From 80c2ba3b0b1d76ac21f578d432f271718949b68b Mon Sep 17 00:00:00 2001 From: Gavin Date: Sun, 23 Mar 2025 22:51:55 -0700 Subject: [PATCH 1/2] Update KIDL code to the most recent kb_sdk_plus version. KIDL code should next be removed from kb_sdk_plus and a jar from this repo used instead. --- RELEASE_NOTES.md | 16 +- .../kbase/jkidl/MemoizingIncludeProvider.java | 44 + src/main/java/us/kbase/jkidl/SpecParser.java | 156 +- src/main/java/us/kbase/jkidl/SpecParser.jj | 59 +- .../kbase/jkidl/SpecParserTokenManager.java | 1 + src/main/java/us/kbase/jkidl/Utils.java | 46 +- .../java/us/kbase/kidl/JSONableVisitor.java | 174 + .../java/us/kbase/kidl/KbAnnotationRange.java | 8 +- .../java/us/kbase/kidl/KbAnnotations.java | 169 +- src/main/java/us/kbase/kidl/KbAuthdef.java | 21 +- src/main/java/us/kbase/kidl/KbFuncdef.java | 86 +- src/main/java/us/kbase/kidl/KbList.java | 27 +- src/main/java/us/kbase/kidl/KbMapping.java | 33 +- src/main/java/us/kbase/kidl/KbModule.java | 106 +- src/main/java/us/kbase/kidl/KbModuleComp.java | 4 +- src/main/java/us/kbase/kidl/KbModuleDef.java | 19 + src/main/java/us/kbase/kidl/KbParameter.java | 48 +- src/main/java/us/kbase/kidl/KbScalar.java | 32 +- src/main/java/us/kbase/kidl/KbService.java | 14 + src/main/java/us/kbase/kidl/KbStruct.java | 65 +- src/main/java/us/kbase/kidl/KbStructItem.java | 14 +- src/main/java/us/kbase/kidl/KbTuple.java | 58 +- src/main/java/us/kbase/kidl/KbType.java | 8 +- src/main/java/us/kbase/kidl/KbTypedef.java | 68 +- .../us/kbase/kidl/KbUnspecifiedObject.java | 26 +- src/main/java/us/kbase/kidl/KidlNode.java | 12 + src/main/java/us/kbase/kidl/KidlParser.java | 242 +- src/main/java/us/kbase/kidl/KidlVisitor.java | 40 + src/main/java/us/kbase/kidl/Utils.java | 6 +- .../java/us/kbase/test/kidl/KidlTest.java | 352 +- .../us/kbase/test/kidl/spec.1.json.properties | 9867 ++++++++++++ .../kbase/test/kidl/spec.10.json.properties | 5146 ++++++ .../kbase/test/kidl/spec.11.json.properties | 2444 +++ .../kbase/test/kidl/spec.12.json.properties | 2780 ++++ .../kbase/test/kidl/spec.13.json.properties | 2756 ++++ .../us/kbase/test/kidl/spec.13.properties | 0 .../kbase/test/kidl/spec.14.json.properties | 3112 ++++ .../kbase/test/kidl/spec.15.json.properties | 1202 ++ .../kbase/test/kidl/spec.16.json.properties | 6958 +++++++++ .../kbase/test/kidl/spec.17.json.properties | 506 + .../kbase/test/kidl/spec.18.json.properties | 2093 +++ .../kbase/test/kidl/spec.19.json.properties | 686 + .../us/kbase/test/kidl/spec.2.json.properties | 726 + .../kbase/test/kidl/spec.20.json.properties | 2981 ++++ .../kbase/test/kidl/spec.21.json.properties | 1792 +++ .../kbase/test/kidl/spec.22.json.properties | 2300 +++ .../kbase/test/kidl/spec.23.json.properties | 118 + .../kbase/test/kidl/spec.24.json.properties | 92 + .../kbase/test/kidl/spec.25.json.properties | 92 + .../us/kbase/test/kidl/spec.3.json.properties | 10089 ++++++++++++ .../us/kbase/test/kidl/spec.4.json.properties | 1313 ++ .../us/kbase/test/kidl/spec.5.json.properties | 12961 ++++++++++++++++ .../us/kbase/test/kidl/spec.5.properties | 2 +- .../us/kbase/test/kidl/spec.6.json.properties | 3614 +++++ .../us/kbase/test/kidl/spec.6.properties | 0 .../us/kbase/test/kidl/spec.7.json.properties | 551 + .../us/kbase/test/kidl/spec.8.json.properties | 1260 ++ .../us/kbase/test/kidl/spec.8.properties | 6 +- .../kbase/test/kidl/spec.i1.json.properties | 72 + .../kbase/test/kidl/spec.i10.json.properties | 64 + .../kbase/test/kidl/spec.i11.json.properties | 663 + .../kbase/test/kidl/spec.i12.json.properties | 1927 +++ .../kbase/test/kidl/spec.i13.json.properties | 64 + .../kbase/test/kidl/spec.i14.json.properties | 64 + .../kbase/test/kidl/spec.i15.json.properties | 165 + .../kbase/test/kidl/spec.i2.json.properties | 72 + .../kbase/test/kidl/spec.i3.json.properties | 82 + .../kbase/test/kidl/spec.i4.json.properties | 90 + .../kbase/test/kidl/spec.i5.json.properties | 110 + .../kbase/test/kidl/spec.i6.json.properties | 2159 +++ .../kbase/test/kidl/spec.i7.json.properties | 64 + .../kbase/test/kidl/spec.i8.json.properties | 64 + .../kbase/test/kidl/spec.i9.json.properties | 64 + 73 files changed, 82543 insertions(+), 582 deletions(-) create mode 100644 src/main/java/us/kbase/jkidl/MemoizingIncludeProvider.java create mode 100644 src/main/java/us/kbase/kidl/JSONableVisitor.java create mode 100644 src/main/java/us/kbase/kidl/KbModuleDef.java create mode 100644 src/main/java/us/kbase/kidl/KidlNode.java create mode 100644 src/main/java/us/kbase/kidl/KidlVisitor.java create mode 100644 src/test/resources/us/kbase/test/kidl/spec.1.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.10.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.11.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.12.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.13.json.properties mode change 100755 => 100644 src/test/resources/us/kbase/test/kidl/spec.13.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.14.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.15.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.16.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.17.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.18.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.19.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.2.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.20.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.21.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.22.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.23.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.24.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.25.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.3.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.4.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.5.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.6.json.properties mode change 100755 => 100644 src/test/resources/us/kbase/test/kidl/spec.6.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.7.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.8.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i1.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i10.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i11.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i12.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i13.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i14.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i15.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i2.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i3.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i4.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i5.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i6.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i7.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i8.json.properties create mode 100644 src/test/resources/us/kbase/test/kidl/spec.i9.json.properties diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index cd6b994..42bd580 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -1,6 +1,20 @@ +# 0.2.0 + +* Updated to code from `kb_sdk_plus` commit `166fe43`. +* It is intended that KIDL parser development now takes place in this repo rather than + `kb_sdk_plus`. +* `kb_sdk_plus`'s code was sourced from `kb_sdk` commit `80aebc4` and updated with the + following changes: + * The unused `async` keyword was removed. + * Code for generating template data structures was moved into `kb_sdk_plus` proper with + the rest of the templating code. + * Other code not involved in parsing KIDL was moved into `kb_sdk_plus` proper. + * For changes between `0.1.0` and `kb_sdk` `80aebc4`, see + the [history of KIDL development](./JKIDL_HISTORY.md). + # 0.1.0 * Initial release * Equivalent to commit `7863aef` of `java_type_compiler` * Equivalent to jar `kbase-kidl-parser-1409261812-7863aef.jar` in the `kbase` folder in - https://github.com/kbase/jars \ No newline at end of file + https://github.com/kbase/jars diff --git a/src/main/java/us/kbase/jkidl/MemoizingIncludeProvider.java b/src/main/java/us/kbase/jkidl/MemoizingIncludeProvider.java new file mode 100644 index 0000000..2ea4501 --- /dev/null +++ b/src/main/java/us/kbase/jkidl/MemoizingIncludeProvider.java @@ -0,0 +1,44 @@ +package us.kbase.jkidl; + +import java.util.HashMap; +import java.util.Map; + +import us.kbase.kidl.KbModule; +import us.kbase.kidl.KidlParseException; + +/** Provides parsed structures for included KIDL specs and memoizes the + * structures. + * @author gaprice@lbl.gov + * + */ +public class MemoizingIncludeProvider implements IncludeProvider { + + private final IncludeProvider wrapped; + private final Map seen = new HashMap(); + + /** Construct the memoizing provider + * @param wrapped an IncludeProvider for which the results will be + * memoized. + */ + public MemoizingIncludeProvider(final IncludeProvider wrapped) { + this.wrapped = wrapped; + } + + @Override + public Map parseInclude(String includeLine) + throws KidlParseException { + final Map parse = wrapped.parseInclude(includeLine); + seen.putAll(parse); + return parse; + } + + /** Note that the Kb* classes are mutable and this function does not make + * a deep copy of the Map. + * @return A mapping of the service name (including the module name) to a + * module for each service encountered in an import. + */ + public Map getParsed() { + return new HashMap(seen); + } + +} diff --git a/src/main/java/us/kbase/jkidl/SpecParser.java b/src/main/java/us/kbase/jkidl/SpecParser.java index 5ab7de0..8d6f255 100644 --- a/src/main/java/us/kbase/jkidl/SpecParser.java +++ b/src/main/java/us/kbase/jkidl/SpecParser.java @@ -25,6 +25,7 @@ import us.kbase.kidl.KbType; import us.kbase.kidl.KbTypedef; import us.kbase.kidl.KbUnspecifiedObject; +import us.kbase.kidl.JSONableVisitor; import us.kbase.kidl.KidlParseException; /** @@ -69,7 +70,7 @@ public static Map parseAsJson(SpecParser p, IncludeProvider ip) throws Pars modList = new ArrayList(); ret.put(module.getServiceName(), modList); } - modList.add(module.toJson()); + modList.add(module.accept(new JSONableVisitor())); } return ret; } @@ -166,6 +167,33 @@ public String getLastComment(Token first) { throw new Error("Missing return statement in function"); } + final public Token Identifier() throws ParseException {Token ret = null; + switch ((jj_ntk==-1)?jj_ntk_f():jj_ntk) { + case S_IDENTIFIER:{ + ret = jj_consume_token(S_IDENTIFIER); + break; + } + case T_required:{ + ret = jj_consume_token(T_required); + break; + } + case T_optional:{ + ret = jj_consume_token(T_optional); + break; + } + case T_none:{ + ret = jj_consume_token(T_none); + break; + } + default: + jj_la1[2] = jj_gen; + jj_consume_token(-1); + throw new ParseException(); + } +{if ("" != null) return ret;} + throw new Error("Missing return statement in function"); + } + /** * Method parses one module. So it iterates over module components (typedefs, funcdefs and auths). * They are separated by semicolon. @@ -179,12 +207,12 @@ public String getLastComment(Token first) { first = jj_consume_token(T_module); comment = getLastComment(first); if (jj_2_1(2147483647)) { - srvToken = jj_consume_token(S_IDENTIFIER); + srvToken = Identifier(); jj_consume_token(T_colon); } else { ; } - nameToken = jj_consume_token(S_IDENTIFIER); + nameToken = Identifier(); ret = new KbModule(srvToken == null ? null : srvToken.toString(), nameToken.toString(), comment); jj_consume_token(T_figure_open_bracket); label_3: @@ -197,7 +225,7 @@ public String getLastComment(Token first) { break; } default: - jj_la1[2] = jj_gen; + jj_la1[3] = jj_gen; break label_3; } switch ((jj_ntk==-1)?jj_ntk_f():jj_ntk) { @@ -214,13 +242,18 @@ public String getLastComment(Token first) { break; } default: - jj_la1[3] = jj_gen; + jj_la1[4] = jj_gen; jj_consume_token(-1); throw new ParseException(); } jj_consume_token(T_semicolon); -lastComment.set(null); - ret.addModuleComponent(comp); +if (!(comp instanceof KbAuthdef)) + lastComment.set(null); + try { + ret.addModuleComponent(comp); + } catch (KidlParseException ex) { + generateParseException(ex); + } } jj_consume_token(T_figure_close_bracket); jj_consume_token(T_semicolon); @@ -239,7 +272,7 @@ public String getLastComment(Token first) { first = jj_consume_token(T_typedef); comment = getLastComment(first); type = Type(curModule, includes); - name = jj_consume_token(S_IDENTIFIER); + name = Identifier(); try { {if ("" != null) return new KbTypedef(curModule.getModuleName(), name.toString(), type, comment);} } catch (KidlParseException ex) { @@ -295,23 +328,29 @@ public String getLastComment(Token first) { jj_consume_token(38); subType = Type(curModule, includes); switch ((jj_ntk==-1)?jj_ntk_f():jj_ntk) { + case T_required: + case T_optional: + case T_none: case S_IDENTIFIER:{ - jj_consume_token(S_IDENTIFIER); + Identifier(); break; } default: - jj_la1[4] = jj_gen; + jj_la1[5] = jj_gen; ; } jj_consume_token(T_comma); subType2 = Type(curModule, includes); switch ((jj_ntk==-1)?jj_ntk_f():jj_ntk) { + case T_required: + case T_optional: + case T_none: case S_IDENTIFIER:{ - jj_consume_token(S_IDENTIFIER); + Identifier(); break; } default: - jj_la1[5] = jj_gen; + jj_la1[6] = jj_gen; ; } jj_consume_token(39); @@ -332,7 +371,7 @@ public String getLastComment(Token first) { break; } default: - jj_la1[6] = jj_gen; + jj_la1[7] = jj_gen; break label_4; } jj_consume_token(T_comma); @@ -349,6 +388,9 @@ public String getLastComment(Token first) { label_5: while (true) { switch ((jj_ntk==-1)?jj_ntk_f():jj_ntk) { + case T_required: + case T_optional: + case T_none: case T_string: case T_int: case T_float: @@ -362,7 +404,7 @@ public String getLastComment(Token first) { break; } default: - jj_la1[7] = jj_gen; + jj_la1[8] = jj_gen; break label_5; } structItem = StructItem(curModule, includes); @@ -374,18 +416,21 @@ public String getLastComment(Token first) { jj_consume_token(T_figure_close_bracket); break; } + case T_required: + case T_optional: + case T_none: case S_IDENTIFIER:{ if (jj_2_2(2147483647)) { - moduleToken = jj_consume_token(S_IDENTIFIER); + moduleToken = Identifier(); jj_consume_token(T_dot); } else { ; } - typeToken = jj_consume_token(S_IDENTIFIER); + typeToken = Identifier(); break; } default: - jj_la1[8] = jj_gen; + jj_la1[9] = jj_gen; jj_consume_token(-1); throw new ParseException(); } @@ -416,7 +461,7 @@ public String getLastComment(Token first) { final public KbStructItem StructItem(KbModule curModule, Map includes) throws ParseException {KbType type; Token name; type = Type(curModule, includes); - name = jj_consume_token(S_IDENTIFIER); + name = Identifier(); {if ("" != null) return new KbStructItem(type, name.toString());} throw new Error("Missing return statement in function"); } @@ -437,7 +482,7 @@ public String getLastComment(Token first) { break; } default: - jj_la1[9] = jj_gen; + jj_la1[10] = jj_gen; jj_consume_token(-1); throw new ParseException(); } @@ -457,9 +502,13 @@ public String getLastComment(Token first) { KbAuthdef auth; first = jj_consume_token(T_funcdef); comment = getLastComment(first); - name = jj_consume_token(S_IDENTIFIER); + name = Identifier(); jj_consume_token(T_round_open_bracket); -ret = new KbFuncdef(name.toString(), comment); +try { + ret = new KbFuncdef(name.toString(), comment); + } catch (KidlParseException ex) { + generateParseException(ex); + } args = OptNameParams(curModule, includes); ret.getParameters().addAll(args); jj_consume_token(T_round_close_bracket); @@ -475,7 +524,7 @@ public String getLastComment(Token first) { break; } default: - jj_la1[10] = jj_gen; + jj_la1[11] = jj_gen; ; } {if ("" != null) return ret;} @@ -488,6 +537,9 @@ public String getLastComment(Token first) { final public List OptNameParams(KbModule curModule, Map includes) throws ParseException {List ret = new ArrayList(); KbParameter param; switch ((jj_ntk==-1)?jj_ntk_f():jj_ntk) { + case T_required: + case T_optional: + case T_none: case T_string: case T_int: case T_float: @@ -507,7 +559,7 @@ public String getLastComment(Token first) { break; } default: - jj_la1[11] = jj_gen; + jj_la1[12] = jj_gen; break label_6; } jj_consume_token(T_comma); @@ -517,7 +569,7 @@ public String getLastComment(Token first) { break; } default: - jj_la1[12] = jj_gen; + jj_la1[13] = jj_gen; ; } {if ("" != null) return ret;} @@ -532,13 +584,16 @@ public String getLastComment(Token first) { String name = null; type = Type(curModule, includes); switch ((jj_ntk==-1)?jj_ntk_f():jj_ntk) { + case T_required: + case T_optional: + case T_none: case S_IDENTIFIER:{ - nameToken = jj_consume_token(S_IDENTIFIER); + nameToken = Identifier(); name = nameToken.toString(); break; } default: - jj_la1[13] = jj_gen; + jj_la1[14] = jj_gen; ; } {if ("" != null) return new KbParameter(type, name);} @@ -561,17 +616,34 @@ private boolean jj_2_2(int xla) finally { jj_save(1, xla); } } - private boolean jj_3_1() + private boolean jj_3_2() { - if (jj_scan_token(S_IDENTIFIER)) return true; - if (jj_scan_token(T_colon)) return true; + if (jj_3R_7()) return true; + if (jj_scan_token(T_dot)) return true; return false; } - private boolean jj_3_2() + private boolean jj_3R_7() { - if (jj_scan_token(S_IDENTIFIER)) return true; - if (jj_scan_token(T_dot)) return true; + Token xsp; + xsp = jj_scanpos; + if (jj_scan_token(33)) { + jj_scanpos = xsp; + if (jj_scan_token(11)) { + jj_scanpos = xsp; + if (jj_scan_token(12)) { + jj_scanpos = xsp; + if (jj_scan_token(13)) return true; + } + } + } + return false; + } + + private boolean jj_3_1() + { + if (jj_3R_7()) return true; + if (jj_scan_token(T_colon)) return true; return false; } @@ -586,7 +658,7 @@ private boolean jj_3_2() private Token jj_scanpos, jj_lastpos; private int jj_la; private int jj_gen; - final private int[] jj_la1 = new int[14]; + final private int[] jj_la1 = new int[15]; static private int[] jj_la1_0; static private int[] jj_la1_1; static { @@ -594,10 +666,10 @@ private boolean jj_3_2() jj_la1_init_1(); } private static void jj_la1_init_0() { - jj_la1_0 = new int[] {0x0,0x200,0xc400,0xc400,0x0,0x0,0x8000000,0xff0000,0xff0000,0x3800,0x400,0x8000000,0xff0000,0x0,}; + jj_la1_0 = new int[] {0x0,0x200,0x3800,0xc400,0xc400,0x3800,0x3800,0x8000000,0xff3800,0xff3800,0x3800,0x400,0x8000000,0xff3800,0x3800,}; } private static void jj_la1_init_1() { - jj_la1_1 = new int[] {0x20,0x0,0x0,0x0,0x2,0x2,0x0,0x2,0x2,0x0,0x0,0x0,0x2,0x2,}; + jj_la1_1 = new int[] {0x20,0x0,0x2,0x0,0x0,0x2,0x2,0x0,0x2,0x2,0x0,0x0,0x0,0x2,0x2,}; } final private JJCalls[] jj_2_rtns = new JJCalls[2]; private boolean jj_rescan = false; @@ -614,7 +686,7 @@ public SpecParser(java.io.InputStream stream, String encoding) { token = new Token(); jj_ntk = -1; jj_gen = 0; - for (int i = 0; i < 14; i++) jj_la1[i] = -1; + for (int i = 0; i < 15; i++) jj_la1[i] = -1; for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls(); } @@ -629,7 +701,7 @@ public void ReInit(java.io.InputStream stream, String encoding) { token = new Token(); jj_ntk = -1; jj_gen = 0; - for (int i = 0; i < 14; i++) jj_la1[i] = -1; + for (int i = 0; i < 15; i++) jj_la1[i] = -1; for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls(); } @@ -640,7 +712,7 @@ public SpecParser(java.io.Reader stream) { token = new Token(); jj_ntk = -1; jj_gen = 0; - for (int i = 0; i < 14; i++) jj_la1[i] = -1; + for (int i = 0; i < 15; i++) jj_la1[i] = -1; for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls(); } @@ -651,7 +723,7 @@ public void ReInit(java.io.Reader stream) { token = new Token(); jj_ntk = -1; jj_gen = 0; - for (int i = 0; i < 14; i++) jj_la1[i] = -1; + for (int i = 0; i < 15; i++) jj_la1[i] = -1; for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls(); } @@ -661,7 +733,7 @@ public SpecParser(SpecParserTokenManager tm) { token = new Token(); jj_ntk = -1; jj_gen = 0; - for (int i = 0; i < 14; i++) jj_la1[i] = -1; + for (int i = 0; i < 15; i++) jj_la1[i] = -1; for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls(); } @@ -671,7 +743,7 @@ public void ReInit(SpecParserTokenManager tm) { token = new Token(); jj_ntk = -1; jj_gen = 0; - for (int i = 0; i < 14; i++) jj_la1[i] = -1; + for (int i = 0; i < 15; i++) jj_la1[i] = -1; for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls(); } @@ -788,7 +860,7 @@ public ParseException generateParseException() { la1tokens[jj_kind] = true; jj_kind = -1; } - for (int i = 0; i < 14; i++) { + for (int i = 0; i < 15; i++) { if (jj_la1[i] == jj_gen) { for (int j = 0; j < 32; j++) { if ((jj_la1_0[i] & (1<(); ret.put(module.getServiceName(), modList); } - modList.add(module.toJson()); + modList.add(module.accept(new JSONableVisitor())); } return ret; } @@ -236,6 +237,22 @@ Map ModuleList(Map includes): { return ret; } } +Token Identifier(): +{ + Token ret = null; +} +{ ( + ( ret = ) + | + ( ret = "required" ) + | + ( ret = "optional" ) + | + ( ret = "none" ) + ) + { return ret; } +} + /** * Method parses one module. So it iterates over module components (typedefs, funcdefs and auths). * They are separated by semicolon. @@ -255,11 +272,11 @@ KbModule Module(Map includes): comment = getLastComment(first); } [ - LOOKAHEAD ( ":") - srvToken = + LOOKAHEAD (Identifier() ":") + srvToken = Identifier() ":" ] - nameToken = + nameToken = Identifier() { ret = new KbModule(srvToken == null ? null : srvToken.toString(), nameToken.toString(), comment); } "{" ( @@ -276,8 +293,13 @@ KbModule Module(Map includes): ) ";" { - lastComment.set(null); - ret.addModuleComponent(comp); + if (!(comp instanceof KbAuthdef)) + lastComment.set(null); + try { + ret.addModuleComponent(comp); + } catch (KidlParseException ex) { + generateParseException(ex); + } } )* "}" ";" { return ret; } @@ -300,7 +322,7 @@ KbTypedef Typedef(KbModule curModule, Map includes): comment = getLastComment(first); } type = Type(curModule, includes) - name = + name = Identifier() { try { return new KbTypedef(curModule.getModuleName(), name.toString(), type, comment); @@ -350,8 +372,8 @@ KbType Type(KbModule curModule, Map includes): { ret = new KbList(subType); } ) | - ( t = "mapping" "<" subType = Type(curModule, includes) [] "," - subType2 = Type(curModule, includes) [] ">" + ( t = "mapping" "<" subType = Type(curModule, includes) [Identifier()] "," + subType2 = Type(curModule, includes) [Identifier()] ">" { ret = new KbMapping(subType, subType2); } ) | @@ -380,11 +402,11 @@ KbType Type(KbModule curModule, Map includes): | ( [ - LOOKAHEAD ( ".") - moduleToken = + LOOKAHEAD (Identifier() ".") + moduleToken = Identifier() "." ] - typeToken = + typeToken = Identifier() ) ) { if (ret == null) { @@ -417,7 +439,7 @@ KbStructItem StructItem(KbModule curModule, Map includes): } { type = Type(curModule, includes) - name = + name = Identifier() { return new KbStructItem(type, name.toString()); } } @@ -460,9 +482,14 @@ KbFuncdef Funcdef(KbModule curModule, Map includes): { comment = getLastComment(first); } - name = + name = Identifier() "(" - { ret = new KbFuncdef(name.toString(), comment); } + { try { + ret = new KbFuncdef(name.toString(), comment); + } catch (KidlParseException ex) { + generateParseException(ex); + } + } args = OptNameParams(curModule, includes) { ret.getParameters().addAll(args); } ")" @@ -509,7 +536,7 @@ KbParameter OptNameParam(KbModule curModule, Map includes): } { type = Type(curModule, includes) - [ nameToken = + [ nameToken = Identifier() { name = nameToken.toString(); } ] { return new KbParameter(type, name); } diff --git a/src/main/java/us/kbase/jkidl/SpecParserTokenManager.java b/src/main/java/us/kbase/jkidl/SpecParserTokenManager.java index 2f2fe68..2403481 100644 --- a/src/main/java/us/kbase/jkidl/SpecParserTokenManager.java +++ b/src/main/java/us/kbase/jkidl/SpecParserTokenManager.java @@ -22,6 +22,7 @@ import us.kbase.kidl.KbType; import us.kbase.kidl.KbTypedef; import us.kbase.kidl.KbUnspecifiedObject; +import us.kbase.kidl.JSONableVisitor; import us.kbase.kidl.KidlParseException; /** Token Manager. */ diff --git a/src/main/java/us/kbase/jkidl/Utils.java b/src/main/java/us/kbase/jkidl/Utils.java index e3a49fc..2de23f5 100644 --- a/src/main/java/us/kbase/jkidl/Utils.java +++ b/src/main/java/us/kbase/jkidl/Utils.java @@ -22,25 +22,30 @@ public static String trim(String comment) { } sb = sb2; int base = 0; - BufferedReader br = new BufferedReader(new StringReader(sb.toString())); - sb = new StringBuilder(); - try { - for (int lineNum = 0;; lineNum++) { - String l = br.readLine(); - if (l == null) - break; - if (lineNum == 1) - while (base < l.length() && l.charAt(base) == ' ') - base++; - if (l.length() >= base && l.substring(0, base).trim().length() == 0) - l = l.substring(base); - sb.append(l).append('\n'); - } - br.close(); - } catch (IOException ex) { - throw new IllegalStateException("Unexpected error", ex); - } - while (sb.length() > 0) { + BufferedReader br = new BufferedReader(new StringReader(sb.toString())); + sb = new StringBuilder(); + try { + for (int lineNum = 0;; lineNum++) { + String l = br.readLine(); + if (l == null) + break; + if (lineNum == 1) + while (base < l.length() && l.charAt(base) == ' ') + base++; + if (l.length() >= base && l.substring(0, base).trim().length() == 0) + l = l.substring(base); + sb.append(l).append('\n'); + } + br.close(); + } catch (IOException ex) { + throw new IllegalStateException("Unexpected error", ex); + } + trimWhitespaces(sb); + return sb.toString(); + } + + public static void trimWhitespaces(StringBuilder sb) { + while (sb.length() > 0) { char ch = sb.charAt(0); if (ch == ' ' || ch == '\t' || ch == '\r' || ch == '\n') { sb.delete(0, 1); @@ -56,6 +61,5 @@ public static String trim(String comment) { break; } } - return sb.toString(); - } + } } diff --git a/src/main/java/us/kbase/kidl/JSONableVisitor.java b/src/main/java/us/kbase/kidl/JSONableVisitor.java new file mode 100644 index 0000000..deb1b19 --- /dev/null +++ b/src/main/java/us/kbase/kidl/JSONableVisitor.java @@ -0,0 +1,174 @@ +package us.kbase.kidl; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; + +/** + * Transform a KIDL class structure to a JSONable object (e.g. Maps and + * Lists). + */ +public class JSONableVisitor implements KidlVisitor { + + @Override + public Object visit(final KbAuthdef auth) { + //presumably this is yet another holdover from the old typecompiler + //that makes no sense + return "auth_default" + auth.getType(); + } + + @Override + public Object visit(final KbFuncdef func, final List params, + final List returns) { + final Map ret = new TreeMap(); + ret.put("!", "Bio::KBase::KIDL::KBT::Funcdef"); + ret.put("annotations", func.getAnnotations().toJson(false)); + ret.put("authentication", func.getAuthentication()); + ret.put("comment", func.getComment()); + ret.put("name", func.getName()); + ret.put("parameters", params); + ret.put("return_type", returns); + return ret; + } + + @Override + public Object visit(final KbList list, final Object elementType) { + final Map ret = new TreeMap(); + ret.put("!", "Bio::KBase::KIDL::KBT::List"); + ret.put("annotations", new HashMap()); + ret.put("element_type", elementType); + return ret; + } + + @Override + public Object visit(final KbMapping map, final Object keyType, + final Object valueType) { + final Map ret = new TreeMap(); + ret.put("!", "Bio::KBase::KIDL::KBT::Mapping"); + ret.put("key_type", keyType); + ret.put("value_type", valueType); + ret.put("annotations", new HashMap()); + return ret; + } + + @Override + public Object visit(final KbModule module, final List components, + final Map typeMap) { + final List ret = new ArrayList(); + final Map main = new TreeMap(); + main.put("!", "Bio::KBase::KIDL::KBT::DefineModule"); + //may need to add annotations to the class in the future + main.put("annotations", new KbAnnotations().toJson(false)); + if (module.getComment() != null) + main.put("comment", module.getComment()); + main.put("module_components", components); + main.put("module_name", module.getModuleName()); + main.put("options", module.getOptions()); + main.put("service_name", module.getServiceName()); + ret.add(main); + // compatibility with Perl type compiler, obsolete + ret.add(new ArrayList()); + ret.add(typeMap); + return ret; + } + + @Override + public Object visit(final KbParameter param, final Object type) { + final Map ret = new TreeMap(); + if (param.getName() != null) + ret.put("name", param.getName()); + ret.put("type", type); + return ret; + } + + @Override + public Object visit(final KbScalar scalar) { + final Map ret = new TreeMap(); + ret.put("!", "Bio::KBase::KIDL::KBT::Scalar"); + //if (scalarType == Type.stringType) + ret.put("annotations", new HashMap()); + ret.put("scalar_type", scalar.getSpecName()); + return ret; + } + + @Override + public Object visit(final KbStruct struct, final List fields) { + final Map ret = new TreeMap(); + ret.put("!", "Bio::KBase::KIDL::KBT::Struct"); + /* per Roman, this weirdness with the annotations is due to matching + * the output of the old type compiler. Raw structs can't actually + * have annotations, only funcdefs and typedefs + */ + if (struct.getAnnotations() == null) { + final Map ann = new HashMap(); + ann.put("searchable_ws_subset", new HashMap()); + ann.put("metadata", new HashMap()); + ret.put("annotations", ann); + } else { + final Map ann = new HashMap(); + if (struct.getAnnotations().getSearchable() == null) { + ann.put("searchable_ws_subset", new HashMap()); + } + if(struct.getAnnotations().getWsMetadata() == null) { + ann.put("metadata", new HashMap()); + } + ret.put("annotations", ann); + } + if (struct.getComment() != null && struct.getComment().length() > 0) + ret.put("comment", struct.getComment()); + ret.put("items", fields); + if (struct.getModule() != null) + ret.put("module", struct.getModule()); + if (struct.getName() != null) + ret.put("name", struct.getName()); + return ret; + } + + @Override + public Object visit(final KbStructItem field, final Object type) { + Map ret = new TreeMap(); + ret.put("!", "Bio::KBase::KIDL::KBT::StructItem"); + ret.put("item_type", type); + ret.put("name", field.getName()); + ret.put("nullable", field.isNullable() ? "1" : "0"); + return ret; + } + + @Override + public Object visit(final KbTuple tuple, final List elementTypes) { + final Map ret = new TreeMap(); + ret.put("!", "Bio::KBase::KIDL::KBT::Tuple"); + if (tuple.getComment() != null && tuple.getComment().length() > 0) + ret.put("comment", tuple.getComment()); + ret.put("element_names", tuple.getElementNames()); + ret.put("element_types", elementTypes); + ret.put("annotations", new HashMap()); + if (tuple.getName() != null) + ret.put("name", tuple.getName()); + return ret; + } + + @Override + public Object visit(final KbTypedef typedef, final KidlNode parent, + final Object aliasType) { + final Map ret = new TreeMap(); + ret.put("!", "Bio::KBase::KIDL::KBT::Typedef"); + ret.put("alias_type", aliasType); + ret.put("annotations", typedef.getAnnotations().toJson(true)); + ret.put("comment", typedef.getComment()); + ret.put("module", typedef.getModule()); + ret.put("name", typedef.getName()); + return ret; + } + + @Override + public Object visit(final KbUnspecifiedObject obj) { + final Map ret = new TreeMap(); + ret.put("!", "Bio::KBase::KIDL::KBT::UnspecifiedObject"); + ret.put("annotations", new HashMap()); + return ret; + } + +} diff --git a/src/main/java/us/kbase/kidl/KbAnnotationRange.java b/src/main/java/us/kbase/kidl/KbAnnotationRange.java index 3708675..3642460 100644 --- a/src/main/java/us/kbase/kidl/KbAnnotationRange.java +++ b/src/main/java/us/kbase/kidl/KbAnnotationRange.java @@ -150,13 +150,13 @@ Object toJsonSchemaForFloat() { if(isMinSet()) { rangeMap.put("minimum", minValue); if(isExclusiveMin) { - rangeMap.put("exclusiveMinimum",new Boolean(true)); + rangeMap.put("exclusiveMinimum", true); } } if(isMaxSet()) { rangeMap.put("maximum", maxValue); if(isExclusiveMax) { - rangeMap.put("exclusiveMaximum",new Boolean(true)); + rangeMap.put("exclusiveMaximum", true); } } return rangeMap; @@ -169,7 +169,7 @@ Object toJsonSchemaForInt() { rangeMap.put("minimum", rounded ); if(rounded.compareTo(minValue)==0) { if(isExclusiveMin) { - rangeMap.put("exclusiveMinimum",new Boolean(true)); + rangeMap.put("exclusiveMinimum", true); } } } @@ -180,7 +180,7 @@ Object toJsonSchemaForInt() { rangeMap.put("maximum", rounded); if(rounded.compareTo(maxValue)==0) { if(isExclusiveMax) { - rangeMap.put("exclusiveMaximum",new Boolean(true)); + rangeMap.put("exclusiveMaximum", true); } } } diff --git a/src/main/java/us/kbase/kidl/KbAnnotations.java b/src/main/java/us/kbase/kidl/KbAnnotations.java index 052ae4b..f4ebbfa 100644 --- a/src/main/java/us/kbase/kidl/KbAnnotations.java +++ b/src/main/java/us/kbase/kidl/KbAnnotations.java @@ -14,35 +14,55 @@ public class KbAnnotations { private List optional = null; private KbAnnotationId idReference = null; + //TODO ROMAN can this be removed? private KbAnnotationSearch searchableWsSubset = null; private KbAnnotationMetadata wsMetadata = null; private KbAnnotationRange range = null; + private boolean isDeprecated = false; + private String deprecationReplacement = null; private Map unknown = new HashMap(); + /* Implementation notes: + * loadFromMap has two uses: + * 1) loading from XML produced by the old Perl type compiler (obsolete) + * 2) loading from maps produced by toJson in this method. + * Thus, toJson must produce output that loadFromMap can consume. + * + * This class does not have toJsonSchema because only KbType and specific + * annotation classes need toJsonSchema. + */ + @SuppressWarnings("unchecked") KbAnnotations loadFromMap(Map data) throws KidlParseException { - for (Map.Entry enrty : data.entrySet()) { - String key = enrty.getKey().toString(); + for (final Map.Entry entry : data.entrySet()) { + final String key = entry.getKey().toString(); if (key.equals("optional")) { - optional = (List)enrty.getValue(); + optional = (List)entry.getValue(); + } else if (key.equals("deprecated")) { + isDeprecated = true; + final String repl = (String) entry.getValue(); + //is there any other checking we should do here? + if (repl != null && !repl.isEmpty()) { + deprecationReplacement = repl; + } } else if (key.equals("id")) { idReference = new KbAnnotationId(); - idReference.loadFromMap((Map)enrty.getValue()); + idReference.loadFromMap((Map)entry.getValue()); } else if (key.equals("searchable_ws_subset")) { searchableWsSubset = new KbAnnotationSearch(); - searchableWsSubset.loadFromMap((Map)enrty.getValue()); + searchableWsSubset.loadFromMap((Map)entry.getValue()); } else if (key.equals("metadata")) { wsMetadata = new KbAnnotationMetadata(); - wsMetadata.loadFromMap((Map)enrty.getValue()); + wsMetadata.loadFromMap((Map)entry.getValue()); }else if (key.equals("range")) { range = new KbAnnotationRange(); - range.loadFromMap((Map)enrty.getValue()); + range.loadFromMap((Map)entry.getValue()); } else if (key.equals("unknown_annotations")) { - unknown.putAll((Map)enrty.getValue()); + unknown.putAll((Map)entry.getValue()); } else { //throw new KidlParseException("Unknown type of annotation: " + key); if (!unknown.containsKey(key)) - unknown.put(key, enrty.getValue()); + unknown.put(key, entry.getValue()); } } if (optional != null) @@ -51,30 +71,43 @@ KbAnnotations loadFromMap(Map data) throws KidlParseException { return this; } - public KbAnnotations loadFromComment(String comment, KbTypedef caller) throws KidlParseException { - List> lines = new ArrayList>(); - StringTokenizer st = new StringTokenizer(comment, "\r\n"); - while (st.hasMoreTokens()) { - String line = st.nextToken(); - StringTokenizer st2 = new StringTokenizer(line, " \t"); - List words = new ArrayList(); - while (st2.hasMoreTokens()) - words.add(st2.nextToken()); - lines.add(words); - } - for (int pos = 0; pos < lines.size(); pos++) { - if (lines.get(pos).size() == 0) + public KbAnnotations loadFromComment( + final String comment, final KbFuncdef caller) + throws KidlParseException { + final List> lines = tokenize(comment); + for (final List words: lines) { + final String annType = getAnnotationType(words); + if (annType == null) { continue; - List words = lines.get(pos); - String annType = words.get(0); - if (!annType.startsWith("@")) + } + final List value = words.subList(1, words.size()); + if (annType.equals("deprecated")) { + setDeprecated(value); + } else { + // TODO: Probably we should throw an exception here + unknown.put(annType, value); + } + } + return this; + } + + + public KbAnnotations loadFromComment( + final String comment, final KbTypedef caller) + throws KidlParseException { + final List> lines = tokenize(comment); + for (final List words: lines) { + final String annType = getAnnotationType(words); + if (annType == null) { continue; - annType = annType.substring(1); - List value = words.subList(1, words.size()); + } + final List value = words.subList(1, words.size()); if (annType.equals("optional")) { if (optional == null) optional = new ArrayList(); optional.addAll(value); + } else if (annType.equals("deprecated")) { + setDeprecated(value); } else if (annType.equals("id")) { idReference = new KbAnnotationId(); idReference.loadFromComment(value); @@ -96,6 +129,45 @@ public KbAnnotations loadFromComment(String comment, KbTypedef caller) throws Ki } return this; } + + private void setDeprecated(final List value) + throws KidlParseException { + isDeprecated = true; + if (value.size() > 1) { + throw new KidlParseException( + "deprecation annotations may have at most one argument"); + } + final String repl = value.isEmpty() ? null : value.get(0); + if (repl != null && !repl.isEmpty()) { + deprecationReplacement = repl; + } + } + + private String getAnnotationType(final List words) { + //this can't actually happen given the tokenizer setup + if (words.size() == 0) { + return null; + } + final String annType = words.get(0); + if (!annType.startsWith("@")) { + return null; + } + return annType.substring(1); + } + + private List> tokenize(final String comment) { + final List> lines = new ArrayList>(); + final StringTokenizer st = new StringTokenizer(comment, "\r\n"); + while (st.hasMoreTokens()) { + final String line = st.nextToken(); + final StringTokenizer st2 = new StringTokenizer(line, " \t"); + final List words = new ArrayList(); + while (st2.hasMoreTokens()) + words.add(st2.nextToken()); + lines.add(words); + } + return lines; + } public List getOptional() { return optional; @@ -117,16 +189,29 @@ public KbAnnotationRange getRange() { return range; } + public boolean isDeprecated() { + return isDeprecated; + } + + public String getDeprecationReplacement() { + return deprecationReplacement; + } + public Map getUnknown() { return unknown; } public Object toJson(boolean isTypedef) { Map ret = new TreeMap(); - if (optional != null) + if (optional != null) { ret.put("optional", new ArrayList(optional)); - if (idReference != null) + } + if (isDeprecated) { + ret.put("deprecated", deprecationReplacement); + } + if (idReference != null) { ret.put("id", idReference.toJson()); + } if (isTypedef) { Object searchableJson = searchableWsSubset == null ? new HashMap() : searchableWsSubset.toJson(); @@ -142,4 +227,30 @@ public Object toJson(boolean isTypedef) { ret.put("unknown_annotations", unknown); return ret; } + + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("KbAnnotations [optional="); + builder.append(optional); + builder.append(", idReference="); + builder.append(idReference); + builder.append(", searchableWsSubset="); + builder.append(searchableWsSubset); + builder.append(", wsMetadata="); + builder.append(wsMetadata); + builder.append(", range="); + builder.append(range); + builder.append(", isDeprecated="); + builder.append(isDeprecated); + builder.append(", deprecationReplacement="); + builder.append(deprecationReplacement); + builder.append(", unknown="); + builder.append(unknown); + builder.append("]"); + return builder.toString(); + } } diff --git a/src/main/java/us/kbase/kidl/KbAuthdef.java b/src/main/java/us/kbase/kidl/KbAuthdef.java index 256314b..22a7592 100644 --- a/src/main/java/us/kbase/kidl/KbAuthdef.java +++ b/src/main/java/us/kbase/kidl/KbAuthdef.java @@ -5,7 +5,10 @@ */ public class KbAuthdef implements KbModuleComp { private String type; - + + public static final String OPTIONAL = "optional"; + public static final String REQUIRED = "required"; + public KbAuthdef(String type) { this.type = type; } @@ -15,7 +18,19 @@ public String getType() { } @Override - public Object toJson() { - return "auth_default" + type; + public T accept(final KidlVisitor visitor, final KidlNode parent) { + return visitor.visit(this); + } + + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("KbAuthdef [type="); + builder.append(type); + builder.append("]"); + return builder.toString(); } } diff --git a/src/main/java/us/kbase/kidl/KbFuncdef.java b/src/main/java/us/kbase/kidl/KbFuncdef.java index 0219384..82dcdac 100644 --- a/src/main/java/us/kbase/kidl/KbFuncdef.java +++ b/src/main/java/us/kbase/kidl/KbFuncdef.java @@ -2,39 +2,43 @@ import java.util.ArrayList; import java.util.Collections; +import java.util.LinkedList; import java.util.List; import java.util.Map; -import java.util.TreeMap; /** * Class represents function definition in spec-file. */ -public class KbFuncdef implements KbModuleComp { +public class KbFuncdef implements KbModuleDef { private String name; - private boolean async; private String authentication; private String comment; private List parameters; private List returnType; + private KbAnnotations annotations; private Map data = null; public KbFuncdef() {} - - public KbFuncdef(String name, String comment) { + + public KbFuncdef(final String name, final String comment) + throws KidlParseException { this.name = name; - this.async = false; this.comment = comment == null ? "" : comment; parameters = new ArrayList(); returnType = new ArrayList(); + annotations = new KbAnnotations().loadFromComment(this.comment, this); } public KbFuncdef loadFromMap(Map data, String defaultAuth) throws KidlParseException { name = Utils.prop(data, "name"); - async = (0 != Utils.intPropFromString(data, "async")); authentication = Utils.prop(data, "authentication"); // defaultAuth was already involved on kidl stage comment = Utils.prop(data, "comment"); parameters = loadParameters(Utils.propList(data, "parameters"), false); returnType = loadParameters(Utils.propList(data, "return_type"), true); + annotations = new KbAnnotations(); + if (data.containsKey("annotations")) { + annotations.loadFromMap(Utils.propMap(data, "annotations")); + } this.data = data; return this; } @@ -51,14 +55,18 @@ public String getName() { return name; } - public boolean isAsync() { - return async; - } - public String getAuthentication() { return authentication; } - + + public boolean isAuthenticationRequired() { + return KbAuthdef.REQUIRED.equals(authentication); + } + + public boolean isAuthenticationOptional() { + return KbAuthdef.OPTIONAL.equals(authentication); + } + public void setAuthentication(String authentication) { this.authentication = authentication; } @@ -79,24 +87,46 @@ public List getReturnType() { return data; } - private List toJson(List list) { - List ret = new ArrayList(); - for (KbParameter param : list) - ret.add(param.toJson()); - return ret; + + @Override + public KbAnnotations getAnnotations() { + return annotations; } @Override - public Object toJson() { - Map ret = new TreeMap(); - ret.put("!", "Bio::KBase::KIDL::KBT::Funcdef"); - ret.put("annotations", new KbAnnotations().toJson(false)); - ret.put("async", async ? "1" : "0"); - ret.put("authentication", authentication); - ret.put("comment", comment); - ret.put("name", name); - ret.put("parameters", toJson(parameters)); - ret.put("return_type", toJson(returnType)); - return ret; + public T accept(final KidlVisitor visitor, final KidlNode parent) { + final List params = new LinkedList(); + final List returns = new LinkedList(); + for (final KbParameter p: parameters) { + params.add(p.accept(visitor, this)); + } + for (final KbParameter p: returnType) { + returns.add(p.accept(visitor, this)); + } + return visitor.visit(this, params, returns); + } + + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("KbFuncdef [name="); + builder.append(name); + builder.append(", authentication="); + builder.append(authentication); + builder.append(", comment="); + builder.append(comment); + builder.append(", parameters="); + builder.append(parameters); + builder.append(", returnType="); + builder.append(returnType); + builder.append(", annotations="); + builder.append(annotations); + builder.append(", data="); + builder.append(data); + builder.append("]"); + return builder.toString(); } } diff --git a/src/main/java/us/kbase/kidl/KbList.java b/src/main/java/us/kbase/kidl/KbList.java index 4ba4365..81428be 100644 --- a/src/main/java/us/kbase/kidl/KbList.java +++ b/src/main/java/us/kbase/kidl/KbList.java @@ -1,9 +1,7 @@ package us.kbase.kidl; -import java.util.HashMap; import java.util.LinkedHashMap; import java.util.Map; -import java.util.TreeMap; /** * Class represents list in spec-file. @@ -32,12 +30,8 @@ public String getJavaStyleName() { } @Override - public Object toJson() { - Map ret = new TreeMap(); - ret.put("!", "Bio::KBase::KIDL::KBT::List"); - ret.put("annotations", new HashMap()); - ret.put("element_type", elementType.toJson()); - return ret; + public T accept(final KidlVisitor visitor, final KidlNode parent) { + return visitor.visit(this, elementType.accept(visitor, this)); } @Override @@ -48,4 +42,21 @@ public Object toJsonSchema(boolean inner) { ret.put("items", getElementType().toJsonSchema(true)); return ret; } + + @Override + public String getSpecName() { + return "list<" + elementType.getSpecName() + ">"; + } + + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("KbList [elementType="); + builder.append(elementType); + builder.append("]"); + return builder.toString(); + } } diff --git a/src/main/java/us/kbase/kidl/KbMapping.java b/src/main/java/us/kbase/kidl/KbMapping.java index f7afca6..27ea527 100644 --- a/src/main/java/us/kbase/kidl/KbMapping.java +++ b/src/main/java/us/kbase/kidl/KbMapping.java @@ -1,9 +1,7 @@ package us.kbase.kidl; -import java.util.HashMap; import java.util.LinkedHashMap; import java.util.Map; -import java.util.TreeMap; /** * Class represents mapping in spec-file. @@ -37,15 +35,11 @@ public KbType getValueType() { public String getJavaStyleName() { return "Map"; } - + @Override - public Object toJson() { - Map ret = new TreeMap(); - ret.put("!", "Bio::KBase::KIDL::KBT::Mapping"); - ret.put("key_type", keyType.toJson()); - ret.put("value_type", valueType.toJson()); - ret.put("annotations", new HashMap()); - return ret; + public T accept(final KidlVisitor visitor, final KidlNode parent) { + return visitor.visit(this, keyType.accept(visitor, this), + valueType.accept(visitor, this)); } @Override @@ -62,4 +56,23 @@ public Object toJsonSchema(boolean inner) { } return ret; } + + @Override + public String getSpecName() { + return "mapping<" + keyType.getSpecName() + "," + valueType.getSpecName() + ">"; + } + + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("KbMapping [keyType="); + builder.append(keyType); + builder.append(", valueType="); + builder.append(valueType); + builder.append("]"); + return builder.toString(); + } } diff --git a/src/main/java/us/kbase/kidl/KbModule.java b/src/main/java/us/kbase/kidl/KbModule.java index 8a2f0e5..e7e18cf 100644 --- a/src/main/java/us/kbase/kidl/KbModule.java +++ b/src/main/java/us/kbase/kidl/KbModule.java @@ -3,23 +3,24 @@ import java.util.ArrayList; import java.util.Collections; import java.util.LinkedHashMap; +import java.util.LinkedList; import java.util.List; import java.util.Map; +import java.util.Map.Entry; import java.util.TreeMap; /** * Class represents module in spec file. It consists of 3 blocks in parsing structure: * properties, type info, name to type map. */ -public class KbModule { +public class KbModule implements KidlNode { private String moduleName; private String serviceName; private String comment; private List options; private List moduleComponents; - private List typeInfoList; private Map nameToType; - private KbAnnotations annotations; + private Map nameToFuncdef; private String lastAuthTempMode = "none"; private List data = null; @@ -32,52 +33,53 @@ public KbModule(String serviceName, String moduleName, String comment) { this.comment = comment == null ? "" : comment; this.options = new ArrayList(); this.moduleComponents = new ArrayList(); - this.typeInfoList = new ArrayList(); this.nameToType = new LinkedHashMap(); nameToType.put("int", new KbScalar("int")); nameToType.put("float", new KbScalar("float")); nameToType.put("string", new KbScalar("string")); nameToType.put("UnspecifiedObject", new KbUnspecifiedObject()); - annotations = new KbAnnotations(); + this.nameToFuncdef = new LinkedHashMap(); } - public void addModuleComponent(KbModuleComp comp) { + public void addModuleComponent(KbModuleComp comp) throws KidlParseException { moduleComponents.add(comp); if (comp instanceof KbAuthdef) { lastAuthTempMode = ((KbAuthdef)comp).getType(); } else if (comp instanceof KbTypedef) { KbTypedef typeDef = (KbTypedef)comp; + if (nameToType.containsKey(typeDef.getName())) + throw new KidlParseException("Type " + typeDef.getName() + + " was already declared"); nameToType.put(typeDef.getName(), typeDef); - } else if (lastAuthTempMode != null) { - KbFuncdef func = (KbFuncdef)comp; - if (func.getAuthentication() == null) + } else { + KbFuncdef func = (KbFuncdef)comp; + if (nameToFuncdef.containsKey(func.getName())) + throw new KidlParseException("Function " + func.getName() + + " was already declared"); + nameToFuncdef.put(func.getName(), func); + if (lastAuthTempMode != null && func.getAuthentication() == null) func.setAuthentication(lastAuthTempMode); } } - public Object toJson() { - List ret = new ArrayList(); - Map main = new TreeMap(); - main.put("!", "Bio::KBase::KIDL::KBT::DefineModule"); - main.put("annotations", annotations.toJson(false)); - if (comment != null) - main.put("comment", comment); - List comps = new ArrayList(); - for (KbModuleComp comp : moduleComponents) - comps.add(comp.toJson()); - main.put("module_components", comps); - main.put("module_name", moduleName); - main.put("options", options); - main.put("service_name", serviceName); - ret.add(main); - ret.add(new ArrayList()); - Map thirdPart = new TreeMap(); - for (Map.Entry entry : nameToType.entrySet()) - thirdPart.put(entry.getKey(), entry.getValue().toJson()); - ret.add(thirdPart); - return ret; + public T accept(final KidlVisitor visitor) { + return accept(visitor, null); } + @Override + public T accept(final KidlVisitor visitor, final KidlNode parent) { + final List components = new LinkedList(); + for (final KbModuleComp c: moduleComponents) { + components.add(c.accept(visitor, this)); + } + final Map typeMap = new TreeMap(); + for (final Entry entry: nameToType.entrySet()) { + typeMap.put(entry.getKey(), + entry.getValue().accept(visitor, this)); + } + return visitor.visit(this, components, typeMap); + } + public void loadFromList(List data) throws KidlParseException { this.data = data; if (data.size() != 3) @@ -91,32 +93,32 @@ public void loadFromList(List data) throws KidlParseException { moduleComponents = new ArrayList(); List compList = Utils.propList(props, "module_components"); String defaultAuth = null; + nameToFuncdef = new LinkedHashMap(); for (Object item : compList) { if (!Map.class.isInstance(item)) { if (item instanceof String) { - defaultAuth = (String)item; + defaultAuth = ((String)item).replace("auth_default", ""); + moduleComponents.add(new KbAuthdef(defaultAuth)); } else { throw new KidlParseException("List item is not compatible with type " + "[" + Map.class.getName() + "], it has type: " + item.getClass().getName()); } } else { + @SuppressWarnings("rawtypes") Map compProps = (Map)item; String compType = Utils.getPerlSimpleType(compProps); if (compType.equals("Typedef")) { moduleComponents.add(new KbTypedef().loadFromMap(compProps)); } else if (compType.equals("Funcdef")) { - moduleComponents.add(new KbFuncdef().loadFromMap(compProps, defaultAuth)); + KbFuncdef func = new KbFuncdef().loadFromMap(compProps, defaultAuth); + moduleComponents.add(func); + nameToFuncdef.put(func.getName(), func); } else { throw new KidlParseException("Unknown module component type: " + compType); } } } moduleComponents = Collections.unmodifiableList(moduleComponents); - typeInfoList = new ArrayList(); - for (Map infoProps : Utils.repareTypingMap((List)data.get(1))) { - typeInfoList.add(new KbTypeInfo().loadFromMap(infoProps)); - } - typeInfoList = Collections.unmodifiableList(typeInfoList); Map typeMap = (Map)data.get(2); nameToType = new LinkedHashMap(); for (Object key : typeMap.keySet()) { @@ -147,10 +149,6 @@ public List getModuleComponents() { return moduleComponents; } - public List getTypeInfoList() { - return typeInfoList; - } - public Map getNameToType() { return nameToType; } @@ -158,4 +156,30 @@ public Map getNameToType() { public List getData() { return data; } + + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("KbModule [moduleName="); + builder.append(moduleName); + builder.append(", serviceName="); + builder.append(serviceName); + builder.append(", comment="); + builder.append(comment); + builder.append(", options="); + builder.append(options); + builder.append(", moduleComponents="); + builder.append(moduleComponents); + builder.append(", nameToType="); + builder.append(nameToType); + builder.append(", lastAuthTempMode="); + builder.append(lastAuthTempMode); + builder.append(", data="); + builder.append(data); + builder.append("]"); + return builder.toString(); + } } diff --git a/src/main/java/us/kbase/kidl/KbModuleComp.java b/src/main/java/us/kbase/kidl/KbModuleComp.java index db42736..dede60b 100644 --- a/src/main/java/us/kbase/kidl/KbModuleComp.java +++ b/src/main/java/us/kbase/kidl/KbModuleComp.java @@ -4,6 +4,4 @@ * Element of module declaration. This could be Typedef of Funcdef (or Auth string in some cases). * @author rsutormin */ -public interface KbModuleComp { - public Object toJson(); -} +public interface KbModuleComp extends KidlNode {} diff --git a/src/main/java/us/kbase/kidl/KbModuleDef.java b/src/main/java/us/kbase/kidl/KbModuleDef.java new file mode 100644 index 0000000..6459a55 --- /dev/null +++ b/src/main/java/us/kbase/kidl/KbModuleDef.java @@ -0,0 +1,19 @@ +package us.kbase.kidl; + +import java.util.Map; + +/** Element of module declaration - Typedef or Funcdef. + * @author gaprice@lbl.gov + * + */ +public interface KbModuleDef extends KbModuleComp{ + + public String getName(); + + public String getComment(); + + public Map getData(); + + public KbAnnotations getAnnotations(); + +} \ No newline at end of file diff --git a/src/main/java/us/kbase/kidl/KbParameter.java b/src/main/java/us/kbase/kidl/KbParameter.java index 0baf3bf..ff15137 100644 --- a/src/main/java/us/kbase/kidl/KbParameter.java +++ b/src/main/java/us/kbase/kidl/KbParameter.java @@ -1,45 +1,65 @@ package us.kbase.kidl; import java.util.Map; -import java.util.TreeMap; /** * Input or output part of KbFuncdef. * @author rsutormin */ -public class KbParameter { +public class KbParameter implements KidlNode { private String name; + private String nameNotNullIfPossible; private KbType type; public KbParameter() {} public KbParameter(KbType type, String name) { this.name = name; + this.nameNotNullIfPossible = name; this.type = type; } public KbParameter loadFromMap(Map data, boolean isReturn, int paramNum) throws KidlParseException { name = Utils.propOrNull(data, "name"); // Utils.prop(data, "name"); - if (name == null && !isReturn) { - name = "arg" + paramNum; - } type = Utils.createTypeFromMap(Utils.propMap(data, "type")); + nameNotNullIfPossible = name; + if (nameNotNullIfPossible == null && !isReturn) { + nameNotNullIfPossible = "arg" + paramNum; + } return this; } - - public String getName() { + + public String getOriginalName() { return name; } - + + public String getName() { + return nameNotNullIfPossible; + } + public KbType getType() { return type; } - public Object toJson() { - Map ret = new TreeMap(); - if (name != null) - ret.put("name", name); - ret.put("type", type.toJson()); - return ret; + @Override + public T accept(final KidlVisitor visitor, final KidlNode parent) { + return visitor.visit(this, type.accept(visitor, this)); + } + + + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("KbParameter [name="); + builder.append(name); + builder.append(", nameNotNullIfPossible="); + builder.append(nameNotNullIfPossible); + builder.append(", type="); + builder.append(type); + builder.append("]"); + return builder.toString(); } } diff --git a/src/main/java/us/kbase/kidl/KbScalar.java b/src/main/java/us/kbase/kidl/KbScalar.java index ccef527..898107f 100644 --- a/src/main/java/us/kbase/kidl/KbScalar.java +++ b/src/main/java/us/kbase/kidl/KbScalar.java @@ -1,9 +1,7 @@ package us.kbase.kidl; -import java.util.HashMap; import java.util.LinkedHashMap; import java.util.Map; -import java.util.TreeMap; /** * Class represents scalar in spec-file. @@ -47,6 +45,7 @@ public Type getScalarType() { return scalarType; } + @Override public String getSpecName() { String ret = scalarType.toString(); return ret.substring(0, ret.length() - 4); @@ -98,13 +97,8 @@ public KbAnnotationRange getRange() { } @Override - public Object toJson() { - Map ret = new TreeMap(); - ret.put("!", "Bio::KBase::KIDL::KBT::Scalar"); - //if (scalarType == Type.stringType) - ret.put("annotations", new HashMap()); - ret.put("scalar_type", getSpecName()); - return ret; + public T accept(final KidlVisitor visitor, final KidlNode parent) { + return visitor.visit(this); } @SuppressWarnings("unchecked") @@ -126,4 +120,24 @@ public Object toJsonSchema(boolean inner) { } return ret; } + + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("KbScalar [scalarType="); + builder.append(scalarType); + builder.append(", javaStyleType="); + builder.append(javaStyleType); + builder.append(", jsonStyleType="); + builder.append(jsonStyleType); + builder.append(", idReference="); + builder.append(idReference); + builder.append(", range="); + builder.append(range); + builder.append("]"); + return builder.toString(); + } } diff --git a/src/main/java/us/kbase/kidl/KbService.java b/src/main/java/us/kbase/kidl/KbService.java index 052d364..81601a0 100644 --- a/src/main/java/us/kbase/kidl/KbService.java +++ b/src/main/java/us/kbase/kidl/KbService.java @@ -46,4 +46,18 @@ public String getName() { public List getModules() { return modules; } + + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("KbService [name="); + builder.append(name); + builder.append(", modules="); + builder.append(modules); + builder.append("]"); + return builder.toString(); + } } diff --git a/src/main/java/us/kbase/kidl/KbStruct.java b/src/main/java/us/kbase/kidl/KbStruct.java index 439d8cc..e5d5b67 100644 --- a/src/main/java/us/kbase/kidl/KbStruct.java +++ b/src/main/java/us/kbase/kidl/KbStruct.java @@ -2,18 +2,19 @@ import java.util.ArrayList; import java.util.Collections; -import java.util.HashMap; import java.util.LinkedHashMap; import java.util.LinkedHashSet; +import java.util.LinkedList; import java.util.List; import java.util.Map; import java.util.Set; -import java.util.TreeMap; /** * Class represents structure in spec-file. */ public class KbStruct extends KbBasicType { + + // per roman this is only needed for compatibility with the old typecomp private String name; private KbAnnotations annotations; private List items; @@ -97,37 +98,14 @@ public void setModule(String module) { } @Override - public Object toJson() { - Map ret = new TreeMap(); - ret.put("!", "Bio::KBase::KIDL::KBT::Struct"); - if (annotations == null) { - Map ann = new HashMap(); - ann.put("searchable_ws_subset", new HashMap()); - ann.put("metadata", new HashMap()); - ret.put("annotations", ann); - } else { - Map ann = new HashMap(); - if(annotations.getSearchable()==null) { - ann.put("searchable_ws_subset", new HashMap()); - } - if(annotations.getWsMetadata()==null) { - ann.put("metadata", new HashMap()); - } - ret.put("annotations", ann); + public T accept(final KidlVisitor visitor, final KidlNode parent) { + final List fields = new LinkedList(); + for (final KbStructItem f: items) { + fields.add(f.accept(visitor, this)); } - if (comment != null && comment.length() > 0) - ret.put("comment", comment); - List itemList = new ArrayList(); - for (KbStructItem item : items) - itemList.add(item.toJson()); - ret.put("items", itemList); - if (module != null) - ret.put("module", module); - if (name != null) - ret.put("name", name); - return ret; + return visitor.visit(this, fields); } - + @SuppressWarnings("unchecked") @Override public Object toJsonSchema(boolean inner) { @@ -154,4 +132,29 @@ public Object toJsonSchema(boolean inner) { } return ret; } + + @Override + public String getSpecName() { + return "structure"; + } + + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("KbStruct [name="); + builder.append(name); + builder.append(", annotations="); + builder.append(annotations); + builder.append(", items="); + builder.append(items); + builder.append(", comment="); + builder.append(comment); + builder.append(", module="); + builder.append(module); + builder.append("]"); + return builder.toString(); + } } diff --git a/src/main/java/us/kbase/kidl/KbStructItem.java b/src/main/java/us/kbase/kidl/KbStructItem.java index 55a27fc..faa2f86 100644 --- a/src/main/java/us/kbase/kidl/KbStructItem.java +++ b/src/main/java/us/kbase/kidl/KbStructItem.java @@ -2,12 +2,11 @@ import java.util.Map; import java.util.Set; -import java.util.TreeMap; /** * Class represents structure item in spec-file. */ -public class KbStructItem { +public class KbStructItem implements KidlNode { private String name; private boolean nullable; private KbType itemType; @@ -50,12 +49,9 @@ public boolean isOptional() { return optional; } - public Object toJson() { - Map ret = new TreeMap(); - ret.put("!", "Bio::KBase::KIDL::KBT::StructItem"); - ret.put("item_type", itemType.toJson()); - ret.put("name", name); - ret.put("nullable", nullable ? "1" : "0"); - return ret; + @Override + public T accept(final KidlVisitor visitor, final KidlNode parent) { + return visitor.visit(this, itemType.accept(visitor, this)); } + } diff --git a/src/main/java/us/kbase/kidl/KbTuple.java b/src/main/java/us/kbase/kidl/KbTuple.java index 6ef1efa..25fbe68 100644 --- a/src/main/java/us/kbase/kidl/KbTuple.java +++ b/src/main/java/us/kbase/kidl/KbTuple.java @@ -4,9 +4,9 @@ import java.util.Collections; import java.util.HashMap; import java.util.LinkedHashMap; +import java.util.LinkedList; import java.util.List; import java.util.Map; -import java.util.TreeMap; /** * Class represents tuple in spec-file. @@ -14,6 +14,7 @@ public class KbTuple extends KbBasicType { private List elementNames = new ArrayList(); private List elementTypes = new ArrayList(); + // per Roman this is only needed for old type compiler compatibility private String name = null; private String comment = null; @@ -21,7 +22,7 @@ public KbTuple() {} public KbTuple(List types) { elementNames = new ArrayList(); - for (KbType type : types) + for (@SuppressWarnings("unused") KbType type : types) elementNames.add("e_" + (elementNames.size() + 1)); elementNames = Collections.unmodifiableList(elementNames); elementTypes = Collections.unmodifiableList(types); @@ -71,8 +72,6 @@ public void setComment(String comment) { } public String getName() { - if (name == null) - throw new IllegalStateException("Property name was not set for tuple"); return name; } @@ -81,22 +80,14 @@ public void setName(String name) { } @Override - public Object toJson() { - Map ret = new TreeMap(); - ret.put("!", "Bio::KBase::KIDL::KBT::Tuple"); - if (comment != null && comment.length() > 0) - ret.put("comment", comment); - ret.put("element_names", elementNames); - List elementTypeList = new ArrayList(); - for (KbType type : elementTypes) - elementTypeList.add(type.toJson()); - ret.put("element_types", elementTypeList); - ret.put("annotations", new HashMap()); - if (name != null) - ret.put("name", name); - return ret; + public T accept(final KidlVisitor visitor, final KidlNode parent) { + final List elementTypes = new LinkedList(); + for (final KbType t: this.elementTypes) { + elementTypes.add(t.accept(visitor, this)); + } + return visitor.visit(this, elementTypes); } - + @Override public Object toJsonSchema(boolean inner) { Map ret = new LinkedHashMap(); @@ -139,4 +130,33 @@ public void afterCreation() { } elementNames = Collections.unmodifiableList(newElementNames); } + + @Override + public String getSpecName() { + StringBuilder ret = new StringBuilder(); + for (KbType type : elementTypes) { + if (ret.length() > 0) + ret.append(","); + ret.append(type.getSpecName()); + } + return "tuple<" + ret + ">"; + } + + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("KbTuple [elementNames="); + builder.append(elementNames); + builder.append(", elementTypes="); + builder.append(elementTypes); + builder.append(", name="); + builder.append(name); + builder.append(", comment="); + builder.append(comment); + builder.append("]"); + return builder.toString(); + } } diff --git a/src/main/java/us/kbase/kidl/KbType.java b/src/main/java/us/kbase/kidl/KbType.java index 4e72540..fdfd782 100644 --- a/src/main/java/us/kbase/kidl/KbType.java +++ b/src/main/java/us/kbase/kidl/KbType.java @@ -5,11 +5,7 @@ * or KbTypedef (named type). * @author rsutormin */ -public interface KbType { - /** - * Method creates structure to save parsing structure of type in JSON. - */ - public Object toJson(); +public interface KbType extends KidlNode { /** * Method creates structure to save parsing structure of type in JSON schema. * @param inner is important for typedefs, defines if this typedef of top level or not. @@ -20,4 +16,6 @@ public interface KbType { * Method is invoked from parser after type is built and it's time to check internal integrity. */ public void afterCreation(); + + public String getSpecName(); } diff --git a/src/main/java/us/kbase/kidl/KbTypedef.java b/src/main/java/us/kbase/kidl/KbTypedef.java index 78c72d8..59de178 100644 --- a/src/main/java/us/kbase/kidl/KbTypedef.java +++ b/src/main/java/us/kbase/kidl/KbTypedef.java @@ -2,13 +2,12 @@ import java.util.LinkedHashMap; import java.util.Map; -import java.util.TreeMap; /** * Class represents type definition (or named type) in spec-file. * @author rsutormin */ -public class KbTypedef implements KbModuleComp, KbType { +public class KbTypedef implements KbType, KbModuleDef { private String name; private String module; private KbType aliasType; @@ -45,13 +44,18 @@ public KbTypedef loadFromMap(Map data) throws KidlParseException { module = Utils.prop(data, "module"); comment = Utils.prop(data, "comment"); annotations = new KbAnnotations(); - if (data.containsKey("annotations")) + if (data.containsKey("annotations")) { annotations.loadFromMap(Utils.propMap(data, "annotations")); + } aliasType = Utils.createTypeFromMap(Utils.propMap(data, "alias_type"), annotations); this.data = data; return this; } + /* (non-Javadoc) + * @see us.kbase.kidl.KbModuleDef#getName() + */ + @Override public String getName() { return name; } @@ -60,6 +64,10 @@ public String getModule() { return module; } + /* (non-Javadoc) + * @see us.kbase.kidl.KbModuleDef#getComment() + */ + @Override public String getComment() { return comment; } @@ -68,36 +76,61 @@ public KbType getAliasType() { return aliasType; } + /* (non-Javadoc) + * @see us.kbase.kidl.KbModuleDef#getData() + */ + @Override public Map getData() { return data; } + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ @Override public String toString() { - return module + "." + name; + StringBuilder builder = new StringBuilder(); + builder.append("KbTypedef [name="); + builder.append(name); + builder.append(", module="); + builder.append(module); + builder.append(", aliasType="); + builder.append(aliasType); + builder.append(", comment="); + builder.append(comment); + builder.append(", data="); + builder.append(data); + builder.append(", annotations="); + builder.append(annotations); + builder.append("]"); + return builder.toString(); } @Override public int hashCode() { - return toString().hashCode(); + return getSpecName().hashCode(); + } + + @Override + public boolean equals(Object obj) { + return obj != null && + (obj instanceof KbTypedef) && + getSpecName().equals(((KbTypedef)obj).getSpecName()); } + /* (non-Javadoc) + * @see us.kbase.kidl.KbModuleDef#getAnnotations() + */ + @Override public KbAnnotations getAnnotations() { return annotations; } @Override - public Object toJson() { - Map ret = new TreeMap(); - ret.put("!", "Bio::KBase::KIDL::KBT::Typedef"); - ret.put("alias_type", aliasType.toJson()); - ret.put("annotations", annotations.toJson(true)); - ret.put("comment", comment); - ret.put("module", module); - ret.put("name", name); - return ret; + public T accept(final KidlVisitor visitor, final KidlNode parent) { + return visitor.visit(this, parent, aliasType.accept(visitor, this)); } - + @SuppressWarnings("unchecked") @Override public Object toJsonSchema(boolean inner) { @@ -116,4 +149,9 @@ public Object toJsonSchema(boolean inner) { public void afterCreation() { // Default implementation - just do nothing } + + @Override + public String getSpecName() { + return module + "." + name; + } } diff --git a/src/main/java/us/kbase/kidl/KbUnspecifiedObject.java b/src/main/java/us/kbase/kidl/KbUnspecifiedObject.java index fe01968..0c61e6f 100644 --- a/src/main/java/us/kbase/kidl/KbUnspecifiedObject.java +++ b/src/main/java/us/kbase/kidl/KbUnspecifiedObject.java @@ -1,9 +1,7 @@ package us.kbase.kidl; -import java.util.HashMap; import java.util.LinkedHashMap; import java.util.Map; -import java.util.TreeMap; /** * Class represents unspecified object in spec-file. @@ -13,19 +11,17 @@ public class KbUnspecifiedObject extends KbBasicType { public String getJavaStyleName() { return "UObject"; } - + + @Override public String getSpecName() { return "UnspecifiedObject"; } - + @Override - public Object toJson() { - Map ret = new TreeMap(); - ret.put("!", "Bio::KBase::KIDL::KBT::UnspecifiedObject"); - ret.put("annotations", new HashMap()); - return ret; + public T accept(final KidlVisitor visitor, final KidlNode parent) { + return visitor.visit(this); } - + @Override public Object toJsonSchema(boolean inner) { Map ret = new LinkedHashMap(); @@ -33,4 +29,14 @@ public Object toJsonSchema(boolean inner) { ret.put("original-type", "kidl-" + getSpecName()); return ret; } + + /* (non-Javadoc) + * @see java.lang.Object#toString() + */ + @Override + public String toString() { + StringBuilder builder = new StringBuilder(); + builder.append("KbUnspecifiedObject []"); + return builder.toString(); + } } diff --git a/src/main/java/us/kbase/kidl/KidlNode.java b/src/main/java/us/kbase/kidl/KidlNode.java new file mode 100644 index 0000000..83c659b --- /dev/null +++ b/src/main/java/us/kbase/kidl/KidlNode.java @@ -0,0 +1,12 @@ +package us.kbase.kidl; + +public interface KidlNode { + + /** Accept a visitor to this node and return the results of the visitor's + * visit. + * @param visitor the visitor + * @return the result returned from the visitor. + */ + public T accept(KidlVisitor visitor, KidlNode parent); + +} diff --git a/src/main/java/us/kbase/kidl/KidlParser.java b/src/main/java/us/kbase/kidl/KidlParser.java index 0d96a5e..65849d5 100644 --- a/src/main/java/us/kbase/kidl/KidlParser.java +++ b/src/main/java/us/kbase/kidl/KidlParser.java @@ -4,23 +4,14 @@ import java.io.File; import java.io.FileReader; import java.io.IOException; -import java.io.InputStreamReader; -import java.io.PrintWriter; import java.io.Reader; import java.io.StringWriter; import java.util.ArrayList; -import java.util.Collections; -import java.util.HashSet; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; -import java.util.Set; import java.util.TreeMap; -import javax.xml.parsers.ParserConfigurationException; - -import org.xml.sax.SAXException; - import com.fasterxml.jackson.core.JsonGenerationException; import com.fasterxml.jackson.databind.JsonMappingException; import com.fasterxml.jackson.databind.ObjectMapper; @@ -36,29 +27,15 @@ */ public class KidlParser { - public static List parseSpec(File specFile, File tempDir) throws KidlParseException { - return parseSpec(specFile, tempDir, null); + public static List parseSpec(File specFile) throws KidlParseException { + return parseSpec(specFile, null); } - public static List parseSpec(File specFile, File tempDir, + public static List parseSpec(File specFile, Map> modelToTypeJsonSchemaReturn) throws KidlParseException { - return parseSpec(specFile, tempDir, modelToTypeJsonSchemaReturn, null); - } - - public static List parseSpec(File specFile, File tempDir, - Map> modelToTypeJsonSchemaReturn, String kbTop) throws KidlParseException { - return parseSpec(specFile, tempDir, modelToTypeJsonSchemaReturn, kbTop, false); - } - - public static List parseSpec(File specFile, File tempDir, - Map> modelToTypeJsonSchemaReturn, String kbTop, boolean internal) throws KidlParseException { Map map = null; try { - if (internal) { - map = parseSpecInt(specFile, modelToTypeJsonSchemaReturn); - } else { - map = parseSpecExt(specFile, tempDir, modelToTypeJsonSchemaReturn, kbTop); - } + map = parseSpecInt(specFile, modelToTypeJsonSchemaReturn); return parseSpec(map); } catch (KidlParseException ex) { throw ex; @@ -73,201 +50,48 @@ public static List parseSpec(Map parseMap) throws KidlParseExcep public static Map parseSpecInt(File specFile, Map> modelToTypeJsonSchemaReturn) throws Exception { - IncludeProvider ip = new FileIncludeProvider(specFile.getCanonicalFile().getParentFile()); + IncludeProvider ip = new FileIncludeProvider(specFile.getCanonicalFile().getParentFile()); return parseSpecInt(new FileReader(specFile), modelToTypeJsonSchemaReturn, ip); } - + public static Map parseSpecInt(Reader specDocumentReader, Map> modelToTypeJsonSchemaReturn, IncludeProvider ip) throws KidlParseException, JsonGenerationException, JsonMappingException, IOException { - SpecParser p = new SpecParser(new BufferedReader(specDocumentReader)); - Map root; + SpecParser p = new SpecParser(new BufferedReader(specDocumentReader)); + Map root; try { root = p.SpecStatement(ip); specDocumentReader.close(); } catch (ParseException e) { - throw new KidlParseException(e.getMessage()); + throw new KidlParseException(e.getMessage(), e); } - Map> ret = new LinkedHashMap>(); - for (KbModule module : root.values()) { - List modList = ret.get(module.getServiceName()); - if (modList == null) { - modList = new ArrayList(); - ret.put(module.getServiceName(), modList); - } - modList.add(module.toJson()); - } - if (modelToTypeJsonSchemaReturn != null) { - for (Map.Entry entry : root.entrySet()) { - Map typeToSchema = new TreeMap(); - for (KbModuleComp comp : entry.getValue().getModuleComponents()) - if (comp instanceof KbTypedef) { - KbTypedef typedef = (KbTypedef)comp; - Object schemaMap = typedef.toJsonSchema(false); - ObjectMapper mapper = new ObjectMapper(); - mapper.configure(SerializationFeature.INDENT_OUTPUT, true); - StringWriter sw = new StringWriter(); - mapper.writeValue(sw, schemaMap); - sw.close(); - typeToSchema.put(typedef.getName(), sw.toString()); - } - if (typeToSchema.size() > 0) - modelToTypeJsonSchemaReturn.put(entry.getKey(), typeToSchema); - } - } - return ret; - } - - @SuppressWarnings("unchecked") - public static Map parseSpecExt(File specFile, File tempDir, - Map> modelToTypeJsonSchemaReturn, String kbTop) - throws KidlParseException, IOException, InterruptedException, - ParserConfigurationException, SAXException { - if (tempDir == null) - tempDir = new File("."); - File workDir = new File(tempDir, "temp_" + System.currentTimeMillis()); - workDir.mkdir(); - try { - File bashFile = new File(workDir, "comp_server.sh"); - File specDir = specFile.getAbsoluteFile().getParentFile(); - File xmlFile = new File(workDir, "parsing_file.xml"); - if (kbTop == null) - kbTop = System.getenv("KB_TOP"); - String compileTypespecDir = ""; - if (kbTop != null && kbTop.trim().length() > 0) { - compileTypespecDir = kbTop + "/bin/"; - } else { - System.out.println("WARNING: KB_TOP environment variable is not defined, " + - "so compile_typespec is supposed to be in PATH"); + Map> ret = new LinkedHashMap>(); + for (KbModule module : root.values()) { + List modList = ret.get(module.getServiceName()); + if (modList == null) { + modList = new ArrayList(); + ret.put(module.getServiceName(), modList); } - PrintWriter pw = new PrintWriter(bashFile); - pw.println("#!/bin/bash"); - boolean createJsonSchemas = modelToTypeJsonSchemaReturn != null; - pw.println("" + - compileTypespecDir + "compile_typespec --path \"" + specDir.getAbsolutePath() + "\"" + - " --xmldump " + xmlFile.getName() + " " + (createJsonSchemas ? "--jsonschema " : "") + - "\"" + specFile.getAbsolutePath() + "\" " + workDir.getName() - ); - pw.close(); - Process proc = new ProcessBuilder("bash", bashFile.getCanonicalPath()).directory(tempDir) - .redirectErrorStream(true).start(); - BufferedReader br = new BufferedReader(new InputStreamReader(proc.getInputStream())); - StringBuilder errTextSB = new StringBuilder(); - while (true) { - String l = br.readLine(); - if (l == null) - break; - System.out.println("KIDL: " + l); - errTextSB.append(l).append('\n'); - } - br.close(); - proc.waitFor(); - if (!xmlFile.exists()) { - String errText = errTextSB.toString(); - String[] options = {"path", "xmldump", "jsonschema"}; - String caption = null; - for (String opt : options) { - if (errText.contains("Unknown option: " + opt)) { - caption = "It seems that you're using wrong branch of \"typecomp\" module (it should be \"dev-prototypes\")"; - break; - } - } - if (caption == null) - caption = "Parsing file wasn't created"; - throw new KidlParseException(caption + ", here is KIDL output:\n" + errText); - } - Map map = SpecXmlHelper.parseXml(xmlFile); - correctStringAnnotations(map); - Set moduleNames = new HashSet(); - for (Object obj : map.values()) { - List> modList = (List>)obj; - for (List module : modList) { - if (module.size() != 3) - throw new IllegalStateException("Wrong parse structure"); - module.set(1, new ArrayList()); - Map moduleProps = (Map)module.get(0); - String moduleName = moduleProps.get("module_name").toString(); - moduleNames.add(moduleName); - List components = (List)moduleProps.get("module_components"); - for (Object cmp : components) { - if (!(cmp instanceof Map)) - continue; - Map comp = (Map)cmp; - if (comp.get("!").equals("Bio::KBase::KIDL::KBT::Typedef")) { - Map ann = (Map)comp.get("annotations"); - if (ann == null) - ann = new TreeMap(); - if (ann.get("searchable_ws_subset") == null) - ann.put("searchable_ws_subset", new TreeMap()); - if (ann.get("unknown_annotations") == null) - ann.put("unknown_annotations", new TreeMap()); - comp.put("annotations", ann); - } - } - } - } - if (createJsonSchemas) { - File schemasRoot = new File(workDir, "jsonschema"); - if (schemasRoot.exists()) - for (File moduleDir : schemasRoot.listFiles()) { - if (!moduleDir.isDirectory()) - continue; - String moduleName = moduleDir.getName(); - if (!moduleNames.contains(moduleName)) { - continue; - } - Map type2schema = new TreeMap(); - for (File schemaFile : moduleDir.listFiles()) { - if (!schemaFile.getName().endsWith(".json")) - continue; - String typeName = schemaFile.getName(); - typeName = typeName.substring(0, typeName.length() - 5); - StringWriter sw = new StringWriter(); - PrintWriter schemaPw = new PrintWriter(sw); - BufferedReader schemaBr = new BufferedReader(new FileReader(schemaFile)); - while (true) { - String l = schemaBr.readLine(); - if (l == null) - break; - schemaPw.println(l); - } - schemaBr.close(); - schemaPw.close(); - type2schema.put(typeName, sw.toString()); - } - modelToTypeJsonSchemaReturn.put(moduleDir.getName(), type2schema); - } - } - return map; - } finally { - deleteRecursively(workDir); + modList.add(module.accept(new JSONableVisitor())); } - } - - private static void correctStringAnnotations(Object node) { - if (node instanceof Map) { - @SuppressWarnings("unchecked") - Map map = (Map)node; - Object perlType = map.get("!"); - if (perlType != null && perlType instanceof String && - perlType.equals("Bio::KBase::KIDL::KBT::Scalar")) { - String scalarType = (String)map.get("scalar_type"); - if (scalarType.equals("string") && map.get("annotations") == null) - map.put("annotations", Collections.EMPTY_MAP); - } else { - for (Object value : map.values()) - correctStringAnnotations(value); + if (modelToTypeJsonSchemaReturn != null) { + for (Map.Entry entry : root.entrySet()) { + Map typeToSchema = new TreeMap(); + for (KbModuleComp comp : entry.getValue().getModuleComponents()) + if (comp instanceof KbTypedef) { + KbTypedef typedef = (KbTypedef)comp; + Object schemaMap = typedef.toJsonSchema(false); + ObjectMapper mapper = new ObjectMapper(); + mapper.configure(SerializationFeature.INDENT_OUTPUT, true); + StringWriter sw = new StringWriter(); + mapper.writeValue(sw, schemaMap); + sw.close(); + typeToSchema.put(typedef.getName(), sw.toString()); + } + if (typeToSchema.size() > 0) + modelToTypeJsonSchemaReturn.put(entry.getKey(), typeToSchema); } - } else if (node instanceof List) { - for (Object item : ((List)node)) - correctStringAnnotations(item); } - } - - private static void deleteRecursively(File fileOrDir) { - if (fileOrDir.isDirectory()) - for (File f : fileOrDir.listFiles()) - deleteRecursively(f); - fileOrDir.delete(); + return ret; } } diff --git a/src/main/java/us/kbase/kidl/KidlVisitor.java b/src/main/java/us/kbase/kidl/KidlVisitor.java new file mode 100644 index 0000000..2d24b32 --- /dev/null +++ b/src/main/java/us/kbase/kidl/KidlVisitor.java @@ -0,0 +1,40 @@ +package us.kbase.kidl; + +import java.util.List; +import java.util.Map; + +//TODO unit tests with test visitor + +/** An interface implementing the visitor portion of the Visitor design + * pattern for a KIDL parsed structure. + * @author gaprice@lbl.gov + * + * @param The type of data this visitor will process. + */ +public interface KidlVisitor { + + public T visit(KbAuthdef authdef); + + public T visit(KbFuncdef funcdef, List params, List returns); + + public T visit(KbList list, T elementType); + + public T visit(KbMapping map, T keyType, T valueType); + + public T visit(KbModule module, List components, + Map typeMap); + + public T visit(KbParameter param, T type); + + public T visit(KbScalar scalar); + + public T visit(KbStruct struct, List fields); + + public T visit(KbStructItem field, T type); + + public T visit(KbTuple tuple, List elementTypes); + + public T visit(KbTypedef typedef, KidlNode parent, T aliasType); + + public T visit(KbUnspecifiedObject obj); +} diff --git a/src/main/java/us/kbase/kidl/Utils.java b/src/main/java/us/kbase/kidl/Utils.java index a7e0fd4..020900b 100644 --- a/src/main/java/us/kbase/kidl/Utils.java +++ b/src/main/java/us/kbase/kidl/Utils.java @@ -24,6 +24,7 @@ public static Map propMap(Map map, String propName) throws KidlParseEx return propAbstract(map, propName, Map.class); } + @SuppressWarnings("unchecked") private static T propAbstract(Map map, String propName, Class returnType) throws KidlParseException { if (!map.containsKey(propName)) throw new KidlParseException("No property in the map: " + propName); @@ -40,10 +41,12 @@ public static List repareTypingString(List list) throws KidlParseExce return repareTypingAbstract(list, String.class); } + @SuppressWarnings("rawtypes") public static List repareTypingMap(List list) throws KidlParseException { return repareTypingAbstract(list, Map.class); } + @SuppressWarnings("unchecked") private static List repareTypingAbstract(List list, Class itemType) throws KidlParseException { List ret = new ArrayList(); for (Object item : list) { @@ -55,6 +58,7 @@ private static List repareTypingAbstract(List list, Class itemType) return ret; } + @SuppressWarnings("rawtypes") public static List getListOfMapProp(Map data, String propName) throws KidlParseException { return Utils.repareTypingMap(Utils.propList(data, propName)); } @@ -63,7 +67,7 @@ public static String getPerlSimpleType(Map map) throws KidlParseException { return getPerlSimpleType(prop(map, "!")); } - public static String getPerlSimpleType(String type) { + private static String getPerlSimpleType(String type) { return type.contains("::") ? type.substring(type.lastIndexOf("::") + 2) : type; } diff --git a/src/test/java/us/kbase/test/kidl/KidlTest.java b/src/test/java/us/kbase/test/kidl/KidlTest.java index 1286d64..d0cff43 100644 --- a/src/test/java/us/kbase/test/kidl/KidlTest.java +++ b/src/test/java/us/kbase/test/kidl/KidlTest.java @@ -1,5 +1,10 @@ package us.kbase.test.kidl; +import static org.hamcrest.CoreMatchers.is; +import static org.hamcrest.CoreMatchers.nullValue; +import static org.junit.Assert.assertThat; +import static org.junit.Assert.fail; + import java.io.BufferedReader; import java.io.File; import java.io.FileNotFoundException; @@ -29,7 +34,10 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.SerializationFeature; +import us.kbase.jkidl.StaticIncludeProvider; +import us.kbase.kidl.KbAnnotations; import us.kbase.kidl.KbModule; +import us.kbase.kidl.KbModuleDef; import us.kbase.kidl.KbModuleComp; import us.kbase.kidl.KbService; import us.kbase.kidl.KbStruct; @@ -40,27 +48,14 @@ import us.kbase.kidl.KidlParser; public class KidlTest { - - /* TODO TEST many of these tests used to compare the output of the java type compiler with - * the Perl type compiler, which is long gone. As such, those lines have been - * commented out. They need to be updated to compare against expected structures, - * especially if any changes are to be made. - * Another, potentially better option is to update to the latest code in the kb_sdk - * repo, which has removed the need for the Perl type compiler, but see TODO.md in - * the repo root dir. - * For now they're just dumb happy path tests. - */ + public static final String tempDirName = "temp_test"; - private static File prepareWorkDir() throws IOException { + private static File prepareWorkDir() throws Exception { File tempDir = new File(".").getCanonicalFile(); - if (!tempDir.getName().equals("test")) { - tempDir = new File(tempDir, "test"); - if (!tempDir.exists()) - tempDir.mkdir(); - } File workDir = new File(tempDir, "test_kidl"); - if (!workDir.exists()) + if (!workDir.exists()) { workDir.mkdir(); + } return workDir; } @@ -88,9 +83,11 @@ public static void showDiff(String origText, String newText) throws Exception { origWidth = 100; int maxSize = Math.max(origLn.size(), newLn.size()); for (int pos = 0; pos < maxSize; pos++) { - String origL = pos < origLn.size() ? origLn.get(pos) : ""; - String newL = pos < newLn.size() ? newLn.get(pos) : ""; + String origL = pos < origLn.size() ? origLn.get(pos) : ""; + String newL = pos < newLn.size() ? newLn.get(pos) : ""; boolean eq = origL.equals(newL); + if (eq) + continue; if (origL.length() > origWidth) { System.out.println("/" + (eq ? " " : "*") +origL); System.out.println("\\" + (eq ? " " : "*") + newL); @@ -103,6 +100,118 @@ public static void showDiff(String origText, String newText) throws Exception { } } + @Test + public void testDeprecation() throws Exception { + String spec = "module t1 {\n" + + " /* @deprecated bar" + + "*/" + + " typedef int foo;\n" + + " typedef int foo2;\n" + + "};"; + checkDeprecation(spec, "bar", true, null); + + spec = "module t1 {\n" + + " /* @deprecated\n" + + " sometext\n" + + "" + + " " + + " */" + + " typedef int foo;\n" + + " typedef int foo2;\n" + + "};"; + checkDeprecation(spec, null, true, null); + + spec = "module t1 {\n" + + " /* @deprecated baz\n" + + " @wooble wibble" + + " " + + "" + + " */" + + " funcdef whee() returns();\n" + + " /* foo bar\n" + + " " + + "" + + " */" + + " funcdef whee2() returns();\n" + + "};"; + Map unknown = new HashMap(); + unknown.put("wooble", Arrays.asList("wibble")); + checkDeprecation(spec, "baz", true, unknown); + + spec = "module t1 {\n" + + " /* @deprecated bar baz" + + "*/" + + " typedef int foo;\n" + + "};"; + failDeprecation(spec, + "Error at line 2, column 53: deprecation annotations may have at most one argument"); + } + + private void failDeprecation(String spec, String exp) throws Exception { + try { + checkDeprecation(spec, "foo", true, null); + fail("compiled bad spec"); + } catch (KidlParseException kpe) { + assertThat("incorrect exception msg", kpe.getLocalizedMessage(), + is(exp)); + } + } + + @SuppressWarnings("unchecked") + private void checkDeprecation( + final String spec, + final String deptarg, + final boolean isdep, + final Map unknown + ) throws Exception { + Map> schemas = + new HashMap>(); + final Map parsed = (Map) KidlParser.parseSpecInt( + new StringReader(spec), schemas, new StaticIncludeProvider() + ); + final List>> modComps = + ((List>>>>>)parsed.get("t1")) + .get(0).get(0).get("module_components"); + final Map annotations = modComps.get(0).get("annotations"); + assertThat("incorrect deprecation", + annotations.containsKey("deprecated"), is(true)); + if (deptarg != null) { + assertThat("incorrect deprecation target", + (String) annotations.get("deprecated"), + is(deptarg)); + } else { + assertThat("incorrect deprecation target", + annotations.get("deprecated"), is(nullValue())); + } + if (unknown != null) { + Map uk = (Map) annotations.get("unknown_annotations"); + assertThat("incorrect unknown annotations", uk, is(unknown)); + } + final Map stdtarget = modComps.get(1).get("annotations"); + assertThat("incorrect deprection", stdtarget.containsKey("deprecation"), + is(false)); + List reparsed = KidlParser.parseSpec(parsed); + KbAnnotations ann = getAnnotations(reparsed, 0); + assertThat("deprecation incorrect", ann.isDeprecated(), is(isdep)); + assertThat("deprecation target incorrect", + ann.getDeprecationReplacement(), is(deptarg)); + if (unknown != null) { + assertThat("incorrect unknown annotations", + ann.getUnknown(), is(unknown)); + } + ann = getAnnotations(reparsed, 1); + assertThat("deprecation incorrect", ann.isDeprecated(), is(false)); + assertThat("deprecation target incorrect", + ann.getDeprecationReplacement(), is((String)null)); + } + + private KbAnnotations getAnnotations(List reparsed, + int compnum) { + final KbModuleComp td = reparsed.get(0).getModules().get(0) + .getModuleComponents().get(compnum); + return ((KbModuleDef)td).getAnnotations(); + } + @Test public void testJsonSchemas() throws Exception { String[] tests = { @@ -259,55 +368,68 @@ public void testJsonSchemas() throws Exception { " /* Real comment for type1 */\n" + " typedef string test1;\n" + "};", - "module RefCount {" + - "/* @id ws */" + - "typedef string reference;" + - "/* @optional ref */" + - "typedef structure {" + - "reference ref;" + - "} RefType;" + + "module Test15 {" + + " /* @id ws */" + + " typedef string reference;" + + " /* @optional ref */" + + " typedef structure {" + + " reference ref;" + + " } RefType;" + "};" }; boolean ok = true; for (int testNum = 0; testNum < tests.length; testNum++) { - if (testNum + 1 == 14) - continue; File workDir = prepareWorkDir(); File specFile = prepareSpec(workDir, tests[testNum]); - //Map> schemas1 = new HashMap>(); - //Map parse1 = KidlParser.parseSpecExt(specFile, workDir, schemas1, null); + Map parse1 = loadMapFromJsonResource("spec.i" + (testNum + 1)); Map> schemas2 = new HashMap>(); - @SuppressWarnings("unused") Map parse2 = KidlParser.parseSpecInt(specFile, schemas2); - //ok = ok & compareJson(parse1, parse2, "Parsing result for test #" + (testNum + 1)); - //ok = ok & compareJsonSchemas(schemas1, schemas2, "Json schema for test #" + (testNum + 1)); + ok = ok & compareJson(parse1, parse2, "Parsing result for test #" + (testNum + 1)); } Assert.assertTrue(ok); } + public static List getTestSpecNumbers() { + List ret = new ArrayList(); + for (int testNum = 1; testNum <= 22; testNum++) { + if (testNum == 9) { + continue; + } + ret.add(testNum); + } + return ret; + } + + public static InputStream readTestSpec(int testNum) { + return KidlTest.class.getResourceAsStream("spec." + testNum + ".properties"); + } + @Test public void testJsonSchemas2() throws Exception { - for (int testNum = 1; testNum <= 22; testNum++) { - if (testNum == 9) { - continue; - } + boolean ok = true; + for (int testNum : getTestSpecNumbers()) { File workDir = prepareWorkDir(); - InputStream is = this.getClass().getResourceAsStream("spec." + testNum + ".properties"); + InputStream is = readTestSpec(testNum); File specFile = prepareSpec(workDir, is); - parseSpec(testNum, specFile, workDir); + try { + parseSpec(testNum, specFile, workDir); + } catch (Exception ex) { + System.err.println("Error for test " + testNum); + ex.printStackTrace(); + ok = false; + } } + Assert.assertTrue(ok); } private List parseSpec(int testNum, File specFile, File workDir) throws KidlParseException, IOException, InterruptedException, ParserConfigurationException, SAXException, Exception, JsonGenerationException, JsonMappingException, JsonParseException { - //Map> schemas1 = new HashMap>(); - //Map parse1 = KidlParser.parseSpecExt(specFile, workDir, schemas1, null); + Map parse1 = loadMapFromJsonResource("spec." + testNum); Map> schemas2 = new HashMap>(); Map parse = KidlParser.parseSpecInt(specFile, schemas2); - //Assert.assertTrue(compareJson(parse1, parse, "Parsing result for test #" + (testNum + 1))); - //Assert.assertTrue(compareJsonSchemas(schemas1, schemas2, "Json schema for test #" + (testNum + 1))); + Assert.assertTrue(compareJson(parse1, parse, "Parsing result for test #" + (testNum + 1))); return KidlParser.parseSpec(parse); } @@ -364,6 +486,18 @@ public static String rewriteJson(String schema1) throws IOException, return mapper.writeValueAsString(schemaMap); } + @SuppressWarnings("unchecked") + private static Map loadMapFromJsonResource(String resourceName) + throws JsonParseException, JsonMappingException, IOException { + ObjectMapper mapper = new ObjectMapper(); + InputStream is = KidlTest.class.getResourceAsStream(resourceName + ".json.properties"); + try { + return mapper.readValue(is, Map.class); + } finally { + is.close(); + } + } + private static String writeJson(Object obj) throws JsonGenerationException, JsonMappingException, IOException { StringWriter sw = new StringWriter(); @@ -411,7 +545,7 @@ public void testOptionalAnnotation() throws Exception { " float val2;\n" + " } my_struct;\n" + "};"); - List srvList = parseSpec(0, specFile, workDir); + List srvList = parseSpec(23, specFile, workDir); KbModule module = getModule(srvList); List cmpList = module.getModuleComponents(); Assert.assertEquals(1, cmpList.size()); @@ -446,9 +580,9 @@ public void testReferenceId() throws Exception { " float val2;\n" + " } my_struct;\n" + "};"); - List srvList = KidlParser.parseSpec(specFile, workDir, null, null, true); + List srvList = KidlParser.parseSpec(specFile, null); KbModule module = getModule(srvList); - List cmpList = module.getModuleComponents(); + ListcmpList = module.getModuleComponents(); Assert.assertEquals(3, cmpList.size()); for (int i = 0; i < cmpList.size(); i++) { Assert.assertEquals(KbTypedef.class, cmpList.get(i).getClass()); @@ -469,7 +603,7 @@ public void testSyntaxError() throws Exception { " bebebe\n" + "};"); try { - KidlParser.parseSpec(specFile, workDir, null, null, true); + KidlParser.parseSpec(specFile, null); Assert.fail(); } catch (KidlParseException ex) { Assert.assertTrue(ex.getMessage().contains("bebebe")); @@ -592,7 +726,7 @@ public void testSyntaxError() throws Exception { for (int testNum = 0; testNum < specAndResult.length; testNum++) { specFile = prepareSpec(workDir, specAndResult[testNum][0]); try { - KidlParser.parseSpec(specFile, workDir, null, null, true); + KidlParser.parseSpec(specFile, null); Assert.fail(); } catch (Exception ex) { boolean expectedError = ex.getMessage().contains(specAndResult[testNum][1]); @@ -602,6 +736,124 @@ public void testSyntaxError() throws Exception { expectedError); } } + String[][] specAndResult2 = { + { "" + + "module Test {\n typedef structure {\n" + + " int authentication;\n" + + " } test1;\n};", + "AUTHENTICATION" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int required;\n" + + " } test1;\n};" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int optional;\n" + + " } test1;\n};" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int none;\n" + + " } test1;\n};" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int typedef;\n" + + " } test1;\n};", + "TYPEDEF" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int funcdef;\n" + + " } test1;\n};", + "FUNCDEF" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int string;\n" + + " } test1;\n};", + "string" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int int;\n" + + " } test1;\n};", + "int" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int float;\n" + + " } test1;\n};", + "float" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int UnspecifiedObject;\n" + + " } test1;\n};", + "UnspecifiedObject" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int list;\n" + + " } test1;\n};", + "LIST" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int mapping;\n" + + " } test1;\n};", + "MAPPING" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int structure;\n" + + " } test1;\n};", + "STRUCTURE" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int tuple;\n" + + " } test1;\n};", + "TUPLE" + }, + { "" + + "module Test {\n typedef structure {\n" + + " int returns;\n" + + " } test1;\n};", + "RETURNS" + }, + { "" + + "module Test {\n" + + " typedef int type1;\n" + + " typedef int type1;\n" + + "};", + "Type type1 was already declared" + }, + { "" + + "module Test {\n" + + " funcdef func1 () returns ();\n" + + " funcdef func1 () returns ();\n" + + "};", + "Function func1 was already declared" + } + }; + for (int testNum = 0; testNum < specAndResult2.length; testNum++) { + specFile = prepareSpec(workDir, specAndResult2[testNum][0]); + try { + KidlParser.parseSpec(specFile, null); + if (specAndResult2[testNum].length > 1) + Assert.fail("Good for case: " + specAndResult2[testNum][0]); + } catch (Exception ex) { + boolean expectedError = ex.getMessage().toLowerCase().contains( + specAndResult2[testNum][1].toLowerCase()); + if (!expectedError) + ex.printStackTrace(); + Assert.assertTrue("Actual message for test #" + (testNum + 1) + ": " + ex.getMessage(), + expectedError); + } + } } @Test @@ -611,7 +863,7 @@ public void testTupleFieldDuplication() throws Exception { "module Test {\n" + " typedef tuple t;\n" + "};"); - List srvList = parseSpec(0, specFile, workDir); + List srvList = parseSpec(24, specFile, workDir); KbModule module = getModule(srvList); List cmpList = module.getModuleComponents(); Assert.assertEquals(1, cmpList.size()); @@ -631,7 +883,7 @@ public void testTupleFieldWithoutName() throws Exception { "module Test {\n" + " typedef tuple t;\n" + "};"); - List srvList = parseSpec(0, specFile, workDir); + List srvList = parseSpec(25, specFile, workDir); KbModule module = getModule(srvList); List cmpList = module.getModuleComponents(); Assert.assertEquals(1, cmpList.size()); diff --git a/src/test/resources/us/kbase/test/kidl/spec.1.json.properties b/src/test/resources/us/kbase/test/kidl/spec.1.json.properties new file mode 100644 index 0000000..18a38f4 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.1.json.properties @@ -0,0 +1,9867 @@ +{ + "Workspace" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "The workspace service at its core is a storage and retrieval system for \ntyped objects. Objects are organized by the user into one or more workspaces.\n\nFeatures:\n\nVersioning of objects\nData provenenance\nObject to object references\nWorkspace sharing\n***Add stuff here***\n\nNotes about deletion and GC\n\nBINARY DATA:\nAll binary data must be hex encoded prior to storage in a workspace. \nAttempting to send binary data via a workspace client will cause errors.", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A boolean. 0 = false, other = true.", + "module" : "Workspace", + "name" : "boolean" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "WorkspaceIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "module" : "Workspace", + "name" : "WorkspaceIdentity" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about a workspace.\n\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace.\n username owner - name of the user who owns (e.g. created) this workspace.\n timestamp moddate - date when the workspace was last modified.\n permission user_permission - permissions for the authenticated user of\n this workspace.\n permission globalread - whether this workspace is globally readable.", + "element_names" : [ "id", "workspace", "owner", "moddate", "user_permission", "globalread" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + } ], + "name" : "workspace_info" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about a workspace.\n\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace.\n username owner - name of the user who owns (e.g. created) this workspace.\n timestamp moddate - date when the workspace was last modified.\n permission user_permission - permissions for the authenticated user of\n this workspace.\n permission globalread - whether this workspace is globally readable.", + "module" : "Workspace", + "name" : "workspace_info" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object version.\nThe version of the object, starting at 1.", + "module" : "Workspace", + "name" : "obj_ver" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object identifier.\n\nSelect an object by either:\n One, and only one, of the numerical id or name of the workspace,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id wsid - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID\n in KBase format, e.g. kb|ws.78.\n AND \n One, and only one, of the numerical id or name of the object.\n obj_id objid- the numerical ID of the object.\n obj_name name - name of the object.\n OPTIONALLY\n obj_ver ver - the version of the object.\nOR an object reference string:\n obj_ref ref - an object reference string.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "wsid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, + "name" : "objid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object version.\nThe version of the object, starting at 1.", + "module" : "Workspace", + "name" : "obj_ver" + }, + "name" : "ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + }, + "name" : "ref", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object identifier.\n\nSelect an object by either:\n One, and only one, of the numerical id or name of the workspace,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id wsid - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID\n in KBase format, e.g. kb|ws.78.\n AND \n One, and only one, of the numerical id or name of the object.\n obj_id objid- the numerical ID of the object.\n obj_name name - name of the object.\n OPTIONALLY\n obj_ver ver - the version of the object.\nOR an object reference string:\n obj_ref ref - an object reference string.", + "module" : "Workspace", + "name" : "ObjectIdentity" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about an object.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.", + "element_names" : [ "objid", "name", "type", "save_date", "version", "created_by", "wsid", "chsum", "size" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "object_info" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about an object.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.", + "module" : "Workspace", + "name" : "object_info" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about an object, including user provided metadata.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.\n usermeta meta - arbitrary user-supplied metadata about\n the object.", + "element_names" : [ "objid", "name", "type", "save_date", "version", "created_by", "wsid", "chsum", "size", "meta" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + } ], + "name" : "object_info_full" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about an object, including user provided metadata.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.\n usermeta meta - arbitrary user-supplied metadata about\n the object.", + "module" : "Workspace", + "name" : "object_info_full" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, + "name" : "time", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + } + }, + "name" : "method_params", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_command_line", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "input_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "resolved_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_incoming", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_outgoing", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ProvenanceAction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "module" : "Workspace", + "name" : "ProvenanceAction" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Input parameters for the \"create_workspace\" function.\n\n Required arguments:\n ws_name workspace - name of the workspace to be created.\n \n Optional arguments:\n permission globalread - 'r' to set workspace globally readable,\n default 'n'.\n string description - A free-text description of the workspace, 1000\n characters max. Longer strings will be mercilessly and brutally\n truncated.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, + "name" : "globalread", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "CreateWorkspaceParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Input parameters for the \"create_workspace\" function.\n\n Required arguments:\n ws_name workspace - name of the workspace to be created.\n \n Optional arguments:\n permission globalread - 'r' to set workspace globally readable,\n default 'n'.\n string description - A free-text description of the workspace, 1000\n characters max. Longer strings will be mercilessly and brutally\n truncated.", + "module" : "Workspace", + "name" : "CreateWorkspaceParams" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "Creates a new workspace.", + "name" : "create_workspace", + "parameters" : [ { + "name" : "params", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Input parameters for the \"create_workspace\" function.\n\n Required arguments:\n ws_name workspace - name of the workspace to be created.\n \n Optional arguments:\n permission globalread - 'r' to set workspace globally readable,\n default 'n'.\n string description - A free-text description of the workspace, 1000\n characters max. Longer strings will be mercilessly and brutally\n truncated.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, + "name" : "globalread", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "CreateWorkspaceParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Input parameters for the \"create_workspace\" function.\n\n Required arguments:\n ws_name workspace - name of the workspace to be created.\n \n Optional arguments:\n permission globalread - 'r' to set workspace globally readable,\n default 'n'.\n string description - A free-text description of the workspace, 1000\n characters max. Longer strings will be mercilessly and brutally\n truncated.", + "module" : "Workspace", + "name" : "CreateWorkspaceParams" + } + } ], + "return_type" : [ { + "name" : "info", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about a workspace.\n\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace.\n username owner - name of the user who owns (e.g. created) this workspace.\n timestamp moddate - date when the workspace was last modified.\n permission user_permission - permissions for the authenticated user of\n this workspace.\n permission globalread - whether this workspace is globally readable.", + "element_names" : [ "id", "workspace", "owner", "moddate", "user_permission", "globalread" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + } ], + "name" : "workspace_info" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about a workspace.\n\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace.\n username owner - name of the user who owns (e.g. created) this workspace.\n timestamp moddate - date when the workspace was last modified.\n permission user_permission - permissions for the authenticated user of\n this workspace.\n permission globalread - whether this workspace is globally readable.", + "module" : "Workspace", + "name" : "workspace_info" + } + } ] + }, "auth_defaultoptional", { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "Get information associated with a workspace.", + "name" : "get_workspace_info", + "parameters" : [ { + "name" : "wsi", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "WorkspaceIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "module" : "Workspace", + "name" : "WorkspaceIdentity" + } + } ], + "return_type" : [ { + "name" : "info", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about a workspace.\n\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace.\n username owner - name of the user who owns (e.g. created) this workspace.\n timestamp moddate - date when the workspace was last modified.\n permission user_permission - permissions for the authenticated user of\n this workspace.\n permission globalread - whether this workspace is globally readable.", + "element_names" : [ "id", "workspace", "owner", "moddate", "user_permission", "globalread" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + } ], + "name" : "workspace_info" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about a workspace.\n\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace.\n username owner - name of the user who owns (e.g. created) this workspace.\n timestamp moddate - date when the workspace was last modified.\n permission user_permission - permissions for the authenticated user of\n this workspace.\n permission globalread - whether this workspace is globally readable.", + "module" : "Workspace", + "name" : "workspace_info" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "Get a workspace's description.", + "name" : "get_workspace_description", + "parameters" : [ { + "name" : "wsi", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "WorkspaceIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "module" : "Workspace", + "name" : "WorkspaceIdentity" + } + } ], + "return_type" : [ { + "name" : "description", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Input parameters for the \"set_permissions\" function.\n\n One, and only one, of the following is required:\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.\n \n Required arguments:\n permission new_permission - the permission to assign to the users.\n list users - the users whose permissions will be altered.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, + "name" : "new_permission", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + } + }, + "name" : "users", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "SetPermissionsParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Input parameters for the \"set_permissions\" function.\n\n One, and only one, of the following is required:\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.\n \n Required arguments:\n permission new_permission - the permission to assign to the users.\n list users - the users whose permissions will be altered.", + "module" : "Workspace", + "name" : "SetPermissionsParams" + }, "auth_defaultrequired", { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "Set permissions for a workspace.", + "name" : "set_permissions", + "parameters" : [ { + "name" : "params", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Input parameters for the \"set_permissions\" function.\n\n One, and only one, of the following is required:\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.\n \n Required arguments:\n permission new_permission - the permission to assign to the users.\n list users - the users whose permissions will be altered.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, + "name" : "new_permission", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + } + }, + "name" : "users", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "SetPermissionsParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Input parameters for the \"set_permissions\" function.\n\n One, and only one, of the following is required:\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.\n \n Required arguments:\n permission new_permission - the permission to assign to the users.\n list users - the users whose permissions will be altered.", + "module" : "Workspace", + "name" : "SetPermissionsParams" + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "Get permissions for a workspace.", + "name" : "get_permissions", + "parameters" : [ { + "name" : "wsi", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "WorkspaceIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "module" : "Workspace", + "name" : "WorkspaceIdentity" + } + } ], + "return_type" : [ { + "name" : "perms", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object and associated data required for saving.\n\n Required arguments:\n type_string type - the type of the object. Omit the version information\n to use the latest version.\n UnspecifiedObject data - the object data.\n \n Optional arguments:\n One of an object name or id. If no name or id is provided the name\n will be set to 'auto' with the object id appended as a string,\n possibly with -\\d+ appended if that object id already exists as a\n name.\n obj_name name - the name of the object.\n obj_id objid - the id of the object to save over.\n usermeta meta - arbitrary user-supplied metadata for the object,\n not to exceed 16kb.\n list provenance - provenance data for the object.\n boolean hidden - true if this object should not be listed when listing\n workspace objects.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "name" : "data", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, + "name" : "objid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + }, + "name" : "meta", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, + "name" : "time", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + } + }, + "name" : "method_params", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_command_line", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "input_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "resolved_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_incoming", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_outgoing", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ProvenanceAction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "module" : "Workspace", + "name" : "ProvenanceAction" + } + }, + "name" : "provenance", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A boolean. 0 = false, other = true.", + "module" : "Workspace", + "name" : "boolean" + }, + "name" : "hidden", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectSaveData" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object and associated data required for saving.\n\n Required arguments:\n type_string type - the type of the object. Omit the version information\n to use the latest version.\n UnspecifiedObject data - the object data.\n \n Optional arguments:\n One of an object name or id. If no name or id is provided the name\n will be set to 'auto' with the object id appended as a string,\n possibly with -\\d+ appended if that object id already exists as a\n name.\n obj_name name - the name of the object.\n obj_id objid - the id of the object to save over.\n usermeta meta - arbitrary user-supplied metadata for the object,\n not to exceed 16kb.\n list provenance - provenance data for the object.\n boolean hidden - true if this object should not be listed when listing\n workspace objects.", + "module" : "Workspace", + "name" : "ObjectSaveData" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Input parameters for the \"save_objects\" function.\n\n One, and only one, of the following is required:\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.\n \n Required arguments:\n list objects - the objects to save.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object and associated data required for saving.\n\n Required arguments:\n type_string type - the type of the object. Omit the version information\n to use the latest version.\n UnspecifiedObject data - the object data.\n \n Optional arguments:\n One of an object name or id. If no name or id is provided the name\n will be set to 'auto' with the object id appended as a string,\n possibly with -\\d+ appended if that object id already exists as a\n name.\n obj_name name - the name of the object.\n obj_id objid - the id of the object to save over.\n usermeta meta - arbitrary user-supplied metadata for the object,\n not to exceed 16kb.\n list provenance - provenance data for the object.\n boolean hidden - true if this object should not be listed when listing\n workspace objects.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "name" : "data", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, + "name" : "objid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + }, + "name" : "meta", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, + "name" : "time", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + } + }, + "name" : "method_params", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_command_line", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "input_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "resolved_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_incoming", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_outgoing", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ProvenanceAction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "module" : "Workspace", + "name" : "ProvenanceAction" + } + }, + "name" : "provenance", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A boolean. 0 = false, other = true.", + "module" : "Workspace", + "name" : "boolean" + }, + "name" : "hidden", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectSaveData" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object and associated data required for saving.\n\n Required arguments:\n type_string type - the type of the object. Omit the version information\n to use the latest version.\n UnspecifiedObject data - the object data.\n \n Optional arguments:\n One of an object name or id. If no name or id is provided the name\n will be set to 'auto' with the object id appended as a string,\n possibly with -\\d+ appended if that object id already exists as a\n name.\n obj_name name - the name of the object.\n obj_id objid - the id of the object to save over.\n usermeta meta - arbitrary user-supplied metadata for the object,\n not to exceed 16kb.\n list provenance - provenance data for the object.\n boolean hidden - true if this object should not be listed when listing\n workspace objects.", + "module" : "Workspace", + "name" : "ObjectSaveData" + } + }, + "name" : "objects", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "SaveObjectsParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Input parameters for the \"save_objects\" function.\n\n One, and only one, of the following is required:\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.\n \n Required arguments:\n list objects - the objects to save.", + "module" : "Workspace", + "name" : "SaveObjectsParams" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "Save objects to the workspace. Saving over a deleted object undeletes\nit.", + "name" : "save_objects", + "parameters" : [ { + "name" : "params", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Input parameters for the \"save_objects\" function.\n\n One, and only one, of the following is required:\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.\n \n Required arguments:\n list objects - the objects to save.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object and associated data required for saving.\n\n Required arguments:\n type_string type - the type of the object. Omit the version information\n to use the latest version.\n UnspecifiedObject data - the object data.\n \n Optional arguments:\n One of an object name or id. If no name or id is provided the name\n will be set to 'auto' with the object id appended as a string,\n possibly with -\\d+ appended if that object id already exists as a\n name.\n obj_name name - the name of the object.\n obj_id objid - the id of the object to save over.\n usermeta meta - arbitrary user-supplied metadata for the object,\n not to exceed 16kb.\n list provenance - provenance data for the object.\n boolean hidden - true if this object should not be listed when listing\n workspace objects.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "name" : "data", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, + "name" : "objid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + }, + "name" : "meta", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, + "name" : "time", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + } + }, + "name" : "method_params", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_command_line", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "input_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "resolved_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_incoming", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_outgoing", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ProvenanceAction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "module" : "Workspace", + "name" : "ProvenanceAction" + } + }, + "name" : "provenance", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A boolean. 0 = false, other = true.", + "module" : "Workspace", + "name" : "boolean" + }, + "name" : "hidden", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectSaveData" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object and associated data required for saving.\n\n Required arguments:\n type_string type - the type of the object. Omit the version information\n to use the latest version.\n UnspecifiedObject data - the object data.\n \n Optional arguments:\n One of an object name or id. If no name or id is provided the name\n will be set to 'auto' with the object id appended as a string,\n possibly with -\\d+ appended if that object id already exists as a\n name.\n obj_name name - the name of the object.\n obj_id objid - the id of the object to save over.\n usermeta meta - arbitrary user-supplied metadata for the object,\n not to exceed 16kb.\n list provenance - provenance data for the object.\n boolean hidden - true if this object should not be listed when listing\n workspace objects.", + "module" : "Workspace", + "name" : "ObjectSaveData" + } + }, + "name" : "objects", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "SaveObjectsParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Input parameters for the \"save_objects\" function.\n\n One, and only one, of the following is required:\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.\n \n Required arguments:\n list objects - the objects to save.", + "module" : "Workspace", + "name" : "SaveObjectsParams" + } + } ], + "return_type" : [ { + "name" : "info", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about an object.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.", + "element_names" : [ "objid", "name", "type", "save_date", "version", "created_by", "wsid", "chsum", "size" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "object_info" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about an object.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.", + "module" : "Workspace", + "name" : "object_info" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "The data and supplemental info for an object.\n\n UnspecifiedObject data - the object's data.\n object_info_full info - information about the object.\n list provenance - the object's provenance.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "name" : "data", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about an object, including user provided metadata.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.\n usermeta meta - arbitrary user-supplied metadata about\n the object.", + "element_names" : [ "objid", "name", "type", "save_date", "version", "created_by", "wsid", "chsum", "size", "meta" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + } ], + "name" : "object_info_full" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about an object, including user provided metadata.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.\n usermeta meta - arbitrary user-supplied metadata about\n the object.", + "module" : "Workspace", + "name" : "object_info_full" + }, + "name" : "info", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, + "name" : "time", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + } + }, + "name" : "method_params", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_command_line", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "input_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "resolved_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_incoming", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_outgoing", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ProvenanceAction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "module" : "Workspace", + "name" : "ProvenanceAction" + } + }, + "name" : "provenance", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectData" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The data and supplemental info for an object.\n\n UnspecifiedObject data - the object's data.\n object_info_full info - information about the object.\n list provenance - the object's provenance.", + "module" : "Workspace", + "name" : "ObjectData" + }, "auth_defaultoptional", { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "pre alpha version of list_workspaces so there's something to use.\nUntested.", + "name" : "prealpha_list_workspaces", + "parameters" : [ ], + "return_type" : [ { + "name" : "wsinfo", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about a workspace.\n\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace.\n username owner - name of the user who owns (e.g. created) this workspace.\n timestamp moddate - date when the workspace was last modified.\n permission user_permission - permissions for the authenticated user of\n this workspace.\n permission globalread - whether this workspace is globally readable.", + "element_names" : [ "id", "workspace", "owner", "moddate", "user_permission", "globalread" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + } ], + "name" : "workspace_info" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about a workspace.\n\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace.\n username owner - name of the user who owns (e.g. created) this workspace.\n timestamp moddate - date when the workspace was last modified.\n permission user_permission - permissions for the authenticated user of\n this workspace.\n permission globalread - whether this workspace is globally readable.", + "module" : "Workspace", + "name" : "workspace_info" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "pre alpha version of list_objects so there's something to use.\nUntested.", + "name" : "prealpha_list_objects", + "parameters" : [ { + "name" : "wsi", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "WorkspaceIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "module" : "Workspace", + "name" : "WorkspaceIdentity" + } + } ], + "return_type" : [ { + "name" : "objinfo", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about an object.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.", + "element_names" : [ "objid", "name", "type", "save_date", "version", "created_by", "wsid", "chsum", "size" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "object_info" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about an object.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.", + "module" : "Workspace", + "name" : "object_info" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "Get objects from the workspace.", + "name" : "get_objects", + "parameters" : [ { + "name" : "object_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object identifier.\n\nSelect an object by either:\n One, and only one, of the numerical id or name of the workspace,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id wsid - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID\n in KBase format, e.g. kb|ws.78.\n AND \n One, and only one, of the numerical id or name of the object.\n obj_id objid- the numerical ID of the object.\n obj_name name - name of the object.\n OPTIONALLY\n obj_ver ver - the version of the object.\nOR an object reference string:\n obj_ref ref - an object reference string.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "wsid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, + "name" : "objid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object version.\nThe version of the object, starting at 1.", + "module" : "Workspace", + "name" : "obj_ver" + }, + "name" : "ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + }, + "name" : "ref", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object identifier.\n\nSelect an object by either:\n One, and only one, of the numerical id or name of the workspace,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id wsid - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID\n in KBase format, e.g. kb|ws.78.\n AND \n One, and only one, of the numerical id or name of the object.\n obj_id objid- the numerical ID of the object.\n obj_name name - name of the object.\n OPTIONALLY\n obj_ver ver - the version of the object.\nOR an object reference string:\n obj_ref ref - an object reference string.", + "module" : "Workspace", + "name" : "ObjectIdentity" + } + } + } ], + "return_type" : [ { + "name" : "data", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "The data and supplemental info for an object.\n\n UnspecifiedObject data - the object's data.\n object_info_full info - information about the object.\n list provenance - the object's provenance.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "name" : "data", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about an object, including user provided metadata.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.\n usermeta meta - arbitrary user-supplied metadata about\n the object.", + "element_names" : [ "objid", "name", "type", "save_date", "version", "created_by", "wsid", "chsum", "size", "meta" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + } ], + "name" : "object_info_full" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about an object, including user provided metadata.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.\n usermeta meta - arbitrary user-supplied metadata about\n the object.", + "module" : "Workspace", + "name" : "object_info_full" + }, + "name" : "info", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, + "name" : "time", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + } + }, + "name" : "method_params", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_command_line", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "input_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "resolved_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_incoming", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_outgoing", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ProvenanceAction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "module" : "Workspace", + "name" : "ProvenanceAction" + } + }, + "name" : "provenance", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectData" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The data and supplemental info for an object.\n\n UnspecifiedObject data - the object's data.\n object_info_full info - information about the object.\n list provenance - the object's provenance.", + "module" : "Workspace", + "name" : "ObjectData" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "Get information about an object from the workspace.", + "name" : "get_object_info", + "parameters" : [ { + "name" : "object_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object identifier.\n\nSelect an object by either:\n One, and only one, of the numerical id or name of the workspace,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id wsid - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID\n in KBase format, e.g. kb|ws.78.\n AND \n One, and only one, of the numerical id or name of the object.\n obj_id objid- the numerical ID of the object.\n obj_name name - name of the object.\n OPTIONALLY\n obj_ver ver - the version of the object.\nOR an object reference string:\n obj_ref ref - an object reference string.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "wsid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, + "name" : "objid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object version.\nThe version of the object, starting at 1.", + "module" : "Workspace", + "name" : "obj_ver" + }, + "name" : "ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + }, + "name" : "ref", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object identifier.\n\nSelect an object by either:\n One, and only one, of the numerical id or name of the workspace,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id wsid - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID\n in KBase format, e.g. kb|ws.78.\n AND \n One, and only one, of the numerical id or name of the object.\n obj_id objid- the numerical ID of the object.\n obj_name name - name of the object.\n OPTIONALLY\n obj_ver ver - the version of the object.\nOR an object reference string:\n obj_ref ref - an object reference string.", + "module" : "Workspace", + "name" : "ObjectIdentity" + } + } + } ], + "return_type" : [ { + "name" : "info", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about an object, including user provided metadata.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.\n usermeta meta - arbitrary user-supplied metadata about\n the object.", + "element_names" : [ "objid", "name", "type", "save_date", "version", "created_by", "wsid", "chsum", "size", "meta" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + } ], + "name" : "object_info_full" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about an object, including user provided metadata.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.\n usermeta meta - arbitrary user-supplied metadata about\n the object.", + "module" : "Workspace", + "name" : "object_info_full" + } + } + } ] + }, "auth_defaultrequired", { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "Delete objects. All versions of an object are deleted, regardless of\nthe version specified in the ObjectIdentity.", + "name" : "delete_objects", + "parameters" : [ { + "name" : "object_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object identifier.\n\nSelect an object by either:\n One, and only one, of the numerical id or name of the workspace,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id wsid - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID\n in KBase format, e.g. kb|ws.78.\n AND \n One, and only one, of the numerical id or name of the object.\n obj_id objid- the numerical ID of the object.\n obj_name name - name of the object.\n OPTIONALLY\n obj_ver ver - the version of the object.\nOR an object reference string:\n obj_ref ref - an object reference string.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "wsid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, + "name" : "objid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object version.\nThe version of the object, starting at 1.", + "module" : "Workspace", + "name" : "obj_ver" + }, + "name" : "ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + }, + "name" : "ref", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object identifier.\n\nSelect an object by either:\n One, and only one, of the numerical id or name of the workspace,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id wsid - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID\n in KBase format, e.g. kb|ws.78.\n AND \n One, and only one, of the numerical id or name of the object.\n obj_id objid- the numerical ID of the object.\n obj_name name - name of the object.\n OPTIONALLY\n obj_ver ver - the version of the object.\nOR an object reference string:\n obj_ref ref - an object reference string.", + "module" : "Workspace", + "name" : "ObjectIdentity" + } + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "Undelete objects. All versions of an object are undeleted, regardless\nof the version specified in the ObjectIdentity. If an object is not\ndeleted, no error is thrown.", + "name" : "undelete_objects", + "parameters" : [ { + "name" : "object_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object identifier.\n\nSelect an object by either:\n One, and only one, of the numerical id or name of the workspace,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id wsid - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID\n in KBase format, e.g. kb|ws.78.\n AND \n One, and only one, of the numerical id or name of the object.\n obj_id objid- the numerical ID of the object.\n obj_name name - name of the object.\n OPTIONALLY\n obj_ver ver - the version of the object.\nOR an object reference string:\n obj_ref ref - an object reference string.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "wsid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, + "name" : "objid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object version.\nThe version of the object, starting at 1.", + "module" : "Workspace", + "name" : "obj_ver" + }, + "name" : "ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + }, + "name" : "ref", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object identifier.\n\nSelect an object by either:\n One, and only one, of the numerical id or name of the workspace,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id wsid - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID\n in KBase format, e.g. kb|ws.78.\n AND \n One, and only one, of the numerical id or name of the object.\n obj_id objid- the numerical ID of the object.\n obj_name name - name of the object.\n OPTIONALLY\n obj_ver ver - the version of the object.\nOR an object reference string:\n obj_ref ref - an object reference string.", + "module" : "Workspace", + "name" : "ObjectIdentity" + } + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "Delete a workspace. All objects contained in the workspace are deleted.", + "name" : "delete_workspace", + "parameters" : [ { + "name" : "wsi", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "WorkspaceIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "module" : "Workspace", + "name" : "WorkspaceIdentity" + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "Undelete a workspace. All objects contained in the workspace are\nundeleted, regardless of their state at the time the workspace was\ndeleted.", + "name" : "undelete_workspace", + "parameters" : [ { + "name" : "wsi", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "WorkspaceIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "module" : "Workspace", + "name" : "WorkspaceIdentity" + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase Interface Definition Language (KIDL) typespec.", + "module" : "Workspace", + "name" : "typespec" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a type in a KIDL typespec module.", + "module" : "Workspace", + "name" : "typename" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The JSON Schema for a type.", + "module" : "Workspace", + "name" : "jsonschema" + }, "auth_defaultrequired", { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "Request ownership of a module name.", + "name" : "request_module_ownership", + "parameters" : [ { + "name" : "mod", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Parameters for the compile_typespec function.\n\n Required arguments:\n One of:\n typespec spec - the new typespec to compile.\n modulename mod - the module to recompile.\n \n Optional arguments:\n boolean dryrun - Return, but do not save, the results of compiling the \n spec. Default true. Set to false for making permanent changes.\n list new_types - types in the spec to make available in the\n workspace service. When compiling a spec for the first time, if\n this argument is empty no types will be made available. Previously\n available types remain so upon recompilation of a spec or\n compilation of a new spec.\n list remove_types - no longer make these types available in\n the workspace service for the new version of the spec. This does\n not remove versions of types previously compiled.\n mapping dependencies - By default, the\n latest released versions of spec dependencies will be included when\n compiling a spec. Specific versions can be specified here.\n spec_version prev_ver - the id of the previous version of the typespec.\n An error will be thrown if this is set and prev_ver is not the\n most recent version of the typespec. This prevents overwriting of\n changes made since retrieving a spec and compiling an edited spec.\n This argument is ignored if a modulename is passed.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase Interface Definition Language (KIDL) typespec.", + "module" : "Workspace", + "name" : "typespec" + }, + "name" : "spec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "name" : "mod", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a type in a KIDL typespec module.", + "module" : "Workspace", + "name" : "typename" + } + }, + "name" : "new_types", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a type in a KIDL typespec module.", + "module" : "Workspace", + "name" : "typename" + } + }, + "name" : "remove_types", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + } + }, + "name" : "dependencies", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A boolean. 0 = false, other = true.", + "module" : "Workspace", + "name" : "boolean" + }, + "name" : "dryrun", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + }, + "name" : "prev_ver", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "CompileTypespecParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Parameters for the compile_typespec function.\n\n Required arguments:\n One of:\n typespec spec - the new typespec to compile.\n modulename mod - the module to recompile.\n \n Optional arguments:\n boolean dryrun - Return, but do not save, the results of compiling the \n spec. Default true. Set to false for making permanent changes.\n list new_types - types in the spec to make available in the\n workspace service. When compiling a spec for the first time, if\n this argument is empty no types will be made available. Previously\n available types remain so upon recompilation of a spec or\n compilation of a new spec.\n list remove_types - no longer make these types available in\n the workspace service for the new version of the spec. This does\n not remove versions of types previously compiled.\n mapping dependencies - By default, the\n latest released versions of spec dependencies will be included when\n compiling a spec. Specific versions can be specified here.\n spec_version prev_ver - the id of the previous version of the typespec.\n An error will be thrown if this is set and prev_ver is not the\n most recent version of the typespec. This prevents overwriting of\n changes made since retrieving a spec and compiling an edited spec.\n This argument is ignored if a modulename is passed.", + "module" : "Workspace", + "name" : "CompileTypespecParams" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "Compile a new typespec or recompile an existing typespec. \nAlso see the release_types function.", + "name" : "compile_typespec", + "parameters" : [ { + "name" : "params", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Parameters for the compile_typespec function.\n\n Required arguments:\n One of:\n typespec spec - the new typespec to compile.\n modulename mod - the module to recompile.\n \n Optional arguments:\n boolean dryrun - Return, but do not save, the results of compiling the \n spec. Default true. Set to false for making permanent changes.\n list new_types - types in the spec to make available in the\n workspace service. When compiling a spec for the first time, if\n this argument is empty no types will be made available. Previously\n available types remain so upon recompilation of a spec or\n compilation of a new spec.\n list remove_types - no longer make these types available in\n the workspace service for the new version of the spec. This does\n not remove versions of types previously compiled.\n mapping dependencies - By default, the\n latest released versions of spec dependencies will be included when\n compiling a spec. Specific versions can be specified here.\n spec_version prev_ver - the id of the previous version of the typespec.\n An error will be thrown if this is set and prev_ver is not the\n most recent version of the typespec. This prevents overwriting of\n changes made since retrieving a spec and compiling an edited spec.\n This argument is ignored if a modulename is passed.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase Interface Definition Language (KIDL) typespec.", + "module" : "Workspace", + "name" : "typespec" + }, + "name" : "spec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "name" : "mod", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a type in a KIDL typespec module.", + "module" : "Workspace", + "name" : "typename" + } + }, + "name" : "new_types", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a type in a KIDL typespec module.", + "module" : "Workspace", + "name" : "typename" + } + }, + "name" : "remove_types", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + } + }, + "name" : "dependencies", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A boolean. 0 = false, other = true.", + "module" : "Workspace", + "name" : "boolean" + }, + "name" : "dryrun", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + }, + "name" : "prev_ver", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "CompileTypespecParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Parameters for the compile_typespec function.\n\n Required arguments:\n One of:\n typespec spec - the new typespec to compile.\n modulename mod - the module to recompile.\n \n Optional arguments:\n boolean dryrun - Return, but do not save, the results of compiling the \n spec. Default true. Set to false for making permanent changes.\n list new_types - types in the spec to make available in the\n workspace service. When compiling a spec for the first time, if\n this argument is empty no types will be made available. Previously\n available types remain so upon recompilation of a spec or\n compilation of a new spec.\n list remove_types - no longer make these types available in\n the workspace service for the new version of the spec. This does\n not remove versions of types previously compiled.\n mapping dependencies - By default, the\n latest released versions of spec dependencies will be included when\n compiling a spec. Specific versions can be specified here.\n spec_version prev_ver - the id of the previous version of the typespec.\n An error will be thrown if this is set and prev_ver is not the\n most recent version of the typespec. This prevents overwriting of\n changes made since retrieving a spec and compiling an edited spec.\n This argument is ignored if a modulename is passed.", + "module" : "Workspace", + "name" : "CompileTypespecParams" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The JSON Schema for a type.", + "module" : "Workspace", + "name" : "jsonschema" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "Compile a copy of new typespec or recompile an existing typespec which is loaded \nfrom another workspace for synchronization. Method returns new version of module \nin current workspace. Also see the release_types function.", + "name" : "compile_typespec_copy", + "parameters" : [ { + "name" : "external_workspace_url", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "mod", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + } + }, { + "name" : "version_in_external_workspace", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + } + } ], + "return_type" : [ { + "name" : "new_local_version", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "Release a module for general use of its types.\n\nReleases the most recent version of a module. Releasing a module does\ntwo things to the module's types:\n1) If a type's major version is 0, it is changed to 1. A major\n version of 0 implies that the type is in development and may have\n backwards incompatible changes from minor version to minor version.\n Once a type is released, backwards incompatible changes always\n cause a major version increment.\n2) This version of the type becomes the default version, and if a \n specific version is not supplied in a function call, this version\n will be used. This means that newer, unreleased versions of the\n type may be skipped.", + "name" : "release_module", + "parameters" : [ { + "name" : "mod", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + } + } ], + "return_type" : [ { + "name" : "types", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + } + } + } ] + }, "auth_defaultnone", { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Parameters for the list_modules() function.\n\n Optional arguments:\n username owner - only list modules owned by this user.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, + "name" : "owner", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ListModulesParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Parameters for the list_modules() function.\n\n Optional arguments:\n username owner - only list modules owned by this user.", + "module" : "Workspace", + "name" : "ListModulesParams" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "List typespec modules.", + "name" : "list_modules", + "parameters" : [ { + "name" : "params", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Parameters for the list_modules() function.\n\n Optional arguments:\n username owner - only list modules owned by this user.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, + "name" : "owner", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ListModulesParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Parameters for the list_modules() function.\n\n Optional arguments:\n username owner - only list modules owned by this user.", + "module" : "Workspace", + "name" : "ListModulesParams" + } + } ], + "return_type" : [ { + "name" : "modules", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Parameters for the list_module_versions function.\n\n Required arguments:\n One of:\n modulename mod - returns all versions of the module.\n type_string type - returns all versions of the module associated with\n the type.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "name" : "mod", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "name" : "type", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ListModuleVersionsParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Parameters for the list_module_versions function.\n\n Required arguments:\n One of:\n modulename mod - returns all versions of the module.\n type_string type - returns all versions of the module associated with\n the type.", + "module" : "Workspace", + "name" : "ListModuleVersionsParams" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A set of versions from a module.\n\n modulename mod - the name of the module.\n list - a set or subset of versions associated with the\n module.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "name" : "mod", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + } + }, + "name" : "vers", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ModuleVersions" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A set of versions from a module.\n\n modulename mod - the name of the module.\n list - a set or subset of versions associated with the\n module.", + "module" : "Workspace", + "name" : "ModuleVersions" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "List typespec module versions.", + "name" : "list_module_versions", + "parameters" : [ { + "name" : "params", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Parameters for the list_module_versions function.\n\n Required arguments:\n One of:\n modulename mod - returns all versions of the module.\n type_string type - returns all versions of the module associated with\n the type.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "name" : "mod", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "name" : "type", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ListModuleVersionsParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Parameters for the list_module_versions function.\n\n Required arguments:\n One of:\n modulename mod - returns all versions of the module.\n type_string type - returns all versions of the module associated with\n the type.", + "module" : "Workspace", + "name" : "ListModuleVersionsParams" + } + } ], + "return_type" : [ { + "name" : "vers", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A set of versions from a module.\n\n modulename mod - the name of the module.\n list - a set or subset of versions associated with the\n module.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "name" : "mod", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + } + }, + "name" : "vers", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ModuleVersions" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A set of versions from a module.\n\n modulename mod - the name of the module.\n list - a set or subset of versions associated with the\n module.", + "module" : "Workspace", + "name" : "ModuleVersions" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Parameters for the get_module_info function.\n\n Required arguments:\n modulename mod - the name of the module to retrieve.\n \n Optional arguments:\n spec_version ver - the version of the module to retrieve. Defaults to\n the latest version.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "name" : "mod", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + }, + "name" : "ver", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "GetModuleInfoParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Parameters for the get_module_info function.\n\n Required arguments:\n modulename mod - the name of the module to retrieve.\n \n Optional arguments:\n spec_version ver - the version of the module to retrieve. Defaults to\n the latest version.", + "module" : "Workspace", + "name" : "GetModuleInfoParams" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Information about a module.\n\n list owners - the owners of the module.\n spec_version ver - the version of the module.\n typespec spec - the typespec.\n string description - the description of the module from the typespec.\n mapping types - the types associated with this\n module and their JSON schema.\n mapping included_spec_version - names of \n included modules associated with their versions.\n string chsum - the md5 checksum of the object.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + } + }, + "name" : "owners", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + }, + "name" : "ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase Interface Definition Language (KIDL) typespec.", + "module" : "Workspace", + "name" : "typespec" + }, + "name" : "spec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The JSON Schema for a type.", + "module" : "Workspace", + "name" : "jsonschema" + } + }, + "name" : "types", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + } + }, + "name" : "included_spec_version", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "chsum", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ModuleInfo" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about a module.\n\n list owners - the owners of the module.\n spec_version ver - the version of the module.\n typespec spec - the typespec.\n string description - the description of the module from the typespec.\n mapping types - the types associated with this\n module and their JSON schema.\n mapping included_spec_version - names of \n included modules associated with their versions.\n string chsum - the md5 checksum of the object.", + "module" : "Workspace", + "name" : "ModuleInfo" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "", + "name" : "get_module_info", + "parameters" : [ { + "name" : "params", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Parameters for the get_module_info function.\n\n Required arguments:\n modulename mod - the name of the module to retrieve.\n \n Optional arguments:\n spec_version ver - the version of the module to retrieve. Defaults to\n the latest version.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "name" : "mod", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + }, + "name" : "ver", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "GetModuleInfoParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Parameters for the get_module_info function.\n\n Required arguments:\n modulename mod - the name of the module to retrieve.\n \n Optional arguments:\n spec_version ver - the version of the module to retrieve. Defaults to\n the latest version.", + "module" : "Workspace", + "name" : "GetModuleInfoParams" + } + } ], + "return_type" : [ { + "name" : "info", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Information about a module.\n\n list owners - the owners of the module.\n spec_version ver - the version of the module.\n typespec spec - the typespec.\n string description - the description of the module from the typespec.\n mapping types - the types associated with this\n module and their JSON schema.\n mapping included_spec_version - names of \n included modules associated with their versions.\n string chsum - the md5 checksum of the object.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + } + }, + "name" : "owners", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + }, + "name" : "ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase Interface Definition Language (KIDL) typespec.", + "module" : "Workspace", + "name" : "typespec" + }, + "name" : "spec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The JSON Schema for a type.", + "module" : "Workspace", + "name" : "jsonschema" + } + }, + "name" : "types", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + } + }, + "name" : "included_spec_version", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "chsum", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ModuleInfo" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about a module.\n\n list owners - the owners of the module.\n spec_version ver - the version of the module.\n typespec spec - the typespec.\n string description - the description of the module from the typespec.\n mapping types - the types associated with this\n module and their JSON schema.\n mapping included_spec_version - names of \n included modules associated with their versions.\n string chsum - the md5 checksum of the object.", + "module" : "Workspace", + "name" : "ModuleInfo" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Get JSON schema for a type.", + "name" : "get_jsonschema", + "parameters" : [ { + "name" : "type", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + } + } ], + "return_type" : [ { + "name" : "schema", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The JSON Schema for a type.", + "module" : "Workspace", + "name" : "jsonschema" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Translation from types qualified with MD5 to their semantic versions", + "name" : "translate_from_MD5_types", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + } + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Translation from types qualified with semantic versions to their MD5'ed versions", + "name" : "translate_to_MD5_types", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "required", + "comment" : "The administration interface.", + "name" : "administer", + "parameters" : [ { + "name" : "command", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + } + } ], + "return_type" : [ { + "name" : "response", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + } + } ] + } ], + "module_name" : "Workspace", + "options" : [ ], + "service_name" : "Workspace" + }, [ ], { + "CompileTypespecParams" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Parameters for the compile_typespec function.\n\n Required arguments:\n One of:\n typespec spec - the new typespec to compile.\n modulename mod - the module to recompile.\n \n Optional arguments:\n boolean dryrun - Return, but do not save, the results of compiling the \n spec. Default true. Set to false for making permanent changes.\n list new_types - types in the spec to make available in the\n workspace service. When compiling a spec for the first time, if\n this argument is empty no types will be made available. Previously\n available types remain so upon recompilation of a spec or\n compilation of a new spec.\n list remove_types - no longer make these types available in\n the workspace service for the new version of the spec. This does\n not remove versions of types previously compiled.\n mapping dependencies - By default, the\n latest released versions of spec dependencies will be included when\n compiling a spec. Specific versions can be specified here.\n spec_version prev_ver - the id of the previous version of the typespec.\n An error will be thrown if this is set and prev_ver is not the\n most recent version of the typespec. This prevents overwriting of\n changes made since retrieving a spec and compiling an edited spec.\n This argument is ignored if a modulename is passed.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase Interface Definition Language (KIDL) typespec.", + "module" : "Workspace", + "name" : "typespec" + }, + "name" : "spec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "name" : "mod", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a type in a KIDL typespec module.", + "module" : "Workspace", + "name" : "typename" + } + }, + "name" : "new_types", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a type in a KIDL typespec module.", + "module" : "Workspace", + "name" : "typename" + } + }, + "name" : "remove_types", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + } + }, + "name" : "dependencies", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A boolean. 0 = false, other = true.", + "module" : "Workspace", + "name" : "boolean" + }, + "name" : "dryrun", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + }, + "name" : "prev_ver", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "CompileTypespecParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Parameters for the compile_typespec function.\n\n Required arguments:\n One of:\n typespec spec - the new typespec to compile.\n modulename mod - the module to recompile.\n \n Optional arguments:\n boolean dryrun - Return, but do not save, the results of compiling the \n spec. Default true. Set to false for making permanent changes.\n list new_types - types in the spec to make available in the\n workspace service. When compiling a spec for the first time, if\n this argument is empty no types will be made available. Previously\n available types remain so upon recompilation of a spec or\n compilation of a new spec.\n list remove_types - no longer make these types available in\n the workspace service for the new version of the spec. This does\n not remove versions of types previously compiled.\n mapping dependencies - By default, the\n latest released versions of spec dependencies will be included when\n compiling a spec. Specific versions can be specified here.\n spec_version prev_ver - the id of the previous version of the typespec.\n An error will be thrown if this is set and prev_ver is not the\n most recent version of the typespec. This prevents overwriting of\n changes made since retrieving a spec and compiling an edited spec.\n This argument is ignored if a modulename is passed.", + "module" : "Workspace", + "name" : "CompileTypespecParams" + }, + "CreateWorkspaceParams" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Input parameters for the \"create_workspace\" function.\n\n Required arguments:\n ws_name workspace - name of the workspace to be created.\n \n Optional arguments:\n permission globalread - 'r' to set workspace globally readable,\n default 'n'.\n string description - A free-text description of the workspace, 1000\n characters max. Longer strings will be mercilessly and brutally\n truncated.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, + "name" : "globalread", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "CreateWorkspaceParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Input parameters for the \"create_workspace\" function.\n\n Required arguments:\n ws_name workspace - name of the workspace to be created.\n \n Optional arguments:\n permission globalread - 'r' to set workspace globally readable,\n default 'n'.\n string description - A free-text description of the workspace, 1000\n characters max. Longer strings will be mercilessly and brutally\n truncated.", + "module" : "Workspace", + "name" : "CreateWorkspaceParams" + }, + "GetModuleInfoParams" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Parameters for the get_module_info function.\n\n Required arguments:\n modulename mod - the name of the module to retrieve.\n \n Optional arguments:\n spec_version ver - the version of the module to retrieve. Defaults to\n the latest version.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "name" : "mod", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + }, + "name" : "ver", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "GetModuleInfoParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Parameters for the get_module_info function.\n\n Required arguments:\n modulename mod - the name of the module to retrieve.\n \n Optional arguments:\n spec_version ver - the version of the module to retrieve. Defaults to\n the latest version.", + "module" : "Workspace", + "name" : "GetModuleInfoParams" + }, + "ListModuleVersionsParams" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Parameters for the list_module_versions function.\n\n Required arguments:\n One of:\n modulename mod - returns all versions of the module.\n type_string type - returns all versions of the module associated with\n the type.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "name" : "mod", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "name" : "type", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ListModuleVersionsParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Parameters for the list_module_versions function.\n\n Required arguments:\n One of:\n modulename mod - returns all versions of the module.\n type_string type - returns all versions of the module associated with\n the type.", + "module" : "Workspace", + "name" : "ListModuleVersionsParams" + }, + "ListModulesParams" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Parameters for the list_modules() function.\n\n Optional arguments:\n username owner - only list modules owned by this user.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, + "name" : "owner", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ListModulesParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Parameters for the list_modules() function.\n\n Optional arguments:\n username owner - only list modules owned by this user.", + "module" : "Workspace", + "name" : "ListModulesParams" + }, + "ModuleInfo" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Information about a module.\n\n list owners - the owners of the module.\n spec_version ver - the version of the module.\n typespec spec - the typespec.\n string description - the description of the module from the typespec.\n mapping types - the types associated with this\n module and their JSON schema.\n mapping included_spec_version - names of \n included modules associated with their versions.\n string chsum - the md5 checksum of the object.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + } + }, + "name" : "owners", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + }, + "name" : "ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase Interface Definition Language (KIDL) typespec.", + "module" : "Workspace", + "name" : "typespec" + }, + "name" : "spec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The JSON Schema for a type.", + "module" : "Workspace", + "name" : "jsonschema" + } + }, + "name" : "types", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + } + }, + "name" : "included_spec_version", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "chsum", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ModuleInfo" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about a module.\n\n list owners - the owners of the module.\n spec_version ver - the version of the module.\n typespec spec - the typespec.\n string description - the description of the module from the typespec.\n mapping types - the types associated with this\n module and their JSON schema.\n mapping included_spec_version - names of \n included modules associated with their versions.\n string chsum - the md5 checksum of the object.", + "module" : "Workspace", + "name" : "ModuleInfo" + }, + "ModuleVersions" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A set of versions from a module.\n\n modulename mod - the name of the module.\n list - a set or subset of versions associated with the\n module.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "name" : "mod", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + } + }, + "name" : "vers", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ModuleVersions" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A set of versions from a module.\n\n modulename mod - the name of the module.\n list - a set or subset of versions associated with the\n module.", + "module" : "Workspace", + "name" : "ModuleVersions" + }, + "ObjectData" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "The data and supplemental info for an object.\n\n UnspecifiedObject data - the object's data.\n object_info_full info - information about the object.\n list provenance - the object's provenance.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "name" : "data", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about an object, including user provided metadata.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.\n usermeta meta - arbitrary user-supplied metadata about\n the object.", + "element_names" : [ "objid", "name", "type", "save_date", "version", "created_by", "wsid", "chsum", "size", "meta" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + } ], + "name" : "object_info_full" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about an object, including user provided metadata.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.\n usermeta meta - arbitrary user-supplied metadata about\n the object.", + "module" : "Workspace", + "name" : "object_info_full" + }, + "name" : "info", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, + "name" : "time", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + } + }, + "name" : "method_params", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_command_line", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "input_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "resolved_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_incoming", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_outgoing", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ProvenanceAction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "module" : "Workspace", + "name" : "ProvenanceAction" + } + }, + "name" : "provenance", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectData" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The data and supplemental info for an object.\n\n UnspecifiedObject data - the object's data.\n object_info_full info - information about the object.\n list provenance - the object's provenance.", + "module" : "Workspace", + "name" : "ObjectData" + }, + "ObjectIdentity" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object identifier.\n\nSelect an object by either:\n One, and only one, of the numerical id or name of the workspace,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id wsid - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID\n in KBase format, e.g. kb|ws.78.\n AND \n One, and only one, of the numerical id or name of the object.\n obj_id objid- the numerical ID of the object.\n obj_name name - name of the object.\n OPTIONALLY\n obj_ver ver - the version of the object.\nOR an object reference string:\n obj_ref ref - an object reference string.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "wsid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, + "name" : "objid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object version.\nThe version of the object, starting at 1.", + "module" : "Workspace", + "name" : "obj_ver" + }, + "name" : "ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + }, + "name" : "ref", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object identifier.\n\nSelect an object by either:\n One, and only one, of the numerical id or name of the workspace,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id wsid - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID\n in KBase format, e.g. kb|ws.78.\n AND \n One, and only one, of the numerical id or name of the object.\n obj_id objid- the numerical ID of the object.\n obj_name name - name of the object.\n OPTIONALLY\n obj_ver ver - the version of the object.\nOR an object reference string:\n obj_ref ref - an object reference string.", + "module" : "Workspace", + "name" : "ObjectIdentity" + }, + "ObjectSaveData" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object and associated data required for saving.\n\n Required arguments:\n type_string type - the type of the object. Omit the version information\n to use the latest version.\n UnspecifiedObject data - the object data.\n \n Optional arguments:\n One of an object name or id. If no name or id is provided the name\n will be set to 'auto' with the object id appended as a string,\n possibly with -\\d+ appended if that object id already exists as a\n name.\n obj_name name - the name of the object.\n obj_id objid - the id of the object to save over.\n usermeta meta - arbitrary user-supplied metadata for the object,\n not to exceed 16kb.\n list provenance - provenance data for the object.\n boolean hidden - true if this object should not be listed when listing\n workspace objects.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "name" : "data", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, + "name" : "objid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + }, + "name" : "meta", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, + "name" : "time", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + } + }, + "name" : "method_params", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_command_line", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "input_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "resolved_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_incoming", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_outgoing", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ProvenanceAction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "module" : "Workspace", + "name" : "ProvenanceAction" + } + }, + "name" : "provenance", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A boolean. 0 = false, other = true.", + "module" : "Workspace", + "name" : "boolean" + }, + "name" : "hidden", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectSaveData" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object and associated data required for saving.\n\n Required arguments:\n type_string type - the type of the object. Omit the version information\n to use the latest version.\n UnspecifiedObject data - the object data.\n \n Optional arguments:\n One of an object name or id. If no name or id is provided the name\n will be set to 'auto' with the object id appended as a string,\n possibly with -\\d+ appended if that object id already exists as a\n name.\n obj_name name - the name of the object.\n obj_id objid - the id of the object to save over.\n usermeta meta - arbitrary user-supplied metadata for the object,\n not to exceed 16kb.\n list provenance - provenance data for the object.\n boolean hidden - true if this object should not be listed when listing\n workspace objects.", + "module" : "Workspace", + "name" : "ObjectSaveData" + }, + "ProvenanceAction" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, + "name" : "time", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + } + }, + "name" : "method_params", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_command_line", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "input_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "resolved_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_incoming", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_outgoing", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ProvenanceAction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "module" : "Workspace", + "name" : "ProvenanceAction" + }, + "SaveObjectsParams" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Input parameters for the \"save_objects\" function.\n\n One, and only one, of the following is required:\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.\n \n Required arguments:\n list objects - the objects to save.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object and associated data required for saving.\n\n Required arguments:\n type_string type - the type of the object. Omit the version information\n to use the latest version.\n UnspecifiedObject data - the object data.\n \n Optional arguments:\n One of an object name or id. If no name or id is provided the name\n will be set to 'auto' with the object id appended as a string,\n possibly with -\\d+ appended if that object id already exists as a\n name.\n obj_name name - the name of the object.\n obj_id objid - the id of the object to save over.\n usermeta meta - arbitrary user-supplied metadata for the object,\n not to exceed 16kb.\n list provenance - provenance data for the object.\n boolean hidden - true if this object should not be listed when listing\n workspace objects.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "name" : "data", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, + "name" : "objid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + }, + "name" : "meta", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, + "name" : "time", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "service_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + } + }, + "name" : "method_params", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_ver", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "script_command_line", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "input_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + } + }, + "name" : "resolved_ws_objects", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_incoming", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "intermediate_outgoing", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ProvenanceAction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A provenance action.\n\n A provenance action is an action taken while transforming one data\n object to another. There may be several provenance actions taken in\n series. An action is typically running a script, running an api\n command, etc. All of the following are optional, but more information\n provided equates to better data provenance.\n \n resolved_ws_objects should never be set by the user; it is set by the\n workspace service when returning data.\n \n The maximum size of the entire provenance object is 1MB.\n \n timestamp time - the time the action was started.\n string service - the name of the service that performed this action.\n int service_ver - the version of the service that performed this action.\n string method - the method of the service that performed this action.\n list method_params - the parameters of the method\n that performed this action. If an object in the parameters is a\n workspace object, also put the object reference in the\n input_ws_object list.\n string script - the name of the script that performed this action.\n int script_ver - the version of the script that performed this action.\n string script_command_line - the command line provided to the script\n that performed this action. If workspace objects were provided in\n the command line, also put the object reference in the\n input_ws_object list.\n list input_ws_objects - the workspace objects that\n were used as input to this action; typically these will also be\n present as parts of the method_params or the script_command_line\n arguments.\n list resolved_ws_objects - the workspace objects ids from \n input_ws_objects resolved to permanent workspace object references\n by the workspace service.\n list intermediate_incoming - if the previous action produced \n output that 1) was not stored in a referrable way, and 2) is\n used as input for this action, provide it with an arbitrary and\n unique ID here, in the order of the input arguments to this action.\n These IDs can be used in the method_params argument.\n list intermediate_outgoing - if this action produced output\n that 1) was not stored in a referrable way, and 2) is\n used as input for the next action, provide it with an arbitrary and\n unique ID here, in the order of the output values from this action.\n These IDs can be used in the intermediate_incoming argument in the\n next action.\n string description - a free text description of this action.", + "module" : "Workspace", + "name" : "ProvenanceAction" + } + }, + "name" : "provenance", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A boolean. 0 = false, other = true.", + "module" : "Workspace", + "name" : "boolean" + }, + "name" : "hidden", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "ObjectSaveData" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object and associated data required for saving.\n\n Required arguments:\n type_string type - the type of the object. Omit the version information\n to use the latest version.\n UnspecifiedObject data - the object data.\n \n Optional arguments:\n One of an object name or id. If no name or id is provided the name\n will be set to 'auto' with the object id appended as a string,\n possibly with -\\d+ appended if that object id already exists as a\n name.\n obj_name name - the name of the object.\n obj_id objid - the id of the object to save over.\n usermeta meta - arbitrary user-supplied metadata for the object,\n not to exceed 16kb.\n list provenance - provenance data for the object.\n boolean hidden - true if this object should not be listed when listing\n workspace objects.", + "module" : "Workspace", + "name" : "ObjectSaveData" + } + }, + "name" : "objects", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "SaveObjectsParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Input parameters for the \"save_objects\" function.\n\n One, and only one, of the following is required:\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.\n \n Required arguments:\n list objects - the objects to save.", + "module" : "Workspace", + "name" : "SaveObjectsParams" + }, + "SetPermissionsParams" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Input parameters for the \"set_permissions\" function.\n\n One, and only one, of the following is required:\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.\n \n Required arguments:\n permission new_permission - the permission to assign to the users.\n list users - the users whose permissions will be altered.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, + "name" : "new_permission", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + } + }, + "name" : "users", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "SetPermissionsParams" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Input parameters for the \"set_permissions\" function.\n\n One, and only one, of the following is required:\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.\n \n Required arguments:\n permission new_permission - the permission to assign to the users.\n list users - the users whose permissions will be altered.", + "module" : "Workspace", + "name" : "SetPermissionsParams" + }, + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "WorkspaceIdentity" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, + "name" : "workspace", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "name" : "id", + "nullable" : "0" + } ], + "module" : "Workspace", + "name" : "WorkspaceIdentity" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace identifier.\n\n Select a workspace by one, and only one, of the numerical id or name,\n where the name can also be a KBase ID including the numerical id,\n e.g. kb|ws.35.\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace or the workspace ID in KBase\n format, e.g. kb|ws.78.", + "module" : "Workspace", + "name" : "WorkspaceIdentity" + }, + "boolean" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A boolean. 0 = false, other = true.", + "module" : "Workspace", + "name" : "boolean" + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "jsonschema" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The JSON Schema for a type.", + "module" : "Workspace", + "name" : "jsonschema" + }, + "modulename" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The module name of a KIDL typespec.", + "module" : "Workspace", + "name" : "modulename" + }, + "obj_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, + "obj_name" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, + "obj_ref" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string that uniquely identifies an object in the workspace service.\n\n There are two ways to uniquely identify an object in one string:\n \"[ws_name or id]/[obj_name or id]/[obj_ver]\" - for example,\n \"MyFirstWorkspace/MyFirstObject/3\" would identify the third version\n of an object called MyFirstObject in the workspace called\n MyFirstWorkspace. 42/Panic/1 would identify the first version of\n the object name Panic in workspace 42. Towel/1/6 would identify\n the 6th version of the object with id 1 in the Towel workspace. \n \"kb|ws.[ws_id].obj.[obj_id].ver.[obj_ver]\" - for example, \n \"kb|ws.23.obj.567.ver.2\" would identify the second version of an\n object with id 567 in a workspace with id 23.\n In all cases, if the version number is omitted, the latest version of\n the object is assumed.", + "module" : "Workspace", + "name" : "obj_ref" + }, + "obj_ver" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object version.\nThe version of the object, starting at 1.", + "module" : "Workspace", + "name" : "obj_ver" + }, + "object_info" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about an object.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.", + "element_names" : [ "objid", "name", "type", "save_date", "version", "created_by", "wsid", "chsum", "size" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "object_info" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about an object.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.", + "module" : "Workspace", + "name" : "object_info" + }, + "object_info_full" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about an object, including user provided metadata.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.\n usermeta meta - arbitrary user-supplied metadata about\n the object.", + "element_names" : [ "objid", "name", "type", "save_date", "version", "created_by", "wsid", "chsum", "size", "meta" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of an object.", + "module" : "Workspace", + "name" : "obj_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for an object.\nAny string consisting of alphanumeric characters and the characters\n |._- that is not an integer is acceptable.", + "module" : "Workspace", + "name" : "obj_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + } ], + "name" : "object_info_full" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about an object, including user provided metadata.\n\n obj_id objid - the numerical id of the object.\n obj_name name - the name of the object.\n type_string type - the type of the object.\n timestamp save_date - the save date of the object.\n obj_ver ver - the version of the object.\n username created_by - the user that created the object.\n ws_id wsid - the workspace containing the object.\n string chsum - the md5 checksum of the object.\n int size - the size of the object in bytes.\n usermeta meta - arbitrary user-supplied metadata about\n the object.", + "module" : "Workspace", + "name" : "object_info_full" + }, + "permission" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, + "spec_version" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The version of a typespec.", + "module" : "Workspace", + "name" : "spec_version" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "timestamp" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, + "type_string" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A type string.\nSpecifies the type and its version in a single string in the format\n[module].[typename]-[major].[minor]:\n\nmodule - a string. The module name of the typespec containing the type.\ntypename - a string. The name of the type as assigned by the typedef\n statement.\nmajor - an integer. The major version of the type. A change in the\n major version implies the type has changed in a non-backwards\n compatible way.\nminor - an integer. The minor version of the type. A change in the\n minor version implies that the type has changed in a way that is\n backwards compatible with previous type definitions.\n\nIn many cases, the major and minor versions are optional, and if not\nprovided the most recent version will be used.\n\nExample: MyModule.MyType-3.1", + "module" : "Workspace", + "name" : "type_string" + }, + "typename" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a type in a KIDL typespec module.", + "module" : "Workspace", + "name" : "typename" + }, + "typespec" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase Interface Definition Language (KIDL) typespec.", + "module" : "Workspace", + "name" : "typespec" + }, + "usermeta" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "User provided metadata about an object.\nArbitrary key-value pairs provided by the user.", + "module" : "Workspace", + "name" : "usermeta" + }, + "username" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, + "workspace_info" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Information about a workspace.\n\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace.\n username owner - name of the user who owns (e.g. created) this workspace.\n timestamp moddate - date when the workspace was last modified.\n permission user_permission - permissions for the authenticated user of\n this workspace.\n permission globalread - whether this workspace is globally readable.", + "element_names" : [ "id", "workspace", "owner", "moddate", "user_permission", "globalread" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of a KBase user account.", + "module" : "Workspace", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A time in the format YYYY-MM-DDThh:mm:ssZ, where Z is the difference\nin time to UTC in the format +/-HHMM, eg:\n 2012-12-17T23:24:06-0500 (EST time)\n 2013-04-03T08:56:32+0000 (UTC time)", + "module" : "Workspace", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the permissions a user or users have to a workspace:\n\n 'a' - administrator. All operations allowed.\n 'w' - read/write.\n 'r' - read.\n 'n' - no permissions.", + "module" : "Workspace", + "name" : "permission" + } ], + "name" : "workspace_info" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Information about a workspace.\n\n ws_id id - the numerical ID of the workspace.\n ws_name workspace - name of the workspace.\n username owner - name of the user who owns (e.g. created) this workspace.\n timestamp moddate - date when the workspace was last modified.\n permission user_permission - permissions for the authenticated user of\n this workspace.\n permission globalread - whether this workspace is globally readable.", + "module" : "Workspace", + "name" : "workspace_info" + }, + "ws_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique, permanent numerical ID of a workspace.", + "module" : "Workspace", + "name" : "ws_id" + }, + "ws_name" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as a name for a workspace.\nAny string consisting of alphanumeric characters and \"_\" that is not an\ninteger is acceptable.", + "module" : "Workspace", + "name" : "ws_name" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.10.json.properties b/src/test/resources/us/kbase/test/kidl/spec.10.json.properties new file mode 100644 index 0000000..c1fbc65 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.10.json.properties @@ -0,0 +1,5146 @@ +{ + "KBaseNetworks" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "Module KBaseNetworks version 1.0\nThis module provides access to various types of network-related datasets across all domains of KBase in a unified format.\n\nNetworks are composed of Nodes and Edges. Nodes represent entities from the datasets (e.g., genes, proteins,\nbiclusters, subystems, etc.), and edges represent relationships (e.g., protein-protein interactions,\ngene-subsystem membership, etc.). Networks can contain Nodes and Edges from multiple datasets.\n\nAll methods in this module can be classified into two types: \ni. getting general information about datasets and network types currently available via KBaseNetworks API\n For example: allDatasetSources(), allNetworkTypes(), datasetSource2Datasets()\nii. building various types of Network objects\n For example: buildFirstNeighborNetwork(), buildInternalNetwork()", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of node in a network", + "module" : "KBaseNetworks", + "name" : "NodeType" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of edge in a network", + "module" : "KBaseNetworks", + "name" : "EdgeType" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values; either \"true\" or \"false\"", + "module" : "KBaseNetworks", + "name" : "Boolean" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Provides detailed information about the source of a dataset.\nstring id - A unique KBase identifier of a dataset source\nstring name - A name of a dataset source\n DatasetSourceRef reference - Reference to a dataset source\n string description - General description of a dataset source\n string resourceURL - URL of the public web resource hosting the data represented by this dataset source", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "reference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "resourceURL", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "DatasetSource" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Provides detailed information about the source of a dataset.\nstring id - A unique KBase identifier of a dataset source\nstring name - A name of a dataset source\n DatasetSourceRef reference - Reference to a dataset source\n string description - General description of a dataset source\n string resourceURL - URL of the public web resource hosting the data represented by this dataset source", + "module" : "KBaseNetworks", + "name" : "DatasetSource" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "entityId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of node in a network", + "module" : "KBaseNetworks", + "name" : "NodeType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Node" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "module" : "KBaseNetworks", + "name" : "Node" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values; either \"true\" or \"false\"", + "module" : "KBaseNetworks", + "name" : "Boolean" + }, + "name" : "directed", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "datasetId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Edge" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "module" : "KBaseNetworks", + "name" : "Edge" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a network\nstring id - A unique KBase identifier of a network \n string name - String representation of a network. It should be a concise but informative representation that is easy for a person to read.\nlist edges - A list of all edges in a network\nlist nodes - A list of all nodes in a network\nlist datasets - A list of all datasets used to build a network\nmapping properties - Other properties of a network\nmapping userAnnotations - User annotations of a network", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values; either \"true\" or \"false\"", + "module" : "KBaseNetworks", + "name" : "Boolean" + }, + "name" : "directed", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "datasetId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Edge" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "module" : "KBaseNetworks", + "name" : "Edge" + } + }, + "name" : "edges", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "entityId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of node in a network", + "module" : "KBaseNetworks", + "name" : "NodeType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Node" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "module" : "KBaseNetworks", + "name" : "Node" + } + }, + "name" : "nodes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + } + }, + "name" : "datasets", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Network" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a network\nstring id - A unique KBase identifier of a network \n string name - String representation of a network. It should be a concise but informative representation that is easy for a person to read.\nlist edges - A list of all edges in a network\nlist nodes - A list of all nodes in a network\nlist datasets - A list of all datasets used to build a network\nmapping properties - Other properties of a network\nmapping userAnnotations - User annotations of a network", + "module" : "KBaseNetworks", + "name" : "Network" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of all datasets that can be used to create a network", + "name" : "allDatasets", + "parameters" : [ ], + "return_type" : [ { + "name" : "datasets", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of all dataset sources available in KBase via KBaseNetworks API", + "name" : "allDatasetSources", + "parameters" : [ ], + "return_type" : [ { + "name" : "datasetSources", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Provides detailed information about the source of a dataset.\nstring id - A unique KBase identifier of a dataset source\nstring name - A name of a dataset source\n DatasetSourceRef reference - Reference to a dataset source\n string description - General description of a dataset source\n string resourceURL - URL of the public web resource hosting the data represented by this dataset source", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "reference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "resourceURL", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "DatasetSource" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Provides detailed information about the source of a dataset.\nstring id - A unique KBase identifier of a dataset source\nstring name - A name of a dataset source\n DatasetSourceRef reference - Reference to a dataset source\n string description - General description of a dataset source\n string resourceURL - URL of the public web resource hosting the data represented by this dataset source", + "module" : "KBaseNetworks", + "name" : "DatasetSource" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of all types of networks that can be created", + "name" : "allNetworkTypes", + "parameters" : [ ], + "return_type" : [ { + "name" : "networkTypes", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of all datasets from a given dataset source \n DatasetSourceRef datasetSourceRef - A reference to a dataset source", + "name" : "datasetSource2Datasets", + "parameters" : [ { + "name" : "datasetSourceRef", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + } + } ], + "return_type" : [ { + "name" : "datasets", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of all datasets that can be used to build a network for a particular genome represented by NCBI taxonomy id. \n Taxon taxon - NCBI taxonomy id", + "name" : "taxon2Datasets", + "parameters" : [ { + "name" : "taxon", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + } ], + "return_type" : [ { + "name" : "datasets", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of all datasets that can be used to build a network of a given type.\n NetworkType networkType - The type of network", + "name" : "networkType2Datasets", + "parameters" : [ { + "name" : "networkType", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + } + } ], + "return_type" : [ { + "name" : "datasets", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of all datasets that have at least one interaction for a given KBase entity", + "name" : "entity2Datasets", + "parameters" : [ { + "name" : "entityId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "name" : "datasets", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a \"first-neighbor\" network constructed based on a given list of datasets. A first-neighbor network contains \n\"source\" nodes and all other nodes that have at least one interaction with the \"source\" nodes. \nOnly interactions of given types are considered. \n list datasetIds - List of dataset identifiers to be used for building a network\n list entityIds - List of entity identifiers to be used as source nodes\n list edgeTypes - List of possible edge types to be considered for building a network", + "name" : "buildFirstNeighborNetwork", + "parameters" : [ { + "name" : "datasetIds", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "entityIds", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "edgeTypes", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of edge in a network", + "module" : "KBaseNetworks", + "name" : "EdgeType" + } + } + } ], + "return_type" : [ { + "name" : "network", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a network\nstring id - A unique KBase identifier of a network \n string name - String representation of a network. It should be a concise but informative representation that is easy for a person to read.\nlist edges - A list of all edges in a network\nlist nodes - A list of all nodes in a network\nlist datasets - A list of all datasets used to build a network\nmapping properties - Other properties of a network\nmapping userAnnotations - User annotations of a network", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values; either \"true\" or \"false\"", + "module" : "KBaseNetworks", + "name" : "Boolean" + }, + "name" : "directed", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "datasetId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Edge" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "module" : "KBaseNetworks", + "name" : "Edge" + } + }, + "name" : "edges", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "entityId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of node in a network", + "module" : "KBaseNetworks", + "name" : "NodeType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Node" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "module" : "KBaseNetworks", + "name" : "Node" + } + }, + "name" : "nodes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + } + }, + "name" : "datasets", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Network" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a network\nstring id - A unique KBase identifier of a network \n string name - String representation of a network. It should be a concise but informative representation that is easy for a person to read.\nlist edges - A list of all edges in a network\nlist nodes - A list of all nodes in a network\nlist datasets - A list of all datasets used to build a network\nmapping properties - Other properties of a network\nmapping userAnnotations - User annotations of a network", + "module" : "KBaseNetworks", + "name" : "Network" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a \"first-neighbor\" network constructed basing on a given list of datasets. First-neighbor network contains \n\"source\" nodes and all other nodes that have at least one interaction with the \"source\" nodes. \nOnly interactions of given types are considered. Additional cutOff parameter allows setting a threshold\non the strength of edges to be considered. \n list datasetIds - List of dataset identifiers to be used for building a network\n list entityIds - List of entity identifiers to be used as source nodes\n list edgeTypes - List of possible edge types to be considered for building a network\n float cutOff - The threshold on the strength of edges to be considered for building a network", + "name" : "buildFirstNeighborNetworkLimtedByStrength", + "parameters" : [ { + "name" : "datasetIds", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "entityIds", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "edgeTypes", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of edge in a network", + "module" : "KBaseNetworks", + "name" : "EdgeType" + } + } + }, { + "name" : "cutOff", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + } ], + "return_type" : [ { + "name" : "network", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a network\nstring id - A unique KBase identifier of a network \n string name - String representation of a network. It should be a concise but informative representation that is easy for a person to read.\nlist edges - A list of all edges in a network\nlist nodes - A list of all nodes in a network\nlist datasets - A list of all datasets used to build a network\nmapping properties - Other properties of a network\nmapping userAnnotations - User annotations of a network", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values; either \"true\" or \"false\"", + "module" : "KBaseNetworks", + "name" : "Boolean" + }, + "name" : "directed", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "datasetId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Edge" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "module" : "KBaseNetworks", + "name" : "Edge" + } + }, + "name" : "edges", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "entityId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of node in a network", + "module" : "KBaseNetworks", + "name" : "NodeType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Node" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "module" : "KBaseNetworks", + "name" : "Node" + } + }, + "name" : "nodes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + } + }, + "name" : "datasets", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Network" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a network\nstring id - A unique KBase identifier of a network \n string name - String representation of a network. It should be a concise but informative representation that is easy for a person to read.\nlist edges - A list of all edges in a network\nlist nodes - A list of all nodes in a network\nlist datasets - A list of all datasets used to build a network\nmapping properties - Other properties of a network\nmapping userAnnotations - User annotations of a network", + "module" : "KBaseNetworks", + "name" : "Network" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns an \"internal\" network constructed based on a given list of datasets. \nInternal network contains only the nodes defined by the geneIds parameter, \nand edges representing interactions between these nodes. Only interactions of given types are considered. \n list datasetIds - List of dataset identifiers to be used for building a network\n list geneIds - Identifiers of genes of interest for building a network \n list edgeTypes - List of possible edge types to be considered for building a network", + "name" : "buildInternalNetwork", + "parameters" : [ { + "name" : "datasetIds", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "geneIds", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "edgeTypes", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of edge in a network", + "module" : "KBaseNetworks", + "name" : "EdgeType" + } + } + } ], + "return_type" : [ { + "name" : "network", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a network\nstring id - A unique KBase identifier of a network \n string name - String representation of a network. It should be a concise but informative representation that is easy for a person to read.\nlist edges - A list of all edges in a network\nlist nodes - A list of all nodes in a network\nlist datasets - A list of all datasets used to build a network\nmapping properties - Other properties of a network\nmapping userAnnotations - User annotations of a network", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values; either \"true\" or \"false\"", + "module" : "KBaseNetworks", + "name" : "Boolean" + }, + "name" : "directed", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "datasetId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Edge" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "module" : "KBaseNetworks", + "name" : "Edge" + } + }, + "name" : "edges", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "entityId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of node in a network", + "module" : "KBaseNetworks", + "name" : "NodeType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Node" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "module" : "KBaseNetworks", + "name" : "Node" + } + }, + "name" : "nodes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + } + }, + "name" : "datasets", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Network" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a network\nstring id - A unique KBase identifier of a network \n string name - String representation of a network. It should be a concise but informative representation that is easy for a person to read.\nlist edges - A list of all edges in a network\nlist nodes - A list of all nodes in a network\nlist datasets - A list of all datasets used to build a network\nmapping properties - Other properties of a network\nmapping userAnnotations - User annotations of a network", + "module" : "KBaseNetworks", + "name" : "Network" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns an \"internal\" network constructed based on a given list of datasets. \nInternal network contains the only nodes defined by the geneIds parameter, \nand edges representing interactions between these nodes. Only interactions of given types are considered. \nAdditional cutOff parameter allows to set a threshold on the strength of edges to be considered. \n list datasetIds - List of dataset identifiers to be used for building a network\n list geneIds - Identifiers of genes of interest for building a network \n list edgeTypes - List of possible edge types to be considered for building a network\n float cutOff - The threshold on the strength of edges to be considered for building a network", + "name" : "buildInternalNetworkLimitedByStrength", + "parameters" : [ { + "name" : "datasetIds", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "geneIds", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "edgeTypes", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of edge in a network", + "module" : "KBaseNetworks", + "name" : "EdgeType" + } + } + }, { + "name" : "cutOff", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + } ], + "return_type" : [ { + "name" : "network", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a network\nstring id - A unique KBase identifier of a network \n string name - String representation of a network. It should be a concise but informative representation that is easy for a person to read.\nlist edges - A list of all edges in a network\nlist nodes - A list of all nodes in a network\nlist datasets - A list of all datasets used to build a network\nmapping properties - Other properties of a network\nmapping userAnnotations - User annotations of a network", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values; either \"true\" or \"false\"", + "module" : "KBaseNetworks", + "name" : "Boolean" + }, + "name" : "directed", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "datasetId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Edge" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "module" : "KBaseNetworks", + "name" : "Edge" + } + }, + "name" : "edges", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "entityId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of node in a network", + "module" : "KBaseNetworks", + "name" : "NodeType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Node" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "module" : "KBaseNetworks", + "name" : "Node" + } + }, + "name" : "nodes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + } + }, + "name" : "datasets", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Network" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a network\nstring id - A unique KBase identifier of a network \n string name - String representation of a network. It should be a concise but informative representation that is easy for a person to read.\nlist edges - A list of all edges in a network\nlist nodes - A list of all nodes in a network\nlist datasets - A list of all datasets used to build a network\nmapping properties - Other properties of a network\nmapping userAnnotations - User annotations of a network", + "module" : "KBaseNetworks", + "name" : "Network" + } + } ] + } ], + "module_name" : "KBaseNetworks", + "options" : [ ], + "service_name" : "KBaseNetworks" + }, [ ], { + "Boolean" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values; either \"true\" or \"false\"", + "module" : "KBaseNetworks", + "name" : "Boolean" + }, + "Dataset" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "DatasetSource" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Provides detailed information about the source of a dataset.\nstring id - A unique KBase identifier of a dataset source\nstring name - A name of a dataset source\n DatasetSourceRef reference - Reference to a dataset source\n string description - General description of a dataset source\n string resourceURL - URL of the public web resource hosting the data represented by this dataset source", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "reference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "resourceURL", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "DatasetSource" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Provides detailed information about the source of a dataset.\nstring id - A unique KBase identifier of a dataset source\nstring name - A name of a dataset source\n DatasetSourceRef reference - Reference to a dataset source\n string description - General description of a dataset source\n string resourceURL - URL of the public web resource hosting the data represented by this dataset source", + "module" : "KBaseNetworks", + "name" : "DatasetSource" + }, + "DatasetSourceRef" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "Edge" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values; either \"true\" or \"false\"", + "module" : "KBaseNetworks", + "name" : "Boolean" + }, + "name" : "directed", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "datasetId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Edge" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "module" : "KBaseNetworks", + "name" : "Edge" + }, + "EdgeType" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of edge in a network", + "module" : "KBaseNetworks", + "name" : "EdgeType" + }, + "Network" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a network\nstring id - A unique KBase identifier of a network \n string name - String representation of a network. It should be a concise but informative representation that is easy for a person to read.\nlist edges - A list of all edges in a network\nlist nodes - A list of all nodes in a network\nlist datasets - A list of all datasets used to build a network\nmapping properties - Other properties of a network\nmapping userAnnotations - User annotations of a network", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "nodeId2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values; either \"true\" or \"false\"", + "module" : "KBaseNetworks", + "name" : "Boolean" + }, + "name" : "directed", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "datasetId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Edge" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents an edge in a network.\nstring id - A unique KBase identifier of an edge \n string name - String representation of an edge. It should be a concise but informative representation that is easy for a person to read.\n string nodeId1 - Identifier of the first node (source node, if the edge is directed) connected by a given edge \n string nodeId2 - Identifier of the second node (target node, if the edge is directed) connected by a given edge\n Boolean directed - Specify whether the edge is directed or not. \"true\" if it is directed, \"false\" if it is not directed\n float confidence - Value from 0 to 1 representing a probability that the interaction represented by a given edge is a true interaction\n float strength - Value from 0 to 1 representing a strength of an interaction represented by a given edge\n string datasetId - The identifier of a dataset that provided an interaction represented by a given edge\n mapping properties - Other edge properties\n mapping userAnnotations - User annotations of an edge", + "module" : "KBaseNetworks", + "name" : "Edge" + } + }, + "name" : "edges", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "entityId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of node in a network", + "module" : "KBaseNetworks", + "name" : "NodeType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Node" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "module" : "KBaseNetworks", + "name" : "Node" + } + }, + "name" : "nodes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "name" : "networkType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a dataset that can be accessed as a source for creating a network", + "module" : "KBaseNetworks", + "name" : "DatasetSourceRef" + }, + "name" : "sourceReference", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + } + }, + "name" : "taxons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Dataset" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a particular dataset.\nstring id - A unique KBase identifier of a dataset \n string name - The name of a dataset\n string description - Description of a dataset\n NetworkType networkType - Type of network that can be generated from a given dataset\nDatasetSourceRef sourceReference - Reference to a dataset source\nlist taxons - A list of NCBI taxonomy ids of all organisms for which genomic features (genes, proteins, etc) are used in a given dataset \n mapping properties - Other properties", + "module" : "KBaseNetworks", + "name" : "Dataset" + } + }, + "name" : "datasets", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Network" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a network\nstring id - A unique KBase identifier of a network \n string name - String representation of a network. It should be a concise but informative representation that is easy for a person to read.\nlist edges - A list of all edges in a network\nlist nodes - A list of all nodes in a network\nlist datasets - A list of all datasets used to build a network\nmapping properties - Other properties of a network\nmapping userAnnotations - User annotations of a network", + "module" : "KBaseNetworks", + "name" : "Network" + }, + "NetworkType" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of network that can be created from a dataset", + "module" : "KBaseNetworks", + "name" : "NetworkType" + }, + "Node" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "entityId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of node in a network", + "module" : "KBaseNetworks", + "name" : "NodeType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "userAnnotations", + "nullable" : "0" + } ], + "module" : "KBaseNetworks", + "name" : "Node" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a node in a network.\nstring id - A unique KBase identifier of a node \n string name - String representation of a node. It should be a concise but informative representation that is easy for a person to read.\n string entityId - The identifier of a KBase entity represented by a given node \n NodeType type - The type of a node\n mapping properties - Other properties of a node\n mapping userAnnotations - User annotations of a node", + "module" : "KBaseNetworks", + "name" : "Node" + }, + "NodeType" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of node in a network", + "module" : "KBaseNetworks", + "name" : "NodeType" + }, + "Taxon" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "NCBI taxonomy id", + "module" : "KBaseNetworks", + "name" : "Taxon" + }, + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.11.json.properties b/src/test/resources/us/kbase/test/kidl/spec.11.json.properties new file mode 100644 index 0000000..6945071 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.11.json.properties @@ -0,0 +1,2444 @@ +{ + "Ontology" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "This module provides public interface/APIs for KBase gene ontology (GO) services in a species-independent manner. It encapsulates the basic functionality of extracting domain ontologies (e.g. biological process, molecular function, cellular process) of interest for a given set of species specific genes. It only accepts KBase gene ids. External gene ids need to be converted to KBase ids. Additionally, it also allows gene ontology enrichment analysis (\"hypergeometric\") to be performed on a set of genes that identifies statistically overrepresented GO terms within given gene sets, say for example, GO enrichment of over-expressed genes in drought stress in plant roots. To support these key features, currently this modules provides five API-functions that are backed by custom defined data structures. Majority of these API-functions accept a list of input items (majority of them being text strings) such as list of gene-ids, list of go-ids, list of ontology-domains, and Test type ( \"hypergeometric\") and return the requested results as tabular dataset.", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Plant Species names.\n \n The current list of plant species includes: \n Alyrata: Arabidopsis lyrata\n Athaliana: Arabidopsis thaliana\n Bdistachyon: Brachypodium distachyon\n Creinhardtii: Chlamydomonas reinhardtii\n Gmax: Glycine max\n Oglaberrima: Oryza glaberrima\n Oindica: Oryza sativa indica\n Osativa: Oryza sativa japonica\n Ptrichocarpa: Populus trichocarpa \n Sbicolor: Sorghum bicolor \n Smoellendorffii: Selaginella moellendorffii\n Vvinifera: Vitis vinefera \n Zmays: Zea mays", + "module" : "Ontology", + "name" : "Species" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Unique identifier of a species specific Gene (aka Feature entity in KBase parlence). This ID is an external identifier that exists in the public databases such as Gramene, Ensembl, NCBI etc.", + "module" : "Ontology", + "name" : "GeneID" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Test type, whether it's \"hypergeometric\" and \"chisq\"", + "module" : "Ontology", + "name" : "TestType" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology identifiers", + "module" : "Ontology", + "name" : "GoIDList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a list of GO terms description", + "module" : "Ontology", + "name" : "GoDescList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Unique identifier of a species specific Gene (aka Feature entity in KBase parlence). This ID is an external identifier that exists in the public databases such as Gramene, Ensembl, NCBI etc.", + "module" : "Ontology", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of gene identifiers from same species", + "module" : "Ontology", + "name" : "GeneIDList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology domains", + "module" : "Ontology", + "name" : "DomainList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "StringArray" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology term evidence codes. One ontology term can have one or more evidence codes.", + "module" : "Ontology", + "name" : "EvidenceCodeList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "ontology_type" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + }, + "name" : "ec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "desc", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "GoTermInfo" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfo" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + }, + "name" : "ec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "desc", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "GoTermInfo" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfo" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfoList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + }, + "name" : "ec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "desc", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "GoTermInfo" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfo" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfoList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoIDMap2GoTermInfo" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Unique identifier of a species specific Gene (aka Feature entity in KBase parlence). This ID is an external identifier that exists in the public databases such as Gramene, Ensembl, NCBI etc.", + "module" : "Ontology", + "name" : "GeneID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + }, + "name" : "ec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "desc", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "GoTermInfo" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfo" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfoList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoIDMap2GoTermInfo" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GeneIDMap2GoInfo" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A composite data structure to capture ontology enrichment type object", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, + "name" : "goID", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "goDesc", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "pvalue", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "Enrichment" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A composite data structure to capture ontology enrichment type object", + "module" : "Ontology", + "name" : "Enrichment" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A composite data structure to capture ontology enrichment type object", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, + "name" : "goID", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "goDesc", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "pvalue", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "Enrichment" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A composite data structure to capture ontology enrichment type object", + "module" : "Ontology", + "name" : "Enrichment" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology enrichment objects", + "module" : "Ontology", + "name" : "EnrichmentList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "This function call accepts three parameters: a list of kbase gene-identifiers, a list of ontology domains, and a list of evidence codes. The list of gene identifiers cannot be empty; however the list of ontology domains and the list of evidence codes can be empty. If any of the last two lists is not empty then the gene-id and go-id pairs retrieved from KBase are further filtered by using the desired ontology domains and/or evidence codes supplied as input. So, if you don't want to filter the initial results then it is recommended to provide empty domain and evidence code lists. Finally, this function returns a mapping of kbase gene id to go-ids along with go-description, ontology domain, and evidence code; note that in the returned table of results, each gene-id is associated with a list of one of more go-ids. Also, if no species is provided as input then by default, Arabidopsis thaliana is used as the input species.", + "name" : "get_goidlist", + "parameters" : [ { + "name" : "geneIDList", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Unique identifier of a species specific Gene (aka Feature entity in KBase parlence). This ID is an external identifier that exists in the public databases such as Gramene, Ensembl, NCBI etc.", + "module" : "Ontology", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of gene identifiers from same species", + "module" : "Ontology", + "name" : "GeneIDList" + } + }, { + "name" : "domainList", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology domains", + "module" : "Ontology", + "name" : "DomainList" + } + }, { + "name" : "ecList", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology term evidence codes. One ontology term can have one or more evidence codes.", + "module" : "Ontology", + "name" : "EvidenceCodeList" + } + } ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Unique identifier of a species specific Gene (aka Feature entity in KBase parlence). This ID is an external identifier that exists in the public databases such as Gramene, Ensembl, NCBI etc.", + "module" : "Ontology", + "name" : "GeneID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + }, + "name" : "ec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "desc", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "GoTermInfo" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfo" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfoList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoIDMap2GoTermInfo" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GeneIDMap2GoInfo" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Extract GO term description for a given list of GO identifiers. This function expects an input list of GO-ids (white space or comman separated) and returns a table of three columns, first column being the GO ids, the second column is the GO description and third column is GO domain (biological process, molecular function, cellular component", + "name" : "get_go_description", + "parameters" : [ { + "name" : "goIDList", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology identifiers", + "module" : "Ontology", + "name" : "GoIDList" + } + } ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "StringArray" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "For a given list of kbase gene ids from a particular genome (for example \"Athaliana\" ) find out the significantly enriched GO terms in your gene set. This function accepts four parameters: A list of kbase gene-identifiers, a list of ontology domains (e.g.\"biological process\", \"molecular function\", \"cellular component\"), a list of evidence codes (e.g.\"IEA\",\"IDA\",\"IEP\" etc.), and test type (e.g. \"hypergeometric\"). The list of kbase gene identifiers cannot be empty; however the list of ontology domains and the list of evidence codes can be empty. If any of these two lists is not empty then the gene-id and the go-id pairs retrieved from KBase are further filtered by using the desired ontology domains and/or evidence codes supplied as input. So, if you don't want to filter the initial results then it is recommended to provide empty domain and evidence code lists. Final filtered list of the kbase gene-id to go-ids mapping is used to calculate GO enrichment using hypergeometric test and provides pvalues.The default pvalue cutoff is used as 0.05. Also, if input species is not provided then by default Arabidopsis thaliana is considered the input species. The current released version ignores test type and by default, it uses hypergeometric test. So even if you do not provide TestType, it will do hypergeometric test.", + "name" : "get_go_enrichment", + "parameters" : [ { + "name" : "geneIDList", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Unique identifier of a species specific Gene (aka Feature entity in KBase parlence). This ID is an external identifier that exists in the public databases such as Gramene, Ensembl, NCBI etc.", + "module" : "Ontology", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of gene identifiers from same species", + "module" : "Ontology", + "name" : "GeneIDList" + } + }, { + "name" : "domainList", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology domains", + "module" : "Ontology", + "name" : "DomainList" + } + }, { + "name" : "ecList", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology term evidence codes. One ontology term can have one or more evidence codes.", + "module" : "Ontology", + "name" : "EvidenceCodeList" + } + }, { + "name" : "type", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Test type, whether it's \"hypergeometric\" and \"chisq\"", + "module" : "Ontology", + "name" : "TestType" + } + }, { + "name" : "ontologytype", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "ontology_type" + } + } ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A composite data structure to capture ontology enrichment type object", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, + "name" : "goID", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "goDesc", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "pvalue", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "Enrichment" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A composite data structure to capture ontology enrichment type object", + "module" : "Ontology", + "name" : "Enrichment" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology enrichment objects", + "module" : "Ontology", + "name" : "EnrichmentList" + } + } ] + } ], + "module_name" : "Ontology", + "options" : [ ], + "service_name" : "Ontology" + }, [ ], { + "Domain" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + }, + "DomainList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology domains", + "module" : "Ontology", + "name" : "DomainList" + }, + "Enrichment" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A composite data structure to capture ontology enrichment type object", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, + "name" : "goID", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "goDesc", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "pvalue", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "Enrichment" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A composite data structure to capture ontology enrichment type object", + "module" : "Ontology", + "name" : "Enrichment" + }, + "EnrichmentList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A composite data structure to capture ontology enrichment type object", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, + "name" : "goID", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "goDesc", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "pvalue", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "Enrichment" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A composite data structure to capture ontology enrichment type object", + "module" : "Ontology", + "name" : "Enrichment" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology enrichment objects", + "module" : "Ontology", + "name" : "EnrichmentList" + }, + "EvidenceCode" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + }, + "EvidenceCodeList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology term evidence codes. One ontology term can have one or more evidence codes.", + "module" : "Ontology", + "name" : "EvidenceCodeList" + }, + "GeneID" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Unique identifier of a species specific Gene (aka Feature entity in KBase parlence). This ID is an external identifier that exists in the public databases such as Gramene, Ensembl, NCBI etc.", + "module" : "Ontology", + "name" : "GeneID" + }, + "GeneIDList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Unique identifier of a species specific Gene (aka Feature entity in KBase parlence). This ID is an external identifier that exists in the public databases such as Gramene, Ensembl, NCBI etc.", + "module" : "Ontology", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of gene identifiers from same species", + "module" : "Ontology", + "name" : "GeneIDList" + }, + "GeneIDMap2GoInfo" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Unique identifier of a species specific Gene (aka Feature entity in KBase parlence). This ID is an external identifier that exists in the public databases such as Gramene, Ensembl, NCBI etc.", + "module" : "Ontology", + "name" : "GeneID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + }, + "name" : "ec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "desc", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "GoTermInfo" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfo" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfoList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoIDMap2GoTermInfo" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GeneIDMap2GoInfo" + }, + "GoDesc" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "GoDescList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a list of GO terms description", + "module" : "Ontology", + "name" : "GoDescList" + }, + "GoID" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, + "GoIDList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A list of ontology identifiers", + "module" : "Ontology", + "name" : "GoIDList" + }, + "GoIDMap2GoTermInfo" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoID : Unique GO term id (Source: external Gene Ontology database - http://www.geneontology.org/)", + "module" : "Ontology", + "name" : "GoID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + }, + "name" : "ec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "desc", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "GoTermInfo" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfo" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfoList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoIDMap2GoTermInfo" + }, + "GoTermInfo" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + }, + "name" : "ec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "desc", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "GoTermInfo" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfo" + }, + "GoTermInfoList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Captures which branch of knowledge the GO terms refers to e.g. \"biological_process\", \"molecular_function\", \"cellular_component\" etc.", + "module" : "Ontology", + "name" : "Domain" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Evidence code indicates how the annotation to a particular term is supported. \nThe list of evidence codes includes Experimental, Computational Analysis, Author statement, Curator statement, Automatically assigned and Obsolete evidence codes. This list will be useful in selecting the correct evidence code for an annotation. The details are given below: \n\n+ Experimental Evidence Codes\nEXP: Inferred from Experiment\nIDA: Inferred from Direct Assay\nIPI: Inferred from Physical Interaction\nIMP: Inferred from Mutant Phenotype\nIGI: Inferred from Genetic Interaction\nIEP: Inferred from Expression Pattern\n \n+ Computational Analysis Evidence Codes\nISS: Inferred from Sequence or Structural Similarity\nISO: Inferred from Sequence Orthology\nISA: Inferred from Sequence Alignment\nISM: Inferred from Sequence Model\nIGC: Inferred from Genomic Context\nIBA: Inferred from Biological aspect of Ancestor\nIBD: Inferred from Biological aspect of Descendant\nIKR: Inferred from Key Residues\nIRD: Inferred from Rapid Divergence\nRCA: inferred from Reviewed Computational Analysis\n \n+ Author Statement Evidence Codes\nTAS: Traceable Author Statement\nNAS: Non-traceable Author Statement\n \n+ Curator Statement Evidence Codes\nIC: Inferred by Curator\nND: No biological Data available\n \n+ Automatically-assigned Evidence Codes\nIEA: Inferred from Electronic Annotation\n \n+ Obsolete Evidence Codes\nNR: Not Recorded", + "module" : "Ontology", + "name" : "EvidenceCode" + }, + "name" : "ec", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GoDesc : Human readable text description of the corresponding GO term", + "module" : "Ontology", + "name" : "GoDesc" + }, + "name" : "desc", + "nullable" : "0" + } ], + "module" : "Ontology", + "name" : "GoTermInfo" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfo" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "GoTermInfoList" + }, + "Species" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Plant Species names.\n \n The current list of plant species includes: \n Alyrata: Arabidopsis lyrata\n Athaliana: Arabidopsis thaliana\n Bdistachyon: Brachypodium distachyon\n Creinhardtii: Chlamydomonas reinhardtii\n Gmax: Glycine max\n Oglaberrima: Oryza glaberrima\n Oindica: Oryza sativa indica\n Osativa: Oryza sativa japonica\n Ptrichocarpa: Populus trichocarpa \n Sbicolor: Sorghum bicolor \n Smoellendorffii: Selaginella moellendorffii\n Vvinifera: Vitis vinefera \n Zmays: Zea mays", + "module" : "Ontology", + "name" : "Species" + }, + "StringArray" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "StringArray" + }, + "TestType" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Test type, whether it's \"hypergeometric\" and \"chisq\"", + "module" : "Ontology", + "name" : "TestType" + }, + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "ontology_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Ontology", + "name" : "ontology_type" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.12.json.properties b/src/test/resources/us/kbase/test/kidl/spec.12.json.properties new file mode 100644 index 0000000..84ef76b --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.12.json.properties @@ -0,0 +1,2780 @@ +{ + "Phispy" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "* This service wraps the PhiSpy service as defined at\n* http://sourceforge.net/projects/phispy.", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Following are the standard genome typed object defintions as copied from\n* the genome_annotation service specification.", + "module" : "Phispy", + "name" : "genome_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_type" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "Phispy", + "name" : "region_of_dna" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "Phispy", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "Phispy", + "name" : "location" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "annotation" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "Phispy", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "Phispy", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "function", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_translation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "aliases", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "annotation" + } + }, + "name" : "annotations", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "module" : "Phispy", + "name" : "feature" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Data for DNA contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "dna", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "contig" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Data for DNA contig", + "module" : "Phispy", + "name" : "contig" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "All of the information about particular genome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Following are the standard genome typed object defintions as copied from\n* the genome_annotation service specification.", + "module" : "Phispy", + "name" : "genome_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "scientific_name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "genetic_code", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Data for DNA contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "dna", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "contig" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Data for DNA contig", + "module" : "Phispy", + "name" : "contig" + } + }, + "name" : "contigs", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "Phispy", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "Phispy", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "function", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_translation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "aliases", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "annotation" + } + }, + "name" : "annotations", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "module" : "Phispy", + "name" : "feature" + } + }, + "name" : "features", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "genomeTO" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "All of the information about particular genome", + "module" : "Phispy", + "name" : "genomeTO" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* We define a type that represents the available phispy training sets.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "training_set_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genome_name", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "TrainingSet" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* We define a type that represents the available phispy training sets.", + "module" : "Phispy", + "name" : "TrainingSet" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "* Retrieve all available training sets.", + "name" : "get_all_training_sets", + "parameters" : [ ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* We define a type that represents the available phispy training sets.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "training_set_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genome_name", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "TrainingSet" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* We define a type that represents the available phispy training sets.", + "module" : "Phispy", + "name" : "TrainingSet" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "* Analysis results from the prophage finder.", + "element_names" : [ "e_1", "e_2", "start", "stop", "position", "rank", "my_status", "pp", "final_status", "start_of_attL", "end_of_attL", "start_of_attR", "end_of_attR", "sequence_of_attL", "sequence_of_attR" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "prophage_feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Analysis results from the prophage finder.", + "module" : "Phispy", + "name" : "prophage_feature" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "* Find prophages in the given genome.\n* \n* The underlying tool uses the following files from a SEED directory:\n* contigs\n* Features/peg/tbl\n* assigned_functions\n* Feature/rna/tbl", + "name" : "find_prophages", + "parameters" : [ { + "name" : "training_set_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "All of the information about particular genome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Following are the standard genome typed object defintions as copied from\n* the genome_annotation service specification.", + "module" : "Phispy", + "name" : "genome_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "scientific_name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : 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"Data for DNA contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "dna", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "contig" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Data for DNA contig", + "module" : "Phispy", + "name" : "contig" + } + }, + "name" : "contigs", + "nullable" : "0" + }, { + "!" : 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By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "Phispy", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "Phispy", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "function", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_translation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "aliases", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", 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"genomeTO" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "All of the information about particular genome", + "module" : "Phispy", + "name" : "genomeTO" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "All of the information about particular genome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Following are the standard genome typed object defintions as copied from\n* the genome_annotation service 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SEED", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "Phispy", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "Phispy", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "function", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_translation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "aliases", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "annotation" + } + }, + "name" : "annotations", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "module" : "Phispy", + "name" : "feature" + } + }, + "name" : "features", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "genomeTO" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "All of the information about particular genome", + "module" : "Phispy", + "name" : "genomeTO" + } + }, { + "name" : "analysis", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "* Analysis results from the prophage finder.", + "element_names" : [ "e_1", "e_2", "start", "stop", "position", "rank", "my_status", "pp", "final_status", "start_of_attL", "end_of_attL", "start_of_attR", "end_of_attR", "sequence_of_attL", "sequence_of_attR" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "prophage_feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Analysis results from the prophage finder.", + "module" : "Phispy", + "name" : "prophage_feature" + } + } + } ] + } ], + "module_name" : "Phispy", + "options" : [ ], + "service_name" : "Phispy" + }, [ ], { + "TrainingSet" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* We define a type that represents the available phispy training sets.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "training_set_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genome_name", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "TrainingSet" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* We define a type that represents the available phispy training sets.", + "module" : "Phispy", + "name" : "TrainingSet" + }, + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "annotation" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "annotation" + }, + "contig" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Data for DNA contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "dna", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "contig" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Data for DNA contig", + "module" : "Phispy", + "name" : "contig" + }, + "contig_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, + "feature" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "Phispy", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "Phispy", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "function", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_translation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "aliases", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "annotation" + } + }, + "name" : "annotations", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "module" : "Phispy", + "name" : "feature" + }, + "feature_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_id" + }, + "feature_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_type" + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "genomeTO" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "All of the information about particular genome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Following are the standard genome typed object defintions as copied from\n* the genome_annotation service specification.", + "module" : "Phispy", + "name" : "genome_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "scientific_name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "genetic_code", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Data for DNA contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "dna", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "contig" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Data for DNA contig", + "module" : "Phispy", + "name" : "contig" + } + }, + "name" : "contigs", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "Phispy", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "Phispy", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "function", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_translation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "aliases", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "annotation" + } + }, + "name" : "annotations", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "module" : "Phispy", + "name" : "feature" + } + }, + "name" : "features", + "nullable" : "0" + } ], + "module" : "Phispy", + "name" : "genomeTO" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "All of the information about particular genome", + "module" : "Phispy", + "name" : "genomeTO" + }, + "genome_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Following are the standard genome typed object defintions as copied from\n* the genome_annotation service specification.", + "module" : "Phispy", + "name" : "genome_id" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "location" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "Phispy", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "Phispy", + "name" : "location" + }, + "prophage_feature" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "* Analysis results from the prophage finder.", + "element_names" : [ "e_1", "e_2", "start", "stop", "position", "rank", "my_status", "pp", "final_status", "start_of_attL", "end_of_attL", "start_of_attR", "end_of_attR", "sequence_of_attL", "sequence_of_attR" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "feature_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "prophage_feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Analysis results from the prophage finder.", + "module" : "Phispy", + "name" : "prophage_feature" + }, + "region_of_dna" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Phispy", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "Phispy", + "name" : "region_of_dna" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.13.json.properties b/src/test/resources/us/kbase/test/kidl/spec.13.json.properties new file mode 100644 index 0000000..f89a9cb --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.13.json.properties @@ -0,0 +1,2756 @@ +{ + "PlantExpression" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "Plant Expression Service APIs \n\n This module provides services for plant expression data in support of the coexpression\n network and ontology driven data needs of the plant sciences community. This version of\n the modules supports retrieval of the following information:\n 1. Retrieval of GEO sample ID list for given EO (environmental ontology) and/or PO (plant ontology -plant tissues/organs of interest).\n 2. Retrieval of the expression values for given GEO sample ID list. \n 3. For given expression values tables, it computes co-expression clusters or network (CLI only).\n\nIt will serve queries for tissue and condition specific gene expression co-expression network for biologically interesting genes/samples. Users can search differentially expressed genes in different tissues or in numerous experimental conditions or treatments (e.g various biotic or abiotic stresses). Currently the metadata annotation is provided for a subset of gene expression experiments from the NCBI GEO microarray experiments for Arabidopsis and Poplar. The samples of these experiments are manually annotated using plant ontology (PO) [http://www.plantontology.org/] and environment ontology (EO) [http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/phenotype/environment/environment_ontology.obo]", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external gene id", + "module" : "PlantExpression", + "name" : "GeneID" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Series id from GEO (GSE#)", + "module" : "PlantExpression", + "name" : "SeriesID" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external gene id", + "module" : "PlantExpression", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of external gene ids from species of interest", + "module" : "PlantExpression", + "name" : "GeneIDList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of Sample ids", + "module" : "PlantExpression", + "name" : "SampleIDList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of environment ontologies", + "module" : "PlantExpression", + "name" : "EOIDList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of plant ontologies", + "module" : "PlantExpression", + "name" : "POIDList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Series id from GEO (GSE#)", + "module" : "PlantExpression", + "name" : "SeriesID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "SeriesIDList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Sample" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Sample" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "SampleList" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Sample" + }, + "name" : "series", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external gene id", + "module" : "PlantExpression", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of external gene ids from species of interest", + "module" : "PlantExpression", + "name" : "GeneIDList" + }, + "name" : "genes", + "nullable" : "0" + } ], + "module" : "PlantExpression", + "name" : "Experiment" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Experiment" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Series id from GEO (GSE#)", + "module" : "PlantExpression", + "name" : "SeriesID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Sample" + }, + "name" : "series", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external gene id", + "module" : "PlantExpression", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of external gene ids from species of interest", + "module" : "PlantExpression", + "name" : "GeneIDList" + }, + "name" : "genes", + "nullable" : "0" + } ], + "module" : "PlantExpression", + "name" : "Experiment" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Experiment" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Experiments" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of Sample ids", + "module" : "PlantExpression", + "name" : "SampleIDList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "EOID2Sample" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of Sample ids", + "module" : "PlantExpression", + "name" : "SampleIDList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "POID2Sample" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "POID2Description" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "EOID2Description" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "This function takes a list a GSM id. The GSM id can be stored as a csv file, containing one line. The output is the corresponding replicate id", + "name" : "get_repid_by_sampleid", + "parameters" : [ { + "name" : "ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of Sample ids", + "module" : "PlantExpression", + "name" : "SampleIDList" + } + } ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Sample" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "This function provides the expression data for each experiment corresponding to the given list of series (GSE#s). It first retrieves the experiments sample ids (GSM#s) for each series and subsequently, it extracts the expressed genes and their corresponding expression values for each experiment. It then returns a table of data containing GSE#, GSM#, Expressed Gene ID, and Expression Value.", + "name" : "get_experiments_by_seriesid", + "parameters" : [ { + "name" : "ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Series id from GEO (GSE#)", + "module" : "PlantExpression", + "name" : "SeriesID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "SeriesIDList" + } + } ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Series id from GEO (GSE#)", + "module" : "PlantExpression", + "name" : "SeriesID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Sample" + }, + "name" : "series", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external gene id", + "module" : "PlantExpression", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of external gene ids from species of interest", + "module" : "PlantExpression", + "name" : "GeneIDList" + }, + "name" : "genes", + "nullable" : "0" + } ], + "module" : "PlantExpression", + "name" : "Experiment" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Experiment" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Experiments" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "This function provides the expression values corresponding to each given experiment sample in the input list of sample ids (GSM#s).For each sample in the input list of samples, it extracts the expressed genes (kbase gene identifier) and their corresponding expression values.", + "name" : "get_experiments_by_sampleid", + "parameters" : [ { + "name" : "ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of Sample ids", + "module" : "PlantExpression", + "name" : "SampleIDList" + } + } ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Sample" + }, + "name" : "series", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external gene id", + "module" : "PlantExpression", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of external gene ids from species of interest", + "module" : "PlantExpression", + "name" : "GeneIDList" + }, + "name" : "genes", + "nullable" : "0" + } ], + "module" : "PlantExpression", + "name" : "Experiment" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Experiment" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "This function provides the expression values corresponding to the given sample and for given list of kbase gene identifiers.\nRetrieve the expression values corresponding to each given sample in the input list of samples ((typically NCBI GEO series sample ids: GSM#s) for given list of genes (kbase identifier).", + "name" : "get_experiments_by_sampleid_geneid", + "parameters" : [ { + "name" : "ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of Sample ids", + "module" : "PlantExpression", + "name" : "SampleIDList" + } + }, { + "name" : "gl", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external gene id", + "module" : "PlantExpression", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of external gene ids from species of interest", + "module" : "PlantExpression", + "name" : "GeneIDList" + } + } ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Sample" + }, + "name" : "series", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external gene id", + "module" : "PlantExpression", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of external gene ids from species of interest", + "module" : "PlantExpression", + "name" : "GeneIDList" + }, + "name" : "genes", + "nullable" : "0" + } ], + "module" : "PlantExpression", + "name" : "Experiment" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Experiment" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Retrieve the list of expression samples (GSM#s) that correspond to one or more of the environmental conditions (EO) of interest.", + "name" : "get_eo_sampleidlist", + "parameters" : [ { + "name" : "lst", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of environment ontologies", + "module" : "PlantExpression", + "name" : "EOIDList" + } + } ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of Sample ids", + "module" : "PlantExpression", + "name" : "SampleIDList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "EOID2Sample" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Retrieve the list of expression samples (GSM#s) that corresponds to one or more of the plant tissue/organ (PO) type of interest.", + "name" : "get_po_sampleidlist", + "parameters" : [ { + "name" : "lst", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of plant ontologies", + "module" : "PlantExpression", + "name" : "POIDList" + } + } ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of Sample ids", + "module" : "PlantExpression", + "name" : "SampleIDList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "POID2Sample" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "=head2 getAllPO\n\n Retrieve the list of all plant ontology IDs (POIDs) currently available in the database.", + "name" : "get_all_po", + "parameters" : [ ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "POID2Description" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Retrieve the list of all plant environment ontology IDs (EOIDs) currently available in the database.", + "name" : "get_all_eo", + "parameters" : [ ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "EOID2Description" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Retrieve the list of selected plant ontology IDs (POIDs) description corresponding to an input\nlist of POIDs.", + "name" : "get_po_descriptions", + "parameters" : [ { + "name" : "ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of plant ontologies", + "module" : "PlantExpression", + "name" : "POIDList" + } + } ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "POID2Description" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Retrieve the list of selected plant environment ontology IDs (EOIDs) description corresponding to an input list of EOIDs.", + "name" : "get_eo_descriptions", + "parameters" : [ { + "name" : "ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of environment ontologies", + "module" : "PlantExpression", + "name" : "EOIDList" + } + } ], + "return_type" : [ { + "name" : "results", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "EOID2Description" + } + } ] + } ], + "module_name" : "PlantExpression", + "options" : [ ], + "service_name" : "PlantExpression" + }, [ ], { + "EOID" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + }, + "EOID2Description" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "EOID2Description" + }, + "EOID2Sample" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of Sample ids", + "module" : "PlantExpression", + "name" : "SampleIDList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "EOID2Sample" + }, + "EOIDList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external environment ontology id \n\n The supported EO ids are :\n EO:0007001 UV-B light regimen\n EO:0007002 UV-A light regimen\n EO:0007041 antibiotic regimen\n EO:0007049 soil environment\n EO:0007066 cytokinin regimen\n EO:0007067 hydroponic plant culture media\n EO:0007071 suspension cell culture media\n EO:0007075 high light intensity regimen\n EO:0007079 sulfate fertilizer regimen\n EO:0007105 abscisic acid regimen\n EO:0007106 Stramenopiles\n EO:0007107 Ascomycota\n EO:0007108 Proteobacteria\n EO:0007116 Hemiptera\n EO:0007128 intermittent light regimen\n EO:0007144 Pseudomonas spp.\n EO:0007149 chemical mutagen\n EO:0007158 sandy soil\n EO:0007162 continuous light regimen\n EO:0007173 warm/hot temperature regimen\n EO:0007174 cold temperature regimen\n EO:0007175 temperature environment\n EO:0007183 herbicide regimen\n EO:0007185 salt regimen\n EO:0007193 day light intensity\n EO:0007199 long day length regimen\n EO:0007200 short day length regimen\n EO:0007203 far red light regimen\n EO:0007207 red light regimen\n EO:0007218 blue light regimen\n EO:0007221 visible light regimen\n EO:0007233 Fungi\n EO:0007265 liquid growth media\n EO:0007266 tissue culture growth media\n EO:0007270 continuous dark (no light) regimen\n EO:0007271 low light intensity regimen\n EO:0007303 carbon nutrient regimen\n EO:0007373 mechanical damage\n EO:0007404 drought environment\n EO:0007409 brassinosteroid", + "module" : "PlantExpression", + "name" : "EOID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of environment ontologies", + "module" : "PlantExpression", + "name" : "EOIDList" + }, + "Experiment" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Sample" + }, + "name" : "series", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external gene id", + "module" : "PlantExpression", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of external gene ids from species of interest", + "module" : "PlantExpression", + "name" : "GeneIDList" + }, + "name" : "genes", + "nullable" : "0" + } ], + "module" : "PlantExpression", + "name" : "Experiment" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Experiment" + }, + "Experiments" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Series id from GEO (GSE#)", + "module" : "PlantExpression", + "name" : "SeriesID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Sample" + }, + "name" : "series", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external gene id", + "module" : "PlantExpression", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of external gene ids from species of interest", + "module" : "PlantExpression", + "name" : "GeneIDList" + }, + "name" : "genes", + "nullable" : "0" + } ], + "module" : "PlantExpression", + "name" : "Experiment" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Experiment" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Experiments" + }, + "GeneID" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external gene id", + "module" : "PlantExpression", + "name" : "GeneID" + }, + "GeneIDList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external gene id", + "module" : "PlantExpression", + "name" : "GeneID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of external gene ids from species of interest", + "module" : "PlantExpression", + "name" : "GeneIDList" + }, + "POID" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + }, + "POID2Description" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "POID2Description" + }, + "POID2Sample" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of Sample ids", + "module" : "PlantExpression", + "name" : "SampleIDList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "POID2Sample" + }, + "POIDList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "external plant ontology id \n\n The supported PO ids are :\n PO:0000003 whole plant\n PO:0000005 cultured cell\n PO:0000006 cultured protoplast\n PO:0009005 root\n PO:0009006 shoot\n PO:0009025 leaf\n PO:0009046 flower\n PO:0009049 Inflorescence\n PO:0009001 fruit\n PO:0009010 seed", + "module" : "PlantExpression", + "name" : "POID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of plant ontologies", + "module" : "PlantExpression", + "name" : "POIDList" + }, + "Sample" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Sample" + }, + "SampleID" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "SampleIDList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of Sample ids", + "module" : "PlantExpression", + "name" : "SampleIDList" + }, + "SampleList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "expression sample id from GEO (GSM#)", + "module" : "PlantExpression", + "name" : "SampleID" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "Sample" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "SampleList" + }, + "SeriesID" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Series id from GEO (GSE#)", + "module" : "PlantExpression", + "name" : "SeriesID" + }, + "SeriesIDList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Series id from GEO (GSE#)", + "module" : "PlantExpression", + "name" : "SeriesID" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "SeriesIDList" + }, + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "ValueList" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "PlantExpression", + "name" : "ValueList" + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.13.properties b/src/test/resources/us/kbase/test/kidl/spec.13.properties old mode 100755 new mode 100644 diff --git a/src/test/resources/us/kbase/test/kidl/spec.14.json.properties b/src/test/resources/us/kbase/test/kidl/spec.14.json.properties new file mode 100644 index 0000000..6948688 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.14.json.properties @@ -0,0 +1,3112 @@ +{ + "PROM" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "PROM (Probabilistic Regulation of Metabolism) Service\n\nThis service enables the creation of FBA model constraints objects that are based on regulatory\nnetworks and expression data, as described in [1]. Constraints are constructed by either automatically\naggregating necessary information from the CDS (if available for a given genome), or by adding user\nexpression and regulatory data. PROM provides the capability to simulate transcription factor knockout\nphenotypes. PROM model constraint objects are created in a user's workspace, and can be operated on and\nused in conjunction with an FBA model with the KBase FBA Modeling Service.\n\nNote: for compatibility with the workspace service and legacy reasons, auth tokens are passed in as\nparameters rather than handled automatically by the auto-generated client/server infrastructure. This\nwill be fixed soon in one of the next builds.\n\n[1] Chandrasekarana S. and Price ND. Probabilistic integrative modeling of genome-scale metabolic and\nregulatory networks in Escherichia coli and Mycobacterium tuberculosis. PNAS (2010) 107:17845-50.\n\nAUTHORS:\nMichael Sneddon (mwsneddon@lbl.gov)\nMatt DeJongh (dejongh@hope.edu)\n\ncreated 11/27/2012 - msneddon", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "indicates true or false values, false <= 0, true >=1", + "module" : "PROM", + "name" : "bool" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome", + "module" : "PROM", + "name" : "genome_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a workspace", + "module" : "PROM", + "name" : "workspace_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a gene expression data object.", + "module" : "PROM", + "name" : "boolean_gene_expression_data_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a regulatory network object", + "module" : "PROM", + "name" : "regulatory_network_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Status message used by this service to provide information on the final status of a step", + "module" : "PROM", + "name" : "status" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for the prom constraints object in a user's workpace", + "module" : "PROM", + "name" : "prom_constraints_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a genome object in a user's workspace, used to link a prom_constraint Object to a genome", + "module" : "PROM", + "name" : "genome_object_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Specifies the source of a data object, e.g. KBase or MicrobesOnline", + "module" : "PROM", + "name" : "source" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Specifies the ID of the data object in the source", + "module" : "PROM", + "name" : "source_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the bearer token needed to authenticate on the workspace service, this will eventually\nbe eliminated when this service is updated to use the auto type-compiler auth functionality", + "module" : "PROM", + "name" : "auth_token" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Indicates on/off state of a gene, 1=on, -1=off, 0=unknown", + "module" : "PROM", + "name" : "on_off_state" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simplified representation of gene expression data under a SINGLE condition. Note that the condition\ninformation is not explicitly tracked here. also NOTE: this data object should be migrated to the Expression\nData service, and simply imported here.\n\n mapping on_off_call - a mapping of genome features to on/off calls under the given\n condition (true=on, false=off). It is therefore assumed that\n the features are protein coding genes.\n source expression_data_source - the source of this collection of expression data\n source_id expression_data_source_id - the id of this data object in the workspace", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a gene expression data object.", + "module" : "PROM", + "name" : "boolean_gene_expression_data_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Indicates on/off state of a gene, 1=on, -1=off, 0=unknown", + "module" : "PROM", + "name" : "on_off_state" + } + }, + "name" : "on_off_call", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Specifies the source of a data object, e.g. KBase or MicrobesOnline", + "module" : "PROM", + "name" : "source" + }, + "name" : "expression_data_source", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Specifies the source of a data object, e.g. KBase or MicrobesOnline", + "module" : "PROM", + "name" : "source" + }, + "name" : "expression_data_source_id", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "boolean_gene_expression_data" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simplified representation of gene expression data under a SINGLE condition. Note that the condition\ninformation is not explicitly tracked here. also NOTE: this data object should be migrated to the Expression\nData service, and simply imported here.\n\n mapping on_off_call - a mapping of genome features to on/off calls under the given\n condition (true=on, false=off). It is therefore assumed that\n the features are protein coding genes.\n source expression_data_source - the source of this collection of expression data\n source_id expression_data_source_id - the id of this data object in the workspace", + "module" : "PROM", + "name" : "boolean_gene_expression_data" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A collection of gene expression data for a single genome under a range of conditions. This data is returned\nas a list of IDs for boolean gene expression data objects in the workspace. This is a simple object for creating\na PROM Model. NOTE: this data object should be migrated to the Expression Data service, and simply imported here.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a gene expression data object.", + "module" : "PROM", + "name" : "boolean_gene_expression_data_id" + } + }, + "name" : "expression_data_ids", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "boolean_gene_expression_data_collection" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A collection of gene expression data for a single genome under a range of conditions. This data is returned\nas a list of IDs for boolean gene expression data objects in the workspace. This is a simple object for creating\na PROM Model. NOTE: this data object should be migrated to the Expression Data service, and simply imported here.", + "module" : "PROM", + "name" : "boolean_gene_expression_data_collection" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simplified representation of a regulatory interaction that also stores the probability of the interaction\n(specificially, as the probability the target is on given that the regulator is off), which is necessary for PROM\nto construct FBA constraints. NOTE: this data object should be migrated to the Regulation service, and simply\nimported here. NOTE 2: feature_id may actually be a more general ID, as models can potentially be loaded that\nare not in the kbase namespace. In this case everything, including expression data and the fba model must be in\nthe same namespace.\n\n feature_id TF - the genome feature that is the regulator\n feature_id target - the genome feature that is the target of regulation", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, + "name" : "TF", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, + "name" : "target", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "regulatory_interaction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simplified representation of a regulatory interaction that also stores the probability of the interaction\n(specificially, as the probability the target is on given that the regulator is off), which is necessary for PROM\nto construct FBA constraints. NOTE: this data object should be migrated to the Regulation service, and simply\nimported here. NOTE 2: feature_id may actually be a more general ID, as models can potentially be loaded that\nare not in the kbase namespace. In this case everything, including expression data and the fba model must be in\nthe same namespace.\n\n feature_id TF - the genome feature that is the regulator\n feature_id target - the genome feature that is the target of regulation", + "module" : "PROM", + "name" : "regulatory_interaction" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simplified representation of a regulatory interaction that also stores the probability of the interaction\n(specificially, as the probability the target is on given that the regulator is off), which is necessary for PROM\nto construct FBA constraints. NOTE: this data object should be migrated to the Regulation service, and simply\nimported here. NOTE 2: feature_id may actually be a more general ID, as models can potentially be loaded that\nare not in the kbase namespace. In this case everything, including expression data and the fba model must be in\nthe same namespace.\n\n feature_id TF - the genome feature that is the regulator\n feature_id target - the genome feature that is the target of regulation", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, + "name" : "TF", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, + "name" : "target", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "regulatory_interaction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simplified representation of a regulatory interaction that also stores the probability of the interaction\n(specificially, as the probability the target is on given that the regulator is off), which is necessary for PROM\nto construct FBA constraints. NOTE: this data object should be migrated to the Regulation service, and simply\nimported here. NOTE 2: feature_id may actually be a more general ID, as models can potentially be loaded that\nare not in the kbase namespace. In this case everything, including expression data and the fba model must be in\nthe same namespace.\n\n feature_id TF - the genome feature that is the regulator\n feature_id target - the genome feature that is the target of regulation", + "module" : "PROM", + "name" : "regulatory_interaction" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A collection of regulatory interactions that together form a regulatory network. This is an extremely\nsimplified data object for use in constructing a PROM model. NOTE: this data object should be migrated to\nthe Regulation service, and simply imported here.", + "module" : "PROM", + "name" : "regulatory_network" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Object required by the prom_constraints object which defines the computed probabilities for a target gene. The\nTF regulating this target can be deduced based on the tfMap object.\n\n string target_uuid - id of the target gene in the annotation object namespace\n float tfOffProbability - PROB(target=ON|TF=OFF)\n the probability that the transcriptional target is ON, given that the\n transcription factor is not expressed, as defined in Candrasekarana &\n Price, PNAS 2010 and used to predict cumulative effects of multiple\n regulatory interactions with a single target. Set to null or empty if\n this probability has not been calculated yet.\n float probTTonGivenTFon - PROB(target=ON|TF=ON)\n the probability that the transcriptional target is ON, given that the\n transcription factor is expressed. Set to null or empty if\n this probability has not been calculated yet.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "target_uuid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "tfOnProbability", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "tfOffProbability", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "regulatory_target" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Object required by the prom_constraints object which defines the computed probabilities for a target gene. The\nTF regulating this target can be deduced based on the tfMap object.\n\n string target_uuid - id of the target gene in the annotation object namespace\n float tfOffProbability - PROB(target=ON|TF=OFF)\n the probability that the transcriptional target is ON, given that the\n transcription factor is not expressed, as defined in Candrasekarana &\n Price, PNAS 2010 and used to predict cumulative effects of multiple\n regulatory interactions with a single target. Set to null or empty if\n this probability has not been calculated yet.\n float probTTonGivenTFon - PROB(target=ON|TF=ON)\n the probability that the transcriptional target is ON, given that the\n transcription factor is expressed. Set to null or empty if\n this probability has not been calculated yet.", + "module" : "PROM", + "name" : "regulatory_target" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Object required by the prom_constraints object, this maps a transcription factor by its uuid (in some\nannotation namespace) to a group of regulatory target genes.\n\n string transcriptionFactor_uuid - id of the TF in the annotation object namespace\n list transcriptionFactorMapTarget - collection of regulatory target genes for the TF\n along with associated joint probabilities for each\n target to be on given that the TF is on or off.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "transcriptionFactor_uuid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Object required by the prom_constraints object which defines the computed probabilities for a target gene. The\nTF regulating this target can be deduced based on the tfMap object.\n\n string target_uuid - id of the target gene in the annotation object namespace\n float tfOffProbability - PROB(target=ON|TF=OFF)\n the probability that the transcriptional target is ON, given that the\n transcription factor is not expressed, as defined in Candrasekarana &\n Price, PNAS 2010 and used to predict cumulative effects of multiple\n regulatory interactions with a single target. Set to null or empty if\n this probability has not been calculated yet.\n float probTTonGivenTFon - PROB(target=ON|TF=ON)\n the probability that the transcriptional target is ON, given that the\n transcription factor is expressed. Set to null or empty if\n this probability has not been calculated yet.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "target_uuid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "tfOnProbability", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "tfOffProbability", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "regulatory_target" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Object required by the prom_constraints object which defines the computed probabilities for a target gene. The\nTF regulating this target can be deduced based on the tfMap object.\n\n string target_uuid - id of the target gene in the annotation object namespace\n float tfOffProbability - PROB(target=ON|TF=OFF)\n the probability that the transcriptional target is ON, given that the\n transcription factor is not expressed, as defined in Candrasekarana &\n Price, PNAS 2010 and used to predict cumulative effects of multiple\n regulatory interactions with a single target. Set to null or empty if\n this probability has not been calculated yet.\n float probTTonGivenTFon - PROB(target=ON|TF=ON)\n the probability that the transcriptional target is ON, given that the\n transcription factor is expressed. Set to null or empty if\n this probability has not been calculated yet.", + "module" : "PROM", + "name" : "regulatory_target" + } + }, + "name" : "transcriptionFactorMapTargets", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "tfMap" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Object required by the prom_constraints object, this maps a transcription factor by its uuid (in some\nannotation namespace) to a group of regulatory target genes.\n\n string transcriptionFactor_uuid - id of the TF in the annotation object namespace\n list transcriptionFactorMapTarget - collection of regulatory target genes for the TF\n along with associated joint probabilities for each\n target to be on given that the TF is on or off.", + "module" : "PROM", + "name" : "tfMap" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "the ID of the genome annotation object kept for reference in the prom_constraints object", + "module" : "PROM", + "name" : "annotation_uuid" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object that encapsulates the information necessary to apply PROM-based constraints to an FBA model. This\nincludes a regulatory network consisting of a set of regulatory interactions (implied by the set of tfMap\nobjects) and interaction probabilities as defined in each regulatory_target object. A link the the annotation\nobject is required in order to properly link to an FBA model object. A reference to the expression_data_collection\nused to compute the interaction probabilities is provided for future reference.\n\n prom_constraints_id id - the id of this prom_constraints object in a\n workspace\n annotation_uuid annotation_uuid - the id of the annotation object in the workspace\n which specfies how TFs and targets are named\n list transcriptionFactorMaps - the list of tfMaps which specifies both the\n regulatory network and interaction probabilities\n between TF and target genes\n expression_data_collection_id expression_data_collection_id - the id of the expresion_data_collection object in\n the workspace which was used to compute the\n regulatory interaction probabilities", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for the prom constraints object in a user's workpace", + "module" : "PROM", + "name" : "prom_constraints_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "the ID of the genome annotation object kept for reference in the prom_constraints object", + "module" : "PROM", + "name" : "annotation_uuid" + }, + "name" : "annotation_uuid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Object required by the prom_constraints object, this maps a transcription factor by its uuid (in some\nannotation namespace) to a group of regulatory target genes.\n\n string transcriptionFactor_uuid - id of the TF in the annotation object namespace\n list transcriptionFactorMapTarget - collection of regulatory target genes for the TF\n along with associated joint probabilities for each\n target to be on given that the TF is on or off.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "transcriptionFactor_uuid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Object required by the prom_constraints object which defines the computed probabilities for a target gene. The\nTF regulating this target can be deduced based on the tfMap object.\n\n string target_uuid - id of the target gene in the annotation object namespace\n float tfOffProbability - PROB(target=ON|TF=OFF)\n the probability that the transcriptional target is ON, given that the\n transcription factor is not expressed, as defined in Candrasekarana &\n Price, PNAS 2010 and used to predict cumulative effects of multiple\n regulatory interactions with a single target. Set to null or empty if\n this probability has not been calculated yet.\n float probTTonGivenTFon - PROB(target=ON|TF=ON)\n the probability that the transcriptional target is ON, given that the\n transcription factor is expressed. Set to null or empty if\n this probability has not been calculated yet.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "target_uuid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "tfOnProbability", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "tfOffProbability", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "regulatory_target" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Object required by the prom_constraints object which defines the computed probabilities for a target gene. The\nTF regulating this target can be deduced based on the tfMap object.\n\n string target_uuid - id of the target gene in the annotation object namespace\n float tfOffProbability - PROB(target=ON|TF=OFF)\n the probability that the transcriptional target is ON, given that the\n transcription factor is not expressed, as defined in Candrasekarana &\n Price, PNAS 2010 and used to predict cumulative effects of multiple\n regulatory interactions with a single target. Set to null or empty if\n this probability has not been calculated yet.\n float probTTonGivenTFon - PROB(target=ON|TF=ON)\n the probability that the transcriptional target is ON, given that the\n transcription factor is expressed. Set to null or empty if\n this probability has not been calculated yet.", + "module" : "PROM", + "name" : "regulatory_target" + } + }, + "name" : "transcriptionFactorMapTargets", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "tfMap" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Object required by the prom_constraints object, this maps a transcription factor by its uuid (in some\nannotation namespace) to a group of regulatory target genes.\n\n string transcriptionFactor_uuid - id of the TF in the annotation object namespace\n list transcriptionFactorMapTarget - collection of regulatory target genes for the TF\n along with associated joint probabilities for each\n target to be on given that the TF is on or off.", + "module" : "PROM", + "name" : "tfMap" + } + }, + "name" : "transcriptionFactorMaps", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + }, + "name" : "expression_data_collection_id", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "prom_contstraint" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object that encapsulates the information necessary to apply PROM-based constraints to an FBA model. This\nincludes a regulatory network consisting of a set of regulatory interactions (implied by the set of tfMap\nobjects) and interaction probabilities as defined in each regulatory_target object. A link the the annotation\nobject is required in order to properly link to an FBA model object. A reference to the expression_data_collection\nused to compute the interaction probabilities is provided for future reference.\n\n prom_constraints_id id - the id of this prom_constraints object in a\n workspace\n annotation_uuid annotation_uuid - the id of the annotation object in the workspace\n which specfies how TFs and targets are named\n list transcriptionFactorMaps - the list of tfMaps which specifies both the\n regulatory network and interaction probabilities\n between TF and target genes\n expression_data_collection_id expression_data_collection_id - the id of the expresion_data_collection object in\n the workspace which was used to compute the\n regulatory interaction probabilities", + "module" : "PROM", + "name" : "prom_contstraint" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "This method fetches all gene expression data available in the CDS that is associated with the given genome id. It then\nconstructs an expression_data_collection object in the specified workspace. The method returns the ID of the expression\ndata collection in the workspace, along with a status message that provides details on what was retrieved and if anything\nfailed. If the method does fail, or if there is no data for the given genome, then no expression data collection is\ncreated and no ID is returned.\n\nNote 1: this method currently can take a long time to complete if there are many expression data sets in the CDS\nNote 2: the current implementation relies on on/off calls stored in the CDM (correct as of 1/2013). This will almost\ncertainly change, at which point logic for making on/off calls will be required as input\nNote 3: this method should be migrated to the expression service, which currently does not exist\nNote 4: this method should use the type compiler auth, but for simplicity we now just pass an auth token directly.", + "name" : "get_expression_data_by_genome", + "parameters" : [ { + "name" : "genome_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome", + "module" : "PROM", + "name" : "genome_id" + } + }, { + "name" : "workspace_name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a workspace", + "module" : "PROM", + "name" : "workspace_name" + } + }, { + "name" : "token", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the bearer token needed to authenticate on the workspace service, this will eventually\nbe eliminated when this service is updated to use the auto type-compiler auth functionality", + "module" : "PROM", + "name" : "auth_token" + } + } ], + "return_type" : [ { + "name" : "status", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Status message used by this service to provide information on the final status of a step", + "module" : "PROM", + "name" : "status" + } + }, { + "name" : "expression_data_collection_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "This method creates a new, empty, expression data collection in the specified workspace. If the method was successful,\nthe ID of the expression data set will be returned. The method also returns a status message providing additional\ndetails of the steps that occured or a message that indicates what failed. If the method fails, no expression\ndata ID is returned.", + "name" : "create_expression_data_collection", + "parameters" : [ { + "name" : "workspace_name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a workspace", + "module" : "PROM", + "name" : "workspace_name" + } + }, { + "name" : "token", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the bearer token needed to authenticate on the workspace service, this will eventually\nbe eliminated when this service is updated to use the auto type-compiler auth functionality", + "module" : "PROM", + "name" : "auth_token" + } + } ], + "return_type" : [ { + "name" : "status", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Status message used by this service to provide information on the final status of a step", + "module" : "PROM", + "name" : "status" + } + }, { + "name" : "expression_data_collection_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "This method provides a way to attach a set of boolean expression data to an expression data collection object created\nin the current workspace. Data collections can thus be composed of both CDS data and user data in this way. The method\nreturns a status message providing additional details of the steps that occured or a message that indicates what failed.\nIf the method fails, then all updates to the expression_data_collection are not made, although some of the boolean gene\nexpression data may have been created in the workspace (see status message for IDs of the new expession data objects).\n\nNote: when defining expression data, the id field must be explicitly defined. This will be the ID used to save the expression\ndata in the workspace. If expression data with that ID already exists, this method will overwrite that data and you will\nhave to use the workspace service revert method to undo the change.", + "name" : "add_expression_data_to_collection", + "parameters" : [ { + "name" : "expression_data", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simplified representation of gene expression data under a SINGLE condition. Note that the condition\ninformation is not explicitly tracked here. also NOTE: this data object should be migrated to the Expression\nData service, and simply imported here.\n\n mapping on_off_call - a mapping of genome features to on/off calls under the given\n condition (true=on, false=off). It is therefore assumed that\n the features are protein coding genes.\n source expression_data_source - the source of this collection of expression data\n source_id expression_data_source_id - the id of this data object in the workspace", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a gene expression data object.", + "module" : "PROM", + "name" : "boolean_gene_expression_data_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Indicates on/off state of a gene, 1=on, -1=off, 0=unknown", + "module" : "PROM", + "name" : "on_off_state" + } + }, + "name" : "on_off_call", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Specifies the source of a data object, e.g. KBase or MicrobesOnline", + "module" : "PROM", + "name" : "source" + }, + "name" : "expression_data_source", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Specifies the source of a data object, e.g. KBase or MicrobesOnline", + "module" : "PROM", + "name" : "source" + }, + "name" : "expression_data_source_id", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "boolean_gene_expression_data" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simplified representation of gene expression data under a SINGLE condition. Note that the condition\ninformation is not explicitly tracked here. also NOTE: this data object should be migrated to the Expression\nData service, and simply imported here.\n\n mapping on_off_call - a mapping of genome features to on/off calls under the given\n condition (true=on, false=off). It is therefore assumed that\n the features are protein coding genes.\n source expression_data_source - the source of this collection of expression data\n source_id expression_data_source_id - the id of this data object in the workspace", + "module" : "PROM", + "name" : "boolean_gene_expression_data" + } + } + }, { + "name" : "expression_data_collecion_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + } + }, { + "name" : "workspace_name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a workspace", + "module" : "PROM", + "name" : "workspace_name" + } + }, { + "name" : "token", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the bearer token needed to authenticate on the workspace service, this will eventually\nbe eliminated when this service is updated to use the auto type-compiler auth functionality", + "module" : "PROM", + "name" : "auth_token" + } + } ], + "return_type" : [ { + "name" : "status", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Status message used by this service to provide information on the final status of a step", + "module" : "PROM", + "name" : "status" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Maps the expression data collection stored in a workspace in one genome namespace to an alternate genome namespace. This is useful,\nfor instance, if expression data is available for one genome, but you intend to use it for a related genome or a genome with different\ngene calls. If a gene in the original expression data cannot be found in the translation mapping, then it is ignored and left as is\nso that the number of features in the expression data set is not altered. NOTE!: this is different from the default behavior of\nchange_regulatory_network_namespace, which will drop all genes that are not found in the mapping. If successful, this method\nreturns the expression collection ID of the newly created expression data colleion. This method also returns a status message indicating\nwhat happened or what went wrong.\n\nThe mapping new_features_names should be defined so that existing IDs are the key and the replacement IDs are the\nvalues stored.", + "name" : "change_expression_data_namespace", + "parameters" : [ { + "name" : "expression_data_collection_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + } + }, { + "name" : "new_feature_names", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "workspace_name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a workspace", + "module" : "PROM", + "name" : "workspace_name" + } + }, { + "name" : "token", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the bearer token needed to authenticate on the workspace service, this will eventually\nbe eliminated when this service is updated to use the auto type-compiler auth functionality", + "module" : "PROM", + "name" : "auth_token" + } + } ], + "return_type" : [ { + "name" : "status", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Status message used by this service to provide information on the final status of a step", + "module" : "PROM", + "name" : "status" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "This method fetches a regulatory network from the regulation service that is associated with the given genome id. If there\nare multiple regulome models available for the given genome, then the model with the most regulons is selected. The method\nthen constructs a regulatory network object in the specified workspace. The method returns the ID of the regulatory network\nin the workspace, along with a status message that provides details on what was retrieved and if anything failed. If the\nmethod does fail, or if there is no regulome for the given genome, then no regulatory network ID is returned.\n\nNote 1: this method should be migrated to the regulation service\nNote 2: this method should use the type compiler auth, but for simplicity we now just pass an auth token directly.", + "name" : "get_regulatory_network_by_genome", + "parameters" : [ { + "name" : "genome_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome", + "module" : "PROM", + "name" : "genome_id" + } + }, { + "name" : "workspace_name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a workspace", + "module" : "PROM", + "name" : "workspace_name" + } + }, { + "name" : "token", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the bearer token needed to authenticate on the workspace service, this will eventually\nbe eliminated when this service is updated to use the auto type-compiler auth functionality", + "module" : "PROM", + "name" : "auth_token" + } + } ], + "return_type" : [ { + "name" : "status", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Status message used by this service to provide information on the final status of a step", + "module" : "PROM", + "name" : "status" + } + }, { + "name" : "regulatory_network_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a regulatory network object", + "module" : "PROM", + "name" : "regulatory_network_id" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Maps the regulatory network stored in a workspace in one genome namespace to an alternate genome namespace. This is useful,\nfor instance, if a regulatory network was built and is available for one genome, but you intend to use it for\na related genome or a genome with different gene calls. If a gene in the original regulatory network cannot be found in\nthe translation mapping, then it is simply removed from the new regulatory network. Thus, if you are only changing the names\nof some genes, you still must provide an entry in the input mapping for the genes you wish to keep. If successful, this method\nreturns the regulatory network ID of the newly created regulatory network. This method also returns a status message indicating\nwhat happened or what went wrong.\n\nThe mapping new_features_names should be defined so that existing IDs are the key and the replacement IDs are the\nvalues stored.", + "name" : "change_regulatory_network_namespace", + "parameters" : [ { + "name" : "regulatory_network_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a regulatory network object", + "module" : "PROM", + "name" : "regulatory_network_id" + } + }, { + "name" : "new_feature_names", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "workspace_name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a workspace", + "module" : "PROM", + "name" : "workspace_name" + } + }, { + "name" : "token", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the bearer token needed to authenticate on the workspace service, this will eventually\nbe eliminated when this service is updated to use the auto type-compiler auth functionality", + "module" : "PROM", + "name" : "auth_token" + } + } ], + "return_type" : [ { + "name" : "status", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Status message used by this service to provide information on the final status of a step", + "module" : "PROM", + "name" : "status" + } + }, { + "name" : "new_regulatory_network_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a regulatory network object", + "module" : "PROM", + "name" : "regulatory_network_id" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Named parameters for 'create_prom_constraints' method. Currently all options are required.\n\n genome_object_id genome_object_id - the workspace ID of the genome to link to the prom object\n expression_data_collection_id\n expression_data_collection_id - the workspace ID of the expression data collection needed to\n build the PROM constraints.\n regulatory_network_id regulatory_network_id - the workspace ID of the regulatory network data to use\n workspace_name workspace_name - the name of the workspace to use\n auth_token token - the auth token that has permission to write in the specified workspace", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a genome object in a user's workspace, used to link a prom_constraint Object to a genome", + "module" : "PROM", + "name" : "genome_object_id" + }, + "name" : "genome_object_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + }, + "name" : "expression_data_collection_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a regulatory network object", + "module" : "PROM", + "name" : "regulatory_network_id" + }, + "name" : "regulatory_network_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a workspace", + "module" : "PROM", + "name" : "workspace_name" + }, + "name" : "workspace_name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the bearer token needed to authenticate on the workspace service, this will eventually\nbe eliminated when this service is updated to use the auto type-compiler auth functionality", + "module" : "PROM", + "name" : "auth_token" + }, + "name" : "token", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "create_prom_constraints_parameters" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Named parameters for 'create_prom_constraints' method. Currently all options are required.\n\n genome_object_id genome_object_id - the workspace ID of the genome to link to the prom object\n expression_data_collection_id\n expression_data_collection_id - the workspace ID of the expression data collection needed to\n build the PROM constraints.\n regulatory_network_id regulatory_network_id - the workspace ID of the regulatory network data to use\n workspace_name workspace_name - the name of the workspace to use\n auth_token token - the auth token that has permission to write in the specified workspace", + "module" : "PROM", + "name" : "create_prom_constraints_parameters" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "This method creates a set of Prom constraints for a given genome annotation based on a regulatory network\nand a collection of gene expression data stored on a workspace. Parameters are specified in the\ncreate_prom_constraints_parameters object. A status object is returned indicating success or failure along\nwith a message on what went wrong or statistics on the retrieved objects. If the method was successful, the\nID of the new Prom constraints object is also returned. The Prom constraints can then be used in conjunction\nwith an FBA model using FBA Model Services.", + "name" : "create_prom_constraints", + "parameters" : [ { + "name" : "params", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Named parameters for 'create_prom_constraints' method. Currently all options are required.\n\n genome_object_id genome_object_id - the workspace ID of the genome to link to the prom object\n expression_data_collection_id\n expression_data_collection_id - the workspace ID of the expression data collection needed to\n build the PROM constraints.\n regulatory_network_id regulatory_network_id - the workspace ID of the regulatory network data to use\n workspace_name workspace_name - the name of the workspace to use\n auth_token token - the auth token that has permission to write in the specified workspace", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a genome object in a user's workspace, used to link a prom_constraint Object to a genome", + "module" : "PROM", + "name" : "genome_object_id" + }, + "name" : "genome_object_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + }, + "name" : "expression_data_collection_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a regulatory network object", + "module" : "PROM", + "name" : "regulatory_network_id" + }, + "name" : "regulatory_network_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a workspace", + "module" : "PROM", + "name" : "workspace_name" + }, + "name" : "workspace_name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the bearer token needed to authenticate on the workspace service, this will eventually\nbe eliminated when this service is updated to use the auto type-compiler auth functionality", + "module" : "PROM", + "name" : "auth_token" + }, + "name" : "token", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "create_prom_constraints_parameters" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Named parameters for 'create_prom_constraints' method. Currently all options are required.\n\n genome_object_id genome_object_id - the workspace ID of the genome to link to the prom object\n expression_data_collection_id\n expression_data_collection_id - the workspace ID of the expression data collection needed to\n build the PROM constraints.\n regulatory_network_id regulatory_network_id - the workspace ID of the regulatory network data to use\n workspace_name workspace_name - the name of the workspace to use\n auth_token token - the auth token that has permission to write in the specified workspace", + "module" : "PROM", + "name" : "create_prom_constraints_parameters" + } + } ], + "return_type" : [ { + "name" : "status", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Status message used by this service to provide information on the final status of a step", + "module" : "PROM", + "name" : "status" + } + }, { + "name" : "prom_constraints_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for the prom constraints object in a user's workpace", + "module" : "PROM", + "name" : "prom_constraints_id" + } + } ] + } ], + "module_name" : "PROM", + "options" : [ ], + "service_name" : "PROM" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "annotation_uuid" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "the ID of the genome annotation object kept for reference in the prom_constraints object", + "module" : "PROM", + "name" : "annotation_uuid" + }, + "auth_token" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the bearer token needed to authenticate on the workspace service, this will eventually\nbe eliminated when this service is updated to use the auto type-compiler auth functionality", + "module" : "PROM", + "name" : "auth_token" + }, + "bool" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "indicates true or false values, false <= 0, true >=1", + "module" : "PROM", + "name" : "bool" + }, + "boolean_gene_expression_data" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simplified representation of gene expression data under a SINGLE condition. Note that the condition\ninformation is not explicitly tracked here. also NOTE: this data object should be migrated to the Expression\nData service, and simply imported here.\n\n mapping on_off_call - a mapping of genome features to on/off calls under the given\n condition (true=on, false=off). It is therefore assumed that\n the features are protein coding genes.\n source expression_data_source - the source of this collection of expression data\n source_id expression_data_source_id - the id of this data object in the workspace", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a gene expression data object.", + "module" : "PROM", + "name" : "boolean_gene_expression_data_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Indicates on/off state of a gene, 1=on, -1=off, 0=unknown", + "module" : "PROM", + "name" : "on_off_state" + } + }, + "name" : "on_off_call", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Specifies the source of a data object, e.g. KBase or MicrobesOnline", + "module" : "PROM", + "name" : "source" + }, + "name" : "expression_data_source", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Specifies the source of a data object, e.g. KBase or MicrobesOnline", + "module" : "PROM", + "name" : "source" + }, + "name" : "expression_data_source_id", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "boolean_gene_expression_data" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simplified representation of gene expression data under a SINGLE condition. Note that the condition\ninformation is not explicitly tracked here. also NOTE: this data object should be migrated to the Expression\nData service, and simply imported here.\n\n mapping on_off_call - a mapping of genome features to on/off calls under the given\n condition (true=on, false=off). It is therefore assumed that\n the features are protein coding genes.\n source expression_data_source - the source of this collection of expression data\n source_id expression_data_source_id - the id of this data object in the workspace", + "module" : "PROM", + "name" : "boolean_gene_expression_data" + }, + "boolean_gene_expression_data_collection" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A collection of gene expression data for a single genome under a range of conditions. This data is returned\nas a list of IDs for boolean gene expression data objects in the workspace. This is a simple object for creating\na PROM Model. NOTE: this data object should be migrated to the Expression Data service, and simply imported here.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a gene expression data object.", + "module" : "PROM", + "name" : "boolean_gene_expression_data_id" + } + }, + "name" : "expression_data_ids", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "boolean_gene_expression_data_collection" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A collection of gene expression data for a single genome under a range of conditions. This data is returned\nas a list of IDs for boolean gene expression data objects in the workspace. This is a simple object for creating\na PROM Model. NOTE: this data object should be migrated to the Expression Data service, and simply imported here.", + "module" : "PROM", + "name" : "boolean_gene_expression_data_collection" + }, + "boolean_gene_expression_data_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a gene expression data object.", + "module" : "PROM", + "name" : "boolean_gene_expression_data_id" + }, + "create_prom_constraints_parameters" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Named parameters for 'create_prom_constraints' method. Currently all options are required.\n\n genome_object_id genome_object_id - the workspace ID of the genome to link to the prom object\n expression_data_collection_id\n expression_data_collection_id - the workspace ID of the expression data collection needed to\n build the PROM constraints.\n regulatory_network_id regulatory_network_id - the workspace ID of the regulatory network data to use\n workspace_name workspace_name - the name of the workspace to use\n auth_token token - the auth token that has permission to write in the specified workspace", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a genome object in a user's workspace, used to link a prom_constraint Object to a genome", + "module" : "PROM", + "name" : "genome_object_id" + }, + "name" : "genome_object_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + }, + "name" : "expression_data_collection_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a regulatory network object", + "module" : "PROM", + "name" : "regulatory_network_id" + }, + "name" : "regulatory_network_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a workspace", + "module" : "PROM", + "name" : "workspace_name" + }, + "name" : "workspace_name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the bearer token needed to authenticate on the workspace service, this will eventually\nbe eliminated when this service is updated to use the auto type-compiler auth functionality", + "module" : "PROM", + "name" : "auth_token" + }, + "name" : "token", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "create_prom_constraints_parameters" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Named parameters for 'create_prom_constraints' method. Currently all options are required.\n\n genome_object_id genome_object_id - the workspace ID of the genome to link to the prom object\n expression_data_collection_id\n expression_data_collection_id - the workspace ID of the expression data collection needed to\n build the PROM constraints.\n regulatory_network_id regulatory_network_id - the workspace ID of the regulatory network data to use\n workspace_name workspace_name - the name of the workspace to use\n auth_token token - the auth token that has permission to write in the specified workspace", + "module" : "PROM", + "name" : "create_prom_constraints_parameters" + }, + "expression_data_collection_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + }, + "feature_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "genome_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome", + "module" : "PROM", + "name" : "genome_id" + }, + "genome_object_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a genome object in a user's workspace, used to link a prom_constraint Object to a genome", + "module" : "PROM", + "name" : "genome_object_id" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "kbase_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "on_off_state" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Indicates on/off state of a gene, 1=on, -1=off, 0=unknown", + "module" : "PROM", + "name" : "on_off_state" + }, + "prom_constraints_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for the prom constraints object in a user's workpace", + "module" : "PROM", + "name" : "prom_constraints_id" + }, + "prom_contstraint" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object that encapsulates the information necessary to apply PROM-based constraints to an FBA model. This\nincludes a regulatory network consisting of a set of regulatory interactions (implied by the set of tfMap\nobjects) and interaction probabilities as defined in each regulatory_target object. A link the the annotation\nobject is required in order to properly link to an FBA model object. A reference to the expression_data_collection\nused to compute the interaction probabilities is provided for future reference.\n\n prom_constraints_id id - the id of this prom_constraints object in a\n workspace\n annotation_uuid annotation_uuid - the id of the annotation object in the workspace\n which specfies how TFs and targets are named\n list transcriptionFactorMaps - the list of tfMaps which specifies both the\n regulatory network and interaction probabilities\n between TF and target genes\n expression_data_collection_id expression_data_collection_id - the id of the expresion_data_collection object in\n the workspace which was used to compute the\n regulatory interaction probabilities", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for the prom constraints object in a user's workpace", + "module" : "PROM", + "name" : "prom_constraints_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "the ID of the genome annotation object kept for reference in the prom_constraints object", + "module" : "PROM", + "name" : "annotation_uuid" + }, + "name" : "annotation_uuid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Object required by the prom_constraints object, this maps a transcription factor by its uuid (in some\nannotation namespace) to a group of regulatory target genes.\n\n string transcriptionFactor_uuid - id of the TF in the annotation object namespace\n list transcriptionFactorMapTarget - collection of regulatory target genes for the TF\n along with associated joint probabilities for each\n target to be on given that the TF is on or off.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "transcriptionFactor_uuid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Object required by the prom_constraints object which defines the computed probabilities for a target gene. The\nTF regulating this target can be deduced based on the tfMap object.\n\n string target_uuid - id of the target gene in the annotation object namespace\n float tfOffProbability - PROB(target=ON|TF=OFF)\n the probability that the transcriptional target is ON, given that the\n transcription factor is not expressed, as defined in Candrasekarana &\n Price, PNAS 2010 and used to predict cumulative effects of multiple\n regulatory interactions with a single target. Set to null or empty if\n this probability has not been calculated yet.\n float probTTonGivenTFon - PROB(target=ON|TF=ON)\n the probability that the transcriptional target is ON, given that the\n transcription factor is expressed. Set to null or empty if\n this probability has not been calculated yet.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "target_uuid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "tfOnProbability", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "tfOffProbability", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "regulatory_target" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Object required by the prom_constraints object which defines the computed probabilities for a target gene. The\nTF regulating this target can be deduced based on the tfMap object.\n\n string target_uuid - id of the target gene in the annotation object namespace\n float tfOffProbability - PROB(target=ON|TF=OFF)\n the probability that the transcriptional target is ON, given that the\n transcription factor is not expressed, as defined in Candrasekarana &\n Price, PNAS 2010 and used to predict cumulative effects of multiple\n regulatory interactions with a single target. Set to null or empty if\n this probability has not been calculated yet.\n float probTTonGivenTFon - PROB(target=ON|TF=ON)\n the probability that the transcriptional target is ON, given that the\n transcription factor is expressed. Set to null or empty if\n this probability has not been calculated yet.", + "module" : "PROM", + "name" : "regulatory_target" + } + }, + "name" : "transcriptionFactorMapTargets", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "tfMap" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Object required by the prom_constraints object, this maps a transcription factor by its uuid (in some\nannotation namespace) to a group of regulatory target genes.\n\n string transcriptionFactor_uuid - id of the TF in the annotation object namespace\n list transcriptionFactorMapTarget - collection of regulatory target genes for the TF\n along with associated joint probabilities for each\n target to be on given that the TF is on or off.", + "module" : "PROM", + "name" : "tfMap" + } + }, + "name" : "transcriptionFactorMaps", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace id for a set of expression data on/off calls", + "module" : "PROM", + "name" : "expression_data_collection_id" + }, + "name" : "expression_data_collection_id", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "prom_contstraint" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object that encapsulates the information necessary to apply PROM-based constraints to an FBA model. This\nincludes a regulatory network consisting of a set of regulatory interactions (implied by the set of tfMap\nobjects) and interaction probabilities as defined in each regulatory_target object. A link the the annotation\nobject is required in order to properly link to an FBA model object. A reference to the expression_data_collection\nused to compute the interaction probabilities is provided for future reference.\n\n prom_constraints_id id - the id of this prom_constraints object in a\n workspace\n annotation_uuid annotation_uuid - the id of the annotation object in the workspace\n which specfies how TFs and targets are named\n list transcriptionFactorMaps - the list of tfMaps which specifies both the\n regulatory network and interaction probabilities\n between TF and target genes\n expression_data_collection_id expression_data_collection_id - the id of the expresion_data_collection object in\n the workspace which was used to compute the\n regulatory interaction probabilities", + "module" : "PROM", + "name" : "prom_contstraint" + }, + "regulatory_interaction" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simplified representation of a regulatory interaction that also stores the probability of the interaction\n(specificially, as the probability the target is on given that the regulator is off), which is necessary for PROM\nto construct FBA constraints. NOTE: this data object should be migrated to the Regulation service, and simply\nimported here. NOTE 2: feature_id may actually be a more general ID, as models can potentially be loaded that\nare not in the kbase namespace. In this case everything, including expression data and the fba model must be in\nthe same namespace.\n\n feature_id TF - the genome feature that is the regulator\n feature_id target - the genome feature that is the target of regulation", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, + "name" : "TF", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, + "name" : "target", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "regulatory_interaction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simplified representation of a regulatory interaction that also stores the probability of the interaction\n(specificially, as the probability the target is on given that the regulator is off), which is necessary for PROM\nto construct FBA constraints. NOTE: this data object should be migrated to the Regulation service, and simply\nimported here. NOTE 2: feature_id may actually be a more general ID, as models can potentially be loaded that\nare not in the kbase namespace. In this case everything, including expression data and the fba model must be in\nthe same namespace.\n\n feature_id TF - the genome feature that is the regulator\n feature_id target - the genome feature that is the target of regulation", + "module" : "PROM", + "name" : "regulatory_interaction" + }, + "regulatory_network" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simplified representation of a regulatory interaction that also stores the probability of the interaction\n(specificially, as the probability the target is on given that the regulator is off), which is necessary for PROM\nto construct FBA constraints. NOTE: this data object should be migrated to the Regulation service, and simply\nimported here. NOTE 2: feature_id may actually be a more general ID, as models can potentially be loaded that\nare not in the kbase namespace. In this case everything, including expression data and the fba model must be in\nthe same namespace.\n\n feature_id TF - the genome feature that is the regulator\n feature_id target - the genome feature that is the target of regulation", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, + "name" : "TF", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. KBase IDs may be hierarchical. See the standard KBase documentation\nfor more information.", + "module" : "PROM", + "name" : "kbase_id" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID for a genome feature", + "module" : "PROM", + "name" : "feature_id" + }, + "name" : "target", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "regulatory_interaction" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simplified representation of a regulatory interaction that also stores the probability of the interaction\n(specificially, as the probability the target is on given that the regulator is off), which is necessary for PROM\nto construct FBA constraints. NOTE: this data object should be migrated to the Regulation service, and simply\nimported here. NOTE 2: feature_id may actually be a more general ID, as models can potentially be loaded that\nare not in the kbase namespace. In this case everything, including expression data and the fba model must be in\nthe same namespace.\n\n feature_id TF - the genome feature that is the regulator\n feature_id target - the genome feature that is the target of regulation", + "module" : "PROM", + "name" : "regulatory_interaction" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A collection of regulatory interactions that together form a regulatory network. This is an extremely\nsimplified data object for use in constructing a PROM model. NOTE: this data object should be migrated to\nthe Regulation service, and simply imported here.", + "module" : "PROM", + "name" : "regulatory_network" + }, + "regulatory_network_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A workspace ID for a regulatory network object", + "module" : "PROM", + "name" : "regulatory_network_id" + }, + "regulatory_target" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Object required by the prom_constraints object which defines the computed probabilities for a target gene. The\nTF regulating this target can be deduced based on the tfMap object.\n\n string target_uuid - id of the target gene in the annotation object namespace\n float tfOffProbability - PROB(target=ON|TF=OFF)\n the probability that the transcriptional target is ON, given that the\n transcription factor is not expressed, as defined in Candrasekarana &\n Price, PNAS 2010 and used to predict cumulative effects of multiple\n regulatory interactions with a single target. Set to null or empty if\n this probability has not been calculated yet.\n float probTTonGivenTFon - PROB(target=ON|TF=ON)\n the probability that the transcriptional target is ON, given that the\n transcription factor is expressed. Set to null or empty if\n this probability has not been calculated yet.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "target_uuid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "tfOnProbability", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "tfOffProbability", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "regulatory_target" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Object required by the prom_constraints object which defines the computed probabilities for a target gene. The\nTF regulating this target can be deduced based on the tfMap object.\n\n string target_uuid - id of the target gene in the annotation object namespace\n float tfOffProbability - PROB(target=ON|TF=OFF)\n the probability that the transcriptional target is ON, given that the\n transcription factor is not expressed, as defined in Candrasekarana &\n Price, PNAS 2010 and used to predict cumulative effects of multiple\n regulatory interactions with a single target. Set to null or empty if\n this probability has not been calculated yet.\n float probTTonGivenTFon - PROB(target=ON|TF=ON)\n the probability that the transcriptional target is ON, given that the\n transcription factor is expressed. Set to null or empty if\n this probability has not been calculated yet.", + "module" : "PROM", + "name" : "regulatory_target" + }, + "source" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Specifies the source of a data object, e.g. KBase or MicrobesOnline", + "module" : "PROM", + "name" : "source" + }, + "source_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Specifies the ID of the data object in the source", + "module" : "PROM", + "name" : "source_id" + }, + "status" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Status message used by this service to provide information on the final status of a step", + "module" : "PROM", + "name" : "status" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "tfMap" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Object required by the prom_constraints object, this maps a transcription factor by its uuid (in some\nannotation namespace) to a group of regulatory target genes.\n\n string transcriptionFactor_uuid - id of the TF in the annotation object namespace\n list transcriptionFactorMapTarget - collection of regulatory target genes for the TF\n along with associated joint probabilities for each\n target to be on given that the TF is on or off.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "transcriptionFactor_uuid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Object required by the prom_constraints object which defines the computed probabilities for a target gene. The\nTF regulating this target can be deduced based on the tfMap object.\n\n string target_uuid - id of the target gene in the annotation object namespace\n float tfOffProbability - PROB(target=ON|TF=OFF)\n the probability that the transcriptional target is ON, given that the\n transcription factor is not expressed, as defined in Candrasekarana &\n Price, PNAS 2010 and used to predict cumulative effects of multiple\n regulatory interactions with a single target. Set to null or empty if\n this probability has not been calculated yet.\n float probTTonGivenTFon - PROB(target=ON|TF=ON)\n the probability that the transcriptional target is ON, given that the\n transcription factor is expressed. Set to null or empty if\n this probability has not been calculated yet.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "target_uuid", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "tfOnProbability", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "tfOffProbability", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "regulatory_target" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Object required by the prom_constraints object which defines the computed probabilities for a target gene. The\nTF regulating this target can be deduced based on the tfMap object.\n\n string target_uuid - id of the target gene in the annotation object namespace\n float tfOffProbability - PROB(target=ON|TF=OFF)\n the probability that the transcriptional target is ON, given that the\n transcription factor is not expressed, as defined in Candrasekarana &\n Price, PNAS 2010 and used to predict cumulative effects of multiple\n regulatory interactions with a single target. Set to null or empty if\n this probability has not been calculated yet.\n float probTTonGivenTFon - PROB(target=ON|TF=ON)\n the probability that the transcriptional target is ON, given that the\n transcription factor is expressed. Set to null or empty if\n this probability has not been calculated yet.", + "module" : "PROM", + "name" : "regulatory_target" + } + }, + "name" : "transcriptionFactorMapTargets", + "nullable" : "0" + } ], + "module" : "PROM", + "name" : "tfMap" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Object required by the prom_constraints object, this maps a transcription factor by its uuid (in some\nannotation namespace) to a group of regulatory target genes.\n\n string transcriptionFactor_uuid - id of the TF in the annotation object namespace\n list transcriptionFactorMapTarget - collection of regulatory target genes for the TF\n along with associated joint probabilities for each\n target to be on given that the TF is on or off.", + "module" : "PROM", + "name" : "tfMap" + }, + "workspace_name" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The name of a workspace", + "module" : "PROM", + "name" : "workspace_name" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.15.json.properties b/src/test/resources/us/kbase/test/kidl/spec.15.json.properties new file mode 100644 index 0000000..9e5b53e --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.15.json.properties @@ -0,0 +1,1202 @@ +{ + "ProteinInfo" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "Given a feature ID that is a protein, the protein info service\nreturns various annotations such as domain annotations, orthologs\nin other genomes, and operons.", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A domain_id is an identifier of a protein domain or family\n(e.g., COG593, TIGR00362). Most of these are stable identifiers\nthat come from external curated libraries, such as COG or InterProScan,\nbut some may be unstable identifiers that come from automated\nanalyses like FastBLAST. (The current implementation includes only\nCOG and InterProScan HMM libraries, such as TIGRFam and Pfam.)", + "module" : "ProteinInfo", + "name" : "domain_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A neighbor_threshold is a floating point number indicating a bound\nfor the neighbor score", + "module" : "ProteinInfo", + "name" : "neighbor_threshold" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Neighbor is a hash of fids to a neighbor score", + "module" : "ProteinInfo", + "name" : "neighbor" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Domains are a list of domain_ids.", + "module" : "ProteinInfo", + "name" : "domains" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "ECs are a list of Enzyme Commission identifiers.", + "module" : "ProteinInfo", + "name" : "ec" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GOs are a list of Gene Ontology identifiers.", + "module" : "ProteinInfo", + "name" : "go" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "IPRs are a list of InterPro identifiers.", + "module" : "ProteinInfo", + "name" : "ipr" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An operon is represented by a list of fids\nwhich make up that operon. The order within the list is not\ndefined; the fids_to_locations method can report on the\norder of the fids in the operon.", + "module" : "ProteinInfo", + "name" : "operon" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Orthologs are a list of fids which are orthologous to a given fid.", + "module" : "ProteinInfo", + "name" : "orthologs" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "fids_to_operons takes as input a list of feature\nids and returns a mapping of each fid to the operon\nin which it is found. The list of fids in the operon\nis not necessarily in the order that the fids are found\non the genome. (fids_to_operons is currently not properly\nimplemented.)", + "name" : "fids_to_operons", + "parameters" : [ { + "name" : "fids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An operon is represented by a list of fids\nwhich make up that operon. The order within the list is not\ndefined; the fids_to_locations method can report on the\norder of the fids in the operon.", + "module" : "ProteinInfo", + "name" : "operon" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "fids_to_domains takes as input a list of feature ids, and\nreturns a mapping of each fid to its domains. (This includes COG,\neven though COG is not part of InterProScan.)", + "name" : "fids_to_domains", + "parameters" : [ { + "name" : "fids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Domains are a list of domain_ids.", + "module" : "ProteinInfo", + "name" : "domains" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "domains_to_fids takes as input a list of domain_ids, and\nreturns a mapping of each domain_id to the fids which have that\ndomain. (This includes COG, even though COG is not part of\nInterProScan.)", + "name" : "domains_to_fids", + "parameters" : [ { + "name" : "domain_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Domains are a list of domain_ids.", + "module" : "ProteinInfo", + "name" : "domains" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A domain_id is an identifier of a protein domain or family\n(e.g., COG593, TIGR00362). Most of these are stable identifiers\nthat come from external curated libraries, such as COG or InterProScan,\nbut some may be unstable identifiers that come from automated\nanalyses like FastBLAST. (The current implementation includes only\nCOG and InterProScan HMM libraries, such as TIGRFam and Pfam.)", + "module" : "ProteinInfo", + "name" : "domain_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "fids_to_ipr takes as input a list of feature ids, and returns\na mapping of each fid to its IPR assignments. These can come from\nHMMER or from non-HMM-based InterProScan results.", + "name" : "fids_to_ipr", + "parameters" : [ { + "name" : "fids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "IPRs are a list of InterPro identifiers.", + "module" : "ProteinInfo", + "name" : "ipr" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "fids_to_orthologs takes as input a list of feature ids, and\nreturns a mapping of each fid to its orthologous fids in\nall genomes.", + "name" : "fids_to_orthologs", + "parameters" : [ { + "name" : "fids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Orthologs are a list of fids which are orthologous to a given fid.", + "module" : "ProteinInfo", + "name" : "orthologs" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "fids_to_ec takes as input a list of feature ids, and returns\na mapping of each fid to its Enzyme Commission numbers (EC).", + "name" : "fids_to_ec", + "parameters" : [ { + "name" : "fids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "ECs are a list of Enzyme Commission identifiers.", + "module" : "ProteinInfo", + "name" : "ec" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "fids_to_go takes as input a list of feature ids, and returns\na mapping of each fid to its Gene Ontology assignments (GO).", + "name" : "fids_to_go", + "parameters" : [ { + "name" : "fids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GOs are a list of Gene Ontology identifiers.", + "module" : "ProteinInfo", + "name" : "go" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "fid_to_neighbor takes as input a single feature id, and\na neighbor score threshold and returns a list of neighbors\nwhere neighbor score >= threshold", + "name" : "fid_to_neighbors", + "parameters" : [ { + "name" : "id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + }, { + "name" : "thresh", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A neighbor_threshold is a floating point number indicating a bound\nfor the neighbor score", + "module" : "ProteinInfo", + "name" : "neighbor_threshold" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Neighbor is a hash of fids to a neighbor score", + "module" : "ProteinInfo", + "name" : "neighbor" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "fidlist_to_neighbors takes as input a list of feature ids, and\na minimal neighbor score, and returns a mapping of each fid to\nits neighbors, based on neighbor score >= threshold", + "name" : "fidlist_to_neighbors", + "parameters" : [ { + "name" : "fids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + } + }, { + "name" : "thresh", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A neighbor_threshold is a floating point number indicating a bound\nfor the neighbor score", + "module" : "ProteinInfo", + "name" : "neighbor_threshold" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Neighbor is a hash of fids to a neighbor score", + "module" : "ProteinInfo", + "name" : "neighbor" + } + } + } + } ] + } ], + "module_name" : "ProteinInfo", + "options" : [ ], + "service_name" : "ProteinInfo" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "domain_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A domain_id is an identifier of a protein domain or family\n(e.g., COG593, TIGR00362). Most of these are stable identifiers\nthat come from external curated libraries, such as COG or InterProScan,\nbut some may be unstable identifiers that come from automated\nanalyses like FastBLAST. (The current implementation includes only\nCOG and InterProScan HMM libraries, such as TIGRFam and Pfam.)", + "module" : "ProteinInfo", + "name" : "domain_id" + }, + "domains" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Domains are a list of domain_ids.", + "module" : "ProteinInfo", + "name" : "domains" + }, + "ec" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "ECs are a list of Enzyme Commission identifiers.", + "module" : "ProteinInfo", + "name" : "ec" + }, + "fid" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "go" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "GOs are a list of Gene Ontology identifiers.", + "module" : "ProteinInfo", + "name" : "go" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "ipr" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "IPRs are a list of InterPro identifiers.", + "module" : "ProteinInfo", + "name" : "ipr" + }, + "neighbor" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Neighbor is a hash of fids to a neighbor score", + "module" : "ProteinInfo", + "name" : "neighbor" + }, + "neighbor_threshold" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A neighbor_threshold is a floating point number indicating a bound\nfor the neighbor score", + "module" : "ProteinInfo", + "name" : "neighbor_threshold" + }, + "operon" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An operon is represented by a list of fids\nwhich make up that operon. The order within the list is not\ndefined; the fids_to_locations method can report on the\norder of the fids in the operon.", + "module" : "ProteinInfo", + "name" : "operon" + }, + "orthologs" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A fid is a unique identifier of a feature.", + "module" : "ProteinInfo", + "name" : "fid" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Orthologs are a list of fids which are orthologous to a given fid.", + "module" : "ProteinInfo", + "name" : "orthologs" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.16.json.properties b/src/test/resources/us/kbase/test/kidl/spec.16.json.properties new file mode 100644 index 0000000..52779b4 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.16.json.properties @@ -0,0 +1,6958 @@ +{ + "KBaseRegPrecise" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "Module KBaseRegPrecise version 1.0\n\nThis module provides access to a collection of curated transcriptional regulons from the RegPrecise database (http://regprecise.lbl.gov) \nreconstructed by a comparative genomics approach. It also provides methods for on-the-fly annotation of regulatory interactions in \nnewly submitted bacterial genomes by conservative propagation of curated (reference) regulons.\n\n\nBoth curated and propagated regulons are provided as RegulomeModels. RegulomeModel is a collection of all regulons for a given genome \nreconstructed by a given approach with given parameters. More than one RegulomeModel can exist for a particular genome.", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The source of regulome model. The value can be one of the following:\n\n REGPRECISE_CURATED - indicates that regulome is based on the curated regulons from RegPrecise database\n REGPRECISE_PROPAGATED - indicates that regulom model was automatically built by conservation propagation of RegPrecise reference regulons", + "module" : "KBaseRegPrecise", + "name" : "RegulomeSource" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of regulation. The value can be one of the following: \n\n TF - for regulation by transcription factor\n RNA - for regulation by RNA regulatory element (e.g. riboswitch)", + "module" : "KBaseRegPrecise", + "name" : "RegulationType" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent a Date", + "module" : "KBaseRegPrecise", + "name" : "Date" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values", + "module" : "KBaseRegPrecise", + "name" : "Boolean" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorLocusTag", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents regulator (transcription factor).\n\nstring regulatorId\nUnique identifier of a regulator\n\nstring locusTag\nLocus tag of a regulator\n\nlist evidences\nList of regulator evidences", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulatorId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorLocusTag", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + } + }, + "name" : "evidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Regulator" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents regulator (transcription factor).\n\nstring regulatorId\nUnique identifier of a regulator\n\nstring locusTag\nLocus tag of a regulator\n\nlist evidences\nList of regulator evidences", + "module" : "KBaseRegPrecise", + "name" : "Regulator" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "siteScoreThreshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "srcTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcGenomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + } + }, + "name" : "srcGenes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + } + }, + "name" : "srcSites", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "intergenicDistance", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "maxIntergenicDistance", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of regulated operon predicted during the propagation procedure\n\nlist genes\nList of genes in the operon\n\nlist sites\nList of sites in upstream region of the first gene in the operon\n \nlist operonEvidences\nList of operon evidences supporting the gene content of the operon\n\nlist siteEvidences\nList of site evidences supporting predicted TFBSs", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + } + }, + "name" : "genes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + } + }, + "name" : "sites", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "intergenicDistance", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "maxIntergenicDistance", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + } + }, + "name" : "operonEvidences", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "siteScoreThreshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "srcTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcGenomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + } + }, + "name" : "srcGenes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + } + }, + "name" : "srcSites", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + } + }, + "name" : "siteEvidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "OperonModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of regulated operon predicted during the propagation procedure\n\nlist genes\nList of genes in the operon\n\nlist sites\nList of sites in upstream region of the first gene in the operon\n \nlist operonEvidences\nList of operon evidences supporting the gene content of the operon\n\nlist siteEvidences\nList of site evidences supporting predicted TFBSs", + "module" : "KBaseRegPrecise", + "name" : "OperonModel" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted regulon.\n\nEvidenceType type\nRegulon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nint srcRegPreciseRegulogId \nIdentifier of the source regulog id used as a reference in the propagation procedure", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "srcRegPreciseRegulogId", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulonEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted regulon.\n\nEvidenceType type\nRegulon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nint srcRegPreciseRegulogId \nIdentifier of the source regulog id used as a reference in the propagation procedure", + "module" : "KBaseRegPrecise", + "name" : "RegulonEvidence" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of a predicted regulon.\n\nstring regulonModelId\nIdentifier of a regulon model\n\nstring regulomeModelId\nIdentifier of a regulome model which the regulon belongs to \n\nstring regulatorName\nThe name of the regulator \n \nRegulationType regulationType\nThe type of regulation\n\nlist regulators\nList of regulators assigned to this regulon. More than one regulator can be assigned to a predicted regulon if there are close paralogs\n\nlist operons\nList of models of regulated operons\n\nlist evidences\nList of regulon-specific evidences.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulonModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulomeModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulatorName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of regulation. The value can be one of the following: \n\n TF - for regulation by transcription factor\n RNA - for regulation by RNA regulatory element (e.g. riboswitch)", + "module" : "KBaseRegPrecise", + "name" : "RegulationType" + }, + "name" : "regulationType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents regulator (transcription factor).\n\nstring regulatorId\nUnique identifier of a regulator\n\nstring locusTag\nLocus tag of a regulator\n\nlist evidences\nList of regulator evidences", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulatorId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorLocusTag", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + } + }, + "name" : "evidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Regulator" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents regulator (transcription factor).\n\nstring regulatorId\nUnique identifier of a regulator\n\nstring locusTag\nLocus tag of a regulator\n\nlist evidences\nList of regulator evidences", + "module" : "KBaseRegPrecise", + "name" : "Regulator" + } + }, + "name" : "regulators", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of regulated operon predicted during the propagation procedure\n\nlist genes\nList of genes in the operon\n\nlist sites\nList of sites in upstream region of the first gene in the operon\n \nlist operonEvidences\nList of operon evidences supporting the gene content of the operon\n\nlist siteEvidences\nList of site evidences supporting predicted TFBSs", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + } + }, + "name" : "genes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + } + }, + "name" : "sites", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "intergenicDistance", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "maxIntergenicDistance", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + } + }, + "name" : "operonEvidences", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "siteScoreThreshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "srcTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcGenomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + } + }, + "name" : "srcGenes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + } + }, + "name" : "srcSites", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + } + }, + "name" : "siteEvidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "OperonModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of regulated operon predicted during the propagation procedure\n\nlist genes\nList of genes in the operon\n\nlist sites\nList of sites in upstream region of the first gene in the operon\n \nlist operonEvidences\nList of operon evidences supporting the gene content of the operon\n\nlist siteEvidences\nList of site evidences supporting predicted TFBSs", + "module" : "KBaseRegPrecise", + "name" : "OperonModel" + } + }, + "name" : "operons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted regulon.\n\nEvidenceType type\nRegulon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nint srcRegPreciseRegulogId \nIdentifier of the source regulog id used as a reference in the propagation procedure", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "srcRegPreciseRegulogId", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulonEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted regulon.\n\nEvidenceType type\nRegulon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nint srcRegPreciseRegulogId \nIdentifier of the source regulog id used as a reference in the propagation procedure", + "module" : "KBaseRegPrecise", + "name" : "RegulonEvidence" + } + }, + "name" : "evidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulonModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of a predicted regulon.\n\nstring regulonModelId\nIdentifier of a regulon model\n\nstring regulomeModelId\nIdentifier of a regulome model which the regulon belongs to \n\nstring regulatorName\nThe name of the regulator \n \nRegulationType regulationType\nThe type of regulation\n\nlist regulators\nList of regulators assigned to this regulon. More than one regulator can be assigned to a predicted regulon if there are close paralogs\n\nlist operons\nList of models of regulated operons\n\nlist evidences\nList of regulon-specific evidences.", + "module" : "KBaseRegPrecise", + "name" : "RegulonModel" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Provides a general statistics for a given regulon model.\n\nstring regulonModelId\nIdentifier of a regulon model\n\nstring regulomeModelId\nIdentifier of a regulome model which the regulon belongs to \n\nstring regulatorName\nThe name of the regulator \n \nRegulationType regulationType\nThe type of regulation\n \nint regulatedOperonCount\nThe total number of regulated operons\n\nint regulatedGeneCount\nThe total number of regulated genes\n\nint sitesCount\nThe total number of regulatory sites", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulonModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulomeModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulatorName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of regulation. The value can be one of the following: \n\n TF - for regulation by transcription factor\n RNA - for regulation by RNA regulatory element (e.g. riboswitch)", + "module" : "KBaseRegPrecise", + "name" : "RegulationType" + }, + "name" : "regulationType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "regulatedOperonCount", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "regulatedGeneCount", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "sitesCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulonModelStat" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Provides a general statistics for a given regulon model.\n\nstring regulonModelId\nIdentifier of a regulon model\n\nstring regulomeModelId\nIdentifier of a regulome model which the regulon belongs to \n\nstring regulatorName\nThe name of the regulator \n \nRegulationType regulationType\nThe type of regulation\n \nint regulatedOperonCount\nThe total number of regulated operons\n\nint regulatedGeneCount\nThe total number of regulated genes\n\nint sitesCount\nThe total number of regulatory sites", + "module" : "KBaseRegPrecise", + "name" : "RegulonModelStat" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of regulome.\n\nstring regulomeModelId\nIdentifier of a regulome model\n\nstring genomeId\nIdentifier of a genome id for which the regulome model was created\n\nstring genomeName\nThe name of a genome for which the regulome model was created\n\nint ncbiTaxonomyId\nThe NCBI taxonomy id of a genome for which the regulome model was created\n\nDate createDate\nThe date when the model was created\n\nRegulomeSource regulomeSource\nThe source of a regulome model\n\nstring buildParams\nString representation of parameters used to build a model\n\nint tfRegulonCount\nThe total number of regulons in a model controlled by trancription factors\n\n\nint rnaRegulonCount \nThe total number of regulons in a model controlled by RNA regulatory elements", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulomeModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "ncbiTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent a Date", + "module" : "KBaseRegPrecise", + "name" : "Date" + }, + "name" : "createDate", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The source of regulome model. The value can be one of the following:\n\n REGPRECISE_CURATED - indicates that regulome is based on the curated regulons from RegPrecise database\n REGPRECISE_PROPAGATED - indicates that regulom model was automatically built by conservation propagation of RegPrecise reference regulons", + "module" : "KBaseRegPrecise", + "name" : "RegulomeSource" + }, + "name" : "regulomeSource", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "buildParams", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "tfRegulonCount", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "rnaRegulonCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulomeModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of regulome.\n\nstring regulomeModelId\nIdentifier of a regulome model\n\nstring genomeId\nIdentifier of a genome id for which the regulome model was created\n\nstring genomeName\nThe name of a genome for which the regulome model was created\n\nint ncbiTaxonomyId\nThe NCBI taxonomy id of a genome for which the regulome model was created\n\nDate createDate\nThe date when the model was created\n\nRegulomeSource regulomeSource\nThe source of a regulome model\n\nstring buildParams\nString representation of parameters used to build a model\n\nint tfRegulonCount\nThe total number of regulons in a model controlled by trancription factors\n\n\nint rnaRegulonCount \nThe total number of regulons in a model controlled by RNA regulatory elements", + "module" : "KBaseRegPrecise", + "name" : "RegulomeModel" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a collection of regulome models. \n\nstring collectionId\nIdentifier of a collection\n\nstring name\nThe name of a collection\n\nstring taxonName\nThe taxony name of a collection\n\nstring phylum\nThe phylum of a collection\n\nstring description\nThe description of a collection\n \nDate createDate\nThe date when a colection was created\n\nRegulomeSource regulomeSource\nThe source of a regulomes in a given collection \n\nstring buildParams\nThe parameters used to build regulome modeles from this collection (if construction of all regulome models was submitted a single job)\n \nint regulomeModelCount\nThe total number of regulom models in a collection", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "collectionId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "taxonName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "phylum", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent a Date", + "module" : "KBaseRegPrecise", + "name" : "Date" + }, + "name" : "createDate", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The source of regulome model. The value can be one of the following:\n\n REGPRECISE_CURATED - indicates that regulome is based on the curated regulons from RegPrecise database\n REGPRECISE_PROPAGATED - indicates that regulom model was automatically built by conservation propagation of RegPrecise reference regulons", + "module" : "KBaseRegPrecise", + "name" : "RegulomeSource" + }, + "name" : "regulomeSource", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "buildParams", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "regulomeModelCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulomeModelCollection" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a collection of regulome models. \n\nstring collectionId\nIdentifier of a collection\n\nstring name\nThe name of a collection\n\nstring taxonName\nThe taxony name of a collection\n\nstring phylum\nThe phylum of a collection\n\nstring description\nThe description of a collection\n \nDate createDate\nThe date when a colection was created\n\nRegulomeSource regulomeSource\nThe source of a regulomes in a given collection \n\nstring buildParams\nThe parameters used to build regulome modeles from this collection (if construction of all regulome models was submitted a single job)\n \nint regulomeModelCount\nThe total number of regulom models in a collection", + "module" : "KBaseRegPrecise", + "name" : "RegulomeModelCollection" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents parametrs for building a regulome model by conservative propagation\n\nstring targetGenomeId\nIdentifier of a target genome for annotation of regualtory interactions \n\nstring sourceRegulomeCollectionId\nIdentifier of regulome collection id that should be used as a source (reference).", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "targetGenomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sourceRegulomeCollectionId", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "BuildRegulomeModelParam" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents parametrs for building a regulome model by conservative propagation\n\nstring targetGenomeId\nIdentifier of a target genome for annotation of regualtory interactions \n\nstring sourceRegulomeCollectionId\nIdentifier of regulome collection id that should be used as a source (reference).", + "module" : "KBaseRegPrecise", + "name" : "BuildRegulomeModelParam" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents the state of the annotation (building a regulome model) process.\n \nint processId\nIdentifier of annotation process (job)\n\nint percentDone\nPercent of accomplished tasks\n\nstring description\nDescription of the current step\n\nBoolean done\nWhether the jod is finished or not\n\nstring modelId\nThe identifier of reconstructed regulome model", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "processId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "percentDone", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values", + "module" : "KBaseRegPrecise", + "name" : "Boolean" + }, + "name" : "done", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "modelId", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "ProcessState" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the state of the annotation (building a regulome model) process.\n \nint processId\nIdentifier of annotation process (job)\n\nint percentDone\nPercent of accomplished tasks\n\nstring description\nDescription of the current step\n\nBoolean done\nWhether the jod is finished or not\n\nstring modelId\nThe identifier of reconstructed regulome model", + "module" : "KBaseRegPrecise", + "name" : "ProcessState" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of all regulome model collections.", + "name" : "getRegulomeModelCollections", + "parameters" : [ ], + "return_type" : [ { + "name" : "regulomeModelCollections", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a collection of regulome models. \n\nstring collectionId\nIdentifier of a collection\n\nstring name\nThe name of a collection\n\nstring taxonName\nThe taxony name of a collection\n\nstring phylum\nThe phylum of a collection\n\nstring description\nThe description of a collection\n \nDate createDate\nThe date when a colection was created\n\nRegulomeSource regulomeSource\nThe source of a regulomes in a given collection \n\nstring buildParams\nThe parameters used to build regulome modeles from this collection (if construction of all regulome models was submitted a single job)\n \nint regulomeModelCount\nThe total number of regulom models in a collection", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "collectionId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "taxonName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "phylum", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent a Date", + "module" : "KBaseRegPrecise", + "name" : "Date" + }, + "name" : "createDate", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The source of regulome model. The value can be one of the following:\n\n REGPRECISE_CURATED - indicates that regulome is based on the curated regulons from RegPrecise database\n REGPRECISE_PROPAGATED - indicates that regulom model was automatically built by conservation propagation of RegPrecise reference regulons", + "module" : "KBaseRegPrecise", + "name" : "RegulomeSource" + }, + "name" : "regulomeSource", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "buildParams", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "regulomeModelCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulomeModelCollection" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a collection of regulome models. \n\nstring collectionId\nIdentifier of a collection\n\nstring name\nThe name of a collection\n\nstring taxonName\nThe taxony name of a collection\n\nstring phylum\nThe phylum of a collection\n\nstring description\nThe description of a collection\n \nDate createDate\nThe date when a colection was created\n\nRegulomeSource regulomeSource\nThe source of a regulomes in a given collection \n\nstring buildParams\nThe parameters used to build regulome modeles from this collection (if construction of all regulome models was submitted a single job)\n \nint regulomeModelCount\nThe total number of regulom models in a collection", + "module" : "KBaseRegPrecise", + "name" : "RegulomeModelCollection" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a regulome model collection by a given identifier.\n\nstring collectionId\nIdentifier of a collection of regulome models", + "name" : "getRegulomeModelCollection", + "parameters" : [ { + "name" : "collectionId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "name" : "regulomeModelCollection", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a collection of regulome models. \n\nstring collectionId\nIdentifier of a collection\n\nstring name\nThe name of a collection\n\nstring taxonName\nThe taxony name of a collection\n\nstring phylum\nThe phylum of a collection\n\nstring description\nThe description of a collection\n \nDate createDate\nThe date when a colection was created\n\nRegulomeSource regulomeSource\nThe source of a regulomes in a given collection \n\nstring buildParams\nThe parameters used to build regulome modeles from this collection (if construction of all regulome models was submitted a single job)\n \nint regulomeModelCount\nThe total number of regulom models in a collection", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "collectionId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "taxonName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "phylum", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent a Date", + "module" : "KBaseRegPrecise", + "name" : "Date" + }, + "name" : "createDate", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The source of regulome model. The value can be one of the following:\n\n REGPRECISE_CURATED - indicates that regulome is based on the curated regulons from RegPrecise database\n REGPRECISE_PROPAGATED - indicates that regulom model was automatically built by conservation propagation of RegPrecise reference regulons", + "module" : "KBaseRegPrecise", + "name" : "RegulomeSource" + }, + "name" : "regulomeSource", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "buildParams", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "regulomeModelCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulomeModelCollection" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a collection of regulome models. \n\nstring collectionId\nIdentifier of a collection\n\nstring name\nThe name of a collection\n\nstring taxonName\nThe taxony name of a collection\n\nstring phylum\nThe phylum of a collection\n\nstring description\nThe description of a collection\n \nDate createDate\nThe date when a colection was created\n\nRegulomeSource regulomeSource\nThe source of a regulomes in a given collection \n\nstring buildParams\nThe parameters used to build regulome modeles from this collection (if construction of all regulome models was submitted a single job)\n \nint regulomeModelCount\nThe total number of regulom models in a collection", + "module" : "KBaseRegPrecise", + "name" : "RegulomeModelCollection" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of regulome models for a given collection.\n\nstring collectionId\nIdentifier of a collection of regulome models", + "name" : "getRegulomeModelsByCollectionId", + "parameters" : [ { + "name" : "collectionId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "name" : "regulomeModels", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of regulome.\n\nstring regulomeModelId\nIdentifier of a regulome model\n\nstring genomeId\nIdentifier of a genome id for which the regulome model was created\n\nstring genomeName\nThe name of a genome for which the regulome model was created\n\nint ncbiTaxonomyId\nThe NCBI taxonomy id of a genome for which the regulome model was created\n\nDate createDate\nThe date when the model was created\n\nRegulomeSource regulomeSource\nThe source of a regulome model\n\nstring buildParams\nString representation of parameters used to build a model\n\nint tfRegulonCount\nThe total number of regulons in a model controlled by trancription factors\n\n\nint rnaRegulonCount \nThe total number of regulons in a model controlled by RNA regulatory elements", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulomeModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "ncbiTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent a Date", + "module" : "KBaseRegPrecise", + "name" : "Date" + }, + "name" : "createDate", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The source of regulome model. The value can be one of the following:\n\n REGPRECISE_CURATED - indicates that regulome is based on the curated regulons from RegPrecise database\n REGPRECISE_PROPAGATED - indicates that regulom model was automatically built by conservation propagation of RegPrecise reference regulons", + "module" : "KBaseRegPrecise", + "name" : "RegulomeSource" + }, + "name" : "regulomeSource", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "buildParams", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "tfRegulonCount", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "rnaRegulonCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulomeModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of regulome.\n\nstring regulomeModelId\nIdentifier of a regulome model\n\nstring genomeId\nIdentifier of a genome id for which the regulome model was created\n\nstring genomeName\nThe name of a genome for which the regulome model was created\n\nint ncbiTaxonomyId\nThe NCBI taxonomy id of a genome for which the regulome model was created\n\nDate createDate\nThe date when the model was created\n\nRegulomeSource regulomeSource\nThe source of a regulome model\n\nstring buildParams\nString representation of parameters used to build a model\n\nint tfRegulonCount\nThe total number of regulons in a model controlled by trancription factors\n\n\nint rnaRegulonCount \nThe total number of regulons in a model controlled by RNA regulatory elements", + "module" : "KBaseRegPrecise", + "name" : "RegulomeModel" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of regulome models for a given genome.\n\nstring genomeId\nIdentifier of a genome", + "name" : "getRegulomeModelsByGenomeId", + "parameters" : [ { + "name" : "genomeId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "name" : "regulomeModels", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of regulome.\n\nstring regulomeModelId\nIdentifier of a regulome model\n\nstring genomeId\nIdentifier of a genome id for which the regulome model was created\n\nstring genomeName\nThe name of a genome for which the regulome model was created\n\nint ncbiTaxonomyId\nThe NCBI taxonomy id of a genome for which the regulome model was created\n\nDate createDate\nThe date when the model was created\n\nRegulomeSource regulomeSource\nThe source of a regulome model\n\nstring buildParams\nString representation of parameters used to build a model\n\nint tfRegulonCount\nThe total number of regulons in a model controlled by trancription factors\n\n\nint rnaRegulonCount \nThe total number of regulons in a model controlled by RNA regulatory elements", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulomeModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "ncbiTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent a Date", + "module" : "KBaseRegPrecise", + "name" : "Date" + }, + "name" : "createDate", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The source of regulome model. The value can be one of the following:\n\n REGPRECISE_CURATED - indicates that regulome is based on the curated regulons from RegPrecise database\n REGPRECISE_PROPAGATED - indicates that regulom model was automatically built by conservation propagation of RegPrecise reference regulons", + "module" : "KBaseRegPrecise", + "name" : "RegulomeSource" + }, + "name" : "regulomeSource", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "buildParams", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "tfRegulonCount", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "rnaRegulonCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulomeModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of regulome.\n\nstring regulomeModelId\nIdentifier of a regulome model\n\nstring genomeId\nIdentifier of a genome id for which the regulome model was created\n\nstring genomeName\nThe name of a genome for which the regulome model was created\n\nint ncbiTaxonomyId\nThe NCBI taxonomy id of a genome for which the regulome model was created\n\nDate createDate\nThe date when the model was created\n\nRegulomeSource regulomeSource\nThe source of a regulome model\n\nstring buildParams\nString representation of parameters used to build a model\n\nint tfRegulonCount\nThe total number of regulons in a model controlled by trancription factors\n\n\nint rnaRegulonCount \nThe total number of regulons in a model controlled by RNA regulatory elements", + "module" : "KBaseRegPrecise", + "name" : "RegulomeModel" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of regulome models for a source type.\n\nstring regulomeSource\nThe source type of regulome model", + "name" : "getRegulomeModelsBySourceType", + "parameters" : [ { + "name" : "regulomeSource", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "name" : "regulomeModels", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of regulome.\n\nstring regulomeModelId\nIdentifier of a regulome model\n\nstring genomeId\nIdentifier of a genome id for which the regulome model was created\n\nstring genomeName\nThe name of a genome for which the regulome model was created\n\nint ncbiTaxonomyId\nThe NCBI taxonomy id of a genome for which the regulome model was created\n\nDate createDate\nThe date when the model was created\n\nRegulomeSource regulomeSource\nThe source of a regulome model\n\nstring buildParams\nString representation of parameters used to build a model\n\nint tfRegulonCount\nThe total number of regulons in a model controlled by trancription factors\n\n\nint rnaRegulonCount \nThe total number of regulons in a model controlled by RNA regulatory elements", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulomeModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "ncbiTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent a Date", + "module" : "KBaseRegPrecise", + "name" : "Date" + }, + "name" : "createDate", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The source of regulome model. The value can be one of the following:\n\n REGPRECISE_CURATED - indicates that regulome is based on the curated regulons from RegPrecise database\n REGPRECISE_PROPAGATED - indicates that regulom model was automatically built by conservation propagation of RegPrecise reference regulons", + "module" : "KBaseRegPrecise", + "name" : "RegulomeSource" + }, + "name" : "regulomeSource", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "buildParams", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "tfRegulonCount", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "rnaRegulonCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulomeModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of regulome.\n\nstring regulomeModelId\nIdentifier of a regulome model\n\nstring genomeId\nIdentifier of a genome id for which the regulome model was created\n\nstring genomeName\nThe name of a genome for which the regulome model was created\n\nint ncbiTaxonomyId\nThe NCBI taxonomy id of a genome for which the regulome model was created\n\nDate createDate\nThe date when the model was created\n\nRegulomeSource regulomeSource\nThe source of a regulome model\n\nstring buildParams\nString representation of parameters used to build a model\n\nint tfRegulonCount\nThe total number of regulons in a model controlled by trancription factors\n\n\nint rnaRegulonCount \nThe total number of regulons in a model controlled by RNA regulatory elements", + "module" : "KBaseRegPrecise", + "name" : "RegulomeModel" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a regulome model by a given identifier.\n\nstring regulomeModelId\nIdentifier of a regulome model", + "name" : "getRegulomeModel", + "parameters" : [ { + "name" : "regulomeModelId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "name" : "regulomeModel", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of regulome.\n\nstring regulomeModelId\nIdentifier of a regulome model\n\nstring genomeId\nIdentifier of a genome id for which the regulome model was created\n\nstring genomeName\nThe name of a genome for which the regulome model was created\n\nint ncbiTaxonomyId\nThe NCBI taxonomy id of a genome for which the regulome model was created\n\nDate createDate\nThe date when the model was created\n\nRegulomeSource regulomeSource\nThe source of a regulome model\n\nstring buildParams\nString representation of parameters used to build a model\n\nint tfRegulonCount\nThe total number of regulons in a model controlled by trancription factors\n\n\nint rnaRegulonCount \nThe total number of regulons in a model controlled by RNA regulatory elements", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulomeModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "ncbiTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent a Date", + "module" : "KBaseRegPrecise", + "name" : "Date" + }, + "name" : "createDate", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The source of regulome model. The value can be one of the following:\n\n REGPRECISE_CURATED - indicates that regulome is based on the curated regulons from RegPrecise database\n REGPRECISE_PROPAGATED - indicates that regulom model was automatically built by conservation propagation of RegPrecise reference regulons", + "module" : "KBaseRegPrecise", + "name" : "RegulomeSource" + }, + "name" : "regulomeSource", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "buildParams", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "tfRegulonCount", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "rnaRegulonCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulomeModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of regulome.\n\nstring regulomeModelId\nIdentifier of a regulome model\n\nstring genomeId\nIdentifier of a genome id for which the regulome model was created\n\nstring genomeName\nThe name of a genome for which the regulome model was created\n\nint ncbiTaxonomyId\nThe NCBI taxonomy id of a genome for which the regulome model was created\n\nDate createDate\nThe date when the model was created\n\nRegulomeSource regulomeSource\nThe source of a regulome model\n\nstring buildParams\nString representation of parameters used to build a model\n\nint tfRegulonCount\nThe total number of regulons in a model controlled by trancription factors\n\n\nint rnaRegulonCount \nThe total number of regulons in a model controlled by RNA regulatory elements", + "module" : "KBaseRegPrecise", + "name" : "RegulomeModel" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a geneeral statistics for all regulons from a given regulome model.\n\nstring regulomeModelId\nIdentifier of a regulome model", + "name" : "getRegulonModelStats", + "parameters" : [ { + "name" : "regulomeModelId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "name" : "regulonModelStats", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Provides a general statistics for a given regulon model.\n\nstring regulonModelId\nIdentifier of a regulon model\n\nstring regulomeModelId\nIdentifier of a regulome model which the regulon belongs to \n\nstring regulatorName\nThe name of the regulator \n \nRegulationType regulationType\nThe type of regulation\n \nint regulatedOperonCount\nThe total number of regulated operons\n\nint regulatedGeneCount\nThe total number of regulated genes\n\nint sitesCount\nThe total number of regulatory sites", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulonModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulomeModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulatorName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of regulation. The value can be one of the following: \n\n TF - for regulation by transcription factor\n RNA - for regulation by RNA regulatory element (e.g. riboswitch)", + "module" : "KBaseRegPrecise", + "name" : "RegulationType" + }, + "name" : "regulationType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "regulatedOperonCount", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "regulatedGeneCount", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "sitesCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulonModelStat" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Provides a general statistics for a given regulon model.\n\nstring regulonModelId\nIdentifier of a regulon model\n\nstring regulomeModelId\nIdentifier of a regulome model which the regulon belongs to \n\nstring regulatorName\nThe name of the regulator \n \nRegulationType regulationType\nThe type of regulation\n \nint regulatedOperonCount\nThe total number of regulated operons\n\nint regulatedGeneCount\nThe total number of regulated genes\n\nint sitesCount\nThe total number of regulatory sites", + "module" : "KBaseRegPrecise", + "name" : "RegulonModelStat" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a regulon model by a given identifier.\n\nstring regulonModelId\nIdentifier of a regulon model", + "name" : "getRegulonModel", + "parameters" : [ { + "name" : "regulonModelId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "name" : "regulonModel", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of a predicted regulon.\n\nstring regulonModelId\nIdentifier of a regulon model\n\nstring regulomeModelId\nIdentifier of a regulome model which the regulon belongs to \n\nstring regulatorName\nThe name of the regulator \n \nRegulationType regulationType\nThe type of regulation\n\nlist regulators\nList of regulators assigned to this regulon. More than one regulator can be assigned to a predicted regulon if there are close paralogs\n\nlist operons\nList of models of regulated operons\n\nlist evidences\nList of regulon-specific evidences.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulonModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulomeModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulatorName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of regulation. The value can be one of the following: \n\n TF - for regulation by transcription factor\n RNA - for regulation by RNA regulatory element (e.g. riboswitch)", + "module" : "KBaseRegPrecise", + "name" : "RegulationType" + }, + "name" : "regulationType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents regulator (transcription factor).\n\nstring regulatorId\nUnique identifier of a regulator\n\nstring locusTag\nLocus tag of a regulator\n\nlist evidences\nList of regulator evidences", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulatorId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorLocusTag", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + } + }, + "name" : "evidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Regulator" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents regulator (transcription factor).\n\nstring regulatorId\nUnique identifier of a regulator\n\nstring locusTag\nLocus tag of a regulator\n\nlist evidences\nList of regulator evidences", + "module" : "KBaseRegPrecise", + "name" : "Regulator" + } + }, + "name" : "regulators", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of regulated operon predicted during the propagation procedure\n\nlist genes\nList of genes in the operon\n\nlist sites\nList of sites in upstream region of the first gene in the operon\n \nlist operonEvidences\nList of operon evidences supporting the gene content of the operon\n\nlist siteEvidences\nList of site evidences supporting predicted TFBSs", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + } + }, + "name" : "genes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + } + }, + "name" : "sites", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "intergenicDistance", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "maxIntergenicDistance", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + } + }, + "name" : "operonEvidences", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "siteScoreThreshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "srcTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcGenomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + } + }, + "name" : "srcGenes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + } + }, + "name" : "srcSites", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + } + }, + "name" : "siteEvidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "OperonModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of regulated operon predicted during the propagation procedure\n\nlist genes\nList of genes in the operon\n\nlist sites\nList of sites in upstream region of the first gene in the operon\n \nlist operonEvidences\nList of operon evidences supporting the gene content of the operon\n\nlist siteEvidences\nList of site evidences supporting predicted TFBSs", + "module" : "KBaseRegPrecise", + "name" : "OperonModel" + } + }, + "name" : "operons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted regulon.\n\nEvidenceType type\nRegulon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nint srcRegPreciseRegulogId \nIdentifier of the source regulog id used as a reference in the propagation procedure", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "srcRegPreciseRegulogId", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulonEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted regulon.\n\nEvidenceType type\nRegulon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nint srcRegPreciseRegulogId \nIdentifier of the source regulog id used as a reference in the propagation procedure", + "module" : "KBaseRegPrecise", + "name" : "RegulonEvidence" + } + }, + "name" : "evidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulonModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of a predicted regulon.\n\nstring regulonModelId\nIdentifier of a regulon model\n\nstring regulomeModelId\nIdentifier of a regulome model which the regulon belongs to \n\nstring regulatorName\nThe name of the regulator \n \nRegulationType regulationType\nThe type of regulation\n\nlist regulators\nList of regulators assigned to this regulon. More than one regulator can be assigned to a predicted regulon if there are close paralogs\n\nlist operons\nList of models of regulated operons\n\nlist evidences\nList of regulon-specific evidences.", + "module" : "KBaseRegPrecise", + "name" : "RegulonModel" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Launches the procedure for building regulome model. It returns the processState objects describing the current state. \nThe process state identifier can be later used to monitor the annotation process. \n\nBuildRegulomeModelParam param\nParameters for building regulome model", + "name" : "buildRegulomeModel", + "parameters" : [ { + "name" : "param", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents parametrs for building a regulome model by conservative propagation\n\nstring targetGenomeId\nIdentifier of a target genome for annotation of regualtory interactions \n\nstring sourceRegulomeCollectionId\nIdentifier of regulome collection id that should be used as a source (reference).", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "targetGenomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sourceRegulomeCollectionId", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "BuildRegulomeModelParam" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents parametrs for building a regulome model by conservative propagation\n\nstring targetGenomeId\nIdentifier of a target genome for annotation of regualtory interactions \n\nstring sourceRegulomeCollectionId\nIdentifier of regulome collection id that should be used as a source (reference).", + "module" : "KBaseRegPrecise", + "name" : "BuildRegulomeModelParam" + } + } ], + "return_type" : [ { + "name" : "processState", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents the state of the annotation (building a regulome model) process.\n \nint processId\nIdentifier of annotation process (job)\n\nint percentDone\nPercent of accomplished tasks\n\nstring description\nDescription of the current step\n\nBoolean done\nWhether the jod is finished or not\n\nstring modelId\nThe identifier of reconstructed regulome model", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "processId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "percentDone", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values", + "module" : "KBaseRegPrecise", + "name" : "Boolean" + }, + "name" : "done", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "modelId", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "ProcessState" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the state of the annotation (building a regulome model) process.\n \nint processId\nIdentifier of annotation process (job)\n\nint percentDone\nPercent of accomplished tasks\n\nstring description\nDescription of the current step\n\nBoolean done\nWhether the jod is finished or not\n\nstring modelId\nThe identifier of reconstructed regulome model", + "module" : "KBaseRegPrecise", + "name" : "ProcessState" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns infofrmation for a given process. \n\nint processId\nIdentifier of a process.", + "name" : "getProcessState", + "parameters" : [ { + "name" : "processId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + } ], + "return_type" : [ { + "name" : "processState", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents the state of the annotation (building a regulome model) process.\n \nint processId\nIdentifier of annotation process (job)\n\nint percentDone\nPercent of accomplished tasks\n\nstring description\nDescription of the current step\n\nBoolean done\nWhether the jod is finished or not\n\nstring modelId\nThe identifier of reconstructed regulome model", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "processId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "percentDone", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values", + "module" : "KBaseRegPrecise", + "name" : "Boolean" + }, + "name" : "done", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "modelId", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "ProcessState" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the state of the annotation (building a regulome model) process.\n \nint processId\nIdentifier of annotation process (job)\n\nint percentDone\nPercent of accomplished tasks\n\nstring description\nDescription of the current step\n\nBoolean done\nWhether the jod is finished or not\n\nstring modelId\nThe identifier of reconstructed regulome model", + "module" : "KBaseRegPrecise", + "name" : "ProcessState" + } + } ] + } ], + "module_name" : "KBaseRegPrecise", + "options" : [ ], + "service_name" : "KBaseRegPrecise" + }, [ ], { + "Boolean" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values", + "module" : "KBaseRegPrecise", + "name" : "Boolean" + }, + "BuildRegulomeModelParam" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents parametrs for building a regulome model by conservative propagation\n\nstring targetGenomeId\nIdentifier of a target genome for annotation of regualtory interactions \n\nstring sourceRegulomeCollectionId\nIdentifier of regulome collection id that should be used as a source (reference).", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "targetGenomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sourceRegulomeCollectionId", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "BuildRegulomeModelParam" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents parametrs for building a regulome model by conservative propagation\n\nstring targetGenomeId\nIdentifier of a target genome for annotation of regualtory interactions \n\nstring sourceRegulomeCollectionId\nIdentifier of regulome collection id that should be used as a source (reference).", + "module" : "KBaseRegPrecise", + "name" : "BuildRegulomeModelParam" + }, + "Date" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent a Date", + "module" : "KBaseRegPrecise", + "name" : "Date" + }, + "EvidenceType" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "Gene" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "OperonEvidence" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "intergenicDistance", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "maxIntergenicDistance", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + }, + "OperonModel" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of regulated operon predicted during the propagation procedure\n\nlist genes\nList of genes in the operon\n\nlist sites\nList of sites in upstream region of the first gene in the operon\n \nlist operonEvidences\nList of operon evidences supporting the gene content of the operon\n\nlist siteEvidences\nList of site evidences supporting predicted TFBSs", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + } + }, + "name" : "genes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + } + }, + "name" : "sites", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "intergenicDistance", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "maxIntergenicDistance", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + } + }, + "name" : "operonEvidences", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "siteScoreThreshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "srcTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcGenomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + } + }, + "name" : "srcGenes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + } + }, + "name" : "srcSites", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + } + }, + "name" : "siteEvidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "OperonModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of regulated operon predicted during the propagation procedure\n\nlist genes\nList of genes in the operon\n\nlist sites\nList of sites in upstream region of the first gene in the operon\n \nlist operonEvidences\nList of operon evidences supporting the gene content of the operon\n\nlist siteEvidences\nList of site evidences supporting predicted TFBSs", + "module" : "KBaseRegPrecise", + "name" : "OperonModel" + }, + "ProcessState" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents the state of the annotation (building a regulome model) process.\n \nint processId\nIdentifier of annotation process (job)\n\nint percentDone\nPercent of accomplished tasks\n\nstring description\nDescription of the current step\n\nBoolean done\nWhether the jod is finished or not\n\nstring modelId\nThe identifier of reconstructed regulome model", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "processId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "percentDone", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent boolean values", + "module" : "KBaseRegPrecise", + "name" : "Boolean" + }, + "name" : "done", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "modelId", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "ProcessState" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents the state of the annotation (building a regulome model) process.\n \nint processId\nIdentifier of annotation process (job)\n\nint percentDone\nPercent of accomplished tasks\n\nstring description\nDescription of the current step\n\nBoolean done\nWhether the jod is finished or not\n\nstring modelId\nThe identifier of reconstructed regulome model", + "module" : "KBaseRegPrecise", + "name" : "ProcessState" + }, + "RegulationType" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of regulation. The value can be one of the following: \n\n TF - for regulation by transcription factor\n RNA - for regulation by RNA regulatory element (e.g. riboswitch)", + "module" : "KBaseRegPrecise", + "name" : "RegulationType" + }, + "Regulator" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents regulator (transcription factor).\n\nstring regulatorId\nUnique identifier of a regulator\n\nstring locusTag\nLocus tag of a regulator\n\nlist evidences\nList of regulator evidences", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulatorId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorLocusTag", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + } + }, + "name" : "evidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Regulator" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents regulator (transcription factor).\n\nstring regulatorId\nUnique identifier of a regulator\n\nstring locusTag\nLocus tag of a regulator\n\nlist evidences\nList of regulator evidences", + "module" : "KBaseRegPrecise", + "name" : "Regulator" + }, + "RegulatorEvidence" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorLocusTag", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + }, + "RegulomeModel" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of regulome.\n\nstring regulomeModelId\nIdentifier of a regulome model\n\nstring genomeId\nIdentifier of a genome id for which the regulome model was created\n\nstring genomeName\nThe name of a genome for which the regulome model was created\n\nint ncbiTaxonomyId\nThe NCBI taxonomy id of a genome for which the regulome model was created\n\nDate createDate\nThe date when the model was created\n\nRegulomeSource regulomeSource\nThe source of a regulome model\n\nstring buildParams\nString representation of parameters used to build a model\n\nint tfRegulonCount\nThe total number of regulons in a model controlled by trancription factors\n\n\nint rnaRegulonCount \nThe total number of regulons in a model controlled by RNA regulatory elements", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulomeModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "genomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "ncbiTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent a Date", + "module" : "KBaseRegPrecise", + "name" : "Date" + }, + "name" : "createDate", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The source of regulome model. The value can be one of the following:\n\n REGPRECISE_CURATED - indicates that regulome is based on the curated regulons from RegPrecise database\n REGPRECISE_PROPAGATED - indicates that regulom model was automatically built by conservation propagation of RegPrecise reference regulons", + "module" : "KBaseRegPrecise", + "name" : "RegulomeSource" + }, + "name" : "regulomeSource", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "buildParams", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "tfRegulonCount", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "rnaRegulonCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulomeModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of regulome.\n\nstring regulomeModelId\nIdentifier of a regulome model\n\nstring genomeId\nIdentifier of a genome id for which the regulome model was created\n\nstring genomeName\nThe name of a genome for which the regulome model was created\n\nint ncbiTaxonomyId\nThe NCBI taxonomy id of a genome for which the regulome model was created\n\nDate createDate\nThe date when the model was created\n\nRegulomeSource regulomeSource\nThe source of a regulome model\n\nstring buildParams\nString representation of parameters used to build a model\n\nint tfRegulonCount\nThe total number of regulons in a model controlled by trancription factors\n\n\nint rnaRegulonCount \nThe total number of regulons in a model controlled by RNA regulatory elements", + "module" : "KBaseRegPrecise", + "name" : "RegulomeModel" + }, + "RegulomeModelCollection" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a collection of regulome models. \n\nstring collectionId\nIdentifier of a collection\n\nstring name\nThe name of a collection\n\nstring taxonName\nThe taxony name of a collection\n\nstring phylum\nThe phylum of a collection\n\nstring description\nThe description of a collection\n \nDate createDate\nThe date when a colection was created\n\nRegulomeSource regulomeSource\nThe source of a regulomes in a given collection \n\nstring buildParams\nThe parameters used to build regulome modeles from this collection (if construction of all regulome models was submitted a single job)\n \nint regulomeModelCount\nThe total number of regulom models in a collection", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "collectionId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "taxonName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "phylum", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Helper type to represent a Date", + "module" : "KBaseRegPrecise", + "name" : "Date" + }, + "name" : "createDate", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The source of regulome model. The value can be one of the following:\n\n REGPRECISE_CURATED - indicates that regulome is based on the curated regulons from RegPrecise database\n REGPRECISE_PROPAGATED - indicates that regulom model was automatically built by conservation propagation of RegPrecise reference regulons", + "module" : "KBaseRegPrecise", + "name" : "RegulomeSource" + }, + "name" : "regulomeSource", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "buildParams", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "regulomeModelCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulomeModelCollection" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a collection of regulome models. \n\nstring collectionId\nIdentifier of a collection\n\nstring name\nThe name of a collection\n\nstring taxonName\nThe taxony name of a collection\n\nstring phylum\nThe phylum of a collection\n\nstring description\nThe description of a collection\n \nDate createDate\nThe date when a colection was created\n\nRegulomeSource regulomeSource\nThe source of a regulomes in a given collection \n\nstring buildParams\nThe parameters used to build regulome modeles from this collection (if construction of all regulome models was submitted a single job)\n \nint regulomeModelCount\nThe total number of regulom models in a collection", + "module" : "KBaseRegPrecise", + "name" : "RegulomeModelCollection" + }, + "RegulomeSource" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The source of regulome model. The value can be one of the following:\n\n REGPRECISE_CURATED - indicates that regulome is based on the curated regulons from RegPrecise database\n REGPRECISE_PROPAGATED - indicates that regulom model was automatically built by conservation propagation of RegPrecise reference regulons", + "module" : "KBaseRegPrecise", + "name" : "RegulomeSource" + }, + "RegulonEvidence" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted regulon.\n\nEvidenceType type\nRegulon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nint srcRegPreciseRegulogId \nIdentifier of the source regulog id used as a reference in the propagation procedure", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "srcRegPreciseRegulogId", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulonEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted regulon.\n\nEvidenceType type\nRegulon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nint srcRegPreciseRegulogId \nIdentifier of the source regulog id used as a reference in the propagation procedure", + "module" : "KBaseRegPrecise", + "name" : "RegulonEvidence" + }, + "RegulonModel" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of a predicted regulon.\n\nstring regulonModelId\nIdentifier of a regulon model\n\nstring regulomeModelId\nIdentifier of a regulome model which the regulon belongs to \n\nstring regulatorName\nThe name of the regulator \n \nRegulationType regulationType\nThe type of regulation\n\nlist regulators\nList of regulators assigned to this regulon. More than one regulator can be assigned to a predicted regulon if there are close paralogs\n\nlist operons\nList of models of regulated operons\n\nlist evidences\nList of regulon-specific evidences.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulonModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulomeModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulatorName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of regulation. The value can be one of the following: \n\n TF - for regulation by transcription factor\n RNA - for regulation by RNA regulatory element (e.g. riboswitch)", + "module" : "KBaseRegPrecise", + "name" : "RegulationType" + }, + "name" : "regulationType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents regulator (transcription factor).\n\nstring regulatorId\nUnique identifier of a regulator\n\nstring locusTag\nLocus tag of a regulator\n\nlist evidences\nList of regulator evidences", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulatorId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulatorLocusTag", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a regulator to be considered as an ortholog\n\nEvidenceType type\nRegulator-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n \nstring srcRegulatorId\nUnique identifier of the source regulator by similarity to which the orthology assignment was made\n\nstring srcRegulatorLocusTag; \nLocus tag of the source regulator by similarity to which the orthology assignment was made", + "module" : "KBaseRegPrecise", + "name" : "RegulatorEvidence" + } + }, + "name" : "evidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Regulator" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents regulator (transcription factor).\n\nstring regulatorId\nUnique identifier of a regulator\n\nstring locusTag\nLocus tag of a regulator\n\nlist evidences\nList of regulator evidences", + "module" : "KBaseRegPrecise", + "name" : "Regulator" + } + }, + "name" : "regulators", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a model of regulated operon predicted during the propagation procedure\n\nlist genes\nList of genes in the operon\n\nlist sites\nList of sites in upstream region of the first gene in the operon\n \nlist operonEvidences\nList of operon evidences supporting the gene content of the operon\n\nlist siteEvidences\nList of site evidences supporting predicted TFBSs", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + } + }, + "name" : "genes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + } + }, + "name" : "sites", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "intergenicDistance", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "maxIntergenicDistance", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted operon.\n\nEvidenceType type\nOperon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\n int intergenicDistance\n Maximum observed distance between genes in a predicted operon\n \nint maxIntergenicDistance \n Maximum expected distance between genes in a predicted operon", + "module" : "KBaseRegPrecise", + "name" : "OperonEvidence" + } + }, + "name" : "operonEvidences", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "siteScoreThreshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "srcTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcGenomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + } + }, + "name" : "srcGenes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + } + }, + "name" : "srcSites", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + } + }, + "name" : "siteEvidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "OperonModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of regulated operon predicted during the propagation procedure\n\nlist genes\nList of genes in the operon\n\nlist sites\nList of sites in upstream region of the first gene in the operon\n \nlist operonEvidences\nList of operon evidences supporting the gene content of the operon\n\nlist siteEvidences\nList of site evidences supporting predicted TFBSs", + "module" : "KBaseRegPrecise", + "name" : "OperonModel" + } + }, + "name" : "operons", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted regulon.\n\nEvidenceType type\nRegulon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nint srcRegPreciseRegulogId \nIdentifier of the source regulog id used as a reference in the propagation procedure", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "srcRegPreciseRegulogId", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulonEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted regulon.\n\nEvidenceType type\nRegulon-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nint srcRegPreciseRegulogId \nIdentifier of the source regulog id used as a reference in the propagation procedure", + "module" : "KBaseRegPrecise", + "name" : "RegulonEvidence" + } + }, + "name" : "evidences", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulonModel" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a model of a predicted regulon.\n\nstring regulonModelId\nIdentifier of a regulon model\n\nstring regulomeModelId\nIdentifier of a regulome model which the regulon belongs to \n\nstring regulatorName\nThe name of the regulator \n \nRegulationType regulationType\nThe type of regulation\n\nlist regulators\nList of regulators assigned to this regulon. More than one regulator can be assigned to a predicted regulon if there are close paralogs\n\nlist operons\nList of models of regulated operons\n\nlist evidences\nList of regulon-specific evidences.", + "module" : "KBaseRegPrecise", + "name" : "RegulonModel" + }, + "RegulonModelStat" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Provides a general statistics for a given regulon model.\n\nstring regulonModelId\nIdentifier of a regulon model\n\nstring regulomeModelId\nIdentifier of a regulome model which the regulon belongs to \n\nstring regulatorName\nThe name of the regulator \n \nRegulationType regulationType\nThe type of regulation\n \nint regulatedOperonCount\nThe total number of regulated operons\n\nint regulatedGeneCount\nThe total number of regulated genes\n\nint sitesCount\nThe total number of regulatory sites", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulonModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulomeModelId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "regulatorName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of regulation. The value can be one of the following: \n\n TF - for regulation by transcription factor\n RNA - for regulation by RNA regulatory element (e.g. riboswitch)", + "module" : "KBaseRegPrecise", + "name" : "RegulationType" + }, + "name" : "regulationType", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "regulatedOperonCount", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "regulatedGeneCount", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "sitesCount", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "RegulonModelStat" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Provides a general statistics for a given regulon model.\n\nstring regulonModelId\nIdentifier of a regulon model\n\nstring regulomeModelId\nIdentifier of a regulome model which the regulon belongs to \n\nstring regulatorName\nThe name of the regulator \n \nRegulationType regulationType\nThe type of regulation\n \nint regulatedOperonCount\nThe total number of regulated operons\n\nint regulatedGeneCount\nThe total number of regulated genes\n\nint sitesCount\nThe total number of regulatory sites", + "module" : "KBaseRegPrecise", + "name" : "RegulonModelStat" + }, + "Site" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "SiteEvidence" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Type of evidence. Several types of reconstructed objects (regulons, transcription factors, etc) are provided with evidences to enable \nthe further curation and improving the model that was created by automatic procedure. \n\n OPERON_GENE_DISTANCE_EVIDENCE - evidence for the gene content of operon basing on the intergenic distances\n REGULON_COMPARATIVE_GENOMICS_EVIDENCE - evidence for predcited regulon based on the orthologous regulon from another genome\n REGULATOR_COMPARATIVE_GENOMICS_EVIDENCE - evidence for orthology of transcription factor basing on \n SITE_COMPARATIVE_GENOMICS_EVIDENCE - evidence for TFBS based on the its conservation between several genomes (comparative genomics)", + "module" : "KBaseRegPrecise", + "name" : "EvidenceType" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "description", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "strength", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "confidence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "siteScoreThreshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcRegulomeId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "srcTaxonomyId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "srcGenomeName", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "geneId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "locusTag", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Gene" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents a gene and its basic information\n\nstring geneId\nUnique KBase identifier of a gene\n\nstring locusTag\nLocus tag of a gene\n\nstring name\nGene name", + "module" : "KBaseRegPrecise", + "name" : "Gene" + } + }, + "name" : "srcGenes", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "position", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "score", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "Site" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents either transcription factor binding site, or RNA regulatory element.\n\nstring sequence\nNucletotide sequence of the site\n\nint position\nPosition relative to the first start of the fisrt gene in the regulated operon\n\nfloat score\nScore of the site", + "module" : "KBaseRegPrecise", + "name" : "Site" + } + }, + "name" : "srcSites", + "nullable" : "0" + } ], + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Represents evidence for a predicted TFBS\n\nEvidenceType type\nSite-specific type of evidence\n\nstring description\nDescription of evidence\n\n float strength\n Value from 0 to 1 representing a strength of evidence\n\n float confidence\n Value from 0 to 1 representing a probability of evidence\n\nfloat siteScoreThreshold\nThreshold used to predict TFBS \n\nstring srcRegulomeId\nThe identifier of a regulome model used as a source of reference regulons in comparative analysis (reference regulome). \n\nint srcTaxonomyId\nNCBI taxonomy id of a genome of a reference regulome \n\nstring srcGenomeName\nThe name of a genome of a reference regulome \n \nlist srcGenes\nList of genes from orthologous operon in a reference regulome \n\nlist srcSites\nList of sites from orthologous operon in a reference regulome", + "module" : "KBaseRegPrecise", + "name" : "SiteEvidence" + }, + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.17.json.properties b/src/test/resources/us/kbase/test/kidl/spec.17.json.properties new file mode 100644 index 0000000..9bb46f0 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.17.json.properties @@ -0,0 +1,506 @@ +{ + "Sim" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "The similarity service exposes the SEED similarity server to the KBase. The\nsimilarity server stores precomputed all-to-all BLAST similarities for a\nlarge database of proteins; this database includes all genomes curated by the\nSEED project as well as a variety of third-party protein databases (NCBI\nnr, Uniprot/Swissprot, IMG, etc).\n\nWhile the SEED similarity server does not itself have knowledge of proteins\nwith KBase identifiers, we use the MD5 signature of the protein sequence\nto perform lookups into the similarity server. Similarities returned from\nthe similarity server are also identified with the MD5 signature, and are\nmapped back to KBase identifiers using the information in the KBase Central Store.", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Each similarity returned is encapsulated in a sim_vec tuple. This tuple\ncontains the similar protein identifiers, as well as the columns as seen in the\nblastall -m8 output..\n\nThe columns in the tuple are defined as follows:\n\n 0 id1 query sequence id\n 1 id2 subject sequence id\n 2 iden percentage sequence identity\n 3 ali_ln alignment length\n 4 mismatches number of mismatch\n 5 gaps number of gaps\n 6 b1 query seq match start\n 7 e1 query seq match end\n 8 b2 subject seq match start\n 9 e2 subject seq match end\n 10 psc match e-value\n 11 bsc bit score\n 12 ln1 query sequence length\n 13 ln2 subject sequence length\n 14 tool tool used to produce similarities\n\nAll following fields may vary by tool:\n\n 15 loc1 query seq locations string (b1-e1,b2-e2,b3-e3)\n 16 loc2 subject seq locations string (b1-e1,b2-e2,b3-e3)\n 17 dist tree distance\n\nWe also return this column for any lookups when the kb_function2 flag\nis enabled:\n\n 18 function2 The function associated with id2 in the KBase.", + "element_names" : [ "id1", "id2", "iden", "ali_ln", "mismatches", "gaps", "b1", "e1", "b2", "e2", "psc", "bsc", "ln1", "ln2", "tool", "def2", "ali", "function2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "sim_vec" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Each similarity returned is encapsulated in a sim_vec tuple. This tuple\ncontains the similar protein identifiers, as well as the columns as seen in the\nblastall -m8 output..\n\nThe columns in the tuple are defined as follows:\n\n 0 id1 query sequence id\n 1 id2 subject sequence id\n 2 iden percentage sequence identity\n 3 ali_ln alignment length\n 4 mismatches number of mismatch\n 5 gaps number of gaps\n 6 b1 query seq match start\n 7 e1 query seq match end\n 8 b2 subject seq match start\n 9 e2 subject seq match end\n 10 psc match e-value\n 11 bsc bit score\n 12 ln1 query sequence length\n 13 ln2 subject sequence length\n 14 tool tool used to produce similarities\n\nAll following fields may vary by tool:\n\n 15 loc1 query seq locations string (b1-e1,b2-e2,b3-e3)\n 16 loc2 subject seq locations string (b1-e1,b2-e2,b3-e3)\n 17 dist tree distance\n\nWe also return this column for any lookups when the kb_function2 flag\nis enabled:\n\n 18 function2 The function associated with id2 in the KBase.", + "module" : "Sim", + "name" : "sim_vec" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Option specification. The following options are available for the sims call:\n\n kb_only Only return KBase identifiers (not raw MD5 or other external IDs).\n kb_function2 For KB identifiers, return the function mapped to id2.\n evalue_cutoff Return similarities with an e-value better than this value.\n max_sims Return at most this many similarities. The number of values\n may exceed this due to multiple identifiers mapping to the same sequence.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "kb_only", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "kb_function2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "evalue_cutoff", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "max_sims", + "nullable" : "0" + } ], + "module" : "Sim", + "name" : "options" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Option specification. The following options are available for the sims call:\n\n kb_only Only return KBase identifiers (not raw MD5 or other external IDs).\n kb_function2 For KB identifiers, return the function mapped to id2.\n evalue_cutoff Return similarities with an e-value better than this value.\n max_sims Return at most this many similarities. The number of values\n may exceed this due to multiple identifiers mapping to the same sequence.", + "module" : "Sim", + "name" : "options" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Retrieve precomputed protein similarities given a list of identifiers.\n\nThe options parameter allows simple configuration of the call. The following\nvalues in the structure are interpreted:\n\n kb_only Only return KBase identifiers (not raw MD5 or other external IDs).\n kb_function2 For KB identifiers, return the function mapped to id2.\n evalue_cutoff Return similarities with an e-value better than this value.\n max_sims Return at most this many similarities. The number of values\n may exceed this due to multiple identifiers mapping to the same sequence.\n\nEach similarity returned is encapsulated in a sim_vec tuple. This tuple\ncontains the similar protein identifiers, as well as the columns as seen in the\nblastall -m8 output..\n\nThe return is a list of tuples representing the similarity values. The indexes in the\ntuple are defined as follows:\n\n 0 id1 query sequence id\n 1 id2 subject sequence id\n 2 iden percentage sequence identity\n 3 ali_ln alignment length\n 4 mismatches number of mismatch\n 5 gaps number of gaps\n 6 b1 query seq match start\n 7 e1 query seq match end\n 8 b2 subject seq match start\n 9 e2 subject seq match end\n 10 psc match e-value\n 11 bsc bit score\n 12 ln1 query sequence length\n 13 ln2 subject sequence length\n 14 tool tool used to produce similarities\n\nAll following fields may vary by tool:\n\n 15 loc1 query seq locations string (b1-e1,b2-e2,b3-e3)\n 16 loc2 subject seq locations string (b1-e1,b2-e2,b3-e3)\n 17 dist tree distance\n\nWe also return this column for any lookups when the kb_function2 flag\nis enabled.\n\n 18 function2 The function associated with id2 in the KBase.", + "name" : "sims", + "parameters" : [ { + "name" : "ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "options", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Option specification. The following options are available for the sims call:\n\n kb_only Only return KBase identifiers (not raw MD5 or other external IDs).\n kb_function2 For KB identifiers, return the function mapped to id2.\n evalue_cutoff Return similarities with an e-value better than this value.\n max_sims Return at most this many similarities. The number of values\n may exceed this due to multiple identifiers mapping to the same sequence.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "kb_only", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "kb_function2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "evalue_cutoff", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "max_sims", + "nullable" : "0" + } ], + "module" : "Sim", + "name" : "options" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Option specification. The following options are available for the sims call:\n\n kb_only Only return KBase identifiers (not raw MD5 or other external IDs).\n kb_function2 For KB identifiers, return the function mapped to id2.\n evalue_cutoff Return similarities with an e-value better than this value.\n max_sims Return at most this many similarities. The number of values\n may exceed this due to multiple identifiers mapping to the same sequence.", + "module" : "Sim", + "name" : "options" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Each similarity returned is encapsulated in a sim_vec tuple. This tuple\ncontains the similar protein identifiers, as well as the columns as seen in the\nblastall -m8 output..\n\nThe columns in the tuple are defined as follows:\n\n 0 id1 query sequence id\n 1 id2 subject sequence id\n 2 iden percentage sequence identity\n 3 ali_ln alignment length\n 4 mismatches number of mismatch\n 5 gaps number of gaps\n 6 b1 query seq match start\n 7 e1 query seq match end\n 8 b2 subject seq match start\n 9 e2 subject seq match end\n 10 psc match e-value\n 11 bsc bit score\n 12 ln1 query sequence length\n 13 ln2 subject sequence length\n 14 tool tool used to produce similarities\n\nAll following fields may vary by tool:\n\n 15 loc1 query seq locations string (b1-e1,b2-e2,b3-e3)\n 16 loc2 subject seq locations string (b1-e1,b2-e2,b3-e3)\n 17 dist tree distance\n\nWe also return this column for any lookups when the kb_function2 flag\nis enabled:\n\n 18 function2 The function associated with id2 in the KBase.", + "element_names" : [ "id1", "id2", "iden", "ali_ln", "mismatches", "gaps", "b1", "e1", "b2", "e2", "psc", "bsc", "ln1", "ln2", "tool", "def2", "ali", "function2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "sim_vec" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Each similarity returned is encapsulated in a sim_vec tuple. This tuple\ncontains the similar protein identifiers, as well as the columns as seen in the\nblastall -m8 output..\n\nThe columns in the tuple are defined as follows:\n\n 0 id1 query sequence id\n 1 id2 subject sequence id\n 2 iden percentage sequence identity\n 3 ali_ln alignment length\n 4 mismatches number of mismatch\n 5 gaps number of gaps\n 6 b1 query seq match start\n 7 e1 query seq match end\n 8 b2 subject seq match start\n 9 e2 subject seq match end\n 10 psc match e-value\n 11 bsc bit score\n 12 ln1 query sequence length\n 13 ln2 subject sequence length\n 14 tool tool used to produce similarities\n\nAll following fields may vary by tool:\n\n 15 loc1 query seq locations string (b1-e1,b2-e2,b3-e3)\n 16 loc2 subject seq locations string (b1-e1,b2-e2,b3-e3)\n 17 dist tree distance\n\nWe also return this column for any lookups when the kb_function2 flag\nis enabled:\n\n 18 function2 The function associated with id2 in the KBase.", + "module" : "Sim", + "name" : "sim_vec" + } + } + } ] + } ], + "module_name" : "Sim", + "options" : [ ], + "service_name" : "Sim" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "options" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Option specification. The following options are available for the sims call:\n\n kb_only Only return KBase identifiers (not raw MD5 or other external IDs).\n kb_function2 For KB identifiers, return the function mapped to id2.\n evalue_cutoff Return similarities with an e-value better than this value.\n max_sims Return at most this many similarities. The number of values\n may exceed this due to multiple identifiers mapping to the same sequence.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "kb_only", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "kb_function2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "evalue_cutoff", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "max_sims", + "nullable" : "0" + } ], + "module" : "Sim", + "name" : "options" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Option specification. The following options are available for the sims call:\n\n kb_only Only return KBase identifiers (not raw MD5 or other external IDs).\n kb_function2 For KB identifiers, return the function mapped to id2.\n evalue_cutoff Return similarities with an e-value better than this value.\n max_sims Return at most this many similarities. The number of values\n may exceed this due to multiple identifiers mapping to the same sequence.", + "module" : "Sim", + "name" : "options" + }, + "sim_vec" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "Each similarity returned is encapsulated in a sim_vec tuple. This tuple\ncontains the similar protein identifiers, as well as the columns as seen in the\nblastall -m8 output..\n\nThe columns in the tuple are defined as follows:\n\n 0 id1 query sequence id\n 1 id2 subject sequence id\n 2 iden percentage sequence identity\n 3 ali_ln alignment length\n 4 mismatches number of mismatch\n 5 gaps number of gaps\n 6 b1 query seq match start\n 7 e1 query seq match end\n 8 b2 subject seq match start\n 9 e2 subject seq match end\n 10 psc match e-value\n 11 bsc bit score\n 12 ln1 query sequence length\n 13 ln2 subject sequence length\n 14 tool tool used to produce similarities\n\nAll following fields may vary by tool:\n\n 15 loc1 query seq locations string (b1-e1,b2-e2,b3-e3)\n 16 loc2 subject seq locations string (b1-e1,b2-e2,b3-e3)\n 17 dist tree distance\n\nWe also return this column for any lookups when the kb_function2 flag\nis enabled:\n\n 18 function2 The function associated with id2 in the KBase.", + "element_names" : [ "id1", "id2", "iden", "ali_ln", "mismatches", "gaps", "b1", "e1", "b2", "e2", "psc", "bsc", "ln1", "ln2", "tool", "def2", "ali", "function2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "sim_vec" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Each similarity returned is encapsulated in a sim_vec tuple. This tuple\ncontains the similar protein identifiers, as well as the columns as seen in the\nblastall -m8 output..\n\nThe columns in the tuple are defined as follows:\n\n 0 id1 query sequence id\n 1 id2 subject sequence id\n 2 iden percentage sequence identity\n 3 ali_ln alignment length\n 4 mismatches number of mismatch\n 5 gaps number of gaps\n 6 b1 query seq match start\n 7 e1 query seq match end\n 8 b2 subject seq match start\n 9 e2 subject seq match end\n 10 psc match e-value\n 11 bsc bit score\n 12 ln1 query sequence length\n 13 ln2 subject sequence length\n 14 tool tool used to produce similarities\n\nAll following fields may vary by tool:\n\n 15 loc1 query seq locations string (b1-e1,b2-e2,b3-e3)\n 16 loc2 subject seq locations string (b1-e1,b2-e2,b3-e3)\n 17 dist tree distance\n\nWe also return this column for any lookups when the kb_function2 flag\nis enabled:\n\n 18 function2 The function associated with id2 in the KBase.", + "module" : "Sim", + "name" : "sim_vec" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.18.json.properties b/src/test/resources/us/kbase/test/kidl/spec.18.json.properties new file mode 100644 index 0000000..682018f --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.18.json.properties @@ -0,0 +1,2093 @@ +{ + "MOTranslation" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "This module will translate KBase ids to MicrobesOnline ids and\nvice-versa. For features, it will initially use MD5s to perform\nthe translation.\n\nThe MOTranslation module will ultimately be deprecated, once all\nMicrobesOnline data types are natively stored in KBase. In general\nthe module and methods should not be publicized, and are mainly intended\nto be used internally by other KBase services (specifically the protein\ninfo service).", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "protein is an MD5 in KBase. It is the primary lookup between\nKBase fids and MicrobesOnline locusIds.", + "module" : "MOTranslation", + "name" : "protein" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbaseId can represent any object with a KBase identifier. \nIn the future this may be used to translate between other data\ntypes, such as contig or genome.", + "module" : "MOTranslation", + "name" : "kbaseId" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbaseId can represent any object with a KBase identifier. \nIn the future this may be used to translate between other data\ntypes, such as contig or genome.", + "module" : "MOTranslation", + "name" : "kbaseId" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "genomeId is a kbase id of a genome", + "module" : "MOTranslation", + "name" : "genomeId" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "fid is a feature id in KBase.", + "module" : "MOTranslation", + "name" : "fid" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moLocusId is a locusId in MicrobesOnline. It is analogous to a fid\nin KBase.", + "module" : "MOTranslation", + "name" : "moLocusId" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moScaffoldId is a scaffoldId in MicrobesOnline. It is analogous to\na contig kbId in KBase.", + "module" : "MOTranslation", + "name" : "moScaffoldId" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moTaxonomyId is a taxonomyId in MicrobesOnline. It is somewhat analogous\nto a genome kbId in KBase. It generally stores the NCBI taxonomy ID,\nthough sometimes can store an internal identifier instead.", + "module" : "MOTranslation", + "name" : "moTaxonomyId" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "fids_to_moLocusIds translates a list of fids into MicrobesOnline\nlocusIds. It uses proteins_to_moLocusIds internally.", + "name" : "fids_to_moLocusIds", + "parameters" : [ { + "name" : "fids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "fid is a feature id in KBase.", + "module" : "MOTranslation", + "name" : "fid" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "fid is a feature id in KBase.", + "module" : "MOTranslation", + "name" : "fid" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moLocusId is a locusId in MicrobesOnline. It is analogous to a fid\nin KBase.", + "module" : "MOTranslation", + "name" : "moLocusId" + } + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "proteins_to_moLocusIds translates a list of proteins (MD5s) into\nMicrobesOnline locusIds.", + "name" : "proteins_to_moLocusIds", + "parameters" : [ { + "name" : "proteins", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "protein is an MD5 in KBase. It is the primary lookup between\nKBase fids and MicrobesOnline locusIds.", + "module" : "MOTranslation", + "name" : "protein" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "protein is an MD5 in KBase. It is the primary lookup between\nKBase fids and MicrobesOnline locusIds.", + "module" : "MOTranslation", + "name" : "protein" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moLocusId is a locusId in MicrobesOnline. It is analogous to a fid\nin KBase.", + "module" : "MOTranslation", + "name" : "moLocusId" + } + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "moLocusIds_to_fids translates a list of MicrobesOnline locusIds\ninto KBase fids. It uses moLocusIds_to_proteins internally.", + "name" : "moLocusIds_to_fids", + "parameters" : [ { + "name" : "moLocusIds", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moLocusId is a locusId in MicrobesOnline. It is analogous to a fid\nin KBase.", + "module" : "MOTranslation", + "name" : "moLocusId" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moLocusId is a locusId in MicrobesOnline. It is analogous to a fid\nin KBase.", + "module" : "MOTranslation", + "name" : "moLocusId" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "fid is a feature id in KBase.", + "module" : "MOTranslation", + "name" : "fid" + } + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "moLocusIds_to_proteins translates a list of MicrobesOnline locusIds\ninto proteins (MD5s).", + "name" : "moLocusIds_to_proteins", + "parameters" : [ { + "name" : "moLocusIds", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moLocusId is a locusId in MicrobesOnline. It is analogous to a fid\nin KBase.", + "module" : "MOTranslation", + "name" : "moLocusId" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moLocusId is a locusId in MicrobesOnline. It is analogous to a fid\nin KBase.", + "module" : "MOTranslation", + "name" : "moLocusId" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "protein is an MD5 in KBase. It is the primary lookup between\nKBase fids and MicrobesOnline locusIds.", + "module" : "MOTranslation", + "name" : "protein" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "AA sequence of a protein", + "module" : "MOTranslation", + "name" : "protein_sequence" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "internally consistant and unique id of a protein (could just be integers 0..n), necessary\nfor returning results", + "module" : "MOTranslation", + "name" : "protein_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short note used to convey the status or explanaton of a result, or in some cases a log of the\nmethod that was run", + "module" : "MOTranslation", + "name" : "status" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A structure for specifying the input sequence queries for the map_to_fid method. This structure, for\nnow, assumes you will be making queries with identical genomes, so it requires the start and stop. In the\nfuture, if this assumption is relaxed, then start and stop will be optional parameters. We should probably\nalso add an MD5 string which can optionally be provided so that we don't have to compute it on the fly.\n\n protein_id id - arbitrary ID that must be unique within the set of query sequences\n protein_sequence seq - the one letter code AA sequence of the protein\n position start - the start position of the start codon in the genome contig (may be a larger\n number than stop if the gene is on the reverse strand)\n position stop - the last position of he stop codon in the genome contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "internally consistant and unique id of a protein (could just be integers 0..n), necessary\nfor returning results", + "module" : "MOTranslation", + "name" : "protein_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "AA sequence of a protein", + "module" : "MOTranslation", + "name" : "protein_sequence" + }, + "name" : "seq", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "name" : "start", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "name" : "stop", + "nullable" : "0" + } ], + "module" : "MOTranslation", + "name" : "query_sequence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A structure for specifying the input sequence queries for the map_to_fid method. This structure, for\nnow, assumes you will be making queries with identical genomes, so it requires the start and stop. In the\nfuture, if this assumption is relaxed, then start and stop will be optional parameters. We should probably\nalso add an MD5 string which can optionally be provided so that we don't have to compute it on the fly.\n\n protein_id id - arbitrary ID that must be unique within the set of query sequences\n protein_sequence seq - the one letter code AA sequence of the protein\n position start - the start position of the start codon in the genome contig (may be a larger\n number than stop if the gene is on the reverse strand)\n position stop - the last position of he stop codon in the genome contig", + "module" : "MOTranslation", + "name" : "query_sequence" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A structure for specifying the input md5 queries for the map_to_fid_fast method. This structure assumes\nyou will be making queries with identical genomes, so it requires the start and stop.\n\n protein_id id - arbitrary ID that must be unique within the set of query sequences\n protein md5 - the computed md5 of the protein sequence\n position start - the start position of the start codon in the genome contig (may be a larger\n number than stop if the gene is on the reverse strand)\n position stop - the last position of he stop codon in the genome contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "internally consistant and unique id of a protein (could just be integers 0..n), necessary\nfor returning results", + "module" : "MOTranslation", + "name" : "protein_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "protein is an MD5 in KBase. It is the primary lookup between\nKBase fids and MicrobesOnline locusIds.", + "module" : "MOTranslation", + "name" : "protein" + }, + "name" : "md5", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "name" : "start", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "name" : "stop", + "nullable" : "0" + } ], + "module" : "MOTranslation", + "name" : "query_md5" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A structure for specifying the input md5 queries for the map_to_fid_fast method. This structure assumes\nyou will be making queries with identical genomes, so it requires the start and stop.\n\n protein_id id - arbitrary ID that must be unique within the set of query sequences\n protein md5 - the computed md5 of the protein sequence\n position start - the start position of the start codon in the genome contig (may be a larger\n number than stop if the gene is on the reverse strand)\n position stop - the last position of he stop codon in the genome contig", + "module" : "MOTranslation", + "name" : "query_md5" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simple structure which returns the best matching FID to a given query (see query_sequence) and attaches\na short status string indicating how the match was made, or which consoles you after a match could not\nbe made.\n\n fid best_match - the feature ID of a KBase feature that offers the best mapping to your query\n status status - a short note explaining how the match was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "fid is a feature id in KBase.", + "module" : "MOTranslation", + "name" : "fid" + }, + "name" : "best_match", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short note used to convey the status or explanaton of a result, or in some cases a log of the\nmethod that was run", + "module" : "MOTranslation", + "name" : "status" + }, + "name" : "status", + "nullable" : "0" + } ], + "module" : "MOTranslation", + "name" : "result" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simple structure which returns the best matching FID to a given query (see query_sequence) and attaches\na short status string indicating how the match was made, or which consoles you after a match could not\nbe made.\n\n fid best_match - the feature ID of a KBase feature that offers the best mapping to your query\n status status - a short note explaining how the match was made", + "module" : "MOTranslation", + "name" : "result" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "A general method to lookup the best matching feature id in a specific genome for a given protein sequence.\n\nNOTE: currently the intended use of this method is to map identical genomes with different gene calls, although it still\ncan work for fairly similar genomes. But be warned!! It may produce incorrect results for genomes that differ!\n\nThis method operates by first checking the MD5 and position of each sequence and determining if there is an exact match,\n(or an exact MD5 match +- 30bp). If none are found, then a simple blast search is performed. Currently the blast search\nis completely overkill as it is used simply to look for 50% overlap of genes. Blast was chosen, however, because it is\nanticipated that this, or a very similar implementation of this method, will be used more generally for mapping features\non roughly similar genomes. Keep very much in mind that this method is not designed to be a general homology search, which\nshould be done with more advanced methods. Rather, this method is designed more for bookkeeping purposes when data based on\none genome with a set of gene calls needs to be applied to a genome with a second set of gene calls.\n\nsee also the cooresponds method of the CDMI.", + "name" : "map_to_fid", + "parameters" : [ { + "name" : "query_sequences", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A structure for specifying the input sequence queries for the map_to_fid method. This structure, for\nnow, assumes you will be making queries with identical genomes, so it requires the start and stop. In the\nfuture, if this assumption is relaxed, then start and stop will be optional parameters. We should probably\nalso add an MD5 string which can optionally be provided so that we don't have to compute it on the fly.\n\n protein_id id - arbitrary ID that must be unique within the set of query sequences\n protein_sequence seq - the one letter code AA sequence of the protein\n position start - the start position of the start codon in the genome contig (may be a larger\n number than stop if the gene is on the reverse strand)\n position stop - the last position of he stop codon in the genome contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "internally consistant and unique id of a protein (could just be integers 0..n), necessary\nfor returning results", + "module" : "MOTranslation", + "name" : "protein_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "AA sequence of a protein", + "module" : "MOTranslation", + "name" : "protein_sequence" + }, + "name" : "seq", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "name" : "start", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "name" : "stop", + "nullable" : "0" + } ], + "module" : "MOTranslation", + "name" : "query_sequence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A structure for specifying the input sequence queries for the map_to_fid method. This structure, for\nnow, assumes you will be making queries with identical genomes, so it requires the start and stop. In the\nfuture, if this assumption is relaxed, then start and stop will be optional parameters. We should probably\nalso add an MD5 string which can optionally be provided so that we don't have to compute it on the fly.\n\n protein_id id - arbitrary ID that must be unique within the set of query sequences\n protein_sequence seq - the one letter code AA sequence of the protein\n position start - the start position of the start codon in the genome contig (may be a larger\n number than stop if the gene is on the reverse strand)\n position stop - the last position of he stop codon in the genome contig", + "module" : "MOTranslation", + "name" : "query_sequence" + } + } + }, { + "name" : "genomeId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbaseId can represent any object with a KBase identifier. \nIn the future this may be used to translate between other data\ntypes, such as contig or genome.", + "module" : "MOTranslation", + "name" : "kbaseId" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "genomeId is a kbase id of a genome", + "module" : "MOTranslation", + "name" : "genomeId" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "internally consistant and unique id of a protein (could just be integers 0..n), necessary\nfor returning results", + "module" : "MOTranslation", + "name" : "protein_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simple structure which returns the best matching FID to a given query (see query_sequence) and attaches\na short status string indicating how the match was made, or which consoles you after a match could not\nbe made.\n\n fid best_match - the feature ID of a KBase feature that offers the best mapping to your query\n status status - a short note explaining how the match was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "fid is a feature id in KBase.", + "module" : "MOTranslation", + "name" : "fid" + }, + "name" : "best_match", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short note used to convey the status or explanaton of a result, or in some cases a log of the\nmethod that was run", + "module" : "MOTranslation", + "name" : "status" + }, + "name" : "status", + "nullable" : "0" + } ], + "module" : "MOTranslation", + "name" : "result" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simple structure which returns the best matching FID to a given query (see query_sequence) and attaches\na short status string indicating how the match was made, or which consoles you after a match could not\nbe made.\n\n fid best_match - the feature ID of a KBase feature that offers the best mapping to your query\n status status - a short note explaining how the match was made", + "module" : "MOTranslation", + "name" : "result" + } + } + }, { + "name" : "log", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short note used to convey the status or explanaton of a result, or in some cases a log of the\nmethod that was run", + "module" : "MOTranslation", + "name" : "status" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Performs the same function as map_to_fid, except it does not require protein sequences to be defined. Instead, it assumes\ngenomes are identical and simply looks for genes on the same strand that overlap by at least 50%. Since no sequences are\ncompared, this method is fast. But, since no sequences are compared, this method only makes sense for identical genomes", + "name" : "map_to_fid_fast", + "parameters" : [ { + "name" : "query_md5s", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A structure for specifying the input md5 queries for the map_to_fid_fast method. This structure assumes\nyou will be making queries with identical genomes, so it requires the start and stop.\n\n protein_id id - arbitrary ID that must be unique within the set of query sequences\n protein md5 - the computed md5 of the protein sequence\n position start - the start position of the start codon in the genome contig (may be a larger\n number than stop if the gene is on the reverse strand)\n position stop - the last position of he stop codon in the genome contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "internally consistant and unique id of a protein (could just be integers 0..n), necessary\nfor returning results", + "module" : "MOTranslation", + "name" : "protein_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "protein is an MD5 in KBase. It is the primary lookup between\nKBase fids and MicrobesOnline locusIds.", + "module" : "MOTranslation", + "name" : "protein" + }, + "name" : "md5", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "name" : "start", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "name" : "stop", + "nullable" : "0" + } ], + "module" : "MOTranslation", + "name" : "query_md5" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A structure for specifying the input md5 queries for the map_to_fid_fast method. This structure assumes\nyou will be making queries with identical genomes, so it requires the start and stop.\n\n protein_id id - arbitrary ID that must be unique within the set of query sequences\n protein md5 - the computed md5 of the protein sequence\n position start - the start position of the start codon in the genome contig (may be a larger\n number than stop if the gene is on the reverse strand)\n position stop - the last position of he stop codon in the genome contig", + "module" : "MOTranslation", + "name" : "query_md5" + } + } + }, { + "name" : "genomeId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbaseId can represent any object with a KBase identifier. \nIn the future this may be used to translate between other data\ntypes, such as contig or genome.", + "module" : "MOTranslation", + "name" : "kbaseId" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "genomeId is a kbase id of a genome", + "module" : "MOTranslation", + "name" : "genomeId" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "internally consistant and unique id of a protein (could just be integers 0..n), necessary\nfor returning results", + "module" : "MOTranslation", + "name" : "protein_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simple structure which returns the best matching FID to a given query (see query_sequence) and attaches\na short status string indicating how the match was made, or which consoles you after a match could not\nbe made.\n\n fid best_match - the feature ID of a KBase feature that offers the best mapping to your query\n status status - a short note explaining how the match was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "fid is a feature id in KBase.", + "module" : "MOTranslation", + "name" : "fid" + }, + "name" : "best_match", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short note used to convey the status or explanaton of a result, or in some cases a log of the\nmethod that was run", + "module" : "MOTranslation", + "name" : "status" + }, + "name" : "status", + "nullable" : "0" + } ], + "module" : "MOTranslation", + "name" : "result" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simple structure which returns the best matching FID to a given query (see query_sequence) and attaches\na short status string indicating how the match was made, or which consoles you after a match could not\nbe made.\n\n fid best_match - the feature ID of a KBase feature that offers the best mapping to your query\n status status - a short note explaining how the match was made", + "module" : "MOTranslation", + "name" : "result" + } + } + }, { + "name" : "log", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short note used to convey the status or explanaton of a result, or in some cases a log of the\nmethod that was run", + "module" : "MOTranslation", + "name" : "status" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "A method designed to map MicrobesOnline locus ids to the features of a specific target genome in kbase. Under the hood, this\nmethod simply fetches MicrobesOnline data and calls the 'map_to_fid' method defined in this service. Therefore, all the caveats\nand disclaimers of the 'map_to_fid' method apply to this function as well, so be sure to read the documenation for the 'map_to_fid'\nmethod as well!", + "name" : "moLocusIds_to_fid_in_genome", + "parameters" : [ { + "name" : "moLocusIds", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moLocusId is a locusId in MicrobesOnline. It is analogous to a fid\nin KBase.", + "module" : "MOTranslation", + "name" : "moLocusId" + } + } + }, { + "name" : "genomeId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbaseId can represent any object with a KBase identifier. \nIn the future this may be used to translate between other data\ntypes, such as contig or genome.", + "module" : "MOTranslation", + "name" : "kbaseId" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "genomeId is a kbase id of a genome", + "module" : "MOTranslation", + "name" : "genomeId" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moLocusId is a locusId in MicrobesOnline. It is analogous to a fid\nin KBase.", + "module" : "MOTranslation", + "name" : "moLocusId" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simple structure which returns the best matching FID to a given query (see query_sequence) and attaches\na short status string indicating how the match was made, or which consoles you after a match could not\nbe made.\n\n fid best_match - the feature ID of a KBase feature that offers the best mapping to your query\n status status - a short note explaining how the match was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "fid is a feature id in KBase.", + "module" : "MOTranslation", + "name" : "fid" + }, + "name" : "best_match", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short note used to convey the status or explanaton of a result, or in some cases a log of the\nmethod that was run", + "module" : "MOTranslation", + "name" : "status" + }, + "name" : "status", + "nullable" : "0" + } ], + "module" : "MOTranslation", + "name" : "result" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simple structure which returns the best matching FID to a given query (see query_sequence) and attaches\na short status string indicating how the match was made, or which consoles you after a match could not\nbe made.\n\n fid best_match - the feature ID of a KBase feature that offers the best mapping to your query\n status status - a short note explaining how the match was made", + "module" : "MOTranslation", + "name" : "result" + } + } + }, { + "name" : "log", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short note used to convey the status or explanaton of a result, or in some cases a log of the\nmethod that was run", + "module" : "MOTranslation", + "name" : "status" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Performs the same function as moLocusIds_to_fid_in_genome, but does not retrieve protein sequences for the locus Ids - it simply\nuses md5 information and start/stop positions to identify matches. It is therefore faster, but will not work if genomes are not\nidentical.", + "name" : "moLocusIds_to_fid_in_genome_fast", + "parameters" : [ { + "name" : "moLocusIds", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moLocusId is a locusId in MicrobesOnline. It is analogous to a fid\nin KBase.", + "module" : "MOTranslation", + "name" : "moLocusId" + } + } + }, { + "name" : "genomeId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbaseId can represent any object with a KBase identifier. \nIn the future this may be used to translate between other data\ntypes, such as contig or genome.", + "module" : "MOTranslation", + "name" : "kbaseId" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "genomeId is a kbase id of a genome", + "module" : "MOTranslation", + "name" : "genomeId" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moLocusId is a locusId in MicrobesOnline. It is analogous to a fid\nin KBase.", + "module" : "MOTranslation", + "name" : "moLocusId" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simple structure which returns the best matching FID to a given query (see query_sequence) and attaches\na short status string indicating how the match was made, or which consoles you after a match could not\nbe made.\n\n fid best_match - the feature ID of a KBase feature that offers the best mapping to your query\n status status - a short note explaining how the match was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "fid is a feature id in KBase.", + "module" : "MOTranslation", + "name" : "fid" + }, + "name" : "best_match", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short note used to convey the status or explanaton of a result, or in some cases a log of the\nmethod that was run", + "module" : "MOTranslation", + "name" : "status" + }, + "name" : "status", + "nullable" : "0" + } ], + "module" : "MOTranslation", + "name" : "result" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simple structure which returns the best matching FID to a given query (see query_sequence) and attaches\na short status string indicating how the match was made, or which consoles you after a match could not\nbe made.\n\n fid best_match - the feature ID of a KBase feature that offers the best mapping to your query\n status status - a short note explaining how the match was made", + "module" : "MOTranslation", + "name" : "result" + } + } + }, { + "name" : "log", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short note used to convey the status or explanaton of a result, or in some cases a log of the\nmethod that was run", + "module" : "MOTranslation", + "name" : "status" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "A method to map a MicrobesOnline genome (identified by taxonomy Id) to the set of identical kbase genomes based on an MD5 checksum\nof the contig sequences. If you already know your MD5 value for your genome (computed in the KBase way), then you should avoid this\nmethod and directly query the CDS using the CDMI API, which includes a method 'md5s_to_genomes'.", + "name" : "moTaxonomyId_to_genomes", + "parameters" : [ { + "name" : "moTaxonomyId", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moTaxonomyId is a taxonomyId in MicrobesOnline. It is somewhat analogous\nto a genome kbId in KBase. It generally stores the NCBI taxonomy ID,\nthough sometimes can store an internal identifier instead.", + "module" : "MOTranslation", + "name" : "moTaxonomyId" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbaseId can represent any object with a KBase identifier. \nIn the future this may be used to translate between other data\ntypes, such as contig or genome.", + "module" : "MOTranslation", + "name" : "kbaseId" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "genomeId is a kbase id of a genome", + "module" : "MOTranslation", + "name" : "genomeId" + } + } + } ] + } ], + "module_name" : "MOTranslation", + "options" : [ ], + "service_name" : "MOTranslation" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "fid" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "fid is a feature id in KBase.", + "module" : "MOTranslation", + "name" : "fid" + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "genomeId" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbaseId can represent any object with a KBase identifier. \nIn the future this may be used to translate between other data\ntypes, such as contig or genome.", + "module" : "MOTranslation", + "name" : "kbaseId" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "genomeId is a kbase id of a genome", + "module" : "MOTranslation", + "name" : "genomeId" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "kbaseId" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbaseId can represent any object with a KBase identifier. \nIn the future this may be used to translate between other data\ntypes, such as contig or genome.", + "module" : "MOTranslation", + "name" : "kbaseId" + }, + "moLocusId" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moLocusId is a locusId in MicrobesOnline. It is analogous to a fid\nin KBase.", + "module" : "MOTranslation", + "name" : "moLocusId" + }, + "moScaffoldId" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moScaffoldId is a scaffoldId in MicrobesOnline. It is analogous to\na contig kbId in KBase.", + "module" : "MOTranslation", + "name" : "moScaffoldId" + }, + "moTaxonomyId" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "moTaxonomyId is a taxonomyId in MicrobesOnline. It is somewhat analogous\nto a genome kbId in KBase. It generally stores the NCBI taxonomy ID,\nthough sometimes can store an internal identifier instead.", + "module" : "MOTranslation", + "name" : "moTaxonomyId" + }, + "position" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "protein" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "protein is an MD5 in KBase. It is the primary lookup between\nKBase fids and MicrobesOnline locusIds.", + "module" : "MOTranslation", + "name" : "protein" + }, + "protein_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "internally consistant and unique id of a protein (could just be integers 0..n), necessary\nfor returning results", + "module" : "MOTranslation", + "name" : "protein_id" + }, + "protein_sequence" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "AA sequence of a protein", + "module" : "MOTranslation", + "name" : "protein_sequence" + }, + "query_md5" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A structure for specifying the input md5 queries for the map_to_fid_fast method. This structure assumes\nyou will be making queries with identical genomes, so it requires the start and stop.\n\n protein_id id - arbitrary ID that must be unique within the set of query sequences\n protein md5 - the computed md5 of the protein sequence\n position start - the start position of the start codon in the genome contig (may be a larger\n number than stop if the gene is on the reverse strand)\n position stop - the last position of he stop codon in the genome contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "internally consistant and unique id of a protein (could just be integers 0..n), necessary\nfor returning results", + "module" : "MOTranslation", + "name" : "protein_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "protein is an MD5 in KBase. It is the primary lookup between\nKBase fids and MicrobesOnline locusIds.", + "module" : "MOTranslation", + "name" : "protein" + }, + "name" : "md5", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "name" : "start", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "name" : "stop", + "nullable" : "0" + } ], + "module" : "MOTranslation", + "name" : "query_md5" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A structure for specifying the input md5 queries for the map_to_fid_fast method. This structure assumes\nyou will be making queries with identical genomes, so it requires the start and stop.\n\n protein_id id - arbitrary ID that must be unique within the set of query sequences\n protein md5 - the computed md5 of the protein sequence\n position start - the start position of the start codon in the genome contig (may be a larger\n number than stop if the gene is on the reverse strand)\n position stop - the last position of he stop codon in the genome contig", + "module" : "MOTranslation", + "name" : "query_md5" + }, + "query_sequence" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A structure for specifying the input sequence queries for the map_to_fid method. This structure, for\nnow, assumes you will be making queries with identical genomes, so it requires the start and stop. In the\nfuture, if this assumption is relaxed, then start and stop will be optional parameters. We should probably\nalso add an MD5 string which can optionally be provided so that we don't have to compute it on the fly.\n\n protein_id id - arbitrary ID that must be unique within the set of query sequences\n protein_sequence seq - the one letter code AA sequence of the protein\n position start - the start position of the start codon in the genome contig (may be a larger\n number than stop if the gene is on the reverse strand)\n position stop - the last position of he stop codon in the genome contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "internally consistant and unique id of a protein (could just be integers 0..n), necessary\nfor returning results", + "module" : "MOTranslation", + "name" : "protein_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "AA sequence of a protein", + "module" : "MOTranslation", + "name" : "protein_sequence" + }, + "name" : "seq", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "name" : "start", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Used to indicate a single nucleotide/residue location in a sequence", + "module" : "MOTranslation", + "name" : "position" + }, + "name" : "stop", + "nullable" : "0" + } ], + "module" : "MOTranslation", + "name" : "query_sequence" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A structure for specifying the input sequence queries for the map_to_fid method. This structure, for\nnow, assumes you will be making queries with identical genomes, so it requires the start and stop. In the\nfuture, if this assumption is relaxed, then start and stop will be optional parameters. We should probably\nalso add an MD5 string which can optionally be provided so that we don't have to compute it on the fly.\n\n protein_id id - arbitrary ID that must be unique within the set of query sequences\n protein_sequence seq - the one letter code AA sequence of the protein\n position start - the start position of the start codon in the genome contig (may be a larger\n number than stop if the gene is on the reverse strand)\n position stop - the last position of he stop codon in the genome contig", + "module" : "MOTranslation", + "name" : "query_sequence" + }, + "result" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "A simple structure which returns the best matching FID to a given query (see query_sequence) and attaches\na short status string indicating how the match was made, or which consoles you after a match could not\nbe made.\n\n fid best_match - the feature ID of a KBase feature that offers the best mapping to your query\n status status - a short note explaining how the match was made", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "fid is a feature id in KBase.", + "module" : "MOTranslation", + "name" : "fid" + }, + "name" : "best_match", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short note used to convey the status or explanaton of a result, or in some cases a log of the\nmethod that was run", + "module" : "MOTranslation", + "name" : "status" + }, + "name" : "status", + "nullable" : "0" + } ], + "module" : "MOTranslation", + "name" : "result" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A simple structure which returns the best matching FID to a given query (see query_sequence) and attaches\na short status string indicating how the match was made, or which consoles you after a match could not\nbe made.\n\n fid best_match - the feature ID of a KBase feature that offers the best mapping to your query\n status status - a short note explaining how the match was made", + "module" : "MOTranslation", + "name" : "result" + }, + "status" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short note used to convey the status or explanaton of a result, or in some cases a log of the\nmethod that was run", + "module" : "MOTranslation", + "name" : "status" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.19.json.properties b/src/test/resources/us/kbase/test/kidl/spec.19.json.properties new file mode 100644 index 0000000..084d7ba --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.19.json.properties @@ -0,0 +1,686 @@ +{ + "TaxonomyTranslation" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "The translation service translates between different things. These are mainly\nmappings. A genbank taxonomic scientific name to a genbank taxonomic common\nname; A Seed role to a Geneontology term; MORE \n\nGenbank taxonomic name translations.\n\nGenbank taxonomic name translations allow on the fly translation between\nthe different name classes supported in the NCBI taxonomy database. These\nname classes include:\n\n misspelling, genbank anamorph, scientific name, synonym \n blast name, genbank synonym, equivalent name, includes \n acronym, in-part, anamorph, authority, genbank common name \n genbank acronym, common name, misnomer, teleomorph \n\nAlthough, the most common are translations between scientific name, synonym,\nequivelant name and common name.", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Tax_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "typedef structure {\nstring scientific_name;\nlist common_names;\nlist synonyms;\nlist misspellings;\nlist equivalent_names;\nlist in_parts;\nlist anamorphs;\nlist includes;\nlist acronyms;\nlist authorities;\nlist misnomers;\nlist teleomorphs;\nlist blast_names;\nlist genbank_synonyms;\nlist genbank_anamorphs;\nlist genbank_acronyms;\nlist genbank_common_names;\n } Names;", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "t", + "nullable" : "0" + } ], + "module" : "TaxonomyTranslation", + "name" : "Names" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "typedef structure {\nstring scientific_name;\nlist common_names;\nlist synonyms;\nlist misspellings;\nlist equivalent_names;\nlist in_parts;\nlist anamorphs;\nlist includes;\nlist acronyms;\nlist authorities;\nlist misnomers;\nlist teleomorphs;\nlist blast_names;\nlist genbank_synonyms;\nlist genbank_anamorphs;\nlist genbank_acronyms;\nlist genbank_common_names;\n } Names;", + "module" : "TaxonomyTranslation", + "name" : "Names" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Tax_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "typedef structure {\nstring scientific_name;\nlist common_names;\nlist synonyms;\nlist misspellings;\nlist equivalent_names;\nlist in_parts;\nlist anamorphs;\nlist includes;\nlist acronyms;\nlist authorities;\nlist misnomers;\nlist teleomorphs;\nlist blast_names;\nlist genbank_synonyms;\nlist genbank_anamorphs;\nlist genbank_acronyms;\nlist genbank_common_names;\n } Names;", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "t", + "nullable" : "0" + } ], + "module" : "TaxonomyTranslation", + "name" : "Names" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "typedef structure {\nstring scientific_name;\nlist common_names;\nlist synonyms;\nlist misspellings;\nlist equivalent_names;\nlist in_parts;\nlist anamorphs;\nlist includes;\nlist acronyms;\nlist authorities;\nlist misnomers;\nlist teleomorphs;\nlist blast_names;\nlist genbank_synonyms;\nlist genbank_anamorphs;\nlist genbank_acronyms;\nlist genbank_common_names;\n } Names;", + "module" : "TaxonomyTranslation", + "name" : "Names" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Translations" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns all possible name translations for a given name.", + "name" : "get_all_translations", + "parameters" : [ { + "name" : "name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Name" + } + } ], + "return_type" : [ { + "name" : "translations", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Tax_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "typedef structure {\nstring scientific_name;\nlist common_names;\nlist synonyms;\nlist misspellings;\nlist equivalent_names;\nlist in_parts;\nlist anamorphs;\nlist includes;\nlist acronyms;\nlist authorities;\nlist misnomers;\nlist teleomorphs;\nlist blast_names;\nlist genbank_synonyms;\nlist genbank_anamorphs;\nlist genbank_acronyms;\nlist genbank_common_names;\n } Names;", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "t", + "nullable" : "0" + } ], + "module" : "TaxonomyTranslation", + "name" : "Names" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "typedef structure {\nstring scientific_name;\nlist common_names;\nlist synonyms;\nlist misspellings;\nlist equivalent_names;\nlist in_parts;\nlist anamorphs;\nlist includes;\nlist acronyms;\nlist authorities;\nlist misnomers;\nlist teleomorphs;\nlist blast_names;\nlist genbank_synonyms;\nlist genbank_anamorphs;\nlist genbank_acronyms;\nlist genbank_common_names;\n } Names;", + "module" : "TaxonomyTranslation", + "name" : "Names" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Translations" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a mapping between tax_id and scientific name for a given name.", + "name" : "get_scientific_names_by_name", + "parameters" : [ { + "name" : "name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Name" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Tax_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a mapping between tax_id and a list of all associated names for a given name.", + "name" : "get_all_names_by_name", + "parameters" : [ { + "name" : "name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Name" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Tax_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Name" + } + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the scientific name for a given tax id.", + "name" : "get_scientific_name_by_tax_id", + "parameters" : [ { + "name" : "tax_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Tax_id" + } + } ], + "return_type" : [ { + "name" : "name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Name" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the tax id for a given scientific name.", + "name" : "get_tax_id_by_scientific_name", + "parameters" : [ { + "name" : "name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Name" + } + } ], + "return_type" : [ { + "name" : "tax_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Tax_id" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of tax ids for a given name.", + "name" : "get_tax_ids_by_name", + "parameters" : [ { + "name" : "name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Name" + } + } ], + "return_type" : [ { + "name" : "tax_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Tax_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of names for a given tax id.", + "name" : "get_all_names_by_tax_id", + "parameters" : [ { + "name" : "tax_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Tax_id" + } + } ], + "return_type" : [ { + "name" : "names", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Name" + } + } + } ] + } ], + "module_name" : "TaxonomyTranslation", + "options" : [ ], + "service_name" : "TaxonomyTranslation" + }, [ ], { + "Name" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Name" + }, + "Names" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "typedef structure {\nstring scientific_name;\nlist common_names;\nlist synonyms;\nlist misspellings;\nlist equivalent_names;\nlist in_parts;\nlist anamorphs;\nlist includes;\nlist acronyms;\nlist authorities;\nlist misnomers;\nlist teleomorphs;\nlist blast_names;\nlist genbank_synonyms;\nlist genbank_anamorphs;\nlist genbank_acronyms;\nlist genbank_common_names;\n } Names;", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "t", + "nullable" : "0" + } ], + "module" : "TaxonomyTranslation", + "name" : "Names" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "typedef structure {\nstring scientific_name;\nlist common_names;\nlist synonyms;\nlist misspellings;\nlist equivalent_names;\nlist in_parts;\nlist anamorphs;\nlist includes;\nlist acronyms;\nlist authorities;\nlist misnomers;\nlist teleomorphs;\nlist blast_names;\nlist genbank_synonyms;\nlist genbank_anamorphs;\nlist genbank_acronyms;\nlist genbank_common_names;\n } Names;", + "module" : "TaxonomyTranslation", + "name" : "Names" + }, + "Tax_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Tax_id" + }, + "Translations" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Tax_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "typedef structure {\nstring scientific_name;\nlist common_names;\nlist synonyms;\nlist misspellings;\nlist equivalent_names;\nlist in_parts;\nlist anamorphs;\nlist includes;\nlist acronyms;\nlist authorities;\nlist misnomers;\nlist teleomorphs;\nlist blast_names;\nlist genbank_synonyms;\nlist genbank_anamorphs;\nlist genbank_acronyms;\nlist genbank_common_names;\n } Names;", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "t", + "nullable" : "0" + } ], + "module" : "TaxonomyTranslation", + "name" : "Names" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "typedef structure {\nstring scientific_name;\nlist common_names;\nlist synonyms;\nlist misspellings;\nlist equivalent_names;\nlist in_parts;\nlist anamorphs;\nlist includes;\nlist acronyms;\nlist authorities;\nlist misnomers;\nlist teleomorphs;\nlist blast_names;\nlist genbank_synonyms;\nlist genbank_anamorphs;\nlist genbank_acronyms;\nlist genbank_common_names;\n } Names;", + "module" : "TaxonomyTranslation", + "name" : "Names" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "TaxonomyTranslation", + "name" : "Translations" + }, + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.2.json.properties b/src/test/resources/us/kbase/test/kidl/spec.2.json.properties new file mode 100644 index 0000000..cf2b3ce --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.2.json.properties @@ -0,0 +1,726 @@ +{ + "ERDB_Service" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "ERDB Service API specification\n\nThis service wraps the ERDB software and allows querying the CDS via the ERDB\nusing typecompiler generated clients rather than direct Perl imports of the ERDB\ncode.\n\nThe exposed functions behave, generally, identically to the ERDB functions documented\nL.\nIt is expected that users of this service already understand how to query the CDS via\nthe ERDB.", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "objectNames" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "filterClause" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "parameter" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "parameter" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "parameters" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fields" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "count" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValue" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValue" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValues" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValue" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValues" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "rowlist" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Wrapper for the GetAll function documented L.\nNote that the objectNames and fields arguments must be strings; array references are not allowed.", + "name" : "GetAll", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "objectNames" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "filterClause" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "parameter" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "parameters" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fields" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "count" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValue" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValues" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "rowlist" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "SQLstring" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "WARNING: this is a function of last resort. Try to do what you need to do with the CDMI client or the\nGetAll function first.\nRuns a standard SQL query via the ERDB DB hook. Be sure not to code inputs into the SQL string - put them\nin the parameter list and use ? placeholders in the SQL. Otherwise you risk SQL injection. If you don't\nunderstand this paragraph, do not use this function.\nNote that most likely, the account for this server only has select privileges and cannot modify the\ndatabase.", + "name" : "runSQL", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "SQLstring" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "parameter" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "parameters" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValue" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValues" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "rowlist" + } + } ] + } ], + "module_name" : "ERDB_Service", + "options" : [ ], + "service_name" : "ERDB_Service" + }, [ ], { + "SQLstring" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "SQLstring" + }, + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "count" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "count" + }, + "fieldValue" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValue" + }, + "fieldValues" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValue" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValues" + }, + "fields" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fields" + }, + "filterClause" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "filterClause" + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "objectNames" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "objectNames" + }, + "parameter" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "parameter" + }, + "parameters" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "parameter" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "parameters" + }, + "rowlist" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValue" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "fieldValues" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "ERDB_Service", + "name" : "rowlist" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.20.json.properties b/src/test/resources/us/kbase/test/kidl/spec.20.json.properties new file mode 100644 index 0000000..65257e3 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.20.json.properties @@ -0,0 +1,2981 @@ +{ + "Tree" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "Phylogenetic Tree and Multiple Sequence Alignment Services\n\nThis service provides a set of methods for querying, manipulating, and analyzing multiple\nsequence alignments and phylogenetic trees.\n\nAuthors\n---------\nMichael Sneddon, LBL (mwsneddon@lbl.gov)\nFangfang Xia, ANL (fangfang.xia@gmail.com)\nMatt Henderson, LBL (mhenderson@lbl.gov)", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "indicates true or false values, false <= 0, true >=1", + "module" : "Tree", + "name" : "bool" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "time in units of number of seconds since the epoch", + "module" : "Tree", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "integer number indicating a 1-based position in an amino acid / nucleotide sequence", + "module" : "Tree", + "name" : "position" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format)\nand are returned to you in this format by default.", + "module" : "Tree", + "name" : "newick_tree" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format),\nbut can optionally be converted to the more verbose phyloXML format, which is useful for compatibility or\nwhen additional information/annotations decorate the tree.", + "module" : "Tree", + "name" : "phyloXML_tree" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format),\nbut can optionally be converted to JSON format where the structure of the tree matches the structure of\nthe JSON object. This is useful when interacting with the tree in JavaScript, for instance.", + "module" : "Tree", + "name" : "json_tree" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "String representation of a sequence alignment, the format of which may be different depending on\ninput options for retrieving the alignment.", + "module" : "Tree", + "name" : "alignment" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "String representation of a sequence or set of sequences in FASTA format. The precise alphabet used is\nnot yet specified, but will be similar to sequences stored in KBase with '-' to denote gaps in alignments.", + "module" : "Tree", + "name" : "fasta" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "String representation of a sequence or set of sequences in FASTA format. The precise alphabet used is\nnot yet specified, but will be similar to sequences stored in KBase with '-' to denote gaps in alignments.", + "module" : "Tree", + "name" : "fasta" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "String representation of an alignment in FASTA format. The precise alphabet and syntax of the alignment\nstring is not yet specified, but will be similar to sequences stored in KBase with '-' to denote gaps in\nalignments.", + "module" : "Tree", + "name" : "fasta_alignment" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the parsed node name (may be a kbase_id, but does not have to be). Note that this\nis not the full, raw label in a newick_tree (which may include comments).", + "module" : "Tree", + "name" : "node_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "String in HTML format, used in the KBase Tree library for returning rendered trees.", + "module" : "Tree", + "name" : "html_file" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Meta data associated with a tree.\n\n kbase_id alignment_id - if this tree was built from an alignment, this provides that alignment id\n string type - the type of tree; possible values currently are \"sequence_alignment\" and \"genome\" for trees\n either built from a sequence alignment, or imported directly indexed to genomes.\n string status - set to 'active' if this is the latest built tree for a particular gene family\n timestamp date_created - time at which the tree was built/loaded in seconds since the epoch\n string tree_contruction_method - the name of the software used to construct the tree\n string tree_construction_parameters - any non-default parameters of the tree construction method\n string tree_protocol - simple free-form text which may provide additional details of how the tree was built\n int node_count - total number of nodes in the tree\n int leaf_count - total number of leaf nodes in the tree (generally this cooresponds to the number of sequences)\n string source_db - the source database where this tree originated, if one exists\n string source_id - the id of this tree in an external database, if one exists", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + }, + "name" : "alignment_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "status", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "time in units of number of seconds since the epoch", + "module" : "Tree", + "name" : "timestamp" + }, + "name" : "date_created", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "tree_contruction_method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "tree_construction_parameters", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "tree_protocol", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "node_count", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "leaf_count", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_db", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_id", + "nullable" : "0" + } ], + "module" : "Tree", + "name" : "tree_meta_data" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Meta data associated with a tree.\n\n kbase_id alignment_id - if this tree was built from an alignment, this provides that alignment id\n string type - the type of tree; possible values currently are \"sequence_alignment\" and \"genome\" for trees\n either built from a sequence alignment, or imported directly indexed to genomes.\n string status - set to 'active' if this is the latest built tree for a particular gene family\n timestamp date_created - time at which the tree was built/loaded in seconds since the epoch\n string tree_contruction_method - the name of the software used to construct the tree\n string tree_construction_parameters - any non-default parameters of the tree construction method\n string tree_protocol - simple free-form text which may provide additional details of how the tree was built\n int node_count - total number of nodes in the tree\n int leaf_count - total number of leaf nodes in the tree (generally this cooresponds to the number of sequences)\n string source_db - the source database where this tree originated, if one exists\n string source_id - the id of this tree in an external database, if one exists", + "module" : "Tree", + "name" : "tree_meta_data" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Meta data associated with an alignment.\n\n list tree_ids - the set of trees that were built from this alignment\n string status - set to 'active' if this is the latest alignment for a particular set of sequences\n string sequence_type - indicates what type of sequence is aligned (e.g. protein vs. dna)\n bool is_concatenation - true if the alignment is based on the concatenation of multiple non-contiguous\n sequences, false if each row cooresponds to exactly one sequence (possibly with gaps)\n timestamp date_created - time at which the alignment was built/loaded in seconds since the epoch\n int n_rows - number of rows in the alignment\n int n_cols - number of columns in the alignment\n string alignment_construction_method - the name of the software tool used to build the alignment\n string alignment_construction_parameters - set of non-default parameters used to construct the alignment\n string alignment_protocol - simple free-form text which may provide additional details of how the alignment was built\n string source_db - the source database where this alignment originated, if one exists\n string source_id - the id of this alignment in an external database, if one exists", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + }, + "name" : "tree_ids", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "status", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence_type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "is_concatenation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "time in units of number of seconds since the epoch", + "module" : "Tree", + "name" : "timestamp" + }, + "name" : "date_created", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "n_rows", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "n_cols", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "alignment_construction_method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "alignment_construction_parameters", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "alignment_protocol", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_db", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_id", + "nullable" : "0" + } ], + "module" : "Tree", + "name" : "alignment_meta_data" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Meta data associated with an alignment.\n\n list tree_ids - the set of trees that were built from this alignment\n string status - set to 'active' if this is the latest alignment for a particular set of sequences\n string sequence_type - indicates what type of sequence is aligned (e.g. protein vs. dna)\n bool is_concatenation - true if the alignment is based on the concatenation of multiple non-contiguous\n sequences, false if each row cooresponds to exactly one sequence (possibly with gaps)\n timestamp date_created - time at which the alignment was built/loaded in seconds since the epoch\n int n_rows - number of rows in the alignment\n int n_cols - number of columns in the alignment\n string alignment_construction_method - the name of the software tool used to build the alignment\n string alignment_construction_parameters - set of non-default parameters used to construct the alignment\n string alignment_protocol - simple free-form text which may provide additional details of how the alignment was built\n string source_db - the source database where this alignment originated, if one exists\n string source_id - the id of this alignment in an external database, if one exists", + "module" : "Tree", + "name" : "alignment_meta_data" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a tree in newick format, replace the node names indicated as keys in the 'replacements' mapping\nwith new node names indicated as values in the 'replacements' mapping. Matching is EXACT and will not handle\nregular expression patterns.", + "name" : "replace_node_names", + "parameters" : [ { + "name" : "tree", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format)\nand are returned to you in this format by default.", + "module" : "Tree", + "name" : "newick_tree" + } + }, { + "name" : "replacements", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the parsed node name (may be a kbase_id, but does not have to be). Note that this\nis not the full, raw label in a newick_tree (which may include comments).", + "module" : "Tree", + "name" : "node_name" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the parsed node name (may be a kbase_id, but does not have to be). Note that this\nis not the full, raw label in a newick_tree (which may include comments).", + "module" : "Tree", + "name" : "node_name" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format)\nand are returned to you in this format by default.", + "module" : "Tree", + "name" : "newick_tree" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a tree in newick format, remove the nodes with the given names indicated in the list, and\nsimplify the tree. Simplifying a tree involves removing unnamed internal nodes that have only one\nchild, and removing unnamed leaf nodes. During the removal process, edge lengths (if they exist) are\nconserved so that the summed end to end distance between any two nodes left in the tree will remain the same.", + "name" : "remove_node_names_and_simplify", + "parameters" : [ { + "name" : "tree", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format)\nand are returned to you in this format by default.", + "module" : "Tree", + "name" : "newick_tree" + } + }, { + "name" : "removal_list", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the parsed node name (may be a kbase_id, but does not have to be). Note that this\nis not the full, raw label in a newick_tree (which may include comments).", + "module" : "Tree", + "name" : "node_name" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format)\nand are returned to you in this format by default.", + "module" : "Tree", + "name" : "newick_tree" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a tree in newick format, list the names of the leaf nodes.", + "name" : "extract_leaf_node_names", + "parameters" : [ { + "name" : "tree", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format)\nand are returned to you in this format by default.", + "module" : "Tree", + "name" : "newick_tree" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the parsed node name (may be a kbase_id, but does not have to be). Note that this\nis not the full, raw label in a newick_tree (which may include comments).", + "module" : "Tree", + "name" : "node_name" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a tree in newick format, list the names of ALL the nodes. Note that for some trees, such as\nthose originating from MicrobesOnline, the names of internal nodes may be bootstrap values, but will still\nbe returned by this function.", + "name" : "extract_node_names", + "parameters" : [ { + "name" : "tree", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format)\nand are returned to you in this format by default.", + "module" : "Tree", + "name" : "newick_tree" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the parsed node name (may be a kbase_id, but does not have to be). Note that this\nis not the full, raw label in a newick_tree (which may include comments).", + "module" : "Tree", + "name" : "node_name" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a tree, return the total number of nodes, including internal nodes and the root node.", + "name" : "get_node_count", + "parameters" : [ { + "name" : "tree", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format)\nand are returned to you in this format by default.", + "module" : "Tree", + "name" : "newick_tree" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a tree, return the total number of leaf nodes, (internal and root nodes are ignored). When the\ntree was based on a multiple sequence alignment, the number of leaves will match the number of sequences\nthat were aligned.", + "name" : "get_leaf_count", + "parameters" : [ { + "name" : "tree", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format)\nand are returned to you in this format by default.", + "module" : "Tree", + "name" : "newick_tree" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the specified tree in the specified format, or an empty string if the tree does not exist.\nThe options hash provides a way to return the tree with different labels replaced or with different attached meta\ninformation. Currently, the available flags and understood options are listed below. \n\n options = [\n format => 'newick',\n newick_label => 'none' || 'raw' || 'feature_id' || 'protein_sequence_id' || 'contig_sequence_id',\n newick_bootstrap => 'none' || 'internal_node_labels'\n newick_distance => 'none' || 'raw'\n ];\n \nThe 'format' key indicates what string format the tree should be returned in. Currently, there is only\nsupport for 'newick'. The default value if not specified is 'newick'.\n\nThe 'newick_label' key only affects trees returned as newick format, and specifies what should be\nplaced in the label of each leaf. 'none' indicates that no label is added, so you get the structure\nof the tree only. 'raw' indicates that the raw label mapping the leaf to an alignement row is used.\n'feature_id' indicates that the label will have an examplar feature_id in each label (typically the\nfeature that was originally used to define the sequence). Note that exemplar feature_ids are not\ndefined for all trees, so this may result in an empty tree. 'protein_sequence_id' indicates that the\nkbase id of the protein sequence used in the alignment is used. 'contig_sequence_id' indicates that\nthe contig sequence id is added. Note that trees are typically built with protein sequences OR\ncontig sequences. If you select one type of sequence, but the tree was built with the other type, then\nno labels will be added. The default value if none is specified is 'raw'.\n\nThe 'newick_bootstrap' key allows control over whether bootstrap values are returned if they exist, and\nhow they are returned. 'none' indicates that no bootstrap values are returned. 'internal_node_labels'\nindicates that bootstrap values are returned as internal node labels. Default value is 'internal_node_labels';\n\nThe 'newick_distance' key allows control over whether distance labels are generated or not. If set to\n'none', no distances will be output. Default is 'raw', which outputs the distances exactly as they appeared\nwhen loaded into kbase.", + "name" : "get_tree", + "parameters" : [ { + "name" : "tree_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + }, { + "name" : "options", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the specified alignment in the specified format, or an empty string if the alignment does not exist.\nThe options hash provides a way to return the alignment with different labels replaced or with different attached meta\ninformation. Currently, the available flags and understood options are listed below. \n\n options = [\n format => 'fasta',\n sequence_label => 'none' || 'raw' || 'feature_id' || 'protein_sequence_id' || 'contig_sequence_id',\n ];\n \nThe 'format' key indicates what string format the alignment should be returned in. Currently, there is only\nsupport for 'fasta'. The default value if not specified is 'fasta'.\n\nThe 'sequence_label' specifies what should be placed in the label of each sequence. 'none' indicates that\nno label is added, so you get the sequence only. 'raw' indicates that the raw label of the alignement row\nis used. 'feature_id' indicates that the label will have an examplar feature_id in each label (typically the\nfeature that was originally used to define the sequence). Note that exemplar feature_ids are not\ndefined for all alignments, so this may result in an unlabeled alignment. 'protein_sequence_id' indicates\nthat the kbase id of the protein sequence used in the alignment is used. 'contig_sequence_id' indicates that\nthe contig sequence id is used. Note that trees are typically built with protein sequences OR\ncontig sequences. If you select one type of sequence, but the alignment was built with the other type, then\nno labels will be added. The default value if none is specified is 'raw'.", + "name" : "get_alignment", + "parameters" : [ { + "name" : "alignment_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + }, { + "name" : "options", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "String representation of a sequence alignment, the format of which may be different depending on\ninput options for retrieving the alignment.", + "module" : "Tree", + "name" : "alignment" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Get meta data associated with each of the trees indicated in the list by tree id. Note that some meta\ndata may not be available for trees which are not built from alignments. Also note that this method\ncomputes the number of nodes and leaves for each tree, so may be slow for very large trees or very long\nlists. If you do not need this full meta information structure, it may be faster to directly query the\nCDS for just the field you need using the CDMI.", + "name" : "get_tree_data", + "parameters" : [ { + "name" : "tree_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Meta data associated with a tree.\n\n kbase_id alignment_id - if this tree was built from an alignment, this provides that alignment id\n string type - the type of tree; possible values currently are \"sequence_alignment\" and \"genome\" for trees\n either built from a sequence alignment, or imported directly indexed to genomes.\n string status - set to 'active' if this is the latest built tree for a particular gene family\n timestamp date_created - time at which the tree was built/loaded in seconds since the epoch\n string tree_contruction_method - the name of the software used to construct the tree\n string tree_construction_parameters - any non-default parameters of the tree construction method\n string tree_protocol - simple free-form text which may provide additional details of how the tree was built\n int node_count - total number of nodes in the tree\n int leaf_count - total number of leaf nodes in the tree (generally this cooresponds to the number of sequences)\n string source_db - the source database where this tree originated, if one exists\n string source_id - the id of this tree in an external database, if one exists", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + }, + "name" : "alignment_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "status", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "time in units of number of seconds since the epoch", + "module" : "Tree", + "name" : "timestamp" + }, + "name" : "date_created", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "tree_contruction_method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "tree_construction_parameters", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "tree_protocol", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "node_count", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "leaf_count", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_db", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_id", + "nullable" : "0" + } ], + "module" : "Tree", + "name" : "tree_meta_data" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Meta data associated with a tree.\n\n kbase_id alignment_id - if this tree was built from an alignment, this provides that alignment id\n string type - the type of tree; possible values currently are \"sequence_alignment\" and \"genome\" for trees\n either built from a sequence alignment, or imported directly indexed to genomes.\n string status - set to 'active' if this is the latest built tree for a particular gene family\n timestamp date_created - time at which the tree was built/loaded in seconds since the epoch\n string tree_contruction_method - the name of the software used to construct the tree\n string tree_construction_parameters - any non-default parameters of the tree construction method\n string tree_protocol - simple free-form text which may provide additional details of how the tree was built\n int node_count - total number of nodes in the tree\n int leaf_count - total number of leaf nodes in the tree (generally this cooresponds to the number of sequences)\n string source_db - the source database where this tree originated, if one exists\n string source_id - the id of this tree in an external database, if one exists", + "module" : "Tree", + "name" : "tree_meta_data" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Get meta data associated with each of the trees indicated in the list by tree id. Note that some meta\ndata may not be available for trees which are not built from alignments. Also note that this method\ncomputes the number of nodes and leaves for each tree, so may be slow for very large trees or very long\nlists. If you do not need this full meta information structure, it may be faster to directly query the\nCDS for just the field you need using the CDMI.", + "name" : "get_alignment_data", + "parameters" : [ { + "name" : "alignment_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Meta data associated with an alignment.\n\n list tree_ids - the set of trees that were built from this alignment\n string status - set to 'active' if this is the latest alignment for a particular set of sequences\n string sequence_type - indicates what type of sequence is aligned (e.g. protein vs. dna)\n bool is_concatenation - true if the alignment is based on the concatenation of multiple non-contiguous\n sequences, false if each row cooresponds to exactly one sequence (possibly with gaps)\n timestamp date_created - time at which the alignment was built/loaded in seconds since the epoch\n int n_rows - number of rows in the alignment\n int n_cols - number of columns in the alignment\n string alignment_construction_method - the name of the software tool used to build the alignment\n string alignment_construction_parameters - set of non-default parameters used to construct the alignment\n string alignment_protocol - simple free-form text which may provide additional details of how the alignment was built\n string source_db - the source database where this alignment originated, if one exists\n string source_id - the id of this alignment in an external database, if one exists", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + }, + "name" : "tree_ids", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "status", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence_type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "is_concatenation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "time in units of number of seconds since the epoch", + "module" : "Tree", + "name" : "timestamp" + }, + "name" : "date_created", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "n_rows", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "n_cols", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "alignment_construction_method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "alignment_construction_parameters", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "alignment_protocol", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_db", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_id", + "nullable" : "0" + } ], + "module" : "Tree", + "name" : "alignment_meta_data" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Meta data associated with an alignment.\n\n list tree_ids - the set of trees that were built from this alignment\n string status - set to 'active' if this is the latest alignment for a particular set of sequences\n string sequence_type - indicates what type of sequence is aligned (e.g. protein vs. dna)\n bool is_concatenation - true if the alignment is based on the concatenation of multiple non-contiguous\n sequences, false if each row cooresponds to exactly one sequence (possibly with gaps)\n timestamp date_created - time at which the alignment was built/loaded in seconds since the epoch\n int n_rows - number of rows in the alignment\n int n_cols - number of columns in the alignment\n string alignment_construction_method - the name of the software tool used to build the alignment\n string alignment_construction_parameters - set of non-default parameters used to construct the alignment\n string alignment_protocol - simple free-form text which may provide additional details of how the alignment was built\n string source_db - the source database where this alignment originated, if one exists\n string source_id - the id of this alignment in an external database, if one exists", + "module" : "Tree", + "name" : "alignment_meta_data" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a list of feature ids in kbase, the protein sequence of each feature (if the sequence exists)\nis identified and used to retrieve all trees by ID that were built using the given protein sequence.", + "name" : "get_tree_ids_by_feature", + "parameters" : [ { + "name" : "feature_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a list of kbase ids of a protein sequences (their MD5s), retrieve the tree ids of trees that\nwere built based on these sequences.", + "name" : "get_tree_ids_by_protein_sequence", + "parameters" : [ { + "name" : "protein_sequence_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a list of feature ids in kbase, the protein sequence of each feature (if the sequence exists)\nis identified and used to retrieve all alignments by ID that were built using the given protein sequence.", + "name" : "get_alignment_ids_by_feature", + "parameters" : [ { + "name" : "feature_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a list of kbase ids of a protein sequences (their MD5s), retrieve the alignment ids of trees that\nwere built based on these sequences.", + "name" : "get_alignment_ids_by_protein_sequence", + "parameters" : [ { + "name" : "protein_sequence_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "This method searches for a tree having a source ID that matches the input pattern. This method accepts\none argument, which is the pattern. The pattern is very simple and includes only two special characters,\nwildcard character, '*', and a match-once character, '.' The wildcard character matches any number (including\n0) of any character, the '.' matches exactly one of any character. These special characters can be escaped\nwith a backslash. To match a blackslash literally, you must also escape it. Note that source IDs are\ngenerally defined by the gene family model which was used to identifiy the sequences to be included in\nthe tree. Therefore, matching a source ID is a convenient way to find trees for a specific set of gene\nfamilies.", + "name" : "get_tree_ids_by_source_id_pattern", + "parameters" : [ { + "name" : "pattern", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a tree id, this method returns a mapping from a tree's unique internal ID to\na protein sequence ID.", + "name" : "get_leaf_to_protein_map", + "parameters" : [ { + "name" : "tree_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a tree id, this method returns a mapping from a tree's unique internal ID to\na KBase feature ID if and only if a cannonical feature id exists.", + "name" : "get_leaf_to_feature_map", + "parameters" : [ { + "name" : "tree_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Structure to group input parameters to the compute_abundance_profile method.\n\n kbase_id tree_id - the KBase ID of the tree to compute abundances for; the tree is\n used to identify the set of sequences that were aligned to build\n the tree; each leaf node of a tree built from an alignment will\n be mapped to a sequence; the compute_abundance_profile method\n assumes that trees are built from protein sequences\n string protein_family_name - the name of the protein family used to pull a small set of reads\n from a metagenomic sample; currently only COG families are supported\n string protein_family_source - the name of the source of the protein family; currently supported\n protein families are: 'COG'\n string metagenomic_sample_id - the ID of the metagenomic sample to lookup; see the KBase communities\n service to identifiy metagenomic samples\n int percent_identity_threshold - the minimum acceptable percent identity for hits, provided as a percentage\n and not a fraction (i.e. set to 87.5 for 87.5%)\n int match_length_threshold - the minimum acceptable length of a match to consider a hit", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + }, + "name" : "tree_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_family_name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_family_source", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "metagenomic_sample_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "percent_identity_threshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "match_length_threshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "mg_auth_key", + "nullable" : "0" + } ], + "module" : "Tree", + "name" : "abundance_params" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Structure to group input parameters to the compute_abundance_profile method.\n\n kbase_id tree_id - the KBase ID of the tree to compute abundances for; the tree is\n used to identify the set of sequences that were aligned to build\n the tree; each leaf node of a tree built from an alignment will\n be mapped to a sequence; the compute_abundance_profile method\n assumes that trees are built from protein sequences\n string protein_family_name - the name of the protein family used to pull a small set of reads\n from a metagenomic sample; currently only COG families are supported\n string protein_family_source - the name of the source of the protein family; currently supported\n protein families are: 'COG'\n string metagenomic_sample_id - the ID of the metagenomic sample to lookup; see the KBase communities\n service to identifiy metagenomic samples\n int percent_identity_threshold - the minimum acceptable percent identity for hits, provided as a percentage\n and not a fraction (i.e. set to 87.5 for 87.5%)\n int match_length_threshold - the minimum acceptable length of a match to consider a hit", + "module" : "Tree", + "name" : "abundance_params" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Structure to group output of the compute_abundance_profile method.\n\n mapping abundances - maps the raw row ID of each leaf node in the input tree to the number\n of hits that map to the given leaf; only row IDs with 1 or more hits\n are added to this map, thus missing leaf nodes imply 0 hits\n int n_hits - the total number of hits in this sample to any leaf\n int n_reads - the total number of reads that were identified for the input protein\n family; if the protein family could not be found this will be zero.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, + "name" : "abundances", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "n_hits", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "n_reads", + "nullable" : "0" + } ], + "module" : "Tree", + "name" : "abundance_result" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Structure to group output of the compute_abundance_profile method.\n\n mapping abundances - maps the raw row ID of each leaf node in the input tree to the number\n of hits that map to the given leaf; only row IDs with 1 or more hits\n are added to this map, thus missing leaf nodes imply 0 hits\n int n_hits - the total number of hits in this sample to any leaf\n int n_reads - the total number of reads that were identified for the input protein\n family; if the protein family could not be found this will be zero.", + "module" : "Tree", + "name" : "abundance_result" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given an input KBase tree built from a sequence alignment, a metagenomic sample, and a protein family, this method\nwill tabulate the number of reads that match to every leaf of the input tree. First, a set of assembled reads from\na metagenomic sample are pulled from the KBase communities service which have been determined to be a likely hit\nto the specified protein family. Second, the sequences aligned to generate the tree are retrieved. Third, UCLUST [1]\nis used to map reads to target sequences of the tree. Finally, for each leaf in the tree, the number of hits matching\nthe input search criteria is tabulated and returned. See the defined objects 'abundance_params' and 'abundance_result'\nfor additional details on specifying the input parameters and handling the results.\n\n[1] Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST, Bioinformatics 26(19), 2460-2461.", + "name" : "compute_abundance_profile", + "parameters" : [ { + "name" : "abundance_params", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Structure to group input parameters to the compute_abundance_profile method.\n\n kbase_id tree_id - the KBase ID of the tree to compute abundances for; the tree is\n used to identify the set of sequences that were aligned to build\n the tree; each leaf node of a tree built from an alignment will\n be mapped to a sequence; the compute_abundance_profile method\n assumes that trees are built from protein sequences\n string protein_family_name - the name of the protein family used to pull a small set of reads\n from a metagenomic sample; currently only COG families are supported\n string protein_family_source - the name of the source of the protein family; currently supported\n protein families are: 'COG'\n string metagenomic_sample_id - the ID of the metagenomic sample to lookup; see the KBase communities\n service to identifiy metagenomic samples\n int percent_identity_threshold - the minimum acceptable percent identity for hits, provided as a percentage\n and not a fraction (i.e. set to 87.5 for 87.5%)\n int match_length_threshold - the minimum acceptable length of a match to consider a hit", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + }, + "name" : "tree_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_family_name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_family_source", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "metagenomic_sample_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "percent_identity_threshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "match_length_threshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "mg_auth_key", + "nullable" : "0" + } ], + "module" : "Tree", + "name" : "abundance_params" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Structure to group input parameters to the compute_abundance_profile method.\n\n kbase_id tree_id - the KBase ID of the tree to compute abundances for; the tree is\n used to identify the set of sequences that were aligned to build\n the tree; each leaf node of a tree built from an alignment will\n be mapped to a sequence; the compute_abundance_profile method\n assumes that trees are built from protein sequences\n string protein_family_name - the name of the protein family used to pull a small set of reads\n from a metagenomic sample; currently only COG families are supported\n string protein_family_source - the name of the source of the protein family; currently supported\n protein families are: 'COG'\n string metagenomic_sample_id - the ID of the metagenomic sample to lookup; see the KBase communities\n service to identifiy metagenomic samples\n int percent_identity_threshold - the minimum acceptable percent identity for hits, provided as a percentage\n and not a fraction (i.e. set to 87.5 for 87.5%)\n int match_length_threshold - the minimum acceptable length of a match to consider a hit", + "module" : "Tree", + "name" : "abundance_params" + } + } ], + "return_type" : [ { + "name" : "abundance_result", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Structure to group output of the compute_abundance_profile method.\n\n mapping abundances - maps the raw row ID of each leaf node in the input tree to the number\n of hits that map to the given leaf; only row IDs with 1 or more hits\n are added to this map, thus missing leaf nodes imply 0 hits\n int n_hits - the total number of hits in this sample to any leaf\n int n_reads - the total number of reads that were identified for the input protein\n family; if the protein family could not be found this will be zero.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, + "name" : "abundances", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "n_hits", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "n_reads", + "nullable" : "0" + } ], + "module" : "Tree", + "name" : "abundance_result" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Structure to group output of the compute_abundance_profile method.\n\n mapping abundances - maps the raw row ID of each leaf node in the input tree to the number\n of hits that map to the given leaf; only row IDs with 1 or more hits\n are added to this map, thus missing leaf nodes imply 0 hits\n int n_hits - the total number of hits in this sample to any leaf\n int n_reads - the total number of reads that were identified for the input protein\n family; if the protein family could not be found this will be zero.", + "module" : "Tree", + "name" : "abundance_result" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a tree structure in newick, render it in HTML/JAVASCRIPT and return the page as a string. display_options\nprovides a way to pass parameters to the tree rendering algorithm, but currently no options are recognized.", + "name" : "draw_html_tree", + "parameters" : [ { + "name" : "tree", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format)\nand are returned to you in this format by default.", + "module" : "Tree", + "name" : "newick_tree" + } + }, { + "name" : "display_options", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "String in HTML format, used in the KBase Tree library for returning rendered trees.", + "module" : "Tree", + "name" : "html_file" + } + } ] + } ], + "module_name" : "Tree", + "options" : [ ], + "service_name" : "Tree" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "abundance_params" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Structure to group input parameters to the compute_abundance_profile method.\n\n kbase_id tree_id - the KBase ID of the tree to compute abundances for; the tree is\n used to identify the set of sequences that were aligned to build\n the tree; each leaf node of a tree built from an alignment will\n be mapped to a sequence; the compute_abundance_profile method\n assumes that trees are built from protein sequences\n string protein_family_name - the name of the protein family used to pull a small set of reads\n from a metagenomic sample; currently only COG families are supported\n string protein_family_source - the name of the source of the protein family; currently supported\n protein families are: 'COG'\n string metagenomic_sample_id - the ID of the metagenomic sample to lookup; see the KBase communities\n service to identifiy metagenomic samples\n int percent_identity_threshold - the minimum acceptable percent identity for hits, provided as a percentage\n and not a fraction (i.e. set to 87.5 for 87.5%)\n int match_length_threshold - the minimum acceptable length of a match to consider a hit", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + }, + "name" : "tree_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_family_name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_family_source", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "metagenomic_sample_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "percent_identity_threshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "match_length_threshold", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "mg_auth_key", + "nullable" : "0" + } ], + "module" : "Tree", + "name" : "abundance_params" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Structure to group input parameters to the compute_abundance_profile method.\n\n kbase_id tree_id - the KBase ID of the tree to compute abundances for; the tree is\n used to identify the set of sequences that were aligned to build\n the tree; each leaf node of a tree built from an alignment will\n be mapped to a sequence; the compute_abundance_profile method\n assumes that trees are built from protein sequences\n string protein_family_name - the name of the protein family used to pull a small set of reads\n from a metagenomic sample; currently only COG families are supported\n string protein_family_source - the name of the source of the protein family; currently supported\n protein families are: 'COG'\n string metagenomic_sample_id - the ID of the metagenomic sample to lookup; see the KBase communities\n service to identifiy metagenomic samples\n int percent_identity_threshold - the minimum acceptable percent identity for hits, provided as a percentage\n and not a fraction (i.e. set to 87.5 for 87.5%)\n int match_length_threshold - the minimum acceptable length of a match to consider a hit", + "module" : "Tree", + "name" : "abundance_params" + }, + "abundance_result" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Structure to group output of the compute_abundance_profile method.\n\n mapping abundances - maps the raw row ID of each leaf node in the input tree to the number\n of hits that map to the given leaf; only row IDs with 1 or more hits\n are added to this map, thus missing leaf nodes imply 0 hits\n int n_hits - the total number of hits in this sample to any leaf\n int n_reads - the total number of reads that were identified for the input protein\n family; if the protein family could not be found this will be zero.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, + "name" : "abundances", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "n_hits", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "n_reads", + "nullable" : "0" + } ], + "module" : "Tree", + "name" : "abundance_result" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Structure to group output of the compute_abundance_profile method.\n\n mapping abundances - maps the raw row ID of each leaf node in the input tree to the number\n of hits that map to the given leaf; only row IDs with 1 or more hits\n are added to this map, thus missing leaf nodes imply 0 hits\n int n_hits - the total number of hits in this sample to any leaf\n int n_reads - the total number of reads that were identified for the input protein\n family; if the protein family could not be found this will be zero.", + "module" : "Tree", + "name" : "abundance_result" + }, + "alignment" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "String representation of a sequence alignment, the format of which may be different depending on\ninput options for retrieving the alignment.", + "module" : "Tree", + "name" : "alignment" + }, + "alignment_meta_data" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Meta data associated with an alignment.\n\n list tree_ids - the set of trees that were built from this alignment\n string status - set to 'active' if this is the latest alignment for a particular set of sequences\n string sequence_type - indicates what type of sequence is aligned (e.g. protein vs. dna)\n bool is_concatenation - true if the alignment is based on the concatenation of multiple non-contiguous\n sequences, false if each row cooresponds to exactly one sequence (possibly with gaps)\n timestamp date_created - time at which the alignment was built/loaded in seconds since the epoch\n int n_rows - number of rows in the alignment\n int n_cols - number of columns in the alignment\n string alignment_construction_method - the name of the software tool used to build the alignment\n string alignment_construction_parameters - set of non-default parameters used to construct the alignment\n string alignment_protocol - simple free-form text which may provide additional details of how the alignment was built\n string source_db - the source database where this alignment originated, if one exists\n string source_id - the id of this alignment in an external database, if one exists", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + } + }, + "name" : "tree_ids", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "status", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "sequence_type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "is_concatenation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "time in units of number of seconds since the epoch", + "module" : "Tree", + "name" : "timestamp" + }, + "name" : "date_created", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "n_rows", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "n_cols", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "alignment_construction_method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "alignment_construction_parameters", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "alignment_protocol", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_db", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_id", + "nullable" : "0" + } ], + "module" : "Tree", + "name" : "alignment_meta_data" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Meta data associated with an alignment.\n\n list tree_ids - the set of trees that were built from this alignment\n string status - set to 'active' if this is the latest alignment for a particular set of sequences\n string sequence_type - indicates what type of sequence is aligned (e.g. protein vs. dna)\n bool is_concatenation - true if the alignment is based on the concatenation of multiple non-contiguous\n sequences, false if each row cooresponds to exactly one sequence (possibly with gaps)\n timestamp date_created - time at which the alignment was built/loaded in seconds since the epoch\n int n_rows - number of rows in the alignment\n int n_cols - number of columns in the alignment\n string alignment_construction_method - the name of the software tool used to build the alignment\n string alignment_construction_parameters - set of non-default parameters used to construct the alignment\n string alignment_protocol - simple free-form text which may provide additional details of how the alignment was built\n string source_db - the source database where this alignment originated, if one exists\n string source_id - the id of this alignment in an external database, if one exists", + "module" : "Tree", + "name" : "alignment_meta_data" + }, + "bool" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "indicates true or false values, false <= 0, true >=1", + "module" : "Tree", + "name" : "bool" + }, + "fasta" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "String representation of a sequence or set of sequences in FASTA format. The precise alphabet used is\nnot yet specified, but will be similar to sequences stored in KBase with '-' to denote gaps in alignments.", + "module" : "Tree", + "name" : "fasta" + }, + "fasta_alignment" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "String representation of a sequence or set of sequences in FASTA format. The precise alphabet used is\nnot yet specified, but will be similar to sequences stored in KBase with '-' to denote gaps in alignments.", + "module" : "Tree", + "name" : "fasta" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "String representation of an alignment in FASTA format. The precise alphabet and syntax of the alignment\nstring is not yet specified, but will be similar to sequences stored in KBase with '-' to denote gaps in\nalignments.", + "module" : "Tree", + "name" : "fasta_alignment" + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "html_file" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "String in HTML format, used in the KBase Tree library for returning rendered trees.", + "module" : "Tree", + "name" : "html_file" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "json_tree" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format),\nbut can optionally be converted to JSON format where the structure of the tree matches the structure of\nthe JSON object. This is useful when interacting with the tree in JavaScript, for instance.", + "module" : "Tree", + "name" : "json_tree" + }, + "kbase_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + }, + "newick_tree" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format)\nand are returned to you in this format by default.", + "module" : "Tree", + "name" : "newick_tree" + }, + "node_name" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The string representation of the parsed node name (may be a kbase_id, but does not have to be). Note that this\nis not the full, raw label in a newick_tree (which may include comments).", + "module" : "Tree", + "name" : "node_name" + }, + "phyloXML_tree" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trees are represented in KBase by default in newick format (http://en.wikipedia.org/wiki/Newick_format),\nbut can optionally be converted to the more verbose phyloXML format, which is useful for compatibility or\nwhen additional information/annotations decorate the tree.", + "module" : "Tree", + "name" : "phyloXML_tree" + }, + "position" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "integer number indicating a 1-based position in an amino acid / nucleotide sequence", + "module" : "Tree", + "name" : "position" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "timestamp" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "time in units of number of seconds since the epoch", + "module" : "Tree", + "name" : "timestamp" + }, + "tree" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string representation of a phylogenetic tree. The format/syntax of the string is\nspecified by using one of the available typedefs declaring a particular format, such as 'newick_tree',\n'phyloXML_tree' or 'json_tree'. When a format is not explictily specified, it is possible to return\ntrees in different formats depending on addtional parameters. Regardless of format, all leaf nodes\nin trees built from MSAs are indexed to a specific MSA row. You can use the appropriate functionality\nof the API to replace these IDs with other KBase Ids instead. Internal nodes may or may not be named.\nNodes, depending on the format, may also be annotated with structured data such as bootstrap values and\ndistances.", + "module" : "Tree", + "name" : "tree" + }, + "tree_meta_data" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Meta data associated with a tree.\n\n kbase_id alignment_id - if this tree was built from an alignment, this provides that alignment id\n string type - the type of tree; possible values currently are \"sequence_alignment\" and \"genome\" for trees\n either built from a sequence alignment, or imported directly indexed to genomes.\n string status - set to 'active' if this is the latest built tree for a particular gene family\n timestamp date_created - time at which the tree was built/loaded in seconds since the epoch\n string tree_contruction_method - the name of the software used to construct the tree\n string tree_construction_parameters - any non-default parameters of the tree construction method\n string tree_protocol - simple free-form text which may provide additional details of how the tree was built\n int node_count - total number of nodes in the tree\n int leaf_count - total number of leaf nodes in the tree (generally this cooresponds to the number of sequences)\n string source_db - the source database where this tree originated, if one exists\n string source_id - the id of this tree in an external database, if one exists", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\". KBase IDs are typed. The types are\ndesignated using a short string. For instance,\" g\" denotes a genome, \"tree\" denotes a Tree, and\n\"aln\" denotes a sequence alignment. KBase IDs may be hierarchical. For example, if a KBase genome\nidentifier is \"kb|g.1234\", a protein encoding gene within that genome may be represented as\n\"kb|g.1234.peg.771\".", + "module" : "Tree", + "name" : "kbase_id" + }, + "name" : "alignment_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "status", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "time in units of number of seconds since the epoch", + "module" : "Tree", + "name" : "timestamp" + }, + "name" : "date_created", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "tree_contruction_method", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "tree_construction_parameters", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "tree_protocol", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "node_count", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "leaf_count", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_db", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_id", + "nullable" : "0" + } ], + "module" : "Tree", + "name" : "tree_meta_data" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Meta data associated with a tree.\n\n kbase_id alignment_id - if this tree was built from an alignment, this provides that alignment id\n string type - the type of tree; possible values currently are \"sequence_alignment\" and \"genome\" for trees\n either built from a sequence alignment, or imported directly indexed to genomes.\n string status - set to 'active' if this is the latest built tree for a particular gene family\n timestamp date_created - time at which the tree was built/loaded in seconds since the epoch\n string tree_contruction_method - the name of the software used to construct the tree\n string tree_construction_parameters - any non-default parameters of the tree construction method\n string tree_protocol - simple free-form text which may provide additional details of how the tree was built\n int node_count - total number of nodes in the tree\n int leaf_count - total number of leaf nodes in the tree (generally this cooresponds to the number of sequences)\n string source_db - the source database where this tree originated, if one exists\n string source_id - the id of this tree in an external database, if one exists", + "module" : "Tree", + "name" : "tree_meta_data" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.21.json.properties b/src/test/resources/us/kbase/test/kidl/spec.21.json.properties new file mode 100644 index 0000000..87c0a73 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.21.json.properties @@ -0,0 +1,1792 @@ +{ + "KB" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "test module for type validation with annotations", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "exclusiveMinimum" : "0", + "maximum" : "30.3", + "minimum" : "-12.5" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range [-12.5,30.3]", + "module" : "KB", + "name" : "f1" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "1", + "exclusiveMinimum" : "0", + "maximum" : "30", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range [0,30)", + "module" : "KB", + "name" : "f2" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "exclusiveMinimum" : "1", + "maximum" : "30", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range (0,30]", + "module" : "KB", + "name" : "f3" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "maximum" : "30" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range ,30]", + "module" : "KB", + "name" : "f4" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMinimum" : "0", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range 0,", + "module" : "KB", + "name" : "f5" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMinimum" : "0", + "minimum" : "5" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range [5,]", + "module" : "KB", + "name" : "i1" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "1", + "maximum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range [,0)", + "module" : "KB", + "name" : "i2" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "exclusiveMinimum" : "1", + "maximum" : "10", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range (0,10]", + "module" : "KB", + "name" : "i3" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "exclusiveMinimum" : "0", + "maximum" : "1", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range 0,1", + "module" : "KB", + "name" : "i4" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMinimum" : "1", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range (0,", + "module" : "KB", + "name" : "i6" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "1", + "exclusiveMinimum" : "0", + "maximum" : "3.99", + "minimum" : "0.12" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "int value that should produce min of 1 inclusive and max of 3 inclusive\n@range [0.12, 3.99)", + "module" : "KB", + "name" : "if1" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "searchable_ws_subset" : { } + }, + "comment" : "@metadata ws f1\n@optional f1 f2 f3 f4 f5 i1 i2 i3 i4 i5 i6", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "exclusiveMinimum" : "0", + "maximum" : "30.3", + "minimum" : "-12.5" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range [-12.5,30.3]", + "module" : "KB", + "name" : "f1" + }, + "name" : "f1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "1", + "exclusiveMinimum" : "0", + "maximum" : "30", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range [0,30)", + "module" : "KB", + "name" : "f2" + }, + "name" : "f2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "exclusiveMinimum" : "1", + "maximum" : "30", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range (0,30]", + "module" : "KB", + "name" : "f3" + }, + "name" : "f3", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "maximum" : "30" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range ,30]", + "module" : "KB", + "name" : "f4" + }, + "name" : "f4", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMinimum" : "0", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range 0,", + "module" : "KB", + "name" : "f5" + }, + "name" : "f5", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMinimum" : "0", + "minimum" : "5" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range [5,]", + "module" : "KB", + "name" : "i1" + }, + "name" : "i1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "1", + "maximum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range [,0)", + "module" : "KB", + "name" : "i2" + }, + "name" : "i2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "exclusiveMinimum" : "1", + "maximum" : "10", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range (0,10]", + "module" : "KB", + "name" : "i3" + }, + "name" : "i3", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "exclusiveMinimum" : "0", + "maximum" : "1", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range 0,1", + "module" : "KB", + "name" : "i4" + }, + "name" : "i4", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "i5", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMinimum" : "1", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range (0,", + "module" : "KB", + "name" : "i6" + }, + "name" : "i6", + "nullable" : "0" + } ], + "module" : "KB", + "name" : "NumberObj" + }, + "annotations" : { + "metadata" : { + "ws" : { + "f1" : "f1" + } + }, + "optional" : [ "f1", "f2", "f3", "f4", "f5", "i1", "i2", "i3", "i4", "i5", "i6" ], + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@metadata ws f1\n@optional f1 f2 f3 f4 f5 i1 i2 i3 i4 i5 i6", + "module" : "KB", + "name" : "NumberObj" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "exclusiveMinimum" : "0", + "maximum" : "1.0E+99", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range [0,1.0E+99]", + "module" : "KB", + "name" : "bf1" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "exclusiveMinimum" : "0", + "maximum" : "98765432101234567890", + "minimum" : "-98765432101234567890" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range [-98765432101234567890,98765432101234567890]", + "module" : "KB", + "name" : "bi1" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "1", + "exclusiveMinimum" : "1", + "maximum" : "98765432101234567890", + "minimum" : "-98765432101234567890" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range (-98765432101234567890,98765432101234567890)", + "module" : "KB", + "name" : "bi2" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMinimum" : "1", + "minimum" : "-98765432101234567890" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range (-98765432101234567890,", + "module" : "KB", + "name" : "bi3" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "1", + "maximum" : "98765432101234567890" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range ,98765432101234567890)", + "module" : "KB", + "name" : "bi4" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMinimum" : "0", + "minimum" : "-98765432101234567890" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range [-98765432101234567890,", + "module" : "KB", + "name" : "bi5" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "maximum" : "98765432101234567890" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range ,98765432101234567890]", + "module" : "KB", + "name" : "bi6" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : 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}, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range [,0)", + "module" : "KB", + "name" : "i2" + }, + "i3" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "exclusiveMinimum" : "1", + "maximum" : "10", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range (0,10]", + "module" : "KB", + "name" : "i3" + }, + "i4" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "0", + "exclusiveMinimum" : "0", + "maximum" : "1", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range 0,1", + "module" : "KB", + "name" : "i4" + }, + "i6" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMinimum" : "1", + "minimum" : "0" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@range (0,", + "module" : "KB", + "name" : "i6" + }, + "if1" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "range" : { + "exclusiveMaximum" : "1", + "exclusiveMinimum" : "0", + "maximum" : "3.99", + "minimum" : "0.12" + }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "int value that should produce min of 1 inclusive and max of 3 inclusive\n@range [0.12, 3.99)", + "module" : "KB", + "name" : "if1" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.22.json.properties b/src/test/resources/us/kbase/test/kidl/spec.22.json.properties new file mode 100644 index 0000000..7571e7b --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.22.json.properties @@ -0,0 +1,2300 @@ +{ + "KB" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + 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"Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "seq", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "length", + "nullable" : "0" + } ], + "module" : "KB", + "name" : "Subdata" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { + "fields" : { + "name" : { } + }, + "keys" : { } + }, + "unknown_annotations" : { } + }, + "comment" : "@searchable ws_subset name", + "module" : "KB", + "name" : "Subdata" + } + } + }, + "name" : "dml", + "nullable" : "0" + } ], + "module" : "KB", + "name" : "NestedData" + }, + "annotations" : { + "metadata" : { }, + "optional" : [ "dl", "dm", "dml" ], + "searchable_ws_subset" : { + "fields" : { + "d" : { + "length" : { }, + "name" : { } + }, + "dl" : { + "[*]" : { + "name" : { } + } + }, + "dm" : { + "*" : { + "length" : { }, + "seq" : { } + } + }, + "dml" : { + "*" : { + "[*]" : { + "name" : { } + } + } + } + }, + "keys" : { } + }, + "unknown_annotations" : { } + }, + "comment" : "@optional dl dm dml\n@searchable ws_subset d.(name,length)\n@searchable ws_subset dl.[*].name\n@searchable ws_subset dm.*.(seq,length)\n@searchable ws_subset dml.*.[*].name", + "module" : "KB", + "name" : "NestedData" + }, + "NoExtractionData" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "data", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "stuff", + "nullable" : "0" + } ], + "module" : "KB", + "name" : "NoExtractionData" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "KB", + "name" : "NoExtractionData" + }, + "SimpleStructure" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { }, + "comment" : "@optional size\n@searchable ws_subset name,alias\n@searchable ws_subset size\n@searchable ws_subset width\n@metadata ws name AS My Name\n@metadata ws size AS Size\n@metadata ws width as width\n@metadata ws length(name) as name length", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "alias", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "size", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "maxsize", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "width", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "maxwidth", + "nullable" : "0" + } ], + "module" : "KB", + "name" : "SimpleStructure" + }, + "annotations" : { + "metadata" : { + "ws" : { + "My Name" : "name", + "Size" : "size", + "name length" : "length(name)", + "width" : "width" + } + }, + "optional" : [ "size" ], + "searchable_ws_subset" : { + "fields" : { + "alias" : { }, + "name" : { }, + "size" : { }, + "width" : { } + }, + "keys" : { } + }, + "unknown_annotations" : { } + }, + "comment" : "@optional size\n@searchable ws_subset name,alias\n@searchable ws_subset size\n@searchable ws_subset width\n@metadata ws name AS My Name\n@metadata ws size AS Size\n@metadata ws width as width\n@metadata ws length(name) as name length", + "module" : "KB", + "name" : "SimpleStructure" + }, + "Subdata" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { } + }, + "comment" : "@searchable ws_subset name", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "seq", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "length", + "nullable" : "0" + } ], + "module" : "KB", + "name" : "Subdata" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { + "fields" : { + "name" : { } + }, + "keys" : { } + }, + "unknown_annotations" : { } + }, + "comment" : "@searchable ws_subset name", + "module" : "KB", + "name" : "Subdata" + }, + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "otherstring" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "KB", + "name" : "otherstring" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.23.json.properties b/src/test/resources/us/kbase/test/kidl/spec.23.json.properties new file mode 100644 index 0000000..5e3207f --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.23.json.properties @@ -0,0 +1,118 @@ +{ + "Test" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "@optional val2\n@new_annotation val1", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "val1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "val2", + "nullable" : "0" + } ], + "module" : "Test", + "name" : "my_struct" + }, + "annotations" : { + "metadata" : { }, + "optional" : [ "val2" ], + "searchable_ws_subset" : { }, + "unknown_annotations" : { + "new_annotation" : [ "val1" ] + } + }, + "comment" : "@optional val2\n@new_annotation val1", + "module" : "Test", + "name" : "my_struct" + } ], + "module_name" : "Test", + "options" : [ ], + "service_name" : "Test" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "my_struct" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "@optional val2\n@new_annotation val1", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "val1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "val2", + "nullable" : "0" + } ], + "module" : "Test", + "name" : "my_struct" + }, + "annotations" : { + "metadata" : { }, + "optional" : [ "val2" ], + "searchable_ws_subset" : { }, + "unknown_annotations" : { + "new_annotation" : [ "val1" ] + } + }, + "comment" : "@optional val2\n@new_annotation val1", + "module" : "Test", + "name" : "my_struct" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.24.json.properties b/src/test/resources/us/kbase/test/kidl/spec.24.json.properties new file mode 100644 index 0000000..458c239 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.24.json.properties @@ -0,0 +1,92 @@ +{ + "Test" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "fid_1", "fid_2", "fid_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "t" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test", + "name" : "t" + } ], + "module_name" : "Test", + "options" : [ ], + "service_name" : "Test" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "t" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "fid_1", "fid_2", "fid_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "t" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test", + "name" : "t" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.25.json.properties b/src/test/resources/us/kbase/test/kidl/spec.25.json.properties new file mode 100644 index 0000000..d26de71 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.25.json.properties @@ -0,0 +1,92 @@ +{ + "Test" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "t" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test", + "name" : "t" + } ], + "module_name" : "Test", + "options" : [ ], + "service_name" : "Test" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "t" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "t" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test", + "name" : "t" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.3.json.properties b/src/test/resources/us/kbase/test/kidl/spec.3.json.properties new file mode 100644 index 0000000..00f234d --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.3.json.properties @@ -0,0 +1,10089 @@ +{ + "Experiment" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "Experiment Service API specification\n\nThis service provides various methods for extracting data from the Experiment portion of the CDS.", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as an ID for a workspace. Any string consisting of alphanumeric characters and \"-\" is acceptable", + "module" : "Experiment", + "name" : "workspace_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string indicating the \"type\" of an object stored in a workspace. Acceptable types are returned by the \"get_types()\" command", + "module" : "Experiment", + "name" : "object_type" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "ID of an object stored in the workspace. Any string consisting of alphanumeric characters and \"-\" is acceptable", + "module" : "Experiment", + "name" : "object_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Single letter indicating permissions on access to workspace. Options are: 'a' for administative access, 'w' for read/write access, 'r' for read access, and 'n' for no access.", + "module" : "Experiment", + "name" : "permission" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of KBase useraccount to which permissions for workspaces are mapped", + "module" : "Experiment", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Exact time for workspace operations. e.g. 2012-12-17T23:24:06", + "module" : "Experiment", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A 36 character string referring to a particular instance of an object in a workspace that lasts forever. Objects should always be retreivable using this ID", + "module" : "Experiment", + "name" : "workspace_ref" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "id", "type", "moddate", "instance", "command", "lastmodifier", "owner", "workspace", "ref", "chsum", "metadata" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "ID of an object stored in the workspace. Any string consisting of alphanumeric characters and \"-\" is acceptable", + "module" : "Experiment", + "name" : "object_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string indicating the \"type\" of an object stored in a workspace. Acceptable types are returned by the \"get_types()\" command", + "module" : "Experiment", + "name" : "object_type" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Exact time for workspace operations. e.g. 2012-12-17T23:24:06", + "module" : "Experiment", + "name" : "timestamp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of KBase useraccount to which permissions for workspaces are mapped", + "module" : "Experiment", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of KBase useraccount to which permissions for workspaces are mapped", + "module" : "Experiment", + "name" : "username" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as an ID for a workspace. Any string consisting of alphanumeric characters and \"-\" is acceptable", + "module" : "Experiment", + "name" : "workspace_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A 36 character string referring to a particular instance of an object in a workspace that lasts forever. Objects should always be retreivable using this ID", + "module" : "Experiment", + "name" : "workspace_ref" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "name" : "object_metadata" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "object_metadata" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "END IMPORTED OBJECTS ----------", + "module" : "Experiment", + "name" : "boolean" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compounds" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "molar_ratio" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "molar_ratio" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "cpd_to_molar" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "molar_ratio" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "cpd_to_molar" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_relationships" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the child compounds of the input compounds and their molar ratio\nequivalents to the parent/input. The MR is -1 if the molar ratio is\nunknown.\nIf the input compounds have no children the returned mapping contains\nthe input compound and 1 as the molar ratio.\nIntermediate compounds in the tree between child (e.g. a compound that\nhas no more children) and input/parent compound are not returned.", + "name" : "getChildCompounds", + "parameters" : [ { + "name" : "parents", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compounds" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "molar_ratio" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "cpd_to_molar" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_relationships" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the parent compounds of the input compounds and the molar ratio\nof the child compound to the parent compound. Note this is the same value\nas returned by the getChildCompounds function, not the inverse of that\nvalue. The MR is -1 if the molar ratio is unknown.\nIf the input compounds have no parents the returned mapping contains\nthe input compound and 1 as the molar ratio.\nIntermediate compounds in the tree between parent (e.g. a compound that\nhas no more parents) and input/child compound are not returned.", + "name" : "getParentCompounds", + "parameters" : [ { + "name" : "children", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compounds" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "molar_ratio" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "cpd_to_molar" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_relationships" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a representation of the compound tree from the parent compounds to\ntheir ultimate children. All intermediate compounds in the tree are \nincluded. This takes the form of a mapping between a parent and its \nimmediate children and a subsequent mapping between those children and the \nmolar ratio from parent:child. To traverse the tree, choose the parent of\ninterest, retrieve the child:molar ratio mapping, and continue down the\ntree with each child, retrieving its children from the mapping returned\nby the function. If a compound has no children it is not included in the\nmapping.", + "name" : "getChildAndIntermediateCompounds", + "parameters" : [ { + "name" : "parents", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compounds" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "molar_ratio" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "cpd_to_molar" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_relationships" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a representation of the compound tree from the child compounds to\ntheir ultimate parents. All intermediate compounds in the tree are \nincluded. This takes the form of a mapping between the child and its \nimmediate parents and a subsequent mapping between those parents and the \nmolar ratio from parent:child. To traverse the tree, choose the child of\ninterest, retrieve the parent:molar ratio mapping, and continue up the tree\nwith each parent, retrieving its parents from the mapping returned\nby the function. If a compound has no parents it is not included in the \nmapping.", + "name" : "getParentAndIntermediateCompounds", + "parameters" : [ { + "name" : "children", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compounds" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "molar_ratio" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "cpd_to_molar" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_relationships" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "media_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "media_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "exclude_medias" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "exclude_compounds" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "END IMPORTED OBJECTS ----------", + "module" : "Experiment", + "name" : "boolean" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "exclude_solid" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "END IMPORTED OBJECTS ----------", + "module" : "Experiment", + "name" : "boolean" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "exclude_undefined" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "media_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "medias" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Find medias matching the input requirements. Media IDs in exclude_medias\nwill not be returned under any circumstances. Medias containing the\ncompounds in exclude_compounds, their parent compounds, and any \nintermediate compounds will be excluded. The arguments exclude_solid and\nexclude_undefined will prevent solid and undefined medias, respectively,\nfrom inclusion in the results.", + "name" : "findMedias", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "media_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "exclude_medias" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "compound_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "exclude_compounds" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "END IMPORTED OBJECTS ----------", + "module" : "Experiment", + "name" : "boolean" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "exclude_solid" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "END IMPORTED OBJECTS ----------", + "module" : "Experiment", + "name" : "boolean" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "exclude_undefined" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "media_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "medias" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "environment_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "environment_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "environments" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "sourceID", "description", "temperature", "oxygenConcentration", "pH", "mediaID", "conditions", "parameters" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "envEF" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "envEF" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "environment_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "sourceID", "description", "temperature", "oxygenConcentration", "pH", "mediaID", "conditions", "parameters" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "envEF" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "envEF" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "envEFs" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Return Environment objects in exchange format. Compounds are returned\nas loaded and are not resolved to the subcompounds. Entries with no values\nare returned as null (e.g. if the environment has no additional compounds\nthe conditions field in envEF will be undef/None/null).", + "name" : "getEnvironmentsInExchangeFormat", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "environment_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "environments" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "environment_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "sourceID", "description", "temperature", "oxygenConcentration", "pH", "mediaID", "conditions", "parameters" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } ], + "name" : "envEF" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "envEF" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "envEFs" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "group_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "group_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "groups" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "time_point" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "time_point" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "environment_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "time_to_env" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Defines whether an experimental unit refers to metadata about a grouping\nor time series, value is either 'Y' or 'N'", + "module" : "Experiment", + "name" : "meta" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Defines whether an experimental unit refers to metadata about a grouping\nor time series, value is either 'Y' or 'N'", + "module" : "Experiment", + "name" : "meta" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "groupMeta" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Defines whether an experimental unit refers to metadata about a grouping\nor time series, value is either 'Y' or 'N'", + "module" : "Experiment", + "name" : "meta" + }, + "annotations" : { + "metadata" : { }, + 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"annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "group_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Defines whether an experimental unit refers to metadata about a grouping\nor time series, value is either 'Y' or 'N'", + "module" : "Experiment", + "name" : "meta" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "groupMeta" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "location" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "time_series_id" + }, + "name" : "timeSeriesId", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Defines whether an experimental unit refers to metadata about a grouping\nor time series, value is either 'Y' or 'N'", + "module" : "Experiment", + "name" : "meta" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "timeMeta" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "time_point" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "environment_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "time_to_env" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "meta_to_time" + }, + "name" : "timepoints", + "nullable" : "0" + } ], + "module" : "Experiment", + "name" : "env_by_time" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "env_by_time" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "loc_to_time_info" 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"comment" : "", + "module" : "Experiment", + "name" : "maxKnockouts" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "END IMPORTED OBJECTS ----------", + "module" : "Experiment", + "name" : "boolean" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "onlyWildtype" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "END IMPORTED OBJECTS ----------", + "module" : "Experiment", + "name" : "boolean" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "onlyAggregate" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "feature_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" 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"searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "strain_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "feature_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "knockouts" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "strainToKOs" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the strains and their knockouts that match the given genome,\nmaximum knockout count, and wildtype and aggregate data boolean flags.", + "name" : "findStrainsAndKOs", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "genome_id" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "maxKnockouts" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "END IMPORTED OBJECTS ----------", + "module" : "Experiment", + "name" : "boolean" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "onlyWildtype" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + 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{ + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "feature_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "knockouts" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "strainToKOs" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "experimentMeta_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "min_temp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "max_temp" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "min_oxygen" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "max_oxygen" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "max_pH" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + 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Fundamentally the data consists of a mapping\nof an environment, consisting of a list of compounds, and a set of gene\nknockouts to a fitness value or a growth boolean. By default, the data \nis processed such that data rows (where a row is an environment, set of \nknockouts, and a fitness value) with identical compounds and knockouts \nare merged into a single row by taking the maximum of the identical \nrows.\n\nThe return value consists of a mapping of ExperimentalUnitGroup IDs to a\nstructure containing several pieces of data about the group: 1) the list \nof compounds in the environment of the group, 2) some summary statistics\nabout the entire group (e.g. including all rows, not just the returned\nmerged rows), 3) the ID of the environment of the group, 4) if \nrequested, a list of all fitness values in the group for the purposes of\nthresholding and finally, 5) the list of data rows containing, by \ndefault, the knockout list, an empty compound list, and the fitness \nvalue (see options below regarding the compound list).\n\nThe fitness value entry can consist of either a continuous fitness value\n(see measurement description IDs kb|measdesc.0 and 1) or a growth\nboolean (see kb|measdesc.5). Groups, in this case, will typically be \nmicroarrays or RNAseq experiments. Data that is not associated with any\ngroup is mapped from an empty string ('') instead of a KBase \nexperimental unit group ID. For this 'group' statistics are not provided\nand the compounds and environment ID are provided on a per row basis \nrather than once for the entire group. No time series data is ever \nreturned.\n\nInput values are:\ngenome - the KBase ID of the genome to pull data from\n\nmaxKnockouts - the maximum number of knockouts allowed for any strain\n in the return data (defaults to no limit) \n\nonlyWildType - only strains marked as wildtype will be returned (default\n false (0))\n\nonlyAggregate - only strains that represent aggregate data from multiple\n strains will be returned (default true (1))\n\nexperimentMetaIDs - the KBase IDs of the experimentMeta entities from \n which to return data (default all)\n\nexcludeGroups - the data related to the ExperimentalUnitGroup KBase IDs \n in this list will be excluded from the results.\n\nonlyGroups - only the data related to the ExperimentalUnitGroup KBase IDs \n in this list will be included in the results. excludeGroups\n will be ignored. An empty list results in no restrictions\n (default) except those in excludeGroups.\n\ngrowthBoolean - if true, returns data consisting of a growth boolean (1\n for grows, 0 for doesn't grow) rather than fitness values.\n Defaults to returning fitness values. There is no guarantee\n that a particular strain/environment combination with\n growth boolean data has fitness value data as well and \n vice versa.\n\nexcludeMedias - data using the media specified by the KBase media IDs in\n this list will not be returned.\n\nonlyMedias - only data using the medias in this list will be returned. If\n this list is not empty excludeMedias and excludeCompounds\n are ignored. If all three lists are empty no restrictions\n are placed on the medias allowed.\n\nexcludeCompounds - any data using medias or environments containing these\n compounds or any of their parent compounds will not \n be returned.\n\ndropCompounds - these compounds will be silently removed from the data \n before it is returned. Typically used to remove compounds\n such as VitB12 which can interfere with FBA results. Does \n not prevent using medias or environments containing the \n compound. Only an exact match will be removed from the \n returned data - children and parent compounds will remain\n in the data.\n\nexcludeSolid - any data using solid medias will be excluded if true (1).\n Defaults to false (0).\n\nexcludeUndefined - any data using undefined medias will be excluded if\n true (1). Defaults to false (0).\n\ntemperatureRange - any data outside the given temperature range will be \n excluded from the results. Defaults to no limits.\n\noxygenRange - any data outside the given oxygen range will be excluded \n from the results. Defaults to no limits. Recall that -1\n signifies the presence of an unknown but substantial \n quantity of oxygen (as in an unmonitored shake flask,\n for example).\n\npHRange - any data outside the given pH range will be excluded from the \n results. Defaults to no limits. If a range is given, data\n without pH data will not be returned.\n\naggMethod - the method by which to aggregate data rows with identical\n compound lists and knockouts. The choices are 'max', \n 'min', or 'none' which return the maximum or minimum \n growth / fitness value or performs no aggregation,\n respectively. The default is max, which is appropriate\n for nutrient compounds, but less so for inhibitors.\n Vice versa for min.\n\noxygenCutoff - environments with a greater oxygen concentration than\n this value will have oxygen added to the compound\n list if it doesn't already exist. Defaults to 0.000002.\n If the oxygen value is < 0 oxygen is always added to \n the compound list.\n\nallValues - returns a list of all fitness values in each group for\n the purposes of statistical thresholding. By default\n an empty list is returned.\n\nmergeCompounds - if true, rather than returning one list of compounds per group,\n each row of the data contains the compounds \n list. In this case the group level list of compounds\n will be empty. Note that the transfer and storage\n costs for the data will probably go up significantly\n if this option is enabled.\n\nparentCompounds - by default, the compounds returned are the ultimate\n subcompounds of the media and environment compound\n lists. 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+ "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "feature_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "knockouts" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "strainToKOs" + }, + "strain_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "strain_id" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "timeMeta" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Defines whether an experimental unit refers to metadata about a grouping\nor time series, value is either 'Y' or 'N'", + "module" : "Experiment", + "name" : "meta" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "timeMeta" + }, + "time_point" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "time_point" + }, + "time_series_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "time_series_id" + }, + "time_to_env" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "time_point" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "environment_id" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Experiment", + "name" : "time_to_env" + }, + "timestamp" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Exact time for workspace operations. e.g. 2012-12-17T23:24:06", + "module" : "Experiment", + "name" : "timestamp" + }, + "username" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Login name of KBase useraccount to which permissions for workspaces are mapped", + "module" : "Experiment", + "name" : "username" + }, + "workspace_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A string used as an ID for a workspace. Any string consisting of alphanumeric characters and \"-\" is acceptable", + "module" : "Experiment", + "name" : "workspace_id" + }, + "workspace_ref" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A 36 character string referring to a particular instance of an object in a workspace that lasts forever. Objects should always be retreivable using this ID", + "module" : "Experiment", + "name" : "workspace_ref" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.4.json.properties b/src/test/resources/us/kbase/test/kidl/spec.4.json.properties new file mode 100644 index 0000000..a5e5680 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.4.json.properties @@ -0,0 +1,1313 @@ +{ + "FileType" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "KBase File Type Manager Service\n\nThis service tracks the type of files that KBase software recognizes and\nproperties of these file types (such as acceptable file extensions). File types\nexist in a hierarchy (e.g. XML is a type of TEXT file) and are uniquely identified\nby a short unique string id. File types are loosely coupled to different types\nof data supported by KBase.\n\nIn the future, this service may provide some validation capabilities to ensure\nthat a given file matches some basic properties of file type, e.g. a valid XML\ndocument.\n\ncreated 10/18/2012 - msneddon", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The full display name of the file type (e.g. 'Text File', 'HyperText Markup Language File')", + "module" : "FileType", + "name" : "file_type_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short string indicating a possible file extension", + "module" : "FileType", + "name" : "file_extension" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object that encapsulates properties of a file type. Note that unless otherwise stated, any\nmethod which returns a file_type also includes all inhereted valid_file_extensions and properties.\n\nfile_type_id id\n the unique string based id of this file type\n \nfile_type_name name\n the human readable long name of the file type\n\nlist valid_file_extensions\n a list of extensions that are associated with this file type. Note that in some cases this will\n include extensions that are inhereted from parent file types (e.g. a valid extension to a tab\n delimited file may be 'tab', but also 'txt' because it is a text file as well)\n\nmapping properties\n a simple mapping of key/value pairs used to describe attributes of the file type. These in general\n can have any string as a key, but note that the following keys have been adopted for most file\n types by convention. Note that if these properties are not defined, then they are inherited from\n a parent file_type object\n default-extension - gives the single default extension\n default-web-renderer - the name/id of the widget that should be used by default to view the\n contents of this file type", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The full display name of the file type (e.g. 'Text File', 'HyperText Markup Language File')", + "module" : "FileType", + "name" : "file_type_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short string indicating a possible file extension", + "module" : "FileType", + "name" : "file_extension" + } + }, + "name" : "valid_file_extensions", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "FileType", + "name" : "file_type" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object that encapsulates properties of a file type. Note that unless otherwise stated, any\nmethod which returns a file_type also includes all inhereted valid_file_extensions and properties.\n\nfile_type_id id\n the unique string based id of this file type\n \nfile_type_name name\n the human readable long name of the file type\n\nlist valid_file_extensions\n a list of extensions that are associated with this file type. Note that in some cases this will\n include extensions that are inhereted from parent file types (e.g. a valid extension to a tab\n delimited file may be 'tab', but also 'txt' because it is a text file as well)\n\nmapping properties\n a simple mapping of key/value pairs used to describe attributes of the file type. These in general\n can have any string as a key, but note that the following keys have been adopted for most file\n types by convention. Note that if these properties are not defined, then they are inherited from\n a parent file_type object\n default-extension - gives the single default extension\n default-web-renderer - the name/id of the widget that should be used by default to view the\n contents of this file type", + "module" : "FileType", + "name" : "file_type" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the specified file_type object including all inherited file extensions and properties, or\nan empty object if the file_type_id is not valid", + "name" : "get_file_type", + "parameters" : [ { + "name" : "id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object that encapsulates properties of a file type. Note that unless otherwise stated, any\nmethod which returns a file_type also includes all inhereted valid_file_extensions and properties.\n\nfile_type_id id\n the unique string based id of this file type\n \nfile_type_name name\n the human readable long name of the file type\n\nlist valid_file_extensions\n a list of extensions that are associated with this file type. Note that in some cases this will\n include extensions that are inhereted from parent file types (e.g. a valid extension to a tab\n delimited file may be 'tab', but also 'txt' because it is a text file as well)\n\nmapping properties\n a simple mapping of key/value pairs used to describe attributes of the file type. These in general\n can have any string as a key, but note that the following keys have been adopted for most file\n types by convention. Note that if these properties are not defined, then they are inherited from\n a parent file_type object\n default-extension - gives the single default extension\n default-web-renderer - the name/id of the widget that should be used by default to view the\n contents of this file type", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The full display name of the file type (e.g. 'Text File', 'HyperText Markup Language File')", + "module" : "FileType", + "name" : "file_type_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short string indicating a possible file extension", + "module" : "FileType", + "name" : "file_extension" + } + }, + "name" : "valid_file_extensions", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "FileType", + "name" : "file_type" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object that encapsulates properties of a file type. Note that unless otherwise stated, any\nmethod which returns a file_type also includes all inhereted valid_file_extensions and properties.\n\nfile_type_id id\n the unique string based id of this file type\n \nfile_type_name name\n the human readable long name of the file type\n\nlist valid_file_extensions\n a list of extensions that are associated with this file type. Note that in some cases this will\n include extensions that are inhereted from parent file types (e.g. a valid extension to a tab\n delimited file may be 'tab', but also 'txt' because it is a text file as well)\n\nmapping properties\n a simple mapping of key/value pairs used to describe attributes of the file type. These in general\n can have any string as a key, but note that the following keys have been adopted for most file\n types by convention. Note that if these properties are not defined, then they are inherited from\n a parent file_type object\n default-extension - gives the single default extension\n default-web-renderer - the name/id of the widget that should be used by default to view the\n contents of this file type", + "module" : "FileType", + "name" : "file_type" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the specified file_type object with THIS file_type object's extensions and properties ONLY,\nnot any of the extensions or properties inhereted by a parent. Therefore be careful since you may not\nhave all valid file extensions and properties for this file type!", + "name" : "get_this_file_type_only", + "parameters" : [ { + "name" : "id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object that encapsulates properties of a file type. Note that unless otherwise stated, any\nmethod which returns a file_type also includes all inhereted valid_file_extensions and properties.\n\nfile_type_id id\n the unique string based id of this file type\n \nfile_type_name name\n the human readable long name of the file type\n\nlist valid_file_extensions\n a list of extensions that are associated with this file type. Note that in some cases this will\n include extensions that are inhereted from parent file types (e.g. a valid extension to a tab\n delimited file may be 'tab', but also 'txt' because it is a text file as well)\n\nmapping properties\n a simple mapping of key/value pairs used to describe attributes of the file type. These in general\n can have any string as a key, but note that the following keys have been adopted for most file\n types by convention. Note that if these properties are not defined, then they are inherited from\n a parent file_type object\n default-extension - gives the single default extension\n default-web-renderer - the name/id of the widget that should be used by default to view the\n contents of this file type", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The full display name of the file type (e.g. 'Text File', 'HyperText Markup Language File')", + "module" : "FileType", + "name" : "file_type_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short string indicating a possible file extension", + "module" : "FileType", + "name" : "file_extension" + } + }, + "name" : "valid_file_extensions", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "FileType", + "name" : "file_type" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object that encapsulates properties of a file type. Note that unless otherwise stated, any\nmethod which returns a file_type also includes all inhereted valid_file_extensions and properties.\n\nfile_type_id id\n the unique string based id of this file type\n \nfile_type_name name\n the human readable long name of the file type\n\nlist valid_file_extensions\n a list of extensions that are associated with this file type. Note that in some cases this will\n include extensions that are inhereted from parent file types (e.g. a valid extension to a tab\n delimited file may be 'tab', but also 'txt' because it is a text file as well)\n\nmapping properties\n a simple mapping of key/value pairs used to describe attributes of the file type. These in general\n can have any string as a key, but note that the following keys have been adopted for most file\n types by convention. Note that if these properties are not defined, then they are inherited from\n a parent file_type object\n default-extension - gives the single default extension\n default-web-renderer - the name/id of the widget that should be used by default to view the\n contents of this file type", + "module" : "FileType", + "name" : "file_type" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the specified file_type name, or an empty string if file_type_id is not valid.", + "name" : "get_file_type_name", + "parameters" : [ { + "name" : "id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The full display name of the file type (e.g. 'Text File', 'HyperText Markup Language File')", + "module" : "FileType", + "name" : "file_type_name" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the specified file_type names, or an empty string if file_type_id is not valid.", + "name" : "get_file_type_names", + "parameters" : [ { + "name" : "ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The full display name of the file type (e.g. 'Text File', 'HyperText Markup Language File')", + "module" : "FileType", + "name" : "file_type_name" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a default extension for the given filetype.", + "name" : "get_default_extension", + "parameters" : [ { + "name" : "id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short string indicating a possible file extension", + "module" : "FileType", + "name" : "file_extension" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a default extensions for the given filetypes.", + "name" : "get_default_extensions", + "parameters" : [ { + "name" : "ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short string indicating a possible file extension", + "module" : "FileType", + "name" : "file_extension" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the specified file_type property, or an empty string if file_type_name is not valid\nor the property is undefined. This method also searches any inhereted properties.", + "name" : "get_file_type_property", + "parameters" : [ { + "name" : "id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + }, { + "name" : "key", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the file_type ids of any file types with names that are an exact match ignoring\ncase to the input name. There is no gaurantee that file type names are unique. Note that this\nmethod is generally slow because it must search over every possible file type.", + "name" : "get_file_type_id_by_full_name", + "parameters" : [ { + "name" : "name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The full display name of the file type (e.g. 'Text File', 'HyperText Markup Language File')", + "module" : "FileType", + "name" : "file_type_name" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given an extension, get a list of possible file types that could apply, including any file_types\nthat inheret this extension from parent file types.", + "name" : "get_possible_file_type_by_extension", + "parameters" : [ { + "name" : "extension", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short string indicating a possible file extension", + "module" : "FileType", + "name" : "file_extension" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given an extension, get a list of file types which use this extension as its DEFAULT file type.", + "name" : "get_possible_file_type_by_default_extension", + "parameters" : [ { + "name" : "extension", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short string indicating a possible file extension", + "module" : "FileType", + "name" : "file_extension" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the id of the parent file_type, or-1 if no parent exists or the input file_type_id is not valid.", + "name" : "get_parent", + "parameters" : [ { + "name" : "id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of all children of this file type", + "name" : "get_all_children", + "parameters" : [ { + "name" : "id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the full lineage of the given file_type in order starting from the root, so that the first element\nof the list is the root of the hierarchy, and the last element is the parent of the given file type. Returns\nan empty list if the id is not valid or the id was already the root.", + "name" : "get_ancestry", + "parameters" : [ { + "name" : "id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of all decendents (ordered as a breadth first traversal)", + "name" : "get_all_descendants", + "parameters" : [ { + "name" : "id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns the file type hierarchy as a newick string, which can be parsed and manipulated by\nvarious tree libraries, such as the KBase Phylogenetic Tree services.", + "name" : "dump_file_type_hierarchy_in_newick", + "parameters" : [ ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a pretty string representation of the full hierarchy of every supported file listed by file\ntype id. This should be used for display purposes only!", + "name" : "dump_file_type_hierarchy_pretty", + "parameters" : [ ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of every file type id that is currently defined in alphabetical order", + "name" : "all_file_type_ids", + "parameters" : [ ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Returns a list of every file type id and the value of the associated property. Thus you can\nquickly list all filetypes and, say, a default renderer if defined for each file type.", + "name" : "all_file_type_property", + "parameters" : [ { + "name" : "propertyName", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + } ] + } ], + "module_name" : "FileType", + "options" : [ ], + "service_name" : "FileType" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "file_extension" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short string indicating a possible file extension", + "module" : "FileType", + "name" : "file_extension" + }, + "file_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "An object that encapsulates properties of a file type. Note that unless otherwise stated, any\nmethod which returns a file_type also includes all inhereted valid_file_extensions and properties.\n\nfile_type_id id\n the unique string based id of this file type\n \nfile_type_name name\n the human readable long name of the file type\n\nlist valid_file_extensions\n a list of extensions that are associated with this file type. Note that in some cases this will\n include extensions that are inhereted from parent file types (e.g. a valid extension to a tab\n delimited file may be 'tab', but also 'txt' because it is a text file as well)\n\nmapping properties\n a simple mapping of key/value pairs used to describe attributes of the file type. These in general\n can have any string as a key, but note that the following keys have been adopted for most file\n types by convention. Note that if these properties are not defined, then they are inherited from\n a parent file_type object\n default-extension - gives the single default extension\n default-web-renderer - the name/id of the widget that should be used by default to view the\n contents of this file type", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The full display name of the file type (e.g. 'Text File', 'HyperText Markup Language File')", + "module" : "FileType", + "name" : "file_type_name" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A short string indicating a possible file extension", + "module" : "FileType", + "name" : "file_extension" + } + }, + "name" : "valid_file_extensions", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "properties", + "nullable" : "0" + } ], + "module" : "FileType", + "name" : "file_type" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "An object that encapsulates properties of a file type. Note that unless otherwise stated, any\nmethod which returns a file_type also includes all inhereted valid_file_extensions and properties.\n\nfile_type_id id\n the unique string based id of this file type\n \nfile_type_name name\n the human readable long name of the file type\n\nlist valid_file_extensions\n a list of extensions that are associated with this file type. Note that in some cases this will\n include extensions that are inhereted from parent file types (e.g. a valid extension to a tab\n delimited file may be 'tab', but also 'txt' because it is a text file as well)\n\nmapping properties\n a simple mapping of key/value pairs used to describe attributes of the file type. These in general\n can have any string as a key, but note that the following keys have been adopted for most file\n types by convention. Note that if these properties are not defined, then they are inherited from\n a parent file_type object\n default-extension - gives the single default extension\n default-web-renderer - the name/id of the widget that should be used by default to view the\n contents of this file type", + "module" : "FileType", + "name" : "file_type" + }, + "file_type_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The unique ID of a file type, which cannot contain any spaces (e.g. file, text, html)", + "module" : "FileType", + "name" : "file_type_id" + }, + "file_type_name" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "The full display name of the file type (e.g. 'Text File', 'HyperText Markup Language File')", + "module" : "FileType", + "name" : "file_type_name" + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.5.json.properties b/src/test/resources/us/kbase/test/kidl/spec.5.json.properties new file mode 100644 index 0000000..97a899c --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.5.json.properties @@ -0,0 +1,12961 @@ +{ + "GenomeAnnotation" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "API Access to the Genome Annotation Service.\n\nProvides support for gene calling, functional annotation, re-annotation. Use to extract annotation in\nformation about an existing genome, or to create new annotations.", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "md5" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "md5" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "md5s" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "genome_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "annotation" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : 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By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "function" + } ], + "name" : "fid_data_tuple" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid_data_tuple" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "md5" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "function" + } ], + "name" : "fid_data_tuple" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid_data_tuple" + } + }, + "annotations" : { + 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"Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "dna", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "contig" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Data for DNA contig", + "module" : "GenomeAnnotation", + "name" : "contig" + } + }, + "name" : "contigs", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : 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"element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "annotation" + } + }, + "name" : "annotations", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "module" : "GenomeAnnotation", + "name" : "feature" + } + }, + "name" : "features", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "genomeTO" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "All of the information about particular genome", + "module" : "GenomeAnnotation", + "name" : "genomeTO" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Metabolic reconstruction\nrepresents the set of subsystems that we infer are present in this genome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : 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By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "function", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_translation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "aliases", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "annotation" + } + }, + "name" : "annotations", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "module" : "GenomeAnnotation", + "name" : "feature" + } + }, + "name" : "features", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "genomeTO" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "All of the information about particular genome", + "module" : "GenomeAnnotation", + "name" : "genomeTO" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "md5" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". 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By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "function" + } ], + "name" : "fid_data_tuple" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid_data_tuple" + } + }, + "annotations" : { + 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Be warned.", + "name" : "annotate_genome", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "All of the information about particular genome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "genome_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "scientific_name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "genetic_code", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Data for DNA contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "dna", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "contig" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Data for DNA contig", + "module" : "GenomeAnnotation", + "name" : "contig" + } + }, + "name" : "contigs", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : 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annoation in style of SEED", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : 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By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : 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By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "function", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_translation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "aliases", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "annotation" + } + }, + "name" : "annotations", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "module" : "GenomeAnnotation", + "name" : "feature" + } + }, + "name" : "features", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "genomeTO" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "All of the information about particular genome", + "module" : "GenomeAnnotation", + "name" : "genomeTO" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "All of the information about particular genome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + 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"Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "dna", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "contig" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Data for DNA contig", + "module" : "GenomeAnnotation", + "name" : "contig" + } + }, + "name" : "contigs", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "function", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_translation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "aliases", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "annotation" + } + }, + "name" : "annotations", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "module" : "GenomeAnnotation", + "name" : "feature" + } + }, + "name" : "features", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "genomeTO" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "All of the information about particular genome", + "module" : "GenomeAnnotation", + "name" : "genomeTO" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "* Given a genome object populated with feature data, reannotate\n* the features that have protein translations. Return the updated\n* genome object.", + "name" : "annotate_proteins", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "All of the information about particular genome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "genome_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "scientific_name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "domain", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "genetic_code", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "source_id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Data for DNA contig", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "dna", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "contig" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Data for DNA contig", + "module" : "GenomeAnnotation", + "name" : "contig" + } + }, + "name" : "contigs", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_id" + }, + "name" : "id", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : 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\"a region\". 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By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : 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By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : 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By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : 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By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "function" + } ], + "name" : "fid_data_tuple" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid_data_tuple" + }, + "fid_data_tuples" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "md5" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "function" + } ], + "name" : "fid_data_tuple" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid_data_tuple" + } + }, + "annotations" : { + 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{ + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "name" : "location", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "feature_type" + }, + "name" : "type", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "function", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "protein_translation", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "aliases", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "comment", "annotator", "annotation_time" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "annotation" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "annotation" + } + }, + "name" : "annotations", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "feature" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "represents a feature on the genome\nlocation on the contig with a type,\nand if a protein has translation,\nany aliases associated\ncurrent history of annoation in style of SEED", + "module" : "GenomeAnnotation", + "name" : "feature" + } + }, + "name" : "features", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "genomeTO" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "All of the information about particular genome", + "module" : "GenomeAnnotation", + "name" : "genomeTO" + }, + "genome_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "genome_id" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "location" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "a \"location\" refers to a sequence of regions", + "module" : "GenomeAnnotation", + "name" : "location" + }, + "md5" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "md5" + }, + "md5s" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "md5" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "md5s" + }, + "reconstructionTO" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "Metabolic reconstruction\nrepresents the set of subsystems that we infer are present in this genome", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "subsystem" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "variant" + } ], + "name" : "variant_of_subsystem" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "variant_of_subsystem" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "variant_subsystem_pairs" + }, + "name" : "subsystems", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "role" + } ], + "name" : "fid_role_pair" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid_role_pair" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid_role_pairs" + }, + "name" : "bindings", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "function" + } ], + "name" : "fid_function_pair" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid_function_pair" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "fid_function_pairs" + }, + "name" : "assignments", + "nullable" : "0" + } ], + "module" : "GenomeAnnotation", + "name" : "reconstructionTO" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Metabolic reconstruction\nrepresents the set of subsystems that we infer are present in this genome", + "module" : "GenomeAnnotation", + "name" : "reconstructionTO" + }, + "region_of_dna" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "element_names" : [ "e_1", "begin", "strand", "length" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "contig_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ], + "name" : "region_of_dna" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A region of DNA is maintained as a tuple of four components:\n\n the contig\n the beginning position (from 1)\n the strand\n the length\n\n We often speak of \"a region\". By \"location\", we mean a sequence\n of regions from the same genome (perhaps from distinct contigs).", + "module" : "GenomeAnnotation", + "name" : "region_of_dna" + }, + "role" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "role" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "subsystem" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "subsystem" + }, + "variant" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "variant" + }, + "variant_of_subsystem" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "subsystem" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "variant" + } ], + "name" : "variant_of_subsystem" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "variant_of_subsystem" + }, + "variant_subsystem_pairs" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "subsystem" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "variant" + } ], + "name" : "variant_of_subsystem" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "variant_of_subsystem" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "GenomeAnnotation", + "name" : "variant_subsystem_pairs" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.5.properties b/src/test/resources/us/kbase/test/kidl/spec.5.properties index f67202e..4498a26 100644 --- a/src/test/resources/us/kbase/test/kidl/spec.5.properties +++ b/src/test/resources/us/kbase/test/kidl/spec.5.properties @@ -100,7 +100,7 @@ module GenomeAnnotation /* * Given a genome object populated with contig data, perform gene calling * and functional annotation and return the annotated genome. - * + * * NOTE: Many of these "transformations" modify the input hash and * copy the pointer. Be warned. */ diff --git a/src/test/resources/us/kbase/test/kidl/spec.6.json.properties b/src/test/resources/us/kbase/test/kidl/spec.6.json.properties new file mode 100644 index 0000000..6a3b5d7 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.6.json.properties @@ -0,0 +1,3614 @@ +{ + "Genotype_PhenotypeAPI" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of genome eg. kb|g.3899", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_genome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "genome name eg. Arabidopsis thaliana", + "module" : "Genotype_PhenotypeAPI", + "name" : "genome_name" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the experiment eg. kb|g.3899.exp.1", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_study_experiment" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Design information about the experiment eg. SNP Array chip or resequencing experiment eg. ~250K SNPs x 107 phenotpes", + "module" : "Genotype_PhenotypeAPI", + "name" : "design_experiment" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Name of the individual or program that are the originators of the experiment eg. 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TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "position is the location of variant on the chromosome", + "module" : "Genotype_PhenotypeAPI", + "name" : "position" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosomal positions: list of positions define by tuple chromosome, position; position can be from several different chromosomes", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosomal_positions" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosome is the source id (eg. TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "start is the start position of chromosomal location", + "module" : "Genotype_PhenotypeAPI", + "name" : "start" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "end is the end position of chromosomal location", + "module" : "Genotype_PhenotypeAPI", + "name" : "end" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosomal locations: chromosome start end", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosomal_locations" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "pvaluecutoff" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait_list_pvalue:List of traits and pvalue", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait_list_pvalue" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "kbase_gene" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "source id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of genes", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene_list" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "phenotype/trait measurement protocol", + "module" : "Genotype_PhenotypeAPI", + "name" : "protocol" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait ontology", + "module" : "Genotype_PhenotypeAPI", + "name" : "to_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "unit of measurement of a phenotype/trait", + "module" : "Genotype_PhenotypeAPI", + "name" : "unit_of_measure" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "experiment_details: kb_study_experiment, experiment design, orginator", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait_metadata" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "kbase_gene" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "source id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of genes", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene_list" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trait details and list of genes", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene_list_with_trait_metadata" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of genome eg. kb|g.3899", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_genome" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of genomes", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_genome_list" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "get genomes with trait/phenotype data", + "name" : "genomes_with_trait", + "parameters" : [ ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of genome eg. kb|g.3899", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_genome" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of genomes", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_genome_list" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "get all experiments corresponding to a genome.", + "name" : "get_experiments", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of genome eg. kb|g.3899", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_genome" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the experiment eg. kb|g.3899.exp.1", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_study_experiment" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Design information about the experiment eg. SNP Array chip or resequencing experiment eg. ~250K SNPs x 107 phenotpes", + "module" : "Genotype_PhenotypeAPI", + "name" : "design_experiment" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Name of the individual or program that are the originators of the experiment eg. Atwell S, et. al.", + "module" : "Genotype_PhenotypeAPI", + "name" : "originator" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "experiment_details: kb_study_experiment, experiment design, orginator", + "module" : "Genotype_PhenotypeAPI", + "name" : "experiment_details" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "get list of traits in an experiment", + "name" : "get_traits", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the experiment eg. kb|g.3899.exp.1", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_study_experiment" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "phenotype/trait measurement protocol", + "module" : "Genotype_PhenotypeAPI", + "name" : "protocol" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait ontology", + "module" : "Genotype_PhenotypeAPI", + "name" : "to_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "unit of measurement of a phenotype/trait", + "module" : "Genotype_PhenotypeAPI", + "name" : "unit_of_measure" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "experiment_details: kb_study_experiment, experiment design, orginator", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait_metadata" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a trait id and pvalue cutoff, the trait metadata and significant variations above the pvalue cutoff", + "name" : "traits_to_variations", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "pvaluecutoff" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "phenotype/trait measurement protocol", + "module" : "Genotype_PhenotypeAPI", + "name" : "protocol" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait ontology", + "module" : "Genotype_PhenotypeAPI", + "name" : "to_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "unit of measurement of a phenotype/trait", + "module" : "Genotype_PhenotypeAPI", + "name" : "unit_of_measure" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "experiment_details: kb_study_experiment, experiment design, orginator", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait_metadata" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosome is the source id (eg. TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "position is the location of variant on the chromosome", + "module" : "Genotype_PhenotypeAPI", + "name" : "position" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "pvalue" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kb_chromosome is the kbase id of the chromosome eg. kb|g.22476.c.2496", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_chromosome" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "variation_details has the output for manhattan plot", + "module" : "Genotype_PhenotypeAPI", + "name" : "variation_details" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "variation_details with trait metadata", + "module" : "Genotype_PhenotypeAPI", + "name" : "variation_details_with_trait_metadata" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "variation details is a data structure with 4 columns, this function converts it into 2 columns for use in other functions", + "name" : "chromosome_position_from_variation_details", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosome is the source id (eg. TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "position is the location of variant on the chromosome", + "module" : "Genotype_PhenotypeAPI", + "name" : "position" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "pvalue" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kb_chromosome is the kbase id of the chromosome eg. kb|g.22476.c.2496", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_chromosome" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "variation_details has the output for manhattan plot", + "module" : "Genotype_PhenotypeAPI", + "name" : "variation_details" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosome is the source id (eg. TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "position is the location of variant on the chromosome", + "module" : "Genotype_PhenotypeAPI", + "name" : "position" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosomal positions: list of positions define by tuple chromosome, position; position can be from several different chromosomes", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosomal_positions" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a trait, directly get the trait metadata and gene list.", + "name" : "traits_to_genes", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "pvaluecutoff" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "distance" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "phenotype/trait measurement protocol", + "module" : "Genotype_PhenotypeAPI", + "name" : "protocol" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait ontology", + "module" : "Genotype_PhenotypeAPI", + "name" : "to_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "unit of measurement of a phenotype/trait", + "module" : "Genotype_PhenotypeAPI", + "name" : "unit_of_measure" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "experiment_details: kb_study_experiment, experiment design, orginator", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait_metadata" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "kbase_gene" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "source id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of genes", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene_list" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trait details and list of genes", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene_list_with_trait_metadata" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a set of variations (genomic locations), identify the genes near the variations", + "name" : "variations_to_genes", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosome is the source id (eg. TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "position is the location of variant on the chromosome", + "module" : "Genotype_PhenotypeAPI", + "name" : "position" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosomal positions: list of positions define by tuple chromosome, position; position can be from several different chromosomes", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosomal_positions" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "distance" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "kbase_gene" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "source id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of genes", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene_list" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a set of traits, identify variants that are common to those traits above a certain pvalue cutoff", + "name" : "find_common_snps", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "pvaluecutoff" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait_list_pvalue:List of traits and pvalue", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait_list_pvalue" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosome is the source id (eg. TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "position is the location of variant on the chromosome", + "module" : "Genotype_PhenotypeAPI", + "name" : "position" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosomal positions: list of positions define by tuple chromosome, position; position can be from several different chromosomes", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosomal_positions" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given pvalue range, list of chromosomal positions, and distance, this function find snp’s with pvalue within the given pvalue range. It then identifies genes within given distance and return list of genes. This function is written to take selection from manhattan plot as input and feed results to other widget", + "name" : "selected_locations_to_genes", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "pmin is minimum selected pvalue", + "module" : "Genotype_PhenotypeAPI", + "name" : "pmin" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "pmax is maximum selected pvalue", + "module" : "Genotype_PhenotypeAPI", + "name" : "pmax" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosome is the source id (eg. TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "start is the start position of chromosomal location", + "module" : "Genotype_PhenotypeAPI", + "name" : "start" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "end is the end position of chromosomal location", + "module" : "Genotype_PhenotypeAPI", + "name" : "end" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosomal locations: chromosome start end", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosomal_locations" + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "distance" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "kbase_gene" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "source id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of genes", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene_list" + } + } ] + } ], + "module_name" : "Genotype_PhenotypeAPI", + "options" : [ ], + "service_name" : "Genotype_PhenotypeAPI" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "chromosomal_locations" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosome is the source id (eg. TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "start is the start position of chromosomal location", + "module" : "Genotype_PhenotypeAPI", + "name" : "start" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "end is the end position of chromosomal location", + "module" : "Genotype_PhenotypeAPI", + "name" : "end" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosomal locations: chromosome start end", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosomal_locations" + }, + "chromosomal_positions" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosome is the source id (eg. TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "position is the location of variant on the chromosome", + "module" : "Genotype_PhenotypeAPI", + "name" : "position" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosomal positions: list of positions define by tuple chromosome, position; position can be from several different chromosomes", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosomal_positions" + }, + "chromosome" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosome is the source id (eg. TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, + "design_experiment" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Design information about the experiment eg. SNP Array chip or resequencing experiment eg. ~250K SNPs x 107 phenotpes", + "module" : "Genotype_PhenotypeAPI", + "name" : "design_experiment" + }, + "distance" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "distance" + }, + "end" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "end is the end position of chromosomal location", + "module" : "Genotype_PhenotypeAPI", + "name" : "end" + }, + "experiment_details" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the experiment eg. kb|g.3899.exp.1", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_study_experiment" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Design information about the experiment eg. SNP Array chip or resequencing experiment eg. ~250K SNPs x 107 phenotpes", + "module" : "Genotype_PhenotypeAPI", + "name" : "design_experiment" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Name of the individual or program that are the originators of the experiment eg. Atwell S, et. al.", + "module" : "Genotype_PhenotypeAPI", + "name" : "originator" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "experiment_details: kb_study_experiment, experiment design, orginator", + "module" : "Genotype_PhenotypeAPI", + "name" : "experiment_details" + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "gene" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "source id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene" + }, + "gene_list" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "kbase_gene" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "source id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of genes", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene_list" + }, + "gene_list_with_trait_metadata" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "phenotype/trait measurement protocol", + "module" : "Genotype_PhenotypeAPI", + "name" : "protocol" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait ontology", + "module" : "Genotype_PhenotypeAPI", + "name" : "to_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "unit of measurement of a phenotype/trait", + "module" : "Genotype_PhenotypeAPI", + "name" : "unit_of_measure" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "experiment_details: kb_study_experiment, experiment design, orginator", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait_metadata" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "kbase_gene" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "source id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of genes", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene_list" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Trait details and list of genes", + "module" : "Genotype_PhenotypeAPI", + "name" : "gene_list_with_trait_metadata" + }, + "genome_name" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "genome name eg. Arabidopsis thaliana", + "module" : "Genotype_PhenotypeAPI", + "name" : "genome_name" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "kb_chromosome" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kb_chromosome is the kbase id of the chromosome eg. kb|g.22476.c.2496", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_chromosome" + }, + "kb_genome" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of genome eg. kb|g.3899", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_genome" + }, + "kb_genome_list" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of genome eg. kb|g.3899", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_genome" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "list of genomes", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_genome_list" + }, + "kb_study_experiment" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the experiment eg. kb|g.3899.exp.1", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_study_experiment" + }, + "kbase_gene" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kbase id of the gene", + "module" : "Genotype_PhenotypeAPI", + "name" : "kbase_gene" + }, + "originator" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Name of the individual or program that are the originators of the experiment eg. Atwell S, et. al.", + "module" : "Genotype_PhenotypeAPI", + "name" : "originator" + }, + "pmax" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "pmax is maximum selected pvalue", + "module" : "Genotype_PhenotypeAPI", + "name" : "pmax" + }, + "pmin" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "pmin is minimum selected pvalue", + "module" : "Genotype_PhenotypeAPI", + "name" : "pmin" + }, + "position" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "position is the location of variant on the chromosome", + "module" : "Genotype_PhenotypeAPI", + "name" : "position" + }, + "protocol" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "phenotype/trait measurement protocol", + "module" : "Genotype_PhenotypeAPI", + "name" : "protocol" + }, + "pvalue" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "pvalue" + }, + "pvaluecutoff" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "pvaluecutoff" + }, + "rankcutoff" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "rankcutoff" + }, + "region" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "region" + }, + "start" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "start is the start position of chromosomal location", + "module" : "Genotype_PhenotypeAPI", + "name" : "start" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "to_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait ontology", + "module" : "Genotype_PhenotypeAPI", + "name" : "to_id" + }, + "trait" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + }, + "trait_list_pvalue" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "pvaluecutoff" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait_list_pvalue:List of traits and pvalue", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait_list_pvalue" + }, + "trait_metadata" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "phenotype/trait measurement protocol", + "module" : "Genotype_PhenotypeAPI", + "name" : "protocol" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait ontology", + "module" : "Genotype_PhenotypeAPI", + "name" : "to_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "unit of measurement of a phenotype/trait", + "module" : "Genotype_PhenotypeAPI", + "name" : "unit_of_measure" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "experiment_details: kb_study_experiment, experiment design, orginator", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait_metadata" + }, + "unit_of_measure" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "unit of measurement of a phenotype/trait", + "module" : "Genotype_PhenotypeAPI", + "name" : "unit_of_measure" + }, + "variation_details" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosome is the source id (eg. TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "position is the location of variant on the chromosome", + "module" : "Genotype_PhenotypeAPI", + "name" : "position" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "pvalue" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kb_chromosome is the kbase id of the chromosome eg. kb|g.22476.c.2496", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_chromosome" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "variation_details has the output for manhattan plot", + "module" : "Genotype_PhenotypeAPI", + "name" : "variation_details" + }, + "variation_details_with_trait_metadata" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait is the kbase id of the trait. kb|g.3899.trait.191", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "phenotype/trait measurement protocol", + "module" : "Genotype_PhenotypeAPI", + "name" : "protocol" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "trait ontology", + "module" : "Genotype_PhenotypeAPI", + "name" : "to_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "unit of measurement of a phenotype/trait", + "module" : "Genotype_PhenotypeAPI", + "name" : "unit_of_measure" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "experiment_details: kb_study_experiment, experiment design, orginator", + "module" : "Genotype_PhenotypeAPI", + "name" : "trait_metadata" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3", "e_4" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "chromosome is the source id (eg. TAIR id) of the chromosome eg. 1", + "module" : "Genotype_PhenotypeAPI", + "name" : "chromosome" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "position is the location of variant on the chromosome", + "module" : "Genotype_PhenotypeAPI", + "name" : "position" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Genotype_PhenotypeAPI", + "name" : "pvalue" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "kb_chromosome is the kbase id of the chromosome eg. kb|g.22476.c.2496", + "module" : "Genotype_PhenotypeAPI", + "name" : "kb_chromosome" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "variation_details has the output for manhattan plot", + "module" : "Genotype_PhenotypeAPI", + "name" : "variation_details" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "variation_details with trait metadata", + "module" : "Genotype_PhenotypeAPI", + "name" : "variation_details_with_trait_metadata" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.6.properties b/src/test/resources/us/kbase/test/kidl/spec.6.properties old mode 100755 new mode 100644 diff --git a/src/test/resources/us/kbase/test/kidl/spec.7.json.properties b/src/test/resources/us/kbase/test/kidl/spec.7.json.properties new file mode 100644 index 0000000..d5b5359 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.7.json.properties @@ -0,0 +1,551 @@ +{ + "IDServerAPI" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "The KBase ID server provides access to the mappings between KBase identifiers and\nexternal identifiers (the original identifiers for data that was migrated from\nother databases into KBase).", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\".\n\nKBase IDs are typed. The types are designated using a short string. For instance,\n\"g\" denotes a genome, \"fp\" denotes a feature representing a protein-encoding gene, etc.\n\nKBase IDs may be hierarchical. If a KBase genome identifier is \"kb|g.1234\", a protein\nwithin that genome may be represented as \"kb|g.1234.fp.771\".", + "module" : "IDServerAPI", + "name" : "kbase_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Each external database is represented using a short string. Microbes Online is \"MOL\",\nthe SEED is \"SEED\", etc.", + "module" : "IDServerAPI", + "name" : "external_db" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "External database identifiers are strings. They are the precise identifier used\nby that database. It is important to note that if a database uses the same \nidentifier space for more than one data type (for instance, if integers are used for\nidentifying both genomes and genes, and if the same number is valid for both a\ngenome and a gene) then the distinction must be made by using separate exgternal database\nstrings for the different types; e.g. DBNAME-GENE and DBNAME-GENOME for a \ndatabase DBNAME that has overlapping namespace for genes and genomes).", + "module" : "IDServerAPI", + "name" : "external_id" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase identifier prefix. This is a string that starts with \"kb|\" and includes either a\nsingle type designator (e.g. \"kb|g\") or is a prefix for a hierarchical identifier (e.g.\n\"kb|g.1234.fp\").", + "module" : "IDServerAPI", + "name" : "kbase_id_prefix" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a set of KBase identifiers, look up the associated external identifiers.\nIf no external ID is associated with the KBase id, no entry will be present in the return.", + "name" : "kbase_ids_to_external_ids", + "parameters" : [ { + "name" : "ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\".\n\nKBase IDs are typed. The types are designated using a short string. For instance,\n\"g\" denotes a genome, \"fp\" denotes a feature representing a protein-encoding gene, etc.\n\nKBase IDs may be hierarchical. If a KBase genome identifier is \"kb|g.1234\", a protein\nwithin that genome may be represented as \"kb|g.1234.fp.771\".", + "module" : "IDServerAPI", + "name" : "kbase_id" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\".\n\nKBase IDs are typed. The types are designated using a short string. For instance,\n\"g\" denotes a genome, \"fp\" denotes a feature representing a protein-encoding gene, etc.\n\nKBase IDs may be hierarchical. If a KBase genome identifier is \"kb|g.1234\", a protein\nwithin that genome may be represented as \"kb|g.1234.fp.771\".", + "module" : "IDServerAPI", + "name" : "kbase_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Each external database is represented using a short string. Microbes Online is \"MOL\",\nthe SEED is \"SEED\", etc.", + "module" : "IDServerAPI", + "name" : "external_db" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "External database identifiers are strings. They are the precise identifier used\nby that database. It is important to note that if a database uses the same \nidentifier space for more than one data type (for instance, if integers are used for\nidentifying both genomes and genes, and if the same number is valid for both a\ngenome and a gene) then the distinction must be made by using separate exgternal database\nstrings for the different types; e.g. DBNAME-GENE and DBNAME-GENOME for a \ndatabase DBNAME that has overlapping namespace for genes and genomes).", + "module" : "IDServerAPI", + "name" : "external_id" + } ] + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Given a set of external identifiers, look up the associated KBase identifiers.\nIf no KBase ID is associated with the external id, no entry will be present in the return.", + "name" : "external_ids_to_kbase_ids", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Each external database is represented using a short string. Microbes Online is \"MOL\",\nthe SEED is \"SEED\", etc.", + "module" : "IDServerAPI", + "name" : "external_db" + } + }, { + "name" : "ext_ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "External database identifiers are strings. They are the precise identifier used\nby that database. It is important to note that if a database uses the same \nidentifier space for more than one data type (for instance, if integers are used for\nidentifying both genomes and genes, and if the same number is valid for both a\ngenome and a gene) then the distinction must be made by using separate exgternal database\nstrings for the different types; e.g. DBNAME-GENE and DBNAME-GENOME for a \ndatabase DBNAME that has overlapping namespace for genes and genomes).", + "module" : "IDServerAPI", + "name" : "external_id" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "External database identifiers are strings. They are the precise identifier used\nby that database. It is important to note that if a database uses the same \nidentifier space for more than one data type (for instance, if integers are used for\nidentifying both genomes and genes, and if the same number is valid for both a\ngenome and a gene) then the distinction must be made by using separate exgternal database\nstrings for the different types; e.g. DBNAME-GENE and DBNAME-GENOME for a \ndatabase DBNAME that has overlapping namespace for genes and genomes).", + "module" : "IDServerAPI", + "name" : "external_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\".\n\nKBase IDs are typed. The types are designated using a short string. For instance,\n\"g\" denotes a genome, \"fp\" denotes a feature representing a protein-encoding gene, etc.\n\nKBase IDs may be hierarchical. If a KBase genome identifier is \"kb|g.1234\", a protein\nwithin that genome may be represented as \"kb|g.1234.fp.771\".", + "module" : "IDServerAPI", + "name" : "kbase_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Register a set of identifiers. All will be assigned identifiers with the given\nprefix.\n\nIf an external ID has already been registered, the existing registration will be returned instead \nof a new ID being allocated.", + "name" : "register_ids", + "parameters" : [ { + "name" : "prefix", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase identifier prefix. This is a string that starts with \"kb|\" and includes either a\nsingle type designator (e.g. \"kb|g\") or is a prefix for a hierarchical identifier (e.g.\n\"kb|g.1234.fp\").", + "module" : "IDServerAPI", + "name" : "kbase_id_prefix" + } + }, { + "name" : "db_name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Each external database is represented using a short string. Microbes Online is \"MOL\",\nthe SEED is \"SEED\", etc.", + "module" : "IDServerAPI", + "name" : "external_db" + } + }, { + "name" : "ids", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "External database identifiers are strings. They are the precise identifier used\nby that database. It is important to note that if a database uses the same \nidentifier space for more than one data type (for instance, if integers are used for\nidentifying both genomes and genes, and if the same number is valid for both a\ngenome and a gene) then the distinction must be made by using separate exgternal database\nstrings for the different types; e.g. DBNAME-GENE and DBNAME-GENOME for a \ndatabase DBNAME that has overlapping namespace for genes and genomes).", + "module" : "IDServerAPI", + "name" : "external_id" + } + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "External database identifiers are strings. They are the precise identifier used\nby that database. It is important to note that if a database uses the same \nidentifier space for more than one data type (for instance, if integers are used for\nidentifying both genomes and genes, and if the same number is valid for both a\ngenome and a gene) then the distinction must be made by using separate exgternal database\nstrings for the different types; e.g. DBNAME-GENE and DBNAME-GENOME for a \ndatabase DBNAME that has overlapping namespace for genes and genomes).", + "module" : "IDServerAPI", + "name" : "external_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\".\n\nKBase IDs are typed. The types are designated using a short string. For instance,\n\"g\" denotes a genome, \"fp\" denotes a feature representing a protein-encoding gene, etc.\n\nKBase IDs may be hierarchical. If a KBase genome identifier is \"kb|g.1234\", a protein\nwithin that genome may be represented as \"kb|g.1234.fp.771\".", + "module" : "IDServerAPI", + "name" : "kbase_id" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Allocate a set of identifiers. This allows efficient registration of a large\nnumber of identifiers (e.g. several thousand features in a genome).\n\nThe return is the first identifier allocated.", + "name" : "allocate_id_range", + "parameters" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase identifier prefix. This is a string that starts with \"kb|\" and includes either a\nsingle type designator (e.g. \"kb|g\") or is a prefix for a hierarchical identifier (e.g.\n\"kb|g.1234.fp\").", + "module" : "IDServerAPI", + "name" : "kbase_id_prefix" + } + }, { + "name" : "count", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + } ], + "return_type" : [ { + "name" : "starting_value", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "none", + "comment" : "Register the mappings for a set of external identifiers. The\nKBase identifiers used here were previously allocated using allocate_id_range.\n\nDoes not return a value.", + "name" : "register_allocated_ids", + "parameters" : [ { + "name" : "prefix", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase identifier prefix. This is a string that starts with \"kb|\" and includes either a\nsingle type designator (e.g. \"kb|g\") or is a prefix for a hierarchical identifier (e.g.\n\"kb|g.1234.fp\").", + "module" : "IDServerAPI", + "name" : "kbase_id_prefix" + } + }, { + "name" : "db_name", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Each external database is represented using a short string. Microbes Online is \"MOL\",\nthe SEED is \"SEED\", etc.", + "module" : "IDServerAPI", + "name" : "external_db" + } + }, { + "name" : "assignments", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "External database identifiers are strings. They are the precise identifier used\nby that database. It is important to note that if a database uses the same \nidentifier space for more than one data type (for instance, if integers are used for\nidentifying both genomes and genes, and if the same number is valid for both a\ngenome and a gene) then the distinction must be made by using separate exgternal database\nstrings for the different types; e.g. DBNAME-GENE and DBNAME-GENOME for a \ndatabase DBNAME that has overlapping namespace for genes and genomes).", + "module" : "IDServerAPI", + "name" : "external_id" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + } + } ], + "return_type" : [ ] + } ], + "module_name" : "IDServerAPI", + "options" : [ ], + "service_name" : "IDServerAPI" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "external_db" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Each external database is represented using a short string. Microbes Online is \"MOL\",\nthe SEED is \"SEED\", etc.", + "module" : "IDServerAPI", + "name" : "external_db" + }, + "external_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "External database identifiers are strings. They are the precise identifier used\nby that database. It is important to note that if a database uses the same \nidentifier space for more than one data type (for instance, if integers are used for\nidentifying both genomes and genes, and if the same number is valid for both a\ngenome and a gene) then the distinction must be made by using separate exgternal database\nstrings for the different types; e.g. DBNAME-GENE and DBNAME-GENOME for a \ndatabase DBNAME that has overlapping namespace for genes and genomes).", + "module" : "IDServerAPI", + "name" : "external_id" + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "kbase_id" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase ID is a string starting with the characters \"kb|\".\n\nKBase IDs are typed. The types are designated using a short string. For instance,\n\"g\" denotes a genome, \"fp\" denotes a feature representing a protein-encoding gene, etc.\n\nKBase IDs may be hierarchical. If a KBase genome identifier is \"kb|g.1234\", a protein\nwithin that genome may be represented as \"kb|g.1234.fp.771\".", + "module" : "IDServerAPI", + "name" : "kbase_id" + }, + "kbase_id_prefix" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "A KBase identifier prefix. This is a string that starts with \"kb|\" and includes either a\nsingle type designator (e.g. \"kb|g\") or is a prefix for a hierarchical identifier (e.g.\n\"kb|g.1234.fp\").", + "module" : "IDServerAPI", + "name" : "kbase_id_prefix" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.8.json.properties b/src/test/resources/us/kbase/test/kidl/spec.8.json.properties new file mode 100644 index 0000000..37d4fab --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.8.json.properties @@ -0,0 +1,1260 @@ +{ + "InvocationService" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "* The Invocation Service provides a mechanism by which KBase clients may\n* invoke command-line programs hosted on the KBase infrastructure. \n* \n* The service provides a simple directory structure for storage of intermediate\n* files, and exposes a limited set of shell command functionality.", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* A directory entry. Used as the return from list_files.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "full_path", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "mod_date", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "directory" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* A directory entry. Used as the return from list_files.", + "module" : "InvocationService", + "name" : "directory" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* A file entry. Used as the return from list_files.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "full_path", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "mod_date", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "size", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "file" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* A file entry. Used as the return from list_files.", + "module" : "InvocationService", + "name" : "file" + }, "auth_defaultoptional", { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Begin a new session. A session_id is an uninterpreted string that\n* identifies a workspace with in the Invocation Service, and serves to\n* scope the data stored in that workspace.\n* \n* If start_session is invoked with valid authentication (via the standard\n* KBase authentication mechanisms), the session_id is ignored, and an\n* empty session_id returned. Throughout this service interface, if\n* any call is made using authentication the given session_id will be ignored.", + "name" : "start_session", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "name" : "actual_session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Enumerate the files in the session, assuming the current working\n* directory is cwd, and the filename to be listed is d. Think of this\n* as the equivalent of \"cd $cwd; ls $d\".", + "name" : "list_files", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "cwd", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "d", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* A directory entry. Used as the return from list_files.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "full_path", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "mod_date", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "directory" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* A directory entry. Used as the return from list_files.", + "module" : "InvocationService", + "name" : "directory" + } + } + }, { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* A file entry. Used as the return from list_files.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "full_path", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "mod_date", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "size", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "file" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* A file entry. Used as the return from list_files.", + "module" : "InvocationService", + "name" : "file" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Remove the given file from the given directory.", + "name" : "remove_files", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "cwd", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "filename", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Rename the given file.", + "name" : "rename_file", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "cwd", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "from", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "to", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Copy the given file to the given destination.", + "name" : "copy", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "cwd", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "from", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "to", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Create a new directory.", + "name" : "make_directory", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "cwd", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "directory", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Remove a directory.", + "name" : "remove_directory", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "cwd", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "directory", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Change to the given directory. Returns the new cwd.", + "name" : "change_directory", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "cwd", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "directory", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Write contents to the given file.", + "name" : "put_file", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "filename", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "contents", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "cwd", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Retrieve the contents of the given file.", + "name" : "get_file", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "filename", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "cwd", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "name" : "contents", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Run the given command pipeline. Returns the stdout and stderr for the pipeline.\n* \n* If max_output_size is greater than zero, limits the output of the command\n* to max_output_size lines.", + "name" : "run_pipeline", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "pipeline", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "input", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "max_output_size", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, { + "name" : "cwd", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "name" : "output", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "errors", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Experimental routine.", + "name" : "run_pipeline2", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "pipeline", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "input", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "max_output_size", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, { + "name" : "cwd", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ { + "name" : "output", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "errors", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } + }, { + "name" : "stdweb", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Exit the session.", + "name" : "exit_session", + "parameters" : [ { + "name" : "session_id", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ], + "return_type" : [ ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* Description of a command. Contains the command name and a link to documentation.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "cmd", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "link", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "command_desc" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Description of a command. Contains the command name and a link to documentation.", + "module" : "InvocationService", + "name" : "command_desc" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* Description of a command group, a set of common commands.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "title", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* Description of a command. Contains the command name and a link to documentation.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "cmd", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "link", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "command_desc" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Description of a command. Contains the command name and a link to documentation.", + "module" : "InvocationService", + "name" : "command_desc" + } + }, + "name" : "items", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "command_group_desc" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Description of a command group, a set of common commands.", + "module" : "InvocationService", + "name" : "command_group_desc" + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Retrieve the set of valid commands.\n* \n* Note that this does not require authentication or a valid session, and thus\n* may be used to set up a graphical interface before a login is done.", + "name" : "valid_commands", + "parameters" : [ ], + "return_type" : [ { + "type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* Description of a command group, a set of common commands.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "title", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* Description of a command. Contains the command name and a link to documentation.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "cmd", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "link", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "command_desc" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Description of a command. Contains the command name and a link to documentation.", + "module" : "InvocationService", + "name" : "command_desc" + } + }, + "name" : "items", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "command_group_desc" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Description of a command group, a set of common commands.", + "module" : "InvocationService", + "name" : "command_group_desc" + } + } + } ] + }, { + "!" : "Bio::KBase::KIDL::KBT::Funcdef", + "annotations" : { + "unknown_annotations" : { } + }, + "authentication" : "optional", + "comment" : "* Retrieve the tutorial text for the given tutorial step, along with the\n* the step numbers for the previous and next steps in the tutorial.", + "name" : "get_tutorial_text", + "parameters" : [ { + "name" : "step", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + } ], + "return_type" : [ { + "name" : "text", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, { + "name" : "prev", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, { + "name" : "next", + "type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + } ] + } ], + "module_name" : "InvocationService", + "options" : [ ], + "service_name" : "InvocationService" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "command_desc" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* Description of a command. Contains the command name and a link to documentation.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "cmd", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "link", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "command_desc" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Description of a command. Contains the command name and a link to documentation.", + "module" : "InvocationService", + "name" : "command_desc" + }, + "command_group_desc" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* Description of a command group, a set of common commands.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "title", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* Description of a command. Contains the command name and a link to documentation.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "cmd", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "link", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "command_desc" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Description of a command. Contains the command name and a link to documentation.", + "module" : "InvocationService", + "name" : "command_desc" + } + }, + "name" : "items", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "command_group_desc" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* Description of a command group, a set of common commands.", + "module" : "InvocationService", + "name" : "command_group_desc" + }, + "directory" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* A directory entry. Used as the return from list_files.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "full_path", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "mod_date", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "directory" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* A directory entry. Used as the return from list_files.", + "module" : "InvocationService", + "name" : "directory" + }, + "file" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "* A file entry. Used as the return from list_files.", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "name", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "full_path", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "mod_date", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "size", + "nullable" : "0" + } ], + "module" : "InvocationService", + "name" : "file" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "* A file entry. Used as the return from list_files.", + "module" : "InvocationService", + "name" : "file" + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.8.properties b/src/test/resources/us/kbase/test/kidl/spec.8.properties index c4b0db9..5f176c7 100644 --- a/src/test/resources/us/kbase/test/kidl/spec.8.properties +++ b/src/test/resources/us/kbase/test/kidl/spec.8.properties @@ -32,7 +32,7 @@ module InvocationService * Begin a new session. A session_id is an uninterpreted string that * identifies a workspace with in the Invocation Service, and serves to * scope the data stored in that workspace. - * + * * If start_session is invoked with valid authentication (via the standard * KBase authentication mechanisms), the session_id is ignored, and an * empty session_id returned. Throughout this service interface, if @@ -89,7 +89,7 @@ module InvocationService /* * Run the given command pipeline. Returns the stdout and stderr for the pipeline. - * + * * If max_output_size is greater than zero, limits the output of the command * to max_output_size lines. */ @@ -126,7 +126,7 @@ module InvocationService /* * Retrieve the set of valid commands. - * + * * Note that this does not require authentication or a valid session, and thus * may be used to set up a graphical interface before a login is done. */ diff --git a/src/test/resources/us/kbase/test/kidl/spec.i1.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i1.json.properties new file mode 100644 index 0000000..362be49 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i1.json.properties @@ -0,0 +1,72 @@ +{ + "Test1" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test1", + "name" : "test1" + } ], + "module_name" : "Test1", + "options" : [ ], + "service_name" : "Test1" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "test1" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test1", + "name" : "test1" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.i10.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i10.json.properties new file mode 100644 index 0000000..a086146 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i10.json.properties @@ -0,0 +1,64 @@ +{ + "Test10" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "line1 \n \n line2", + "module" : "Test10", + "name" : "test1" + } ], + "module_name" : "Test10", + "options" : [ ], + "service_name" : "Test10" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "test1" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "line1 \n \n line2", + "module" : "Test10", + "name" : "test1" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.i11.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i11.json.properties new file mode 100644 index 0000000..a603991 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i11.json.properties @@ -0,0 +1,663 @@ +{ + "Test11" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "id" : { + "attributes" : [ "Test11.test2", "Test11.test2b" ], + "type" : "ws" + }, + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@id ws Test11.test2 Test11.test2b", + "module" : "Test11", + "name" : "test1" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "id" : { + "attributes" : [ "Test11.test2", "Test11.test2b" ], + "type" : "ws" + }, + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@id ws Test11.test2 Test11.test2b", + "module" : "Test11", + "name" : "test1" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test11", + "name" : "id_map" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "id" : { + "attributes" : [ "Test11.test2", "Test11.test2b" ], + "type" : "ws" + }, + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@id ws Test11.test2 Test11.test2b", + "module" : "Test11", + "name" : "test1" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test11", + "name" : "value_map" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "id" : { + "attributes" : [ "Test11.test2", "Test11.test2b" ], + "type" : "ws" + }, + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@id ws Test11.test2 Test11.test2b", + "module" : "Test11", + "name" : "test1" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test11", + "name" : "test1new" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "id" : { + "attributes" : [ "Test11.test2", "Test11.test2b" ], + "type" : "ws" + }, + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@id ws Test11.test2 Test11.test2b", + "module" : "Test11", + "name" : "test1" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test11", + "name" : "test1new" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test11", + "name" : "id_map_new" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "val1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "val2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "val3", + "nullable" : "0" + } ], + "module" : "Test11", + "name" : "test2" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test11", + "name" : "test2" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "id" : { + "attributes" : [ ], + "type" : "kb" + }, + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@id kb", + "module" : "Test11", + "name" : "test3" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : 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+ "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.i14.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i14.json.properties new file mode 100644 index 0000000..94e4be1 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i14.json.properties @@ -0,0 +1,64 @@ +{ + "Test14" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Real comment for type1", + "module" : "Test14", + "name" : "test1" + } ], + "module_name" : "Test14", + "options" : [ ], + "service_name" : "Test14" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "test1" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "Real comment for type1", + "module" : "Test14", + "name" : "test1" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.i15.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i15.json.properties new file mode 100644 index 0000000..56cb7d3 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i15.json.properties @@ -0,0 +1,165 @@ +{ + "Test15" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "id" : { + "attributes" : [ ], + "type" : "ws" + }, + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@id ws", + "module" : "Test15", + "name" : "reference" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "@optional ref", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "id" : { + "attributes" : [ ], + "type" : "ws" + }, + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@id ws", + "module" : "Test15", + "name" : "reference" + }, + "name" : "ref", + "nullable" : "0" + } ], + "module" : "Test15", + "name" : "RefType" + }, + "annotations" : { + "metadata" : { }, + "optional" : [ "ref" ], + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@optional ref", + "module" : "Test15", + "name" : "RefType" + } ], + "module_name" : "Test15", + "options" : [ ], + "service_name" : "Test15" + }, [ ], { + "RefType" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "@optional ref", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "id" : { + "attributes" : [ ], + "type" : "ws" + }, + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@id ws", + "module" : "Test15", + "name" : "reference" + }, + "name" : "ref", + "nullable" : "0" + } ], + "module" : "Test15", + "name" : "RefType" + }, + "annotations" : { + "metadata" : { }, + "optional" : [ "ref" ], + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@optional ref", + "module" : "Test15", + "name" : "RefType" + }, + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "reference" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "id" : { + "attributes" : [ ], + "type" : "ws" + }, + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@id ws", + "module" : "Test15", + "name" : "reference" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.i2.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i2.json.properties new file mode 100644 index 0000000..2fea488 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i2.json.properties @@ -0,0 +1,72 @@ +{ + "Test2" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test2", + "name" : "test1" + } ], + "module_name" : "Test2", + "options" : [ ], + "service_name" : "Test2" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "test1" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test2", + "name" : "test1" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.i3.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i3.json.properties new file mode 100644 index 0000000..8c8d10e --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i3.json.properties @@ -0,0 +1,82 @@ +{ + "Test3" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test3", + "name" : "test1" + } ], + "module_name" : "Test3", + "options" : [ ], + "service_name" : "Test3" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "test1" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test3", + "name" : "test1" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.i4.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i4.json.properties new file mode 100644 index 0000000..ce9257c --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i4.json.properties @@ -0,0 +1,90 @@ +{ + "Test4" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test4", + "name" : "test1" + } ], + "module_name" : "Test4", + "options" : [ ], + "service_name" : "Test4" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "test1" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } ] + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test4", + "name" : "test1" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.i5.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i5.json.properties new file mode 100644 index 0000000..a45b459 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i5.json.properties @@ -0,0 +1,110 @@ +{ + "Test5" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "val1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "val2", + "nullable" : "0" + } ], + "module" : "Test5", + "name" : "test1" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test5", + "name" : "test1" + } ], + "module_name" : "Test5", + "options" : [ ], + "service_name" : "Test5" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "test1" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "name" : "val1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "val2", + "nullable" : "0" + } ], + "module" : "Test5", + "name" : "test1" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test5", + "name" : "test1" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.i6.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i6.json.properties new file mode 100644 index 0000000..d79945a --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i6.json.properties @@ -0,0 +1,2159 @@ +{ + "Test6" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "test", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test6", + "name" : "test1" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test6", + "name" : "test2" + }, 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"int" + }, + "name" : "val2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "val1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "var3", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, + "name" : "var4", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } ] + }, + "name" : "var5", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "name" : "val6", + "nullable" : "0" + } ], + "module" : "Test6", + "name" : "testA" + }, + "annotations" : { + "metadata" : { }, + "optional" : [ "var3" ], + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@optional var3", + "module" : "Test6", + "name" : "testA" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "@optional var3", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "val2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "val1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "var3", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, + "name" : "var4", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } ] + }, + "name" : "var5", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "name" : "val6", + "nullable" : "0" + } ], + "module" : "Test6", + "name" : "testA" + }, + "annotations" : { + "metadata" : { }, + "optional" : [ "var3" ], + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@optional var3", + "module" : "Test6", + "name" : "testA" + }, { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "@optional var3", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "val2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "val1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "var3", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, + "name" : "var4", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } ] + }, + "name" : "var5", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "name" : "val6", + "nullable" : "0" + } ], + "module" : "Test6", + "name" : "testA" + }, + "annotations" : { + "metadata" : { }, + "optional" : [ "var3" ], + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@optional var3", + "module" : "Test6", + "name" : "testA" + } ], + "name" : "testD" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test6", + "name" : "testD" + }, + "testE" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "@optional val1\n@optional id", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Struct", + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { } + }, + "comment" : "@optional var3", + "items" : [ { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "name" : "val2", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "name" : "val1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::List", + "annotations" : { }, + "element_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + } + }, + "name" : "var3", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Mapping", + "annotations" : { }, + "key_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "value_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + } + }, + "name" : "var4", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Tuple", + "annotations" : { }, + "element_names" : [ "e_1", "e_2", "e_3" ], + "element_types" : [ { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + } ] + }, + "name" : "var5", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "name" : "val6", + "nullable" : "0" + } ], + "module" : "Test6", + "name" : "testA" + }, + "annotations" : { + "metadata" : { }, + "optional" : [ "var3" ], + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@optional var3", + "module" : "Test6", + "name" : "testA" + }, + "name" : "val1", + "nullable" : "0" + }, { + "!" : "Bio::KBase::KIDL::KBT::StructItem", + "item_type" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "", + "module" : "Test6", + "name" : "test1" + }, + "name" : "id", + "nullable" : "0" + } ], + "module" : "Test6", + "name" : "testE" + }, + "annotations" : { + "metadata" : { }, + "optional" : [ "val1", "id" ], + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "@optional val1\n@optional id", + "module" : "Test6", + "name" : "testE" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.i7.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i7.json.properties new file mode 100644 index 0000000..4f80ac5 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i7.json.properties @@ -0,0 +1,64 @@ +{ + "Test7" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "line1 \nline2 \n line3", + "module" : "Test7", + "name" : "test1" + } ], + "module_name" : "Test7", + "options" : [ ], + "service_name" : "Test7" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "test1" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "line1 \nline2 \n line3", + "module" : "Test7", + "name" : "test1" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.i8.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i8.json.properties new file mode 100644 index 0000000..387d954 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i8.json.properties @@ -0,0 +1,64 @@ +{ + "Test8" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "line1 \nline2", + "module" : "Test8", + "name" : "test1" + } ], + "module_name" : "Test8", + "options" : [ ], + "service_name" : "Test8" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "test1" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "line1 \nline2", + "module" : "Test8", + "name" : "test1" + } + } ] ] +} \ No newline at end of file diff --git a/src/test/resources/us/kbase/test/kidl/spec.i9.json.properties b/src/test/resources/us/kbase/test/kidl/spec.i9.json.properties new file mode 100644 index 0000000..1417628 --- /dev/null +++ b/src/test/resources/us/kbase/test/kidl/spec.i9.json.properties @@ -0,0 +1,64 @@ +{ + "Test9" : [ [ { + "!" : "Bio::KBase::KIDL::KBT::DefineModule", + "annotations" : { + "unknown_annotations" : { } + }, + "comment" : "", + "module_components" : [ { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "line1 r\n line2\n line3\n line4\n line5", + "module" : "Test9", + "name" : "test1" + } ], + "module_name" : "Test9", + "options" : [ ], + "service_name" : "Test9" + }, [ ], { + "UnspecifiedObject" : { + "!" : "Bio::KBase::KIDL::KBT::UnspecifiedObject", + "annotations" : { } + }, + "float" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "float" + }, + "int" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "int" + }, + "string" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "test1" : { + "!" : "Bio::KBase::KIDL::KBT::Typedef", + "alias_type" : { + "!" : "Bio::KBase::KIDL::KBT::Scalar", + "annotations" : { }, + "scalar_type" : "string" + }, + "annotations" : { + "metadata" : { }, + "searchable_ws_subset" : { }, + "unknown_annotations" : { } + }, + "comment" : "line1 r\n line2\n line3\n line4\n line5", + "module" : "Test9", + "name" : "test1" + } + } ] ] +} \ No newline at end of file From 2faa21f402a06c1871fc4aedaa460b06ef30dab6 Mon Sep 17 00:00:00 2001 From: Gavin Date: Thu, 27 Mar 2025 11:47:40 -0700 Subject: [PATCH 2/2] Remove complete TODO --- TODO.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/TODO.md b/TODO.md index 1c25669..5813c22 100644 --- a/TODO.md +++ b/TODO.md @@ -1,9 +1,3 @@ -* Update this code with the most recent code from kb_sdk. - * Before the update, the template data extraction code (e.g. the `forTemplates()` method - and dependencies) should be removed from the KIDL parser code. The code should be for parsing - and regenerating KIDL files, not handling templating. - * Similarly, the HTML generation code should be moved into the KIDL code, perhaps in - `kidlhtml` or `kidl.html`. * Possibly move everything under the `kidl` namespace, including `jkidl`. * Update the javacc jar to something from maven & add Gradle target to compile the spec parser. * Compilation probably never needs to be done again, so it can wait. \ No newline at end of file