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Fix Abdera ArrayIndexOutOfBoundsException with non-existent atom-entry-study.xml in SWORD jar (upstream ideally) #893

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Fix Abdera ArrayIndexOutOfBoundsException with non-existent atom-entry-study.xml in SWORD jar (upstream ideally)#893
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esotiri
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Type: Buga defect
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Beta 8 - Dataverse 4.0

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@raprasad
raprasad
opened on Sep 2, 2014

Author Name: Philip Durbin (@pdurbin)
Original Redmine Issue: 3305, https://redmine.hmdc.harvard.edu/issues/3305
Original Date: 2013-09-16

If you attempt to create a study via SWORD with an Atom entry file that doesn't exist you will see "org.apache.abdera.parser.ParseException: java.lang.ArrayIndexOutOfBoundsException" from the client side...

murphy:dvn pdurbin$ file atom-entry-study.xml
atom-entry-study.xml: cannot open `atom-entry-study.xml' (No such file or directory)
murphy:dvn pdurbin$ curl --insecure -s --data-binary "@atom-entry-study.xml" -H "Content-Type: application/atom+xml" -u sword:sword https://localhost:8181/dvn/api/data-deposit/v1/swordv2/collection/dataverse/sword | xmllint -format -
<?xml version="1.0"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
  <head>
    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
    <title>GlassFish Server Open Source Edition 3.1.2.2 - Error report</title>
    <style type="text/css">
<!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}HR {color : #525D76;}-->
    </style>
  </head>
  <body>
    <h1>HTTP Status 500 - </h1>
    <hr />
    <p><b>type</b> Exception report</p>
    <p>
      <b>message</b>
    </p>
    <p><b>description</b>The server encountered an internal error () that prevented it from fulfilling this request.</p>
    <p>
      <b>exception</b>
      ```org.apache.abdera.parser.ParseException: java.lang.ArrayIndexOutOfBoundsException

</p>
<p>
  <b>note</b>
  <u>The full stack traces of the exception and its root causes are available in the GlassFish Server Open Source Edition 3.1.2.2 logs.</u>
</p>
<hr />
<h3>GlassFish Server Open Source Edition 3.1.2.2</h3>
murphy:dvn pdurbin$ 

... and in the Glassfish server.log, this error appears:

[#|2013-09-16T08:19:33.170-0400|WARNING|glassfis###1.2|javax.enterprise.system.container.web.com.sun.enterprise.web|_ThreadID=33;_ThreadName=Thread-4;|StandardWrapperValve[edu.harvard.iq.dvn.core.web.servlet.SWORDv2CollectionServlet]: PWC1406: Servlet.service() for servlet edu.harvard.iq.dvn.core.web.servlet.SWORDv2CollectionServlet threw exception
org.apache.abdera.parser.ParseException: java.lang.ArrayIndexOutOfBoundsException
at org.apache.abdera.parser.stax.FOMParser.parse(FOMParser.java:128)
at org.apache.abdera.util.AbstractParser.parse(AbstractParser.java:65)
at org.swordapp.server.SwordAPIEndpoint.addDepositPropertiesFromEntry(SwordAPIEndpoint.java:334)
at org.swordapp.server.CollectionAPI.post(CollectionAPI.java:156)
at edu.harvard.iq.dvn.core.web.servlet.SWORDv2CollectionServlet.doPost(SWORDv2CollectionServlet.java:37)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:688)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:770)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:343)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:217)
at com.ocpsoft.pretty.PrettyFilter.doFilter(PrettyFilter.java:115)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:217)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:279)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:328)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)
at com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)
at com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)
at com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)
at com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)
at com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)
at com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)
at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)
at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)
at com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)
at com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)
at com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)
at com.sun.grizzly.ContextTask.run(ContextTask.java:71)
at com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)
at com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.ArrayIndexOutOfBoundsException
at java.lang.System.arraycopy(Native Method)
at java.io.PushbackInputStream.unread(PushbackInputStream.java:218)
at org.apache.abdera.i18n.text.io.DynamicPushbackInputStream.unread(DynamicPushbackInputStream.java:91)
at org.apache.abdera.i18n.text.io.PeekAheadInputStream.peek(PeekAheadInputStream.java:61)
at org.apache.abdera.i18n.text.io.PeekAheadInputStream.peek(PeekAheadInputStream.java:52)
at org.apache.abdera.i18n.text.io.CharsetSniffingInputStream.detectEncoding(CharsetSniffingInputStream.java:110)
at org.apache.abdera.parser.stax.util.FOMSniffingInputStream.detectEncoding(FOMSniffingInputStream.java:39)
at org.apache.abdera.i18n.text.io.CharsetSniffingInputStream.(CharsetSniffingInputStream.java:81)
at org.apache.abdera.i18n.text.io.CharsetSniffingInputStream.(CharsetSniffingInputStream.java:74)
at org.apache.abdera.parser.stax.util.FOMSniffingInputStream.(FOMSniffingInputStream.java:35)
at org.apache.abdera.parser.stax.FOMParser.parse(FOMParser.java:107)
... 37 more
|#]


org.swordapp.server.SwordAPIEndpoint.addDepositPropertiesFromEntry(SwordAPIEndpoint.java:334) corresponds to https://github.com/IQSS/swordv2-java-server-library/blob/aeaef8342361bf3de7e9fc8f2a979cd742bc31ae/src/main/java/org/swordapp/server/SwordAPIEndpoint.java#L334 which is unmodified from https://github.com/swordapp/JavaServer2.0/blob/master/src/main/java/org/swordapp/server/SwordAPIEndpoint.java#L334

Here is the relevant block of code:

328 protected void addDepositPropertiesFromEntry(Deposit deposit, HttpServletRequest req)
329 throws IOException
330 {
331 InputStream entryPart = req.getInputStream();
332 Abdera abdera = new Abdera();
333 Parser parser = abdera.getParser();
334 Document entryDoc = parser.parse(entryPart);
335 Entry entry = entryDoc.getRoot();
336 deposit.setEntry(entry);
337 }


We should probably start by reporting this on the SWORD mailing list ( https://lists.sourceforge.net/lists/listinfo/sword-app-tech ) or submit another pull request as we did with https://github.com/swordapp/JavaServer2.0/pull/3

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