From 2e2a7c0dc0f2b0a2950e3dc89de86a1588e11429 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Tue, 14 Jan 2025 14:44:27 +0000 Subject: [PATCH 01/30] Duplicated '_midpoint' function from 'murfey.client.contexts.tomo' to preserve client-server independence --- src/murfey/server/__init__.py | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/src/murfey/server/__init__.py b/src/murfey/server/__init__.py index 823df3063..16dfce9ce 100644 --- a/src/murfey/server/__init__.py +++ b/src/murfey/server/__init__.py @@ -48,7 +48,6 @@ import murfey.server.prometheus as prom import murfey.server.websocket import murfey.util.db as db -from murfey.client.contexts.tomo import _midpoint from murfey.server.murfey_db import url # murfey_db from murfey.util import LogFilter from murfey.util.config import ( @@ -165,6 +164,24 @@ def _mc_path(mov_path: Path) -> str: return [_mc_path(Path(r.movie_path)) for r in results] +def _midpoint(angles: List[float]) -> int: + """ + Duplicate of the function in 'murfey.client.contexts.tomo', so as to preserve + client-server independence. + """ + if not angles: + return 0 + if len(angles) <= 2: + return round(angles[0]) + sorted_angles = sorted(angles) + return round( + sorted_angles[len(sorted_angles) // 2] + if sorted_angles[len(sorted_angles) // 2] + and sorted_angles[len(sorted_angles) // 2 + 1] + else 0 + ) + + def get_job_ids(tilt_series_id: int, appid: int) -> JobIDs: results = murfey_db.exec( select( From 69888076b841c3ad1ba9cbd294a54c2eda9cd003 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Tue, 14 Jan 2025 15:20:56 +0000 Subject: [PATCH 02/30] Moved 'midpoint' function to 'murfey.util.tomo' to function duplication --- src/murfey/client/contexts/tomo.py | 17 ++--------------- src/murfey/server/__init__.py | 21 ++------------------- src/murfey/server/api/__init__.py | 4 ++-- src/murfey/util/tomo.py | 16 ++++++++++++++++ 4 files changed, 22 insertions(+), 36 deletions(-) create mode 100644 src/murfey/util/tomo.py diff --git a/src/murfey/client/contexts/tomo.py b/src/murfey/client/contexts/tomo.py index e9bcd2aaf..f09dad951 100644 --- a/src/murfey/client/contexts/tomo.py +++ b/src/murfey/client/contexts/tomo.py @@ -21,6 +21,7 @@ ) from murfey.util import authorised_requests, capture_post, get_machine_config_client from murfey.util.mdoc import get_block, get_global_data, get_num_blocks +from murfey.util.tomo import midpoint logger = logging.getLogger("murfey.client.contexts.tomo") @@ -64,20 +65,6 @@ def _construct_tilt_series_name(file_path: Path) -> str: return "_".join(split_name[:-5]) -def _midpoint(angles: List[float]) -> int: - if not angles: - return 0 - if len(angles) <= 2: - return round(angles[0]) - sorted_angles = sorted(angles) - return round( - sorted_angles[len(sorted_angles) // 2] - if sorted_angles[len(sorted_angles) // 2] - and sorted_angles[len(sorted_angles) // 2 + 1] - else 0 - ) - - class ProcessFileIncomplete(BaseModel): dest: Path source: Path @@ -738,7 +725,7 @@ def gather_metadata( if environment else None ) - mdoc_metadata["manual_tilt_offset"] = -_midpoint( + mdoc_metadata["manual_tilt_offset"] = -midpoint( [float(b["TiltAngle"]) for b in blocks] ) mdoc_metadata["source"] = str(self._basepath) diff --git a/src/murfey/server/__init__.py b/src/murfey/server/__init__.py index 16dfce9ce..57b10dcc7 100644 --- a/src/murfey/server/__init__.py +++ b/src/murfey/server/__init__.py @@ -59,6 +59,7 @@ ) from murfey.util.processing_params import default_spa_parameters from murfey.util.state import global_state +from murfey.util.tomo import midpoint try: from murfey.server.ispyb import TransportManager # Session @@ -164,24 +165,6 @@ def _mc_path(mov_path: Path) -> str: return [_mc_path(Path(r.movie_path)) for r in results] -def _midpoint(angles: List[float]) -> int: - """ - Duplicate of the function in 'murfey.client.contexts.tomo', so as to preserve - client-server independence. - """ - if not angles: - return 0 - if len(angles) <= 2: - return round(angles[0]) - sorted_angles = sorted(angles) - return round( - sorted_angles[len(sorted_angles) // 2] - if sorted_angles[len(sorted_angles) // 2] - and sorted_angles[len(sorted_angles) // 2 + 1] - else 0 - ) - - def get_job_ids(tilt_series_id: int, appid: int) -> JobIDs: results = murfey_db.exec( select( @@ -2593,7 +2576,7 @@ def feedback_callback(header: dict, message: dict) -> None: ) if not stack_file.parent.exists(): stack_file.parent.mkdir(parents=True) - tilt_offset = _midpoint([float(get_angle(t)) for t in tilts]) + tilt_offset = midpoint([float(get_angle(t)) for t in tilts]) zocalo_message = { "recipes": ["em-tomo-align"], "parameters": { diff --git a/src/murfey/server/api/__init__.py b/src/murfey/server/api/__init__.py index 6f5d411e9..d6232f9ac 100644 --- a/src/murfey/server/api/__init__.py +++ b/src/murfey/server/api/__init__.py @@ -33,7 +33,6 @@ import murfey.server.websocket as ws import murfey.util.eer from murfey.server import ( - _midpoint, _murfey_id, _transport_object, check_tilt_series_mc, @@ -108,6 +107,7 @@ ) from murfey.util.processing_params import default_spa_parameters from murfey.util.state import global_state +from murfey.util.tomo import midpoint log = logging.getLogger("murfey.server.api") @@ -840,7 +840,7 @@ def register_completed_tilt_series( ) if not stack_file.parent.exists(): stack_file.parent.mkdir(parents=True) - tilt_offset = _midpoint([float(get_angle(t)) for t in tilts]) + tilt_offset = midpoint([float(get_angle(t)) for t in tilts]) zocalo_message = { "recipes": ["em-tomo-align"], "parameters": { diff --git a/src/murfey/util/tomo.py b/src/murfey/util/tomo.py new file mode 100644 index 000000000..dc7314ec1 --- /dev/null +++ b/src/murfey/util/tomo.py @@ -0,0 +1,16 @@ +def midpoint(angles: list[float]) -> int: + """ + Utility function to calculate the midpoint of the angles used in a tilt series. + Used primarily in the tomography workflow. + """ + if not angles: + return 0 + if len(angles) <= 2: + return round(angles[0]) + sorted_angles = sorted(angles) + return round( + sorted_angles[len(sorted_angles) // 2] + if sorted_angles[len(sorted_angles) // 2] + and sorted_angles[len(sorted_angles) // 2 + 1] + else 0 + ) From a67ae92f4cfb75c7e1eb67b41ca4c9e7ea355f05 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Tue, 14 Jan 2025 15:40:56 +0000 Subject: [PATCH 03/30] Added new optional dependency key for client-side instrument server --- pyproject.toml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index d956932fa..44c532795 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -53,6 +53,10 @@ developer = [ "pre-commit", # Formatting, linting, type checking, etc. "pytest", # Test code functionality ] +instrument-server = [ + "fastapi[standard]", + "uvicorn[standard]", +] server = [ # "matplotlib", # For visual statistical analysis of images "aiohttp", From 45590a9750768a3510ad936fd1b52015c07fe8e5 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Tue, 14 Jan 2025 15:55:28 +0000 Subject: [PATCH 04/30] Replaced remaining instances of 'procrunner' with 'subprocess' --- pyproject.toml | 1 - src/murfey/cli/transfer.py | 4 ++-- src/murfey/instrument_server/api.py | 4 ++-- src/murfey/util/rsync.py | 24 +++++++++++++----------- 4 files changed, 17 insertions(+), 16 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 44c532795..620f8b37b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,7 +42,6 @@ cicd = [ "pytest-cov", # Used by Azure Pipelines for PyTest coverage reports ] client = [ - "procrunner", "textual==0.42.0", "websocket-client", "xmltodict", diff --git a/src/murfey/cli/transfer.py b/src/murfey/cli/transfer.py index 3c03c8e05..4b23793c4 100644 --- a/src/murfey/cli/transfer.py +++ b/src/murfey/cli/transfer.py @@ -1,10 +1,10 @@ from __future__ import annotations import argparse +import subprocess from pathlib import Path from urllib.parse import urlparse -import procrunner import requests from rich.console import Console from rich.prompt import Confirm @@ -76,6 +76,6 @@ def run(): cmd.extend(list(Path(args.source or ".").glob("*"))) cmd.append(f"{murfey_url.hostname}::{args.destination}") - result = procrunner.run(cmd) + result = subprocess.run(cmd) if result.returncode: console.print(f"[red]rsync failed returning code {result.returncode}") diff --git a/src/murfey/instrument_server/api.py b/src/murfey/instrument_server/api.py index c2bee0516..2081e0a50 100644 --- a/src/murfey/instrument_server/api.py +++ b/src/murfey/instrument_server/api.py @@ -1,6 +1,7 @@ from __future__ import annotations import secrets +import subprocess import time from datetime import datetime from functools import partial @@ -9,7 +10,6 @@ from typing import Annotated, Dict, List, Optional, Union from urllib.parse import urlparse -import procrunner import requests from fastapi import APIRouter, Depends, HTTPException, status from fastapi.security import OAuth2PasswordBearer @@ -283,7 +283,7 @@ def upload_gain_reference(session_id: MurfeySessionID, gain_reference: GainRefer str(gain_reference.gain_path), f"{urlparse(_get_murfey_url(), allow_fragments=False).hostname}::{gain_reference.visit_path}/{gain_reference.gain_destination_dir}/{secure_filename(gain_reference.gain_path.name)}", ] - gain_rsync = procrunner.run(cmd) + gain_rsync = subprocess.run(cmd) if gain_rsync.returncode: safe_gain_path = ( str(gain_reference.gain_path).replace("\r\n", "").replace("\n", "") diff --git a/src/murfey/util/rsync.py b/src/murfey/util/rsync.py index 51836f692..1a9b14bb4 100644 --- a/src/murfey/util/rsync.py +++ b/src/murfey/util/rsync.py @@ -1,11 +1,10 @@ from __future__ import annotations import logging +import subprocess from pathlib import Path from typing import Callable, Dict, List, Optional, Tuple, Union -import procrunner - from murfey.util import Processor from murfey.util.file_monitor import Monitor @@ -32,7 +31,7 @@ def __init__( self.received_bytes = 0 self.byte_rate: float = 0 self.total_size = 0 - self.runner_return: List[procrunner.ReturnObject] = [] + self.runner_return: List[subprocess.CompletedProcess] = [] self._root = root self._sub_structure: Optional[Path] = None self._notify = notify or (lambda f: None) @@ -53,7 +52,7 @@ def _run_rsync( retry: bool = True, ): """ - Run rsync -v on a list of files using procrunner. + Run rsync -v on a list of files using subprocess. :param root: root path of files for transferring; structure below the root is preserved :type root: pathlib.Path object @@ -109,17 +108,20 @@ def _single_rsync( else: cmd.append(str(self._finaldir / sub_struct) + "/") self._transferring = True - runner = procrunner.run( + runner = subprocess.run( cmd, - callback_stdout=self._parse_rsync_stdout, - callback_stderr=self._parse_rsync_stderr, + capture_output=True, ) + for line in runner.stdout.decode("utf-8", "replace").split("\n"): + self._parse_rsync_stdout(line) + for line in runner.stderr.decode("utf-8", "replace").split("\n"): + self._parse_rsync_stderr(line) self.runner_return.append(runner) self.failed.extend(root / sub_struct / f for f in self._failed_tmp) if retry: self._in.put(root / sub_struct / f for f in self._failed_tmp) - def _parse_rsync_stdout(self, stdout: bytes): + def _parse_rsync_stdout(self, stdout: bytes | str): """ Parse rsync stdout to collect information such as the paths of transferred files and the amount of data transferred. @@ -127,7 +129,7 @@ def _parse_rsync_stdout(self, stdout: bytes): :param stdout: stdout of rsync process :type stdout: bytes """ - stringy_stdout = str(stdout) + stringy_stdout = str(stdout) if isinstance(stdout, bytes) else stdout if stringy_stdout: if self._transferring: if stringy_stdout.startswith("sent"): @@ -158,14 +160,14 @@ def _parse_rsync_stdout(self, stdout: bytes): stringy_stdout.replace("total size", "").split()[1] ) - def _parse_rsync_stderr(self, stderr: bytes): + def _parse_rsync_stderr(self, stderr: bytes | str): """ Parse rsync stderr to collect information on any files that failed to transfer. :param stderr: stderr of rsync process :type stderr: bytes """ - stringy_stderr = str(stderr) + stringy_stderr = str(stderr) if isinstance(stderr, bytes) else stderr if stringy_stderr: if ( stringy_stderr.startswith("rsync: link_stat") From 2bb132a8c40dcb0e6dd5c648e4044daf4aa41123 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Tue, 14 Jan 2025 15:59:29 +0000 Subject: [PATCH 05/30] Updated descriptive comments on 'pyproject.toml' --- pyproject.toml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 620f8b37b..4bb53f9e8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,14 +32,14 @@ classifiers = [ dependencies = [ "backports.entry_points_selectable", "defusedxml", # For safely parsing XML files - "pydantic<2", # Locked to <2 by zocalo + "pydantic<2", # Locked to <2 by cygwin terminal "requests", "rich", "werkzeug", ] [project.optional-dependencies] cicd = [ - "pytest-cov", # Used by Azure Pipelines for PyTest coverage reports + "pytest-cov", # Used for generating PyTest coverage reports ] client = [ "textual==0.42.0", @@ -57,7 +57,6 @@ instrument-server = [ "uvicorn[standard]", ] server = [ - # "matplotlib", # For visual statistical analysis of images "aiohttp", "cryptography", "fastapi[standard]", From bb0ec71601ec35e50904e770d0ddf566d91df199 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Tue, 14 Jan 2025 16:07:17 +0000 Subject: [PATCH 06/30] Implemented sanitisation to satisfy CodeQL warning on uncontrolled command line input --- src/murfey/instrument_server/api.py | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/src/murfey/instrument_server/api.py b/src/murfey/instrument_server/api.py index 2081e0a50..229acfa9b 100644 --- a/src/murfey/instrument_server/api.py +++ b/src/murfey/instrument_server/api.py @@ -21,7 +21,7 @@ from murfey.client.multigrid_control import MultigridController from murfey.client.rsync import RSyncer from murfey.client.watchdir_multigrid import MultigridDirWatcher -from murfey.util import sanitise_nonpath, secure_path +from murfey.util import sanitise, sanitise_nonpath, secure_path from murfey.util.instrument_models import MultigridWatcherSpec from murfey.util.models import File, Token @@ -278,19 +278,16 @@ class GainReference(BaseModel): @router.post("/sessions/{session_id}/upload_gain_reference") def upload_gain_reference(session_id: MurfeySessionID, gain_reference: GainReference): + safe_gain_path = sanitise(str(gain_reference.gain_path)) + safe_visit_path = sanitise(gain_reference.visit_path) + safe_destination_dir = sanitise(gain_reference.gain_destination_dir) cmd = [ "rsync", - str(gain_reference.gain_path), - f"{urlparse(_get_murfey_url(), allow_fragments=False).hostname}::{gain_reference.visit_path}/{gain_reference.gain_destination_dir}/{secure_filename(gain_reference.gain_path.name)}", + safe_gain_path, + f"{urlparse(_get_murfey_url(), allow_fragments=False).hostname}::{safe_visit_path}/{safe_destination_dir}/{secure_filename(gain_reference.gain_path.name)}", ] gain_rsync = subprocess.run(cmd) if gain_rsync.returncode: - safe_gain_path = ( - str(gain_reference.gain_path).replace("\r\n", "").replace("\n", "") - ) - safe_visit_path = gain_reference.visit_path.replace("\r\n", "").replace( - "\n", "" - ) logger.warning( f"Gain reference file {safe_gain_path} was not successfully transferred to {safe_visit_path}/processing" ) From b3c8e3dd98594561fcc203b2ded435a54d93df57 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Wed, 15 Jan 2025 14:05:26 +0000 Subject: [PATCH 07/30] Added 'jose' as an 'instrument-server' dependency --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 4bb53f9e8..450042362 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,6 +54,7 @@ developer = [ ] instrument-server = [ "fastapi[standard]", + "jose", "uvicorn[standard]", ] server = [ From b55ae5fe5aa24fd55fc596a07366e3d01555f736 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Wed, 15 Jan 2025 14:06:02 +0000 Subject: [PATCH 08/30] Added 'jose' as a 'server' dependency --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 450042362..2ea86545a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -63,6 +63,7 @@ server = [ "fastapi[standard]", "ispyb", # Responsible for setting requirements for SQLAlchemy and mysql-connector-python; v10.0.0: sqlalchemy <2, mysql-connector-python >=8.0.32 "jinja2", + "jose", "mrcfile", "numpy", "packaging", From 933cfe6090d9d9bf1d8a49bb87c98bf52e3338ff Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Wed, 15 Jan 2025 14:21:36 +0000 Subject: [PATCH 09/30] Package is 'python-jose[cryptography], not 'jose' --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 2ea86545a..1ee9240d2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,7 +54,7 @@ developer = [ ] instrument-server = [ "fastapi[standard]", - "jose", + "python-jose[cryptography]", "uvicorn[standard]", ] server = [ @@ -63,7 +63,6 @@ server = [ "fastapi[standard]", "ispyb", # Responsible for setting requirements for SQLAlchemy and mysql-connector-python; v10.0.0: sqlalchemy <2, mysql-connector-python >=8.0.32 "jinja2", - "jose", "mrcfile", "numpy", "packaging", From 72548e2bc1372c3a982a0bef16ce5767b6c1b1a0 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Wed, 15 Jan 2025 16:20:42 +0000 Subject: [PATCH 10/30] Updated '_parse_rsync_stdout/stderr()' functions to read stringified lines --- src/murfey/util/rsync.py | 74 ++++++++++++++++++---------------------- 1 file changed, 33 insertions(+), 41 deletions(-) diff --git a/src/murfey/util/rsync.py b/src/murfey/util/rsync.py index 1a9b14bb4..84953b39a 100644 --- a/src/murfey/util/rsync.py +++ b/src/murfey/util/rsync.py @@ -121,7 +121,7 @@ def _single_rsync( if retry: self._in.put(root / sub_struct / f for f in self._failed_tmp) - def _parse_rsync_stdout(self, stdout: bytes | str): + def _parse_rsync_stdout(self, line: str): """ Parse rsync stdout to collect information such as the paths of transferred files and the amount of data transferred. @@ -129,51 +129,43 @@ def _parse_rsync_stdout(self, stdout: bytes | str): :param stdout: stdout of rsync process :type stdout: bytes """ - stringy_stdout = str(stdout) if isinstance(stdout, bytes) else stdout - if stringy_stdout: - if self._transferring: - if stringy_stdout.startswith("sent"): - self._transferring = False - byte_info = stringy_stdout.split() - self.sent_bytes = int( - byte_info[byte_info.index("sent") + 1].replace(",", "") - ) - self.received_bytes = int( - byte_info[byte_info.index("received") + 1].replace(",", "") - ) - self.byte_rate = float( - byte_info[byte_info.index("bytes/sec") - 1].replace(",", "") - ) - elif len(stringy_stdout.split()) == 1: - if self._root and self._sub_structure: - self._notify( - self._finaldir / self._sub_structure / stringy_stdout - ) - self._out.put(self._root / self._sub_structure / stringy_stdout) - else: - logger.warning( - f"root or substructure not set for transfer of {stringy_stdout}" - ) - else: - if "total size" in stringy_stdout: - self.total_size = int( - stringy_stdout.replace("total size", "").split()[1] + if self._transferring: + if line.startswith("sent"): + self._transferring = False + byte_info = line.split() + self.sent_bytes = int( + byte_info[byte_info.index("sent") + 1].replace(",", "") + ) + self.received_bytes = int( + byte_info[byte_info.index("received") + 1].replace(",", "") + ) + self.byte_rate = float( + byte_info[byte_info.index("bytes/sec") - 1].replace(",", "") + ) + elif len(line.split()) == 1: + if self._root and self._sub_structure: + self._notify(self._finaldir / self._sub_structure / line) + self._out.put(self._root / self._sub_structure / line) + else: + logger.warning( + f"root or substructure not set for transfer of {line}" ) + else: + if "total size" in line: + self.total_size = int(line.replace("total size", "").split()[1]) - def _parse_rsync_stderr(self, stderr: bytes | str): + def _parse_rsync_stderr(self, line: str): """ Parse rsync stderr to collect information on any files that failed to transfer. :param stderr: stderr of rsync process :type stderr: bytes """ - stringy_stderr = str(stderr) if isinstance(stderr, bytes) else stderr - if stringy_stderr: - if ( - stringy_stderr.startswith("rsync: link_stat") - or stringy_stderr.startswith("rsync: [sender] link_stat") - ) and "failed" in stringy_stderr: - failed_msg = stringy_stderr.split() - self._failed_tmp.append( - failed_msg[failed_msg.index("failed:") - 1].replace('"', "") - ) + if ( + line.startswith("rsync: link_stat") + or line.startswith("rsync: [sender] link_stat") + ) and "failed" in line: + failed_msg = line.split() + self._failed_tmp.append( + failed_msg[failed_msg.index("failed:") - 1].replace('"', "") + ) From e35c6fe8e7c1f25c02f35fb448a558d25d26c7a6 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Wed, 15 Jan 2025 17:01:26 +0000 Subject: [PATCH 11/30] Increased large files threshold to 600kB in pre-commit config --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 00200fe5a..ee9a38db6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -8,7 +8,7 @@ repos: hooks: - id: check-added-large-files name: Checking for added large files - args: ["--maxkb=200"] + args: ["--maxkb=600"] fail_fast: True - id: check-case-conflict name: Checking for name case conflicts From 087934b5ce20b396853cc9b42874f0f94d490657 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Wed, 15 Jan 2025 17:02:25 +0000 Subject: [PATCH 12/30] Added Dockerfiles for Murfey services to repo, and add build context for Murfey frontend --- Dockerfiles/murfey-frontend | 47 + Dockerfiles/murfey-instrument-server | 52 + Dockerfiles/murfey-rsync | 14 + Dockerfiles/murfey-server | 53 + murfey-frontend/README.md | 70 + murfey-frontend/mime.types | 99 + murfey-frontend/nginx/conf.d | 28 + murfey-frontend/openapi.yaml | 1869 +++ murfey-frontend/package.json | 58 + murfey-frontend/public/favicon.ico | Bin 0 -> 3870 bytes murfey-frontend/public/images/diamondgs.png | Bin 0 -> 1931 bytes murfey-frontend/public/index.html | 43 + murfey-frontend/public/logo192.png | Bin 0 -> 5347 bytes murfey-frontend/public/logo512.png | Bin 0 -> 9664 bytes murfey-frontend/public/manifest.json | 25 + murfey-frontend/public/robots.txt | 3 + murfey-frontend/src/components/forms.tsx | 195 + .../src/components/gridSquareCard.tsx | 147 + .../src/components/instrumentCard.tsx | 58 + murfey-frontend/src/components/navbar.tsx | 170 + .../src/components/protectedRoutes.tsx | 20 + .../src/components/setupStepper.tsx | 65 + .../src/components/upstreamVisitsCard.tsx | 48 + murfey-frontend/src/index.css | 13 + murfey-frontend/src/index.tsx | 149 + .../src/loaders/dataCollectionGroups.tsx | 33 + murfey-frontend/src/loaders/general.tsx | 49 + murfey-frontend/src/loaders/gridSquares.tsx | 80 + murfey-frontend/src/loaders/hub.tsx | 22 + murfey-frontend/src/loaders/jwt.tsx | 43 + murfey-frontend/src/loaders/machineConfig.tsx | 27 + murfey-frontend/src/loaders/magTable.tsx | 46 + .../src/loaders/multigridSetup.tsx | 21 + .../src/loaders/possibleGainRefs.tsx | 84 + .../src/loaders/processingParameters.tsx | 34 + murfey-frontend/src/loaders/rsyncers.tsx | 94 + murfey-frontend/src/loaders/sessionSetup.tsx | 22 + .../src/loaders/session_clients.tsx | 116 + murfey-frontend/src/loaders/visits.tsx | 33 + murfey-frontend/src/logo.svg | 1 + murfey-frontend/src/reportWebVitals.js | 13 + .../src/routes/DataCollectionGroups.tsx | 87 + murfey-frontend/src/routes/Error.tsx | 59 + .../src/routes/GainRefTransfer.tsx | 158 + murfey-frontend/src/routes/GridSquares.tsx | 75 + murfey-frontend/src/routes/Home.tsx | 206 + murfey-frontend/src/routes/Hub.tsx | 97 + murfey-frontend/src/routes/Login.tsx | 75 + murfey-frontend/src/routes/MagTable.tsx | 168 + murfey-frontend/src/routes/MultigridSetup.tsx | 166 + murfey-frontend/src/routes/NewSession.tsx | 185 + .../src/routes/ProcessingParameters.tsx | 184 + murfey-frontend/src/routes/Root.tsx | 21 + murfey-frontend/src/routes/Session.tsx | 418 + murfey-frontend/src/routes/SessionLinker.tsx | 140 + murfey-frontend/src/routes/SessionSetup.tsx | 168 + murfey-frontend/src/routes/UserParameters.tsx | 40 + murfey-frontend/src/schema/main.ts | 4335 ++++++ murfey-frontend/src/setupTests.js | 5 + murfey-frontend/src/styles/colours.tsx | 16 + murfey-frontend/src/styles/components.ts | 325 + murfey-frontend/src/styles/main.css | 29 + murfey-frontend/src/styles/theme.tsx | 49 + murfey-frontend/src/utils/api/client.tsx | 162 + murfey-frontend/src/utils/generic.tsx | 15 + murfey-frontend/tsconfig.json | 21 + murfey-frontend/yarn.lock | 11673 ++++++++++++++++ 67 files changed, 22821 insertions(+) create mode 100644 Dockerfiles/murfey-frontend create mode 100644 Dockerfiles/murfey-instrument-server create mode 100644 Dockerfiles/murfey-rsync create mode 100644 Dockerfiles/murfey-server create mode 100644 murfey-frontend/README.md create mode 100644 murfey-frontend/mime.types create mode 100644 murfey-frontend/nginx/conf.d create mode 100644 murfey-frontend/openapi.yaml create mode 100644 murfey-frontend/package.json create mode 100644 murfey-frontend/public/favicon.ico create mode 100644 murfey-frontend/public/images/diamondgs.png create mode 100644 murfey-frontend/public/index.html create mode 100644 murfey-frontend/public/logo192.png create mode 100644 murfey-frontend/public/logo512.png create mode 100644 murfey-frontend/public/manifest.json create mode 100644 murfey-frontend/public/robots.txt create mode 100644 murfey-frontend/src/components/forms.tsx create mode 100644 murfey-frontend/src/components/gridSquareCard.tsx create mode 100644 murfey-frontend/src/components/instrumentCard.tsx create mode 100644 murfey-frontend/src/components/navbar.tsx create mode 100644 murfey-frontend/src/components/protectedRoutes.tsx create mode 100644 murfey-frontend/src/components/setupStepper.tsx create mode 100644 murfey-frontend/src/components/upstreamVisitsCard.tsx create mode 100644 murfey-frontend/src/index.css create mode 100644 murfey-frontend/src/index.tsx create mode 100644 murfey-frontend/src/loaders/dataCollectionGroups.tsx create mode 100644 murfey-frontend/src/loaders/general.tsx create mode 100644 murfey-frontend/src/loaders/gridSquares.tsx create mode 100644 murfey-frontend/src/loaders/hub.tsx create mode 100644 murfey-frontend/src/loaders/jwt.tsx create mode 100644 murfey-frontend/src/loaders/machineConfig.tsx create mode 100644 murfey-frontend/src/loaders/magTable.tsx create mode 100644 murfey-frontend/src/loaders/multigridSetup.tsx create mode 100644 murfey-frontend/src/loaders/possibleGainRefs.tsx create mode 100644 murfey-frontend/src/loaders/processingParameters.tsx create mode 100644 murfey-frontend/src/loaders/rsyncers.tsx create mode 100644 murfey-frontend/src/loaders/sessionSetup.tsx create mode 100644 murfey-frontend/src/loaders/session_clients.tsx create mode 100644 murfey-frontend/src/loaders/visits.tsx create mode 100644 murfey-frontend/src/logo.svg create mode 100644 murfey-frontend/src/reportWebVitals.js create mode 100644 murfey-frontend/src/routes/DataCollectionGroups.tsx create mode 100644 murfey-frontend/src/routes/Error.tsx create mode 100644 murfey-frontend/src/routes/GainRefTransfer.tsx create mode 100644 murfey-frontend/src/routes/GridSquares.tsx create mode 100644 murfey-frontend/src/routes/Home.tsx create mode 100644 murfey-frontend/src/routes/Hub.tsx create mode 100644 murfey-frontend/src/routes/Login.tsx create mode 100644 murfey-frontend/src/routes/MagTable.tsx create mode 100644 murfey-frontend/src/routes/MultigridSetup.tsx create mode 100644 murfey-frontend/src/routes/NewSession.tsx create mode 100644 murfey-frontend/src/routes/ProcessingParameters.tsx create mode 100644 murfey-frontend/src/routes/Root.tsx create mode 100644 murfey-frontend/src/routes/Session.tsx create mode 100644 murfey-frontend/src/routes/SessionLinker.tsx create mode 100644 murfey-frontend/src/routes/SessionSetup.tsx create mode 100644 murfey-frontend/src/routes/UserParameters.tsx create mode 100644 murfey-frontend/src/schema/main.ts create mode 100644 murfey-frontend/src/setupTests.js create mode 100644 murfey-frontend/src/styles/colours.tsx create mode 100644 murfey-frontend/src/styles/components.ts create mode 100644 murfey-frontend/src/styles/main.css create mode 100644 murfey-frontend/src/styles/theme.tsx create mode 100644 murfey-frontend/src/utils/api/client.tsx create mode 100644 murfey-frontend/src/utils/generic.tsx create mode 100644 murfey-frontend/tsconfig.json create mode 100644 murfey-frontend/yarn.lock diff --git a/Dockerfiles/murfey-frontend b/Dockerfiles/murfey-frontend new file mode 100644 index 000000000..dec866090 --- /dev/null +++ b/Dockerfiles/murfey-frontend @@ -0,0 +1,47 @@ +# Build commmand template: +# podman build --build-arg API_ENDPOINT= ... --no-cache -t murfey-frontend: -f /path/to/Dockerfiles/murfey-frontend path/to/murfey-frontend + +FROM docker.io/library/node:22.13.0-alpine3.20 as build +# FROM docker.io/library/node:20.11.0-alpine3.19 as build + +# Set arguments and environment variables +ARG DEPLOY_TYPE="production" +ARG API_ENDPOINT="http://localhost:8000/" +ARG DEV_CONTACT="daniel.hatton@diamond.ac.uk" +ARG VERSION=0.0.1 +ARG FEEDBACK_URL="http://localhost:8080/" + +ENV REACT_APP_DEPLOY_TYPE=${DEPLOY_TYPE} +ENV REACT_APP_HUB_ENDPOINT=${API_ENDPOINT} +ENV REACT_APP_VERSION=${VERSION} +ENV REACT_APP_DEV_CONTACT=${DEV_CONTACT} +ENV REACT_APP_AUTH_TYPE="oidc" +ENV REACT_APP_FEEDBACK_URL=${FEEDBACK_URL} + +# Set working directory to build installation in +WORKDIR /usr/src/app + +# Install all Yarn dependencies listed in package.json using versions listed in +# .lock file as unless they are not sufficient to satisfy package requirements +COPY ./package.json ./yarn.lock ./ +RUN yarn install --immutable --check-cache + +# Copy across files needed to build the app and build it +COPY ./ ./ +RUN yarn build + +# Start second stage of build(?) +FROM docker.io/nginxinc/nginx-unprivileged:alpine3.20-slim +# FROM docker.io/nginxinc/nginx-unprivileged:alpine3.18-slim +COPY --from=build --chown=nginx /usr/src/app/build /usr/share/nginx/html +COPY --chown=nginx nginx/conf.d /tmp/nginx/nginx.conf +COPY --chown=nginx mime.types /tmp/nginx/mime.types + +EXPOSE 8080 +CMD [ \ + "nginx", \ + "-c", \ + "/tmp/nginx/nginx.conf", \ + "-g", \ + "daemon off;" \ +] diff --git a/Dockerfiles/murfey-instrument-server b/Dockerfiles/murfey-instrument-server new file mode 100644 index 000000000..2391692ac --- /dev/null +++ b/Dockerfiles/murfey-instrument-server @@ -0,0 +1,52 @@ +# Build command template +# podman build --build-arg groupid= --build-arg userid= --build-arg groupname= --no-cache -f path/to/Dockerfiles/murfey-instrument-server -t murfey-instrument-server: path/to/python-murfey + +# Set up the Python base image to build with +FROM docker.io/library/python:3.12.8-slim-bullseye as build + +# Define external build arguments +ARG groupid +ARG groupname +ARG userid + +# Add system dependencies for the developer/build environment +# Add the group and user ID to be used by Murfey +RUN apt-get update && \ + apt-get upgrade -y && \ + apt-get install -y --no-install-recommends \ + build-essential \ + busybox \ + git \ + net-tools \ + libpq-dev && \ + busybox --install &&\ + rm -rf /var/lib/apt/lists/* && \ + groupadd -r -g "${groupid}" "${groupname}" && useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" + +# Copy essential Murfey source files across from repo +COPY --chown="${userid}":"${groupid}" src/murfey/ /repos/python-murfey/src/murfey/ +COPY --chown="${userid}":"${groupid}" \ + pyproject.toml \ + setup.py \ + api-spec.yaml \ + AUTHORS.rst \ + catalog-info.yaml \ + LICENSE \ + MANIFEST.in \ + README.md \ + /repos/python-murfey/ + +# Set the repo as the current working directory +WORKDIR /repos/python-murfey + +# Set up a virtual environment and install Murfey +RUN python -m venv /venv && \ + chmod -R a+x /venv && \ + /venv/bin/python -m pip install --upgrade \ + pip \ + build \ + importlib-metadata &&\ + /venv/bin/python -m pip install .[client,instrument-server] + +# Prepend the virtual environment to PATH +ENV PATH=/venv/bin:$PATH diff --git a/Dockerfiles/murfey-rsync b/Dockerfiles/murfey-rsync new file mode 100644 index 000000000..88c75a159 --- /dev/null +++ b/Dockerfiles/murfey-rsync @@ -0,0 +1,14 @@ +# Template build command +# podman build --build-arg groupid= --build-arg userid= --build-arg groupname= --no-cache -f path/to/Dockerfiles/murfey-rsync + +FROM docker.io/library/alpine:3.20 +# FROM alpine:3.14 + +ARG groupid +ARG groupname +ARG userid + +# Add any system dependencies for the developer/build environment here +RUN apk add --no-cache rsync + +RUN addgroup -S -g "${groupid}" "${groupname}" && adduser -S "${groupname}" -G "${groupname}" -u "${userid}" -s /bin/sh diff --git a/Dockerfiles/murfey-server b/Dockerfiles/murfey-server new file mode 100644 index 000000000..b934108e5 --- /dev/null +++ b/Dockerfiles/murfey-server @@ -0,0 +1,53 @@ +# Template build command +# podman build --build-arg groupid= --build-arg userid= --build-arg groupname= --no-cache -f path/to/Dockerfiles/murfey-server -t murfey-server: path/to/python-murfey + +# Set up the Python base image to build with +FROM docker.io/library/python:3.12.8-slim-bullseye as build + +# Define external build arguments +ARG groupid +ARG groupname +ARG userid + +# Add system dependencies for the developer/build environment +# Add the group and user ID to be used by Murfey +RUN apt-get update && \ + apt-get upgrade -y && \ + apt-get install -y --no-install-recommends \ + build-essential \ + busybox \ + git \ + net-tools \ + libpq-dev && \ + busybox --install &&\ + rm -rf /var/lib/apt/lists/* && \ + groupadd -r -g "${groupid}" "${groupname}" && useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" + +# Copy essential Murfey source files across from repo +COPY --chown="${userid}":"${groupid}" src/murfey/ /repos/python-murfey/src/murfey/ +COPY --chown="${userid}":"${groupid}" \ + pyproject.toml \ + setup.py \ + api-spec.yaml \ + AUTHORS.rst \ + catalog-info.yaml \ + LICENSE \ + MANIFEST.in \ + README.md \ + /repos/python-murfey/ + +# Set the repo as the current working directory +WORKDIR /repos/python-murfey + +# Set up a virtual environment and install Murfey +RUN python -m venv /venv && \ + chmod -R a+x /venv && \ + /venv/bin/python -m pip install --upgrade \ + pip \ + build \ + importlib-metadata \ + psycopg2-binary && \ + /venv/bin/python -m pip install .[server] + +# Prepend the virtual environment to PATH +ENV PATH=/venv/bin:$PATH diff --git a/murfey-frontend/README.md b/murfey-frontend/README.md new file mode 100644 index 000000000..c0541f9c0 --- /dev/null +++ b/murfey-frontend/README.md @@ -0,0 +1,70 @@ +# Getting Started with Create React App + +This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app). + +## Available Scripts + +In the project directory, you can run: + +### `yarn start` + +Runs the app in the development mode.\ +Open [http://localhost:3000](http://localhost:3000) to view it in your browser. + +The page will reload when you make changes.\ +You may also see any lint errors in the console. + +### `yarn test` + +Launches the test runner in the interactive watch mode.\ +See the section about [running tests](https://facebook.github.io/create-react-app/docs/running-tests) for more information. + +### `yarn build` + +Builds the app for production to the `build` folder.\ +It correctly bundles React in production mode and optimizes the build for the best performance. + +The build is minified and the filenames include the hashes.\ +Your app is ready to be deployed! + +See the section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information. + +### `yarn eject` + +**Note: this is a one-way operation. Once you `eject`, you can't go back!** + +If you aren't satisfied with the build tool and configuration choices, you can `eject` at any time. This command will remove the single build dependency from your project. + +Instead, it will copy all the configuration files and the transitive dependencies (webpack, Babel, ESLint, etc) right into your project so you have full control over them. All of the commands except `eject` will still work, but they will point to the copied scripts so you can tweak them. At this point you're on your own. + +You don't have to ever use `eject`. The curated feature set is suitable for small and middle deployments, and you shouldn't feel obligated to use this feature. However we understand that this tool wouldn't be useful if you couldn't customize it when you are ready for it. + +## Learn More + +You can learn more in the [Create React App documentation](https://facebook.github.io/create-react-app/docs/getting-started). + +To learn React, check out the [React documentation](https://reactjs.org/). + +### Code Splitting + +This section has moved here: [https://facebook.github.io/create-react-app/docs/code-splitting](https://facebook.github.io/create-react-app/docs/code-splitting) + +### Analyzing the Bundle Size + +This section has moved here: [https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size](https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size) + +### Making a Progressive Web App + +This section has moved here: [https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app](https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app) + +### Advanced Configuration + +This section has moved here: [https://facebook.github.io/create-react-app/docs/advanced-configuration](https://facebook.github.io/create-react-app/docs/advanced-configuration) + +### Deployment + +This section has moved here: [https://facebook.github.io/create-react-app/docs/deployment](https://facebook.github.io/create-react-app/docs/deployment) + +### `yarn build` fails to minify + +This section has moved here: [https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify](https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify) diff --git a/murfey-frontend/mime.types b/murfey-frontend/mime.types new file mode 100644 index 000000000..d77e2680c --- /dev/null +++ b/murfey-frontend/mime.types @@ -0,0 +1,99 @@ +types { + text/html html htm shtml; + text/css css; + text/xml xml; + image/gif gif; + image/jpeg jpeg jpg; + application/javascript js; + application/atom+xml atom; + application/rss+xml rss; + + text/mathml mml; + text/plain txt; + text/vnd.sun.j2me.app-descriptor jad; + text/vnd.wap.wml wml; + text/x-component htc; + + image/avif avif; + image/png png; + image/svg+xml svg svgz; + image/tiff tif tiff; + image/vnd.wap.wbmp wbmp; + image/webp webp; + image/x-icon ico; + image/x-jng jng; + image/x-ms-bmp bmp; + + font/woff woff; + font/woff2 woff2; + + application/java-archive jar war ear; + application/json json; + application/mac-binhex40 hqx; + application/msword doc; + application/pdf pdf; + application/postscript ps eps ai; + application/rtf rtf; + application/vnd.apple.mpegurl m3u8; + application/vnd.google-earth.kml+xml kml; + application/vnd.google-earth.kmz kmz; + application/vnd.ms-excel xls; + application/vnd.ms-fontobject eot; + application/vnd.ms-powerpoint ppt; + application/vnd.oasis.opendocument.graphics odg; + application/vnd.oasis.opendocument.presentation odp; + application/vnd.oasis.opendocument.spreadsheet ods; + application/vnd.oasis.opendocument.text odt; + application/vnd.openxmlformats-officedocument.presentationml.presentation + pptx; + application/vnd.openxmlformats-officedocument.spreadsheetml.sheet + xlsx; + application/vnd.openxmlformats-officedocument.wordprocessingml.document + docx; + application/vnd.wap.wmlc wmlc; + application/wasm wasm; + application/x-7z-compressed 7z; + application/x-cocoa cco; + application/x-java-archive-diff jardiff; + application/x-java-jnlp-file jnlp; + application/x-makeself run; + application/x-perl pl pm; + application/x-pilot prc pdb; + application/x-rar-compressed rar; + application/x-redhat-package-manager rpm; + application/x-sea sea; + application/x-shockwave-flash swf; + application/x-stuffit sit; + application/x-tcl tcl tk; + application/x-x509-ca-cert der pem crt; + application/x-xpinstall xpi; + application/xhtml+xml xhtml; + application/xspf+xml xspf; + application/zip zip; + + application/octet-stream bin exe dll; + application/octet-stream deb; + application/octet-stream dmg; + application/octet-stream iso img; + application/octet-stream msi msp msm; + + audio/midi mid midi kar; + audio/mpeg mp3; + audio/ogg ogg; + audio/x-m4a m4a; + audio/x-realaudio ra; + + video/3gpp 3gpp 3gp; + video/mp2t ts; + video/mp4 mp4; + video/mpeg mpeg mpg; + video/quicktime mov; + video/webm webm; + video/x-flv flv; + video/x-m4v m4v; + video/x-mng mng; + video/x-ms-asf asx asf; + video/x-ms-wmv wmv; + video/x-msvideo avi; +} + diff --git a/murfey-frontend/nginx/conf.d b/murfey-frontend/nginx/conf.d new file mode 100644 index 000000000..cd28dd198 --- /dev/null +++ b/murfey-frontend/nginx/conf.d @@ -0,0 +1,28 @@ +worker_processes 3; +pid /tmp/nginx.pid; # Changed from /var/run/nginx.pid +error_log /var/log/nginx/error.log; +events { + worker_connections 10240; +} + +http { + include mime.types; + client_body_temp_path /tmp/client_temp; + proxy_temp_path /tmp/proxy_temp_path; + fastcgi_temp_path /tmp/fastcgi_temp; + uwsgi_temp_path /tmp/uwsgi_temp; + scgi_temp_path /tmp/scgi_temp; + server { + listen 8080; + location / { + root /usr/share/nginx/html; + index index.html index.htm; + try_files $uri $uri/ /index.html; + } + error_page 500 502 503 504 /50x.html; + location = /50x.html { + root /usr/share/nginx/html; + } + } +} + diff --git a/murfey-frontend/openapi.yaml b/murfey-frontend/openapi.yaml new file mode 100644 index 000000000..c4b3b6e5f --- /dev/null +++ b/murfey-frontend/openapi.yaml @@ -0,0 +1,1869 @@ +components: + schemas: + ClientInfo: + properties: + id: + title: Id + type: integer + required: + - id + title: ClientInfo + type: object + CompletedTiltSeries: + properties: + rsync_source: + title: Rsync Source + type: string + tilt_series: + items: + type: string + title: Tilt Series + type: array + required: + - tilt_series + - rsync_source + title: CompletedTiltSeries + type: object + ConnectionFileParameters: + properties: + destinations: + items: + type: string + title: Destinations + type: array + filename: + title: Filename + type: string + required: + - filename + - destinations + title: ConnectionFileParameters + type: object + ContextInfo: + properties: + acquisition_software: + title: Acquisition Software + type: string + experiment_type: + title: Experiment Type + type: string + required: + - experiment_type + - acquisition_software + title: ContextInfo + type: object + DCGroupParameters: + properties: + experiment_type: + title: Experiment Type + type: string + experiment_type_id: + title: Experiment Type Id + type: integer + tag: + title: Tag + type: string + required: + - experiment_type + - experiment_type_id + - tag + title: DCGroupParameters + type: object + DCParameters: + properties: + acquisition_software: + title: Acquisition Software + type: string + c2aperture: + title: C2Aperture + type: number + experiment_type: + title: Experiment Type + type: string + exposure_time: + title: Exposure Time + type: number + file_extension: + title: File Extension + type: string + image_directory: + title: Image Directory + type: string + image_size_x: + title: Image Size X + type: integer + image_size_y: + title: Image Size Y + type: integer + magnification: + title: Magnification + type: number + phase_plate: + default: false + title: Phase Plate + type: boolean + pixel_size_on_image: + title: Pixel Size On Image + type: string + slit_width: + title: Slit Width + type: number + source: + title: Source + type: string + tag: + title: Tag + type: string + total_exposed_dose: + title: Total Exposed Dose + type: number + voltage: + title: Voltage + type: number + required: + - voltage + - pixel_size_on_image + - experiment_type + - image_size_x + - image_size_y + - file_extension + - acquisition_software + - image_directory + - tag + - source + - magnification + title: DCParameters + type: object + File: + properties: + description: + title: Description + type: string + name: + title: Name + type: string + size: + title: Size + type: integer + timestamp: + title: Timestamp + type: number + required: + - name + - description + - size + - timestamp + title: File + type: object + FractionationParameters: + properties: + dose_per_frame: + title: Dose Per Frame + type: number + fractionation: + title: Fractionation + type: integer + fractionation_file_name: + default: eer_fractionation.txt + title: Fractionation File Name + type: string + num_frames: + title: Num Frames + type: integer + required: + - num_frames + - fractionation + - dose_per_frame + title: FractionationParameters + type: object + GainReference: + properties: + gain_ref: + format: path + title: Gain Ref + type: string + rescale: + default: true + title: Rescale + type: boolean + required: + - gain_ref + title: GainReference + type: object + HTTPValidationError: + properties: + detail: + items: + $ref: "#/components/schemas/ValidationError" + title: Detail + type: array + title: HTTPValidationError + type: object + ProcessFile: + properties: + autoproc_program_id: + title: Autoproc Program Id + type: integer + data_collection_id: + title: Data Collection Id + type: integer + description: + title: Description + type: string + dose_per_frame: + title: Dose Per Frame + type: number + eer_fractionation_file: + title: Eer Fractionation File + type: string + extract_downscale: + default: 1 + title: Extract Downscale + type: integer + gain_ref: + title: Gain Ref + type: string + image_number: + title: Image Number + type: integer + mc_binning: + default: 1 + title: Mc Binning + type: integer + mc_uuid: + title: Mc Uuid + type: integer + path: + title: Path + type: string + pixel_size: + title: Pixel Size + type: number + processing_job: + title: Processing Job + type: integer + size: + title: Size + type: integer + timestamp: + title: Timestamp + type: number + voltage: + default: 300 + title: Voltage + type: number + required: + - path + - description + - size + - timestamp + - image_number + - mc_uuid + - pixel_size + - dose_per_frame + title: ProcessFile + type: object + ProcessingJobParameters: + properties: + experiment_type: + default: spa + title: Experiment Type + type: string + parameters: + default: {} + title: Parameters + type: object + recipe: + title: Recipe + type: string + tag: + title: Tag + type: string + required: + - tag + - recipe + title: ProcessingJobParameters + type: object + ProcessingParametersSPA: + properties: + acquisition_software: + title: Acquisition Software + type: string + boxsize: + title: Boxsize + type: integer + c2aperture: + title: C2Aperture + type: number + dose_per_frame: + title: Dose Per Frame + type: number + downscale: + title: Downscale + type: boolean + eer_fractionation: + title: Eer Fractionation + type: integer + experiment_type: + title: Experiment Type + type: string + exposure_time: + title: Exposure Time + type: number + file_extension: + title: File Extension + type: string + gain_ref: + title: Gain Ref + type: string + image_size_x: + title: Image Size X + type: integer + image_size_y: + title: Image Size Y + type: integer + magnification: + title: Magnification + type: integer + mask_diameter: + title: Mask Diameter + type: integer + motion_corr_binning: + title: Motion Corr Binning + type: integer + particle_diameter: + title: Particle Diameter + type: number + phase_plate: + default: false + title: Phase Plate + type: boolean + pixel_size_on_image: + title: Pixel Size On Image + type: string + slit_width: + title: Slit Width + type: number + small_boxsize: + title: Small Boxsize + type: integer + symmetry: + title: Symmetry + type: string + tag: + title: Tag + type: string + total_exposed_dose: + title: Total Exposed Dose + type: number + use_cryolo: + title: Use Cryolo + type: boolean + voltage: + title: Voltage + type: number + required: + - tag + - dose_per_frame + - experiment_type + - voltage + - image_size_x + - image_size_y + - pixel_size_on_image + - motion_corr_binning + - file_extension + - acquisition_software + - use_cryolo + - symmetry + - downscale + - eer_fractionation + title: ProcessingParametersSPA + type: object + RegistrationMessage: + properties: + params: + title: Params + type: object + registration: + title: Registration + type: string + required: + - registration + title: RegistrationMessage + type: object + RsyncerInfo: + properties: + bytes: + default: 0 + title: Bytes + type: integer + client_id: + title: Client Id + type: integer + data_bytes: + default: 0 + title: Data Bytes + type: integer + destination: + title: Destination + type: string + increment_count: + default: 1 + title: Increment Count + type: integer + increment_data_count: + default: 0 + title: Increment Data Count + type: integer + source: + title: Source + type: string + transferring: + default: true + title: Transferring + type: boolean + required: + - source + - destination + - client_id + title: RsyncerInfo + type: object + SPAProcessFile: + properties: + autoproc_program_id: + title: Autoproc Program Id + type: integer + data_collection_id: + title: Data Collection Id + type: integer + description: + title: Description + type: string + dose_per_frame: + title: Dose Per Frame + type: number + eer_fractionation_file: + title: Eer Fractionation File + type: string + extract_downscale: + default: true + title: Extract Downscale + type: boolean + gain_ref: + title: Gain Ref + type: string + image_number: + title: Image Number + type: integer + mc_binning: + default: 1 + title: Mc Binning + type: integer + path: + title: Path + type: string + pixel_size: + title: Pixel Size + type: number + processing_job: + title: Processing Job + type: integer + source: + default: "" + title: Source + type: string + tag: + title: Tag + type: string + required: + - tag + - path + - description + - image_number + title: SPAProcessFile + type: object + SPAProcessingParameters: + properties: + job_id: + title: Job Id + type: integer + required: + - job_id + title: SPAProcessingParameters + type: object + SessionInfo: + properties: + rescale: + default: true + title: Rescale + type: boolean + session_id: + title: Session Id + type: integer + session_name: + default: "" + title: Session Name + type: string + title: SessionInfo + type: object + SmartEMAtlasRequest: + properties: + atlas_path: + format: path + title: Atlas Path + type: string + num_preds: + default: 15 + title: Num Preds + type: integer + output_dir: + format: path + title: Output Dir + type: string + required: + - atlas_path + - output_dir + title: SmartEMAtlasRequest + type: object + SuggestedPathParameters: + properties: + base_path: + format: path + title: Base Path + type: string + touch: + default: false + title: Touch + type: boolean + required: + - base_path + title: SuggestedPathParameters + type: object + TiltInfo: + properties: + movie_path: + title: Movie Path + type: string + rsync_source: + title: Rsync Source + type: string + tilt_series_tag: + title: Tilt Series Tag + type: string + required: + - tilt_series_tag + - movie_path + - rsync_source + title: TiltInfo + type: object + TiltSeriesInfo: + properties: + client_id: + title: Client Id + type: integer + rsync_source: + title: Rsync Source + type: string + tag: + title: Tag + type: string + required: + - client_id + - tag + - rsync_source + title: TiltSeriesInfo + type: object + TiltSeriesProcessingDetails: + properties: + autoproc_program_id: + title: Autoproc Program Id + type: integer + dcid: + title: Dcid + type: integer + file_tilt_list: + title: File Tilt List + type: string + manual_tilt_offset: + title: Manual Tilt Offset + type: integer + motion_corrected_path: + title: Motion Corrected Path + type: string + movie_id: + title: Movie Id + type: integer + name: + title: Name + type: string + pixel_size: + title: Pixel Size + type: number + processing_job: + title: Processing Job + type: integer + required: + - name + - file_tilt_list + - dcid + - processing_job + - autoproc_program_id + - motion_corrected_path + - movie_id + - pixel_size + - manual_tilt_offset + title: TiltSeriesProcessingDetails + type: object + ValidationError: + properties: + loc: + items: + anyOf: + - type: string + - type: integer + title: Location + type: array + msg: + title: Message + type: string + type: + title: Error Type + type: string + required: + - loc + - msg + - type + title: ValidationError + type: object + Visit: + properties: + beamline: + title: Beamline + type: string + end: + format: date-time + title: End + type: string + name: + title: Name + type: string + proposal_title: + title: Proposal Title + type: string + session_id: + title: Session Id + type: integer + start: + format: date-time + title: Start + type: string + required: + - start + - end + - session_id + - name + - beamline + - proposal_title + title: Visit + type: object +info: + title: Murfey server + version: 0.1.0 +openapi: 3.1.0 +paths: + /: + get: + operationId: root__get + responses: + "200": + content: + text/html: + schema: + type: string + description: Successful Response + summary: Root + /bootstrap/: + get: + description: + "Return a website containing instructions for installing the Murfey + client on a + + machine with no internet access." + operationId: get_bootstrap_instructions_bootstrap__get + responses: + "200": + content: + text/html: + schema: + type: string + description: Successful Response + summary: Get Bootstrap Instructions + tags: + - bootstrap + /bootstrap/murfey.whl: + get: + description: + "Return a wheel file containing the latest release version of Murfey. + We should + + not have to worry about the exact Python compatibility here, as long as + + murfey.bootstrap is compatible with all relevant versions of Python. + + This also ignores yanked releases, which again should be fine." + operationId: get_murfey_wheel_bootstrap_murfey_whl_get + responses: + "200": + description: Successful Response + summary: Get Murfey Wheel + tags: + - bootstrap + /bootstrap/pip.whl: + get: + description: + "Return a static version of pip. This does not need to be the newest + or best, + + but has to be compatible with all supported Python versions. + + This is only used during bootstrapping by the client to identify and then + + download the actually newest appropriate version of pip." + operationId: get_pip_wheel_bootstrap_pip_whl_get + responses: + "200": + description: Successful Response + summary: Get Pip Wheel + tags: + - bootstrap + /clients: + get: + operationId: get_clients_clients_get + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + summary: Get Clients + /clients/{client_id}/rsyncers: + get: + operationId: get_rsyncers_for_client_clients__client_id__rsyncers_get + parameters: + - in: path + name: client_id + required: true + schema: + title: Client Id + type: integer + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Get Rsyncers For Client + /clients/{client_id}/session: + delete: + operationId: remove_session_clients__client_id__session_delete + parameters: + - in: path + name: client_id + required: true + schema: + title: Client Id + type: integer + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Remove Session + post: + operationId: link_client_to_session_clients__client_id__session_post + parameters: + - in: path + name: client_id + required: true + schema: + title: Client Id + type: integer + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/SessionInfo" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Link Client To Session + /clients/{client_id}/spa_processing_parameters: + get: + operationId: get_spa_proc_params_clients__client_id__spa_processing_parameters_get + parameters: + - in: path + name: client_id + required: true + schema: + title: Client Id + type: integer + responses: + "200": + content: + application/json: + schema: + items: + type: object + title: + Response Get Spa Proc Params Clients Client Id Spa Processing + Parameters Get + type: array + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Get Spa Proc Params + post: + operationId: register_spa_proc_params_clients__client_id__spa_processing_parameters_post + parameters: + - in: path + name: client_id + required: true + schema: + title: Client Id + type: integer + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ProcessingParametersSPA" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Register Spa Proc Params + /cygwin/setup-x86_64.exe: + get: + description: + "Obtain and past though a Cygwin installer from an official source. + + This is used during client bootstrapping and can download and install the + + Cygwin distribution that then remains on the client machines." + operationId: get_cygwin_setup_cygwin_setup_x86_64_exe_get + responses: + "200": + description: Successful Response + summary: Get Cygwin Setup + tags: + - bootstrap + /cygwin/{request_path}: + get: + description: Forward a Cygwin setup request to an official mirror. + operationId: parse_cygwin_request_cygwin__request_path__get + parameters: + - in: path + name: request_path + required: true + schema: + title: Request Path + type: string + responses: + "200": + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Parse Cygwin Request + tags: + - bootstrap + /feedback: + post: + operationId: send_murfey_message_feedback_post + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/RegistrationMessage" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Send Murfey Message + /machine/: + get: + operationId: machine_info_machine__get + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + summary: Machine Info + /microscope/: + get: + operationId: get_mic_microscope__get + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + summary: Get Mic + /microscope_image/: + get: + operationId: get_mic_image_microscope_image__get + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + summary: Get Mic Image + /new_client_id/: + get: + operationId: new_client_id_new_client_id__get + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + summary: New Client Id + /plugins/{package}: + get: + operationId: get_plugin_wheel_plugins__package__get + parameters: + - in: path + name: package + required: true + schema: + title: Package + type: string + responses: + "200": + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Get Plugin Wheel + tags: + - bootstrap + /pypi/: + get: + description: Obtain list of all PyPI packages via the simple API (PEP 503). + operationId: get_pypi_index_pypi__get + responses: + "200": + description: Successful Response + summary: Get Pypi Index + tags: + - bootstrap + /pypi/{package}/: + get: + description: + "Obtain list of all package downloads from PyPI via the simple + API (PEP 503), + + and rewrite all download URLs to point to this server, + + underneath the current directory." + operationId: get_pypi_package_downloads_list_pypi__package___get + parameters: + - in: path + name: package + required: true + schema: + title: Package + type: string + responses: + "200": + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Get Pypi Package Downloads List + tags: + - bootstrap + /pypi/{package}/{filename}: + get: + description: Obtain and pass through a specific download for a PyPI package. + operationId: get_pypi_file_pypi__package___filename__get + parameters: + - in: path + name: package + required: true + schema: + title: Package + type: string + - in: path + name: filename + required: true + schema: + title: Filename + type: string + responses: + "200": + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Get Pypi File + tags: + - bootstrap + /sessions: + get: + operationId: get_sessions_sessions_get + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + summary: Get Sessions + /sessions/{session_id}: + delete: + operationId: remove_session_by_id_sessions__session_id__delete + parameters: + - in: path + name: session_id + required: true + schema: + title: Session Id + type: integer + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Remove Session By Id + /version: + get: + operationId: get_version_version_get + parameters: + - in: query + name: client_version + required: false + schema: + default: "" + title: Client Version + type: string + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Get Version + /visits/: + get: + operationId: all_visit_info_visits__get + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + summary: All Visit Info + /visits/{visit_name}: + get: + operationId: visit_info_visits__visit_name__get + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Visit Info + post: + operationId: register_client_to_visit_visits__visit_name__post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ClientInfo" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Register Client To Visit + /visits/{visit_name}/align: + post: + operationId: request_tilt_series_alignment_visits__visit_name__align_post + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/TiltSeriesProcessingDetails" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Request Tilt Series Alignment + /visits/{visit_name}/context: + post: + operationId: register_context_visits__visit_name__context_post + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ContextInfo" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Register Context + /visits/{visit_name}/eer_fractionation_file: + post: + operationId: write_eer_fractionation_file_visits__visit_name__eer_fractionation_file_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/FractionationParameters" + required: true + responses: + "200": + content: + application/json: + schema: + title: + Response Write Eer Fractionation File Visits Visit Name Eer + Fractionation File Post + type: object + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Write Eer Fractionation File + /visits/{visit_name}/files: + post: + operationId: add_file_visits__visit_name__files_post + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/File" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Add File + /visits/{visit_name}/increment_rsync_file_count: + post: + operationId: increment_rsync_file_count_visits__visit_name__increment_rsync_file_count_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/RsyncerInfo" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Increment Rsync File Count + /visits/{visit_name}/increment_rsync_transferred_files: + post: + operationId: increment_rsync_transferred_files_visits__visit_name__increment_rsync_transferred_files_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/RsyncerInfo" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Increment Rsync Transferred Files + /visits/{visit_name}/process_gain: + post: + operationId: process_gain_visits__visit_name__process_gain_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/GainReference" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Process Gain + /visits/{visit_name}/rsyncer: + post: + operationId: register_rsyncer_visits__visit_name__rsyncer_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/RsyncerInfo" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Register Rsyncer + /visits/{visit_name}/smartem_atlas/: + post: + operationId: request_smartem_atlas_analysis_visits__visit_name__smartem_atlas__post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/SmartEMAtlasRequest" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Request Smartem Atlas Analysis + /visits/{visit_name}/spa_processing: + post: + operationId: request_spa_processing_visits__visit_name__spa_processing_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/SPAProcessingParameters" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Request Spa Processing + /visits/{visit_name}/suggested_path: + post: + operationId: suggest_path_visits__visit_name__suggested_path_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/SuggestedPathParameters" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Suggest Path + /visits/{visit_name}/tilt: + post: + operationId: register_tilt_visits__visit_name__tilt_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/TiltInfo" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Register Tilt + /visits/{visit_name}/tilt_series: + post: + operationId: register_tilt_series_visits__visit_name__tilt_series_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/TiltSeriesInfo" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Register Tilt Series + /visits/{visit_name}/tomography_preprocess: + post: + operationId: request_tomography_preprocessing_visits__visit_name__tomography_preprocess_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ProcessFile" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Request Tomography Preprocessing + /visits/{visit_name}/write_connections_file: + post: + operationId: write_conn_file_visits__visit_name__write_connections_file_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ConnectionFileParameters" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Write Conn File + /visits/{visit_name}/{client_id}/completed_tilt_series: + post: + operationId: register_completed_tilt_series_visits__visit_name___client_id__completed_tilt_series_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + - in: path + name: client_id + required: true + schema: + title: Client Id + type: integer + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/CompletedTiltSeries" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Register Completed Tilt Series + /visits/{visit_name}/{client_id}/flush_spa_processing: + post: + operationId: flush_spa_processing_visits__visit_name___client_id__flush_spa_processing_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + - in: path + name: client_id + required: true + schema: + title: Client Id + type: integer + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Flush Spa Processing + /visits/{visit_name}/{client_id}/register_data_collection_group: + post: + operationId: register_dc_group_visits__visit_name___client_id__register_data_collection_group_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + - in: path + name: client_id + required: true + schema: + title: Client Id + type: integer + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/DCGroupParameters" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Register Dc Group + /visits/{visit_name}/{client_id}/register_processing_job: + post: + operationId: register_proc_visits__visit_name___client_id__register_processing_job_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + - in: path + name: client_id + required: true + schema: + title: Client Id + type: integer + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/ProcessingJobParameters" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Register Proc + /visits/{visit_name}/{client_id}/spa_preprocess: + post: + operationId: request_spa_preprocessing_visits__visit_name___client_id__spa_preprocess_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + type: string + - in: path + name: client_id + required: true + schema: + title: Client Id + type: integer + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/SPAProcessFile" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Request Spa Preprocessing + /visits/{visit_name}/{client_id}/start_data_collection: + post: + operationId: start_dc_visits__visit_name___client_id__start_data_collection_post + parameters: + - in: path + name: visit_name + required: true + schema: + title: Visit Name + - in: path + name: client_id + required: true + schema: + title: Client Id + type: integer + requestBody: + content: + application/json: + schema: + $ref: "#/components/schemas/DCParameters" + required: true + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Start Dc + /visits_raw: + get: + operationId: get_current_visits_visits_raw_get + responses: + "200": + content: + application/json: + schema: + items: + $ref: "#/components/schemas/Visit" + title: Response Get Current Visits Visits Raw Get + type: array + description: Successful Response + summary: Get Current Visits + /ws/test/{client_id}: + delete: + operationId: close_ws_connection_ws_test__client_id__delete + parameters: + - in: path + name: client_id + required: true + schema: + title: Client Id + type: integer + responses: + "200": + content: + application/json: + schema: {} + description: Successful Response + "422": + content: + application/json: + schema: + $ref: "#/components/schemas/HTTPValidationError" + description: Validation Error + summary: Close Ws Connection + tags: + - websocket +tags: + - description: " + + API endpoints related to installing Murfey on a client. + + + Client machines may not have a direct internet connection, so Murfey allows + + passing through requests to PyPI using the PEP 503 simple API, and download + + requests to the Cygwin website and mirrors. + + + A static HTML page gives instructions on how to install on a network-isolated + + system that has Python already installed. A previously set up system does not + + need to have pip installed in order to bootstrap Murfey. Python and rsync are + + required. + + " + externalDocs: + description: PEP 503 + url: https://www.python.org/dev/peps/pep-0503/ + name: bootstrap diff --git a/murfey-frontend/package.json b/murfey-frontend/package.json new file mode 100644 index 000000000..37f5b1531 --- /dev/null +++ b/murfey-frontend/package.json @@ -0,0 +1,58 @@ +{ + "name": "murfey-frontend", + "version": "0.1.0", + "private": true, + "dependencies": { + "@chakra-ui/icons": "^2.1.1", + "@chakra-ui/react": "^2.8.2", + "@diamondlightsource/ui-components": "^1.0.3", + "@emotion/react": "^11.11.1", + "@emotion/styled": "^11.11.0", + "@tanstack/react-query": "^5.12.2", + "@tanstack/react-query-devtools": "^5.12.2", + "@testing-library/jest-dom": "^5.14.1", + "@testing-library/react": "^13.0.0", + "@testing-library/user-event": "^13.2.1", + "@types/uuid": "^10.0.0", + "framer-motion": "^10.16.12", + "react": "^18.2.0", + "react-collapsible": "^2.10.0", + "react-dom": "^18.2.0", + "react-query": "^3.39.3", + 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HcmV?d00001 diff --git a/murfey-frontend/public/manifest.json b/murfey-frontend/public/manifest.json new file mode 100644 index 000000000..080d6c77a --- /dev/null +++ b/murfey-frontend/public/manifest.json @@ -0,0 +1,25 @@ +{ + "short_name": "React App", + "name": "Create React App Sample", + "icons": [ + { + "src": "favicon.ico", + "sizes": "64x64 32x32 24x24 16x16", + "type": "image/x-icon" + }, + { + "src": "logo192.png", + "type": "image/png", + "sizes": "192x192" + }, + { + "src": "logo512.png", + "type": "image/png", + "sizes": "512x512" + } + ], + "start_url": ".", + "display": "standalone", + "theme_color": "#000000", + "background_color": "#ffffff" +} diff --git a/murfey-frontend/public/robots.txt b/murfey-frontend/public/robots.txt new file mode 100644 index 000000000..e9e57dc4d --- /dev/null +++ b/murfey-frontend/public/robots.txt @@ -0,0 +1,3 @@ +# https://www.robotstxt.org/robotstxt.html +User-agent: * +Disallow: diff --git a/murfey-frontend/src/components/forms.tsx b/murfey-frontend/src/components/forms.tsx new file mode 100644 index 000000000..e654a9ce3 --- /dev/null +++ b/murfey-frontend/src/components/forms.tsx @@ -0,0 +1,195 @@ +import { + Button, + Divider, + Text, + FormControl, + FormLabel, + Input, + NumberInput, + NumberInputField, + NumberInputStepper, + NumberIncrementStepper, + NumberDecrementStepper, + RadioGroup, + Radio, + HStack, + VStack, + Select, + Switch, + Link, +} from "@chakra-ui/react"; +import { Link as LinkRouter } from "react-router-dom"; + +import React, { ReactElement } from "react"; + +const formDataSPA: { [key: string]: any } = { + type: "SPA", + dose_per_frame: 1, + symmetry: "C1", + particle_diameter: null, + extract_downscale: true, + eer_fractionation: 20, +}; + +const formDataTomo: { [key: string]: any } = { + type: "tomo", + dose_per_frame: 0.5, + eer_fractionation: 20, +}; + +const SpaForm = (submissionCallback: (arg0: any) => void) => { + const validateInt = (char: string) => { + return /\d/.test(char); + }; + const validateFloat = (char: string) => { + return /^\d*\.?\d*$/.test(char); + }; + const [symmetryType, setSymmetryType] = React.useState("C"); + const [particleDetection, setParticleDetection] = React.useState(true); + const handleChange = (event: React.ChangeEvent) => { + setSymmetryType(event.target.value); + }; + const handleSwitchChange = (event: React.ChangeEvent) => { + setParticleDetection(!particleDetection); + }; + const setFormElement = ( + event: React.FormEvent, + callback: (arg0: any) => void, + ) => { + event.preventDefault(); + const formData = new FormData(event.currentTarget); + formDataSPA.dose_per_frame = formData.get("dose"); + formDataSPA.symmetry = ((formData.get("symmetry1") as string) + + formData.get("symmetry2")) as string; + formDataSPA.particle_diameter = formData.get("detect-particle-size") + ? null + : formData.get("particle-diameter"); + formDataSPA.eer_fractionation = formData.get("eer-grouping"); + callback(formDataSPA); + }; + + return ( +
setFormElement(e, submissionCallback)}> + + + + + {"Dose per frame [\u212B / pixel]"} + + + + Symmetry + + + + + + + + + + + + + + {"EER grouping (number of EER frames in each fraction)"} + + + + + + Automatically detect particle size + + + + {!particleDetection ? ( + + {"Particle diameter [\u212B]"} + + + ) : ( + <> + )} + + + Downscale in extraction + + + + + + + +
+ ); +}; + +const TomoForm = (submissionCallback: (arg0: any) => void) => { + const setFormElement = ( + event: React.FormEvent, + callback: (arg0: any) => void, + ) => { + event.preventDefault(); + const formData = new FormData(event.currentTarget); + formDataSPA.dose_per_frame = formData.get("dose"); + formDataSPA.eer_fractionation = formData.get("eer-grouping"); + callback(formDataSPA); + }; + return ( +
setFormElement(e, submissionCallback)}> + + + + + {"Dose per frame [\u212B / pixel]"} + + + + + {"EER grouping (number of EER frames in each fraction)"} + + + + + + + +
+ ); +}; + +interface Forms { + [expType: string]: ReactElement; +} + +export const getForm = ( + expType: string, + submissionCallback: (arg0: any) => void, +) => { + let forms = { + spa: SpaForm(submissionCallback), + tomography: TomoForm(submissionCallback), + } as Forms; + return forms[expType]; +}; diff --git a/murfey-frontend/src/components/gridSquareCard.tsx b/murfey-frontend/src/components/gridSquareCard.tsx new file mode 100644 index 000000000..17fc868d7 --- /dev/null +++ b/murfey-frontend/src/components/gridSquareCard.tsx @@ -0,0 +1,147 @@ +import { + CardBody, + Card, + CardHeader, + Image, + Text, + Box, + Tooltip, + VStack, + Slider, + SliderTrack, + SliderFilledTrack, + SliderThumb, +} from "@chakra-ui/react"; + +import { components } from "schema/main"; +import { getFoilHoles, getNumMovies } from "loaders/gridSquares"; + +import { useState, useEffect } from "react"; + +type GridSquare = components["schemas"]["GridSquare"]; +type FoilHole = components["schemas"]["FoilHole"]; + +const getUrl = (endpoint: string) => { + return ( + (sessionStorage.getItem("murfeyServerURL") ?? + process.env.REACT_APP_API_ENDPOINT) + endpoint + ); +}; + +const GridSquareCard = ( + gs: GridSquare, + sessid: string | undefined, + dcgid: string | undefined, +) => { + const [numFoilHoles, setNumFoilHoles] = useState(0); + const [numMovies, setNumMovies] = useState(0); + const [foilHoleXPositions, setFoilHoleXPositions] = useState([]); + const [foilHoleYPositions, setFoilHoleYPositions] = useState([]); + const [foilHoleNames, setFoilHoleNames] = useState([]); + const [foilHoleImages, setFoilHoleImages] = useState<(string | null)[]>([]); + const [sliderValue, setSliderValue] = useState(10); + const foilHoleSetup = (foilHoles: FoilHole[]) => { + let xpositions: number[] = []; + let ypositions = []; + let names: number[] = []; + let images: (string | null)[] = []; + for (let i = 0; i < foilHoles.length; i++) { + const unscaledx = foilHoles[i].x_location; + const x = + gs.thumbnail_size_x && gs.readout_area_x && unscaledx + ? unscaledx * (gs.thumbnail_size_x / gs.readout_area_x) + : unscaledx; + const unscaledy = foilHoles[i].y_location; + const y = + gs.thumbnail_size_y && gs.readout_area_y && unscaledy + ? unscaledy * (gs.thumbnail_size_y / gs.readout_area_y) + : unscaledy; + if (x) xpositions.push(Math.floor(x)); + if (y) ypositions.push(Math.floor(y)); + if (x) names.push(foilHoles[i].name); + const image = foilHoles[i].image; + if (x) image ? images.push(image) : images.push(null); + } + setFoilHoleXPositions(xpositions); + setFoilHoleYPositions(ypositions); + setFoilHoleNames(names); + setFoilHoleImages(images); + setNumFoilHoles(foilHoles.length); + }; + useEffect(() => { + getFoilHoles(sessid ?? "0", dcgid ?? "0", gs.name).then((fhs) => + foilHoleSetup(fhs), + ); + getNumMovies(sessid ?? "0", dcgid ?? "0", gs.name).then((nm) => + setNumMovies(nm), + ); + }, []); + + const zip = (a: number[], b: number[]) => a.map((k, i) => [k, b[i]]); + + const foilHoleTooltip = (fhName: number, fhImage: string | null) => { + const fhImageUrl = getUrl( + `display/sessions/${sessid}/data_collection_groups/${dcgid}/grid_squares/${gs.name}/foil_holes/${fhName}/image`, + ); + return ( + + {fhName} + {fhImage ? : <>} + + ); + }; + + return ( + + {gs.name} + + + + + {zip(foilHoleXPositions, foilHoleYPositions).map((pos, index) => ( + + + + ))} + + + {numFoilHoles} foil holes + {numMovies} movies + setSliderValue(val)} + > + + + + + + + + ); +}; + +export { GridSquareCard }; diff --git a/murfey-frontend/src/components/instrumentCard.tsx b/murfey-frontend/src/components/instrumentCard.tsx new file mode 100644 index 000000000..ee4e95a64 --- /dev/null +++ b/murfey-frontend/src/components/instrumentCard.tsx @@ -0,0 +1,58 @@ +import { + Card, + CardBody, + CardHeader, + Image, + Link, + Text, +} from "@chakra-ui/react"; + +import { Link as LinkRouter } from "react-router-dom"; +import { getInstrumentName } from "loaders/general"; + +import React, { useEffect } from "react"; + +const getUrl = (endpoint: string) => { + return ( + (sessionStorage.getItem("murfeyServerURL") ?? + process.env.REACT_APP_API_ENDPOINT) + endpoint + ); +}; + +const InstrumentCard = () => { + const [instrumentName, setInstrumentName] = React.useState(""); + + const resolveName = async () => { + const name: string = await getInstrumentName(); + setInstrumentName(name); + }; + useEffect(() => { + resolveName(); + }, []); + + return ( + + + + + + + {instrumentName} + + + + ); +}; + +export { InstrumentCard }; diff --git a/murfey-frontend/src/components/navbar.tsx b/murfey-frontend/src/components/navbar.tsx new file mode 100644 index 000000000..178dc0cda --- /dev/null +++ b/murfey-frontend/src/components/navbar.tsx @@ -0,0 +1,170 @@ +import { + Box, + Flex, + HStack, + Link, + IconButton, + useDisclosure, + Image, + Tooltip, + VStack, + BoxProps, + Icon, +} from "@chakra-ui/react"; +import { + MdMenu, + MdClose, + MdSignalWifi4Bar, + MdOutlineSignalWifiBad, +} from "react-icons/md"; +import { TbMicroscope, TbSnowflake } from "react-icons/tb"; +import { getInstrumentConnectionStatus } from "loaders/general"; +import { Link as LinkRouter } from "react-router-dom"; +import React from "react"; + +export interface LinkDescriptor { + label: string; + route: string; +} + +interface BaseLinkProps { + links?: LinkDescriptor[]; + as?: React.ElementType; +} + +export interface NavbarProps extends BaseLinkProps, BoxProps { + logo?: string | null; + children?: React.ReactElement; +} + +const NavLinks = ({ links, as }: BaseLinkProps) => ( + <> + {links + ? links.map((link) => ( + + {link.label} + + )) + : null} + +); + +const Navbar = ({ links, as, children, logo, ...props }: NavbarProps) => { + const { isOpen, onOpen, onClose } = useDisclosure(); + const [instrumentConnectionStatus, setInsrumentConnectionStatus] = + React.useState(false); + + const resolveConnectionStatus = async () => { + const status: boolean = await getInstrumentConnectionStatus(); + setInsrumentConnectionStatus(status); + }; + resolveConnectionStatus(); + + return ( + + + : } + aria-label={"Open Menu"} + display={{ md: "none" }} + bg="transparent" + border="none" + _hover={{ background: "transparent", color: "murfey.500" }} + onClick={isOpen ? onClose : onOpen} + /> + + {logo ? ( + + + Home + + + ) : null} + + + + + + + } + aria-label={"Back to the Hub"} + _hover={{ background: "transparent", color: "murfey.500" }} + /> + + + + + + + + + + {children} + + {isOpen && ( + + + + )} + + ); +}; + +export { Navbar }; diff --git a/murfey-frontend/src/components/protectedRoutes.tsx b/murfey-frontend/src/components/protectedRoutes.tsx new file mode 100644 index 000000000..75cd228b0 --- /dev/null +++ b/murfey-frontend/src/components/protectedRoutes.tsx @@ -0,0 +1,20 @@ +import { Navigate, Outlet } from "react-router-dom"; +import { Box } from "@chakra-ui/react"; +import { Navbar } from "components/navbar"; + +const ProtectedRoutes = () => { + const sessionToken = sessionStorage.getItem("token"); + const standard = ( +
+ + + + + + +
+ ); + return sessionToken ? standard : ; +}; + +export { ProtectedRoutes }; diff --git a/murfey-frontend/src/components/setupStepper.tsx b/murfey-frontend/src/components/setupStepper.tsx new file mode 100644 index 000000000..18c9f4f60 --- /dev/null +++ b/murfey-frontend/src/components/setupStepper.tsx @@ -0,0 +1,65 @@ +import { + Box, + Step, + StepDescription, + StepIcon, + StepIndicator, + StepNumber, + StepSeparator, + StepStatus, + StepTitle, + Stepper, + useSteps, +} from "@chakra-ui/react"; + +import React from "react"; + +const getUrl = (endpoint: string) => { + return ( + (sessionStorage.getItem("murfeyServerURL") ?? + process.env.REACT_APP_API_ENDPOINT) + endpoint + ); +}; + +interface StepperStartConditions { + activeStepIndex: number; +} + +const SetupStepper = ({ activeStepIndex }: StepperStartConditions) => { + const steps = [ + { title: "Visit", description: "Select visit" }, + { title: "Gain reference", description: "Transfer and transform" }, + { title: "Parameters", description: "For processing" }, + { title: "Confirm", description: "Start data transfer" }, + ]; + + const { activeStep } = useSteps({ + index: activeStepIndex, + count: steps.length, + }); + + return ( + + {steps.map((step, index) => ( + + + } + incomplete={} + active={} + /> + + + + {step.title} + {step.description} + + + + + ))} + + ); +}; + +export { SetupStepper }; diff --git a/murfey-frontend/src/components/upstreamVisitsCard.tsx b/murfey-frontend/src/components/upstreamVisitsCard.tsx new file mode 100644 index 000000000..a5b802334 --- /dev/null +++ b/murfey-frontend/src/components/upstreamVisitsCard.tsx @@ -0,0 +1,48 @@ +import { Card, CardBody, Button, CardHeader } from "@chakra-ui/react"; + +import { + getUpstreamVisits, + upstreamDataDownloadRequest, +} from "loaders/general"; +import { MdFileDownload } from "react-icons/md"; + +import React, { useEffect } from "react"; + +interface SessionId { + sessid: number; +} + +const UpstreamVisitCard = ({ sessid }: SessionId) => { + const [upstreamVisits, setUpstreamVisits] = React.useState({}); + + const resolveVisits = async () => { + const visits = await getUpstreamVisits(sessid); + setUpstreamVisits(visits); + console.log(upstreamVisits); + }; + useEffect(() => { + resolveVisits(); + }, []); + + return upstreamVisits ? ( + + Upstream Visit Data Download + {Object.keys(upstreamVisits).map((k) => { + return ( + + + + ); + })} + + ) : ( + <> + ); +}; + +export { UpstreamVisitCard }; diff --git a/murfey-frontend/src/index.css b/murfey-frontend/src/index.css new file mode 100644 index 000000000..4a1df4db7 --- /dev/null +++ b/murfey-frontend/src/index.css @@ -0,0 +1,13 @@ +body { + margin: 0; + font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", "Roboto", "Oxygen", + "Ubuntu", "Cantarell", "Fira Sans", "Droid Sans", "Helvetica Neue", + sans-serif; + -webkit-font-smoothing: antialiased; + -moz-osx-font-smoothing: grayscale; +} + +code { + font-family: source-code-pro, Menlo, Monaco, Consolas, "Courier New", + monospace; +} diff --git a/murfey-frontend/src/index.tsx b/murfey-frontend/src/index.tsx new file mode 100644 index 000000000..17a01add8 --- /dev/null +++ b/murfey-frontend/src/index.tsx @@ -0,0 +1,149 @@ +import React, { Suspense } from "react"; +import { createRoot } from "react-dom/client"; +import { ChakraProvider, createStandaloneToast } from "@chakra-ui/react"; +import { + createBrowserRouter, + Navigate, + RouterProvider, +} from "react-router-dom"; +import { Root } from "routes/Root"; +import { DataCollectionGroups } from "routes/DataCollectionGroups"; +import { GridSquares } from "routes/GridSquares"; +import { Home } from "routes/Home"; +import { Hub } from "routes/Hub"; +import { Session } from "routes/Session"; +import { NewSession } from "routes/NewSession"; +import { SessionLinker } from "routes/SessionLinker"; +import { GainRefTransfer } from "routes/GainRefTransfer"; +import { SessionSetup } from "routes/SessionSetup"; +import { MagTable } from "routes/MagTable"; +import { ProcessingParameters } from "routes/ProcessingParameters"; +import { Error } from "routes/Error"; +import { + clientsLoader, + sessionsLoader, + sessionLoader, +} from "loaders/session_clients"; +import { rsyncerLoader } from "loaders/rsyncers"; +import { visitLoader } from "loaders/visits"; +import { gainRefLoader } from "loaders/possibleGainRefs"; +import { instrumentInfoLoader } from "loaders/hub"; +import { magTableLoader } from "loaders/magTable"; +import { processingParametersLoader } from "loaders/processingParameters"; +import { dataCollectionGroupsLoader } from "loaders/dataCollectionGroups"; +import { theme } from "styles/theme"; +import { QueryClient, QueryClientProvider } from "@tanstack/react-query"; +import { ReactQueryDevtools } from "@tanstack/react-query-devtools"; +import { MultigridSetup } from "routes/MultigridSetup"; +import { machineConfigLoader } from "loaders/machineConfig"; +import { ProtectedRoutes } from "components/protectedRoutes"; +import { Login } from "routes/Login"; +import { gridSquaresLoader } from "loaders/gridSquares"; + +const { ToastContainer } = createStandaloneToast(); +const container = document.getElementById("root")!; +const root = createRoot(container); +const queryClient = new QueryClient({ + defaultOptions: { queries: { staleTime: 1.08e7 } }, +}); + +const router = createBrowserRouter([ + { + path: "/hub", + element: , + errorElement: , + loader: instrumentInfoLoader(queryClient), + }, + { + path: "/login", + element: , + errorElement: , + }, + { + path: "/", + element: , + errorElement: , + children: [ + { + path: "/home", + element: , + errorElement: , + loader: sessionsLoader(queryClient), + }, + { + path: "/sessions/:sessid", + element: , + errorElement: , + loader: ({ params }) => rsyncerLoader(queryClient)(params), + }, + { + path: "/instruments/:instrumentName/new_session", + element: , + errorElement: , + loader: ({ params }) => visitLoader(queryClient)(params), + }, + { + path: "/new_session/setup/:sessid", + element: , + errorElement: , + loader: machineConfigLoader(queryClient), + }, + { + path: "/link_session", + element: , + errorElement: , + loader: clientsLoader(queryClient), + }, + { + path: "/sessions/:sessid/gain_ref_transfer", + element: , + errorElement: , + loader: ({ params }) => gainRefLoader(queryClient)(params), + }, + { + path: "/new_session/parameters/:sessid", + element: , + errorElement: , + loader: ({ params }) => sessionLoader(queryClient)(params), + }, + { + path: "/sessions/:sessid/processing_parameters", + element: , + errorElement: , + loader: ({ params }) => processingParametersLoader(queryClient)(params), + }, + { + path: "/mag_table", + element: , + errorElement: , + loader: magTableLoader(queryClient), + }, + { + path: "/sessions/:sessid/data_collection_groups", + element: , + errorElement: , + loader: ({ params }) => dataCollectionGroupsLoader(queryClient)(params), + }, + { + path: "/sessions/:sessid/data_collection_groups/:dcgid/grid_squares", + element: , + errorElement: , + loader: ({ params }) => gridSquaresLoader(queryClient)(params), + }, + ], + }, +]); + +root.render( + + + + + {process.env.NODE_ENV === "development" && ( + + )} + + , +); + +// loader: ({ params }) => gridSquaresLoader(queryClient)(params), diff --git a/murfey-frontend/src/loaders/dataCollectionGroups.tsx b/murfey-frontend/src/loaders/dataCollectionGroups.tsx new file mode 100644 index 000000000..93af47b6c --- /dev/null +++ b/murfey-frontend/src/loaders/dataCollectionGroups.tsx @@ -0,0 +1,33 @@ +import { QueryClient } from "@tanstack/react-query"; +import { client } from "utils/api/client"; +import { Params } from "react-router-dom"; + +const getDataCollectionGroups = async (sessid: string = "0") => { + console.log("data collection groups gather"); + const response = await client.get( + `sessions/${sessid}/data_collection_groups`, + ); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +const queryBuilder = (sessid: string = "0") => { + return { + queryKey: ["sessionId", sessid], + queryFn: () => getDataCollectionGroups(sessid), + staleTime: 60000, + }; +}; + +export const dataCollectionGroupsLoader = + (queryClient: QueryClient) => async (params: Params) => { + const singleQuery = queryBuilder(params.sessid); + return ( + (await queryClient.getQueryData(singleQuery.queryKey)) ?? + (await queryClient.fetchQuery(singleQuery)) + ); + }; diff --git a/murfey-frontend/src/loaders/general.tsx b/murfey-frontend/src/loaders/general.tsx new file mode 100644 index 000000000..cf628b1d9 --- /dev/null +++ b/murfey-frontend/src/loaders/general.tsx @@ -0,0 +1,49 @@ +import { client } from "utils/api/client"; + +export const getInstrumentName = async () => { + const response = await client.get( + `instruments/${sessionStorage.getItem("instrumentName")}/instrument_name`, + ); + + if (response.status !== 200) { + return null; + } + return response.data; +}; + +export const getInstrumentConnectionStatus = async () => { + const response = await client.get( + `instruments/${sessionStorage.getItem("instrumentName")}/instrument_server`, + {}, + false, + ); + + if (response.status !== 200) { + return false; + } + + return response.data; +}; + +export const getUpstreamVisits = async (sessid: number) => { + const response = await client.get(`sessions/${sessid}/upstream_visits`); + + if (response.status !== 200) { + return null; + } + return response.data; +}; + +export const upstreamDataDownloadRequest = async ( + visitName: string, + sessid: number, +) => { + const response = await client.get( + `visits/${visitName}/${sessid}/upstream_tiff_data_request`, + ); + + if (response.status !== 200) { + return null; + } + return response.data; +}; diff --git a/murfey-frontend/src/loaders/gridSquares.tsx b/murfey-frontend/src/loaders/gridSquares.tsx new file mode 100644 index 000000000..2c5a00d82 --- /dev/null +++ b/murfey-frontend/src/loaders/gridSquares.tsx @@ -0,0 +1,80 @@ +import { QueryClient } from "@tanstack/react-query"; +import { client } from "utils/api/client"; +import { Params } from "react-router-dom"; + +const getGridSquares = async ( + sessid: string = "0", + dataCollectionGroupId: string = "0", +) => { + console.log("getting grid squares"); + const response = await client.get( + `sessions/${sessid}/data_collection_groups/${dataCollectionGroupId}/grid_squares`, + ); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +const getNumMovies = async ( + sessid: string, + dataCollectionGroupId: string, + gridSquareId: number, +) => { + const response = await client.get( + `sessions/${sessid}/data_collection_groups/${dataCollectionGroupId}/grid_squares/${gridSquareId}/num_movies`, + ); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +const getFoilHoles = async ( + sessid: string, + dataCollectionGroupId: string, + gridSquareId: number, +) => { + const response = await client.get( + `sessions/${sessid}/data_collection_groups/${dataCollectionGroupId}/grid_squares/${gridSquareId}/foil_holes`, + ); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +const queryBuilder = ( + sessid: string = "0", + dataCollectionGroupId: string = "0", +) => { + return { + queryKey: [ + "gridSquares", + "sessionId", + sessid, + "dataCollectionGroup", + dataCollectionGroupId, + ], + queryFn: () => getGridSquares(sessid, dataCollectionGroupId), + staleTime: 60000, + }; +}; + +export const gridSquaresLoader = + (queryClient: QueryClient) => async (params: Params) => { + // const singleQuery = queryBuilder(params.sessid, params.dcgid); + const singleQuery = queryBuilder(params.sessid); + return ( + (await queryClient.getQueryData(singleQuery.queryKey)) ?? + (await queryClient.fetchQuery(singleQuery)) + ); + }; + +export { getFoilHoles, getNumMovies }; diff --git a/murfey-frontend/src/loaders/hub.tsx b/murfey-frontend/src/loaders/hub.tsx new file mode 100644 index 000000000..a4fa20d45 --- /dev/null +++ b/murfey-frontend/src/loaders/hub.tsx @@ -0,0 +1,22 @@ +import { QueryClient } from "@tanstack/react-query"; +import { client, getPrefix } from "utils/api/client"; + +const getInstrumentInfo = async () => { + const response = await client.hub_get(`instruments`); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +const query = { + queryKey: ["instrumentInfo"], + queryFn: getInstrumentInfo, + staleTime: 60000, +}; + +export const instrumentInfoLoader = (queryClient: QueryClient) => async () => + (await queryClient.getQueryData(query.queryKey)) ?? + (await queryClient.fetchQuery(query)); diff --git a/murfey-frontend/src/loaders/jwt.tsx b/murfey-frontend/src/loaders/jwt.tsx new file mode 100644 index 000000000..0532a0087 --- /dev/null +++ b/murfey-frontend/src/loaders/jwt.tsx @@ -0,0 +1,43 @@ +import { client } from "utils/api/client"; + +type LoginDetails = { + username: string; + password: string; +}; + +export const getJWT = async (loginDetails: LoginDetails) => { + const formData = new FormData(); + formData.append("username", loginDetails.username); + formData.append("password", loginDetails.password); + + const response = await client.post(`token`, formData); + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +export const handshake = async () => { + const response = await client.post( + `instruments/${sessionStorage.getItem( + "instrumentName", + )}/activate_instrument_server`, + {}, + ); + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +export const sessionHandshake = async (sessid: number) => { + const response = await client.post( + `instruments/${sessionStorage.getItem( + "instrumentName", + )}/sessions/${sessid}/activate_instrument_server`, + {}, + ); + return response.data; +}; diff --git a/murfey-frontend/src/loaders/machineConfig.tsx b/murfey-frontend/src/loaders/machineConfig.tsx new file mode 100644 index 000000000..458bd31d3 --- /dev/null +++ b/murfey-frontend/src/loaders/machineConfig.tsx @@ -0,0 +1,27 @@ +import { QueryClient } from "@tanstack/react-query"; +import { components } from "schema/main"; +import { client } from "utils/api/client"; +import { Params } from "react-router-dom"; +import { parseDate } from "utils/generic"; + +export const getMachineConfigData = async () => { + const response = await client.get( + `instruments/${sessionStorage.getItem("instrumentName")}/machine`, + ); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +const query = { + queryKey: ["machineConfig"], + queryFn: getMachineConfigData, + staleTime: 60000, +}; + +export const machineConfigLoader = (queryClient: QueryClient) => async () => + (await queryClient.getQueryData(query.queryKey)) ?? + (await queryClient.fetchQuery(query)); diff --git a/murfey-frontend/src/loaders/magTable.tsx b/murfey-frontend/src/loaders/magTable.tsx new file mode 100644 index 000000000..4a26ff4b8 --- /dev/null +++ b/murfey-frontend/src/loaders/magTable.tsx @@ -0,0 +1,46 @@ +import { QueryClient } from "@tanstack/react-query"; +import { client } from "utils/api/client"; + +const getMagTableData = async () => { + const response = await client.get(`mag_table`); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +export const addMagTableRow = async ( + magnification: number, + pixelSize: number, +) => { + const response = await client.post(`mag_table/`, [ + { + magnification: magnification, + pixel_size: pixelSize, + }, + ]); + if (response.status !== 200) { + return null; + } + return response.data; +}; + +export const removeMagTableRow = async (magnification: number) => { + const response = await client.delete(`mag_table/${magnification}`); + if (response.status !== 200) { + return null; + } + return response.data; +}; + +const query = { + queryKey: ["magTable"], + queryFn: getMagTableData, + staleTime: 60000, +}; + +export const magTableLoader = (queryClient: QueryClient) => async () => + (await queryClient.getQueryData(query.queryKey)) ?? + (await queryClient.fetchQuery(query)); diff --git a/murfey-frontend/src/loaders/multigridSetup.tsx b/murfey-frontend/src/loaders/multigridSetup.tsx new file mode 100644 index 000000000..51434a3b1 --- /dev/null +++ b/murfey-frontend/src/loaders/multigridSetup.tsx @@ -0,0 +1,21 @@ +import { QueryClient } from "@tanstack/react-query"; +import { client } from "utils/api/client"; +import { components } from "schema/main"; + +type MultigridWatcherSpec = components["schemas"]["MultigridWatcherSetup"]; + +export const startMultigridWatcher = async ( + multigridWatcher: MultigridWatcherSpec, + sessionId: number, +) => { + const response = await client.post( + `sessions/${sessionId}/multigrid_watcher`, + multigridWatcher, + ); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; diff --git a/murfey-frontend/src/loaders/possibleGainRefs.tsx b/murfey-frontend/src/loaders/possibleGainRefs.tsx new file mode 100644 index 000000000..70105a708 --- /dev/null +++ b/murfey-frontend/src/loaders/possibleGainRefs.tsx @@ -0,0 +1,84 @@ +import { QueryClient } from "@tanstack/react-query"; +import { client } from "utils/api/client"; +import { Params } from "react-router-dom"; + +const getGainRefData = async (sessionId: string) => { + const response = await client.get( + `instruments/${sessionStorage.getItem( + "instrumentName", + )}/sessions/${sessionId}/possible_gain_references`, + ); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +export const transferGainReference = async ( + sessionId: number, + gainRef: string, +) => { + const response = await client.post( + `sessions/${sessionId}/upload_gain_reference`, + { + gain_path: gainRef, + }, + ); + if (response.status !== 200) { + return null; + } + return response.data; +}; + +export const prepareGainReference = async ( + sessionId: number, + gainRef: string, + rescale: boolean = false, + eer: boolean = false, + tag: string = "", +) => { + const response = await client.post(`sessions/${sessionId}/process_gain`, { + gain_ref: gainRef, + rescale: rescale, + eer: eer, + tag: tag, + }); + if (response.status !== 200) { + return null; + } + return response.data; +}; + +export const updateCurrentGainReference = async ( + sessionId: number, + gainRef: string, +) => { + const response = await client.put(`sessions/${sessionId}/current_gain_ref`, { + path: gainRef, + }); + if (response.status !== 200) { + return null; + } + return response.data; +}; + +const query = (sessid: string) => { + return { + queryKey: ["gainRefs"], + queryFn: () => getGainRefData(sessid), + staleTime: 60000, + }; +}; + +export const gainRefLoader = + (queryClient: QueryClient) => async (params: Params) => { + if (params.sessid) { + const singleQuery = query(params.sessid); + return ( + (await queryClient.getQueryData(singleQuery.queryKey)) ?? + (await queryClient.fetchQuery(singleQuery)) + ); + } + }; diff --git a/murfey-frontend/src/loaders/processingParameters.tsx b/murfey-frontend/src/loaders/processingParameters.tsx new file mode 100644 index 000000000..78d71e14f --- /dev/null +++ b/murfey-frontend/src/loaders/processingParameters.tsx @@ -0,0 +1,34 @@ +import { QueryClient } from "@tanstack/react-query"; +import { client } from "utils/api/client"; +import { Params } from "react-router-dom"; + +const getProcessingParameterData = async (sessid: string = "0") => { + const response = await client.get( + `sessions/${sessid}/spa_processing_parameters`, + ); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +const queryBuilder = (sessid: string = "0") => { + return { + queryKey: ["sessionId", sessid], + queryFn: () => getProcessingParameterData(sessid), + staleTime: 60000, + }; +}; + +export const processingParametersLoader = + (queryClient: QueryClient) => async (params: Params) => { + const singleQuery = queryBuilder(params.sessid); + return ( + (await queryClient.getQueryData(singleQuery.queryKey)) ?? + (await queryClient.fetchQuery(singleQuery)) + ); + }; + +export { getProcessingParameterData }; diff --git a/murfey-frontend/src/loaders/rsyncers.tsx b/murfey-frontend/src/loaders/rsyncers.tsx new file mode 100644 index 000000000..3d0a81eb0 --- /dev/null +++ b/murfey-frontend/src/loaders/rsyncers.tsx @@ -0,0 +1,94 @@ +import { QueryClient } from "@tanstack/react-query"; +import { components } from "schema/main"; +import { client } from "utils/api/client"; +import { Params } from "react-router-dom"; +import { parseDate } from "utils/generic"; + +const getRsyncerData = async (sessionId: string) => { + const response = await client.get(`sessions/${sessionId}/rsyncers`); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +export const pauseRsyncer = async (sessionId: number, source: string) => { + console.log("stopping rsyncer"); + + const response = await client.post(`sessions/${sessionId}/stop_rsyncer`, { + source: source, + }); + + if (response.status !== 200) { + return null; + } + + console.log(response.data); + + return response.data; +}; + +export const restartRsyncer = async (sessionId: number, source: string) => { + console.log("stopping rsyncer"); + + const response = await client.post(`sessions/${sessionId}/restart_rsyncer`, { + source: source, + }); + + if (response.status !== 200) { + return null; + } + + console.log(response.data); + + return response.data; +}; + +export const finaliseRsyncer = async (sessionId: number, source: string) => { + const response = await client.post(`sessions/${sessionId}/finalise_rsyncer`, { + source: source, + }); + + if (response.status !== 200) { + return null; + } + + console.log(response.data); + + return response.data; +}; + +export const removeRsyncer = async (sessionId: number, source: string) => { + console.log("removing rsyncer"); + + const response = await client.post(`sessions/${sessionId}/remove_rsyncer`, { + source: source, + }); + + if (response.status !== 200) { + return null; + } + + console.log(response.data); + + return response.data; +}; + +const queryBuilder = (sessionId: string = "0") => { + return { + queryKey: ["sessid", sessionId], + queryFn: () => getRsyncerData(sessionId), + staleTime: 60000, + }; +}; + +export const rsyncerLoader = + (queryClient: QueryClient) => async (params: Params) => { + const singleQuery = queryBuilder(params.sessid); + return ( + (await queryClient.getQueryData(singleQuery.queryKey)) ?? + (await queryClient.fetchQuery(singleQuery)) + ); + }; diff --git a/murfey-frontend/src/loaders/sessionSetup.tsx b/murfey-frontend/src/loaders/sessionSetup.tsx new file mode 100644 index 000000000..b5eb257bb --- /dev/null +++ b/murfey-frontend/src/loaders/sessionSetup.tsx @@ -0,0 +1,22 @@ +import { QueryClient } from "@tanstack/react-query"; +import { client } from "utils/api/client"; +import { components } from "schema/main"; + +type ProvidedProcessingParameters = + components["schemas"]["ProvidedProcessingParameters"]; + +export const registerProcessingParameters = async ( + processingParameters: ProvidedProcessingParameters, + sessionId: number, +) => { + const response = await client.post( + `sessions/${sessionId}/provided_processing_parameters`, + processingParameters, + ); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; diff --git a/murfey-frontend/src/loaders/session_clients.tsx b/murfey-frontend/src/loaders/session_clients.tsx new file mode 100644 index 000000000..f7af42db4 --- /dev/null +++ b/murfey-frontend/src/loaders/session_clients.tsx @@ -0,0 +1,116 @@ +import { QueryClient } from "@tanstack/react-query"; +import { components } from "schema/main"; +import { client } from "utils/api/client"; +import { Params } from "react-router-dom"; + +export const includePage = (endpoint: string, limit: number, page: number) => + `${endpoint}${endpoint.includes("?") ? "&" : "?"}page=${ + page - 1 + }&limit=${limit}`; + +const getSessionsData = async () => { + const response = await client.get(`sessions`); + + if (response.status !== 200) { + return null; + } + + return { + current: response.data, + }; +}; + +const getClientData = async () => { + const response = await client.get(`clients`); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +const getSessionData = async (sessid: string = "0") => { + const response = await client.get(`session/${sessid}`); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +export const linkSessionToClient = async ( + client_id: number, + sessionName: string, +) => { + const response = await client.post(`clients/${client_id}/session`, { + session_name: sessionName, + }); + if (response.status !== 200) { + return null; + } + return response.data; +}; + +export const createSession = async ( + visit: string, + sessionName: string, + instrumentName: string, +) => { + const response = await client.post( + `instruments/${instrumentName}/visits/${visit}/session/${sessionName}`, + {}, + ); + if (response.status !== 200) { + return null; + } + return response.data; +}; + +export const deleteSessionData = async (sessid: number) => { + const response = await client.delete(`sessions/${sessid}`); + if (response.status !== 200) { + return null; + } + return response.data; +}; + +const query = { + queryKey: ["homepageSessions", sessionStorage.getItem("instrumentName")], + queryFn: getSessionsData, + staleTime: 60000, +}; + +const clientQuery = { + queryKey: ["homepageClients", sessionStorage.getItem("instrumentName")], + queryFn: getClientData, + staleTime: 60000, +}; + +export const sessionsLoader = (queryClient: QueryClient) => async () => + (await queryClient.getQueryData(query.queryKey)) ?? + (await queryClient.fetchQuery(query)); + +export const clientsLoader = (queryClient: QueryClient) => async () => + (await queryClient.getQueryData(clientQuery.queryKey)) ?? + (await queryClient.fetchQuery(clientQuery)); + +const queryBuilder = (sessid: string = "0") => { + return { + queryKey: ["sessionId", sessid], + queryFn: () => getSessionData(sessid), + staleTime: 60000, + }; +}; + +export const sessionLoader = + (queryClient: QueryClient) => async (params: Params) => { + const singleQuery = queryBuilder(params.sessid); + return ( + (await queryClient.getQueryData(singleQuery.queryKey)) ?? + (await queryClient.fetchQuery(singleQuery)) + ); + }; + +export { getSessionData }; diff --git a/murfey-frontend/src/loaders/visits.tsx b/murfey-frontend/src/loaders/visits.tsx new file mode 100644 index 000000000..8be762354 --- /dev/null +++ b/murfey-frontend/src/loaders/visits.tsx @@ -0,0 +1,33 @@ +import { QueryClient } from "@tanstack/react-query"; +import { client } from "utils/api/client"; +import { Params } from "react-router-dom"; + +const getVisitData = async (instrumentName: string) => { + const response = await client.get(`instruments/${instrumentName}/visits_raw`); + + if (response.status !== 200) { + return null; + } + + return response.data; +}; + +const query = (instrumentName: string) => { + return { + queryKey: ["visits", instrumentName], + queryFn: () => getVisitData(instrumentName), + staleTime: 60000, + }; +}; + +export const visitLoader = + (queryClient: QueryClient) => async (params: Params) => { + if (params.instrumentName) { + const singleQuery = query(params.instrumentName); + return ( + (await queryClient.getQueryData(singleQuery.queryKey)) ?? + (await queryClient.fetchQuery(singleQuery)) + ); + } + return null; + }; diff --git a/murfey-frontend/src/logo.svg b/murfey-frontend/src/logo.svg new file mode 100644 index 000000000..9dfc1c058 --- /dev/null +++ b/murfey-frontend/src/logo.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/murfey-frontend/src/reportWebVitals.js b/murfey-frontend/src/reportWebVitals.js new file mode 100644 index 000000000..9ecd33f9c --- /dev/null +++ b/murfey-frontend/src/reportWebVitals.js @@ -0,0 +1,13 @@ +const reportWebVitals = (onPerfEntry) => { + if (onPerfEntry && onPerfEntry instanceof Function) { + import("web-vitals").then(({ getCLS, getFID, getFCP, getLCP, getTTFB }) => { + getCLS(onPerfEntry); + getFID(onPerfEntry); + getFCP(onPerfEntry); + getLCP(onPerfEntry); + getTTFB(onPerfEntry); + }); + } +}; + +export default reportWebVitals; diff --git a/murfey-frontend/src/routes/DataCollectionGroups.tsx b/murfey-frontend/src/routes/DataCollectionGroups.tsx new file mode 100644 index 000000000..9f8dadbcd --- /dev/null +++ b/murfey-frontend/src/routes/DataCollectionGroups.tsx @@ -0,0 +1,87 @@ +import { Box, Button, Heading, HStack, VStack, Link } from "@chakra-ui/react"; + +import { + useNavigate, + useLoaderData, + useParams, + Link as LinkRouter, +} from "react-router-dom"; +import { components } from "schema/main"; +import { Table } from "@diamondlightsource/ui-components"; +import { SetupStepper } from "components/setupStepper"; +import { + prepareGainReference, + transferGainReference, + updateCurrentGainReference, +} from "loaders/possibleGainRefs"; +import { getMachineConfigData } from "loaders/machineConfig"; + +import { useState } from "react"; + +type DataCollectionGroup = components["schemas"]["DataCollectionGroup"]; + +const DataCollectionGroups = () => { + const dataCollectionGroups = useLoaderData() as { + [key: string]: DataCollectionGroup; + }; + const { sessid } = useParams(); + const navigate = useNavigate(); + + const SelectDataCollectionGroup = async ( + data: Record, + index: number, + ) => { + navigate( + `/sessions/${sessid}/data_collection_groups/${data["id"]}/grid_squares`, + ); + }; + + return ( +
+ + + + + + Data Collection Groups + + + + + + {dataCollectionGroups ? ( + + ) : ( + <> + )} + + + + ); +}; + +export { DataCollectionGroups }; diff --git a/murfey-frontend/src/routes/Error.tsx b/murfey-frontend/src/routes/Error.tsx new file mode 100644 index 000000000..61bc62503 --- /dev/null +++ b/murfey-frontend/src/routes/Error.tsx @@ -0,0 +1,59 @@ +import { Heading, Link, VStack, Box, Text, Code } from "@chakra-ui/react"; +import { useEffect, useState } from "react"; +import { useRouteError } from "react-router-dom"; +import { Navbar } from "@diamondlightsource/ui-components"; + +interface ErrorType { + status: number; + statusText: string; + data?: string; +} + +const Error = () => { + const [heading, setHeading] = useState(""); + const [message, setMessage] = useState(""); + const [details, setDetails] = useState(""); + const error = useRouteError() as ErrorType; + + useEffect(() => { + console.error(error); + if (error.status === 404) { + setHeading("Page not found"); + setMessage("This page does not exist."); + } else { + setHeading("An error has occurred"); + setMessage( + "An unexpected error has occurred. If this persists, please contact the developers. Details:", + ); + setDetails(error.toString()); + } + }, [error]); + + return ( +
+ + + + {heading} + {message} + {details && ( + + {details} + + )} + + Go home + + + +
+ ); +}; + +export { Error }; diff --git a/murfey-frontend/src/routes/GainRefTransfer.tsx b/murfey-frontend/src/routes/GainRefTransfer.tsx new file mode 100644 index 000000000..373442593 --- /dev/null +++ b/murfey-frontend/src/routes/GainRefTransfer.tsx @@ -0,0 +1,158 @@ +import { + Box, + Heading, + HStack, + VStack, + Input, + Checkbox, + Modal, + ModalOverlay, + ModalContent, + ModalBody, + ModalHeader, + Spinner, + Tooltip, +} from "@chakra-ui/react"; + +import { useNavigate, useLoaderData, useSearchParams } from "react-router-dom"; +import { components } from "schema/main"; +import { Table } from "@diamondlightsource/ui-components"; +import { SetupStepper } from "components/setupStepper"; +import { + prepareGainReference, + transferGainReference, + updateCurrentGainReference, +} from "loaders/possibleGainRefs"; +import { getMachineConfigData } from "loaders/machineConfig"; + +import React from "react"; + +type File = components["schemas"]["File"]; + +const GainRefTransfer = () => { + const possibleGainRefs = useLoaderData() as File[] | null; + let [searchParams, setSearchParams] = useSearchParams(); + const navigate = useNavigate(); + const [processing, setProcessing] = React.useState(false); + const [tag, setTag] = React.useState(""); + const [falcon, setFalcon] = React.useState(false); + const [falconPreset, setFalconPreset] = React.useState(false); + + const SelectGainRef = async (data: Record, index: number) => { + setProcessing(true); + const sessid = searchParams.get("sessid"); + const setup = searchParams.get("setup"); + if (sessid) { + const transferStatus = await transferGainReference( + parseInt(sessid), + data["full_path"], + ); + if (true) { + const preparedGainReference = await prepareGainReference( + parseInt(sessid), + data["full_path"], + !falcon, + falcon, + tag, + ); + await updateCurrentGainReference( + parseInt(sessid), + preparedGainReference.gain_ref, + ); + } + } + if (setup) + sessid ? navigate(`/new_session/parameters/${sessid}`) : navigate("/"); + else sessid ? navigate(`/sessions/${sessid}`) : navigate("/"); + setProcessing(false); + }; + + if (!falconPreset) { + setFalconPreset(true); + getMachineConfigData().then((cfg) => setFalcon(cfg.camera === "FALCON")); + } + + return ( +
+ + + + + + Possible Gain Reference Files + + + + + void 0}> + + + Processing gain reference + + + + + + + {searchParams.get("setup") ? ( + + ) : null} + + + + +
+ + setTag(e.target.value)} + /> + + setFalcon(e.target.checked)} + > + Falcon + + + + + + + ); +}; + +export { GainRefTransfer }; diff --git a/murfey-frontend/src/routes/GridSquares.tsx b/murfey-frontend/src/routes/GridSquares.tsx new file mode 100644 index 000000000..431381e8c --- /dev/null +++ b/murfey-frontend/src/routes/GridSquares.tsx @@ -0,0 +1,75 @@ +import { + Box, + Heading, + HStack, + VStack, + CardBody, + Card, + CardHeader, + Image, +} from "@chakra-ui/react"; + +import { useNavigate, useLoaderData, useParams } from "react-router-dom"; +import { components } from "schema/main"; +import { GridSquareCard } from "components/gridSquareCard"; + +type GridSquare = components["schemas"]["GridSquare"]; + +const GridSquares = () => { + console.log("gather grid squares"); + const gridSquares = useLoaderData() as GridSquare[]; + console.log( + "grid squares", + gridSquares, + typeof gridSquares, + gridSquares.length, + ); + const { sessid, dcgid } = useParams(); + + const getUrl = (endpoint: string) => { + return ( + (sessionStorage.getItem("murfeyServerURL") ?? + process.env.REACT_APP_API_ENDPOINT) + endpoint + ); + }; + + const res = ( +
+ + + + + + Grid Squares + + + + + + {gridSquares && gridSquares.length > 0 ? ( + gridSquares.map((gs) => GridSquareCard(gs, sessid, dcgid)) + ) : ( + <> + )} + + +
+ ); + return res; +}; + +export { GridSquares }; diff --git a/murfey-frontend/src/routes/Home.tsx b/murfey-frontend/src/routes/Home.tsx new file mode 100644 index 000000000..5859c0191 --- /dev/null +++ b/murfey-frontend/src/routes/Home.tsx @@ -0,0 +1,206 @@ +import { + Box, + Button, + Divider, + GridItem, + Heading, + HStack, + IconButton, + Link, + Stack, + Stat, + StatLabel, + Tooltip, + VStack, +} from "@chakra-ui/react"; + +import { v4 as uuid4 } from "uuid"; +import { Link as LinkRouter, useLoaderData } from "react-router-dom"; +import { components } from "schema/main"; +import { MdDelete } from "react-icons/md"; +import { deleteSessionData } from "loaders/session_clients"; +import { InstrumentCard } from "components/instrumentCard"; +import useWebSocket from "react-use-websocket"; + +import React, { useEffect } from "react"; + +type SessionClients = components["schemas"]["SessionClients"]; + +interface SessionRowProps { + session_clients: SessionClients[]; + title: string; +} + +const SessionRow = ({ session_clients, title }: SessionRowProps) => { + return ( + + + {title} + + + + {session_clients && session_clients.length > 0 ? ( + session_clients.map((session_client) => { + const session_id = session_client["session"]["id"]; + return ( + <> + + c.connected) + ? "Active (live connections)" + : "Inactive" + } + > + + c.connected) + ? "murfey.500" + : "murfey.400" + } + overflow="auto" + w="calc(100%)" + p={2} + border="1px solid grey" + borderRadius={5} + display={"flex"} + > + + {session_client.session.name}:{" "} + {session_client.session.id} + + + + + } + onClick={() => { + deleteSessionData(session_id); + window.location.reload(); + }} + /> + + + ); + }) + ) : ( + + + No {title} Found + + + )} + + + ); +}; + +const Home = () => { + const sessions = useLoaderData() as { + current: SessionClients[]; + } | null; + const [UUID, setUUID] = React.useState(""); + const baseUrl = + sessionStorage.getItem("murfeyServerURL") ?? + process.env.REACT_APP_API_ENDPOINT; + const url = baseUrl ? baseUrl.replace("http", "ws") : "ws://localhost:8000"; + const parseWebsocketMessage = (message: any) => { + let parsedMessage: any = {}; + try { + parsedMessage = JSON.parse(message); + } catch (err) { + return; + } + if (parsedMessage.message === "refresh") { + window.location.reload(); + } + }; + + //const wsid = uuid1(); + useEffect(() => { + setUUID(uuid4()); + }, []); + useWebSocket(url + `ws/connect/${UUID}`, { + onOpen: () => { + console.log("WebSocket connection established."); + }, + onMessage: (event) => { + parseWebsocketMessage(event.data); + }, + }); + + return ( +
+ Murfey + + + + + + Murfey Sessions + + + Microscope Data Transfer Control System + + + + + + + + + {sessions ? ( + + + + ) : ( + + + No sessions found + + + )} + + + + + + +
+ ); +}; + +export { Home }; diff --git a/murfey-frontend/src/routes/Hub.tsx b/murfey-frontend/src/routes/Hub.tsx new file mode 100644 index 000000000..7358e840b --- /dev/null +++ b/murfey-frontend/src/routes/Hub.tsx @@ -0,0 +1,97 @@ +import { + Card, + CardBody, + CardHeader, + Image, + Link, + Text, + HStack, + Heading, + VStack, + Box, + SimpleGrid, +} from "@chakra-ui/react"; + +import { TbMicroscope, TbSnowflake } from "react-icons/tb"; +import { Link as LinkRouter, useLoaderData } from "react-router-dom"; +import { getInstrumentName } from "loaders/general"; + +import React from "react"; + +const getUrl = (endpoint: string) => { + return process.env.REACT_APP_HUB_ENDPOINT + endpoint; +}; + +type InstrumentInfo = { + instrument_name: string; + display_name: string; + instrument_url: string; +}; + +const Hub = () => { + const instrumentInfo = useLoaderData() as InstrumentInfo[]; + + const sessionStorageSetup = (ininfo: InstrumentInfo) => { + sessionStorage.setItem("murfeyServerURL", ininfo.instrument_url + "/"); + sessionStorage.setItem("instrumentName", ininfo.instrument_name); + }; + + return ( + + + + + {" "} + {" "} + {" "} + Murfey Hub + + + + {instrumentInfo ? ( + instrumentInfo.map((ini) => { + return ( + + sessionStorageSetup(ini)}> + + + + + {ini.display_name} + + + + ); + }) + ) : ( + <> + )} + + + ); +}; + +export { Hub }; diff --git a/murfey-frontend/src/routes/Login.tsx b/murfey-frontend/src/routes/Login.tsx new file mode 100644 index 000000000..9f62d5b5b --- /dev/null +++ b/murfey-frontend/src/routes/Login.tsx @@ -0,0 +1,75 @@ +import { + Button, + Input, + VStack, + Link, + FormControl, + Card, + CardBody, + Heading, + HStack, +} from "@chakra-ui/react"; +import { Link as LinkRouter, useNavigate, Navigate } from "react-router-dom"; +import { TbMicroscope, TbSnowflake } from "react-icons/tb"; + +import { getJWT, handshake } from "loaders/jwt"; + +import React from "react"; + +const Login = () => { + const [username, setUsername] = React.useState(""); + const handleUsername = (event: React.ChangeEvent) => + setUsername(event.target.value); + const [password, setPassword] = React.useState(""); + const handlePassword = (event: React.ChangeEvent) => + setPassword(event.target.value); + + const navigate = useNavigate(); + + return sessionStorage.getItem("murfeyServerURL") ? ( + + + + {" "} + {" "} + {" "} + Murfey Login + + + + + + + + + + + + ) : ( + + ); +}; + +export { Login }; diff --git a/murfey-frontend/src/routes/MagTable.tsx b/murfey-frontend/src/routes/MagTable.tsx new file mode 100644 index 000000000..a120aeae2 --- /dev/null +++ b/murfey-frontend/src/routes/MagTable.tsx @@ -0,0 +1,168 @@ +import { + Button, + Box, + Heading, + HStack, + IconButton, + Input, + VStack, + TableContainer, + Table, + Thead, + Tbody, + Tfoot, + Tr, + Th, + Td, + Text, + TableCaption, + Modal, + ModalOverlay, + ModalHeader, + ModalFooter, + ModalContent, + ModalBody, + ModalCloseButton, + FormControl, + useDisclosure, +} from "@chakra-ui/react"; + +import { CheckIcon, EditIcon } from "@chakra-ui/icons"; + +import { Link as LinkRouter, useLoaderData } from "react-router-dom"; +import { components } from "schema/main"; +import { MdAdd, MdHorizontalRule } from "react-icons/md"; +import { addMagTableRow, removeMagTableRow } from "loaders/magTable"; + +import React from "react"; + +type MagTableRow = components["schemas"]["MagnificationLookup"]; + +const MagTable = () => { + const magTable = useLoaderData() as MagTableRow[] | null; + const { isOpen, onOpen, onClose } = useDisclosure(); + const [numNewRows, setNumNewRows] = React.useState(0); + + const handleRemoveRow = (mag: number) => { + removeMagTableRow(mag); + window.location.reload(); + }; + + const handleForm = (event: React.FormEvent) => { + event.preventDefault(); + const formData = new FormData(event.currentTarget); + const mag = parseInt(formData.get("magnification") as string); + const pixelSize = parseFloat(formData.get("pixelSize") as string); + addMagTableRow(mag, pixelSize); + window.location.reload(); + }; + + return ( +
+ Murfey + + + + + + Magnification Table + + + + + +
+ Magnification Table + + + + + + + + + + + Add Mag Table Row + + +
+ + + + + + + + + + + + + {magTable && magTable.length > 0 ? ( + magTable.map((row) => { + return ( + + + + + + ); + }) + ) : ( + <> + )} + + + + } + size="m" + onClick={onOpen} + > + + +
MagnificationPixel SizeRemove
+ {row.magnification} + + {row.pixel_size} + + } + onClick={() => + handleRemoveRow(row.magnification) + } + > +
+ + + + + +
+ ); +}; + +export { MagTable }; diff --git a/murfey-frontend/src/routes/MultigridSetup.tsx b/murfey-frontend/src/routes/MultigridSetup.tsx new file mode 100644 index 000000000..e2857e3a4 --- /dev/null +++ b/murfey-frontend/src/routes/MultigridSetup.tsx @@ -0,0 +1,166 @@ +import { + Box, + FormControl, + FormLabel, + GridItem, + Heading, + HStack, + IconButton, + Link, + Select, + Stack, + Switch, + VStack, +} from "@chakra-ui/react"; +import { ArrowForwardIcon } from "@chakra-ui/icons"; + +import { Link as LinkRouter, useLoaderData, useParams } from "react-router-dom"; +import { components } from "schema/main"; +import { startMultigridWatcher } from "loaders/multigridSetup"; +import { getSessionData } from "loaders/session_clients"; +import { SetupStepper } from "components/setupStepper"; +import React, { useEffect } from "react"; + +type MachineConfig = components["schemas"]["MachineConfig"]; +type MultigridWatcherSpec = components["schemas"]["MultigridWatcherSetup"]; +type Session = components["schemas"]["Session"]; + +const MultigridSetup = () => { + const machineConfig = useLoaderData() as MachineConfig | null; + const { sessid } = useParams(); + let initialDirectory = ""; + if (machineConfig) { + initialDirectory = machineConfig.data_directories[0]; + } + const [selectedDirectory, setSelectedDirectory] = + React.useState(initialDirectory); + const processByDefault = machineConfig + ? machineConfig.process_by_default + : true; + const [skipExistingProcessing, setSkipExistingProcessing] = + React.useState(!processByDefault); + const [session, setSession] = React.useState(); + + useEffect(() => { + getSessionData(sessid).then((sess) => setSession(sess.session)); + }, []); + const activeStep = session != null ? (session.started ? 4 : 3) : 3; + + const handleDirectorySelection = (e: React.ChangeEvent) => + setSelectedDirectory(e.target.value); + + const handleSelection = () => { + if (typeof sessid !== "undefined") { + console.log(sessid); + startMultigridWatcher( + { + source: selectedDirectory, + skip_existing_processing: skipExistingProcessing, + } as MultigridWatcherSpec, + parseInt(sessid), + ); + } + }; + + return ( +
+ + + + + + Select data directory + + + + + + + + + + + + + + Do not process existing data + { + setSkipExistingProcessing(!skipExistingProcessing); + }} + /> + + + + + } + onClick={handleSelection} + /> + + + + + + + +
+ ); +}; + +export { MultigridSetup }; diff --git a/murfey-frontend/src/routes/NewSession.tsx b/murfey-frontend/src/routes/NewSession.tsx new file mode 100644 index 000000000..d7c3db10a --- /dev/null +++ b/murfey-frontend/src/routes/NewSession.tsx @@ -0,0 +1,185 @@ +import { + Box, + Button, + Divider, + GridItem, + Input, + Heading, + HStack, + Link, + Stack, + Stat, + StatHelpText, + StatLabel, + StatNumber, + Text, + VStack, + Modal, + ModalOverlay, + ModalHeader, + ModalContent, + ModalFooter, + ModalCloseButton, + ModalBody, +} from "@chakra-ui/react"; + +import { useDisclosure } from "@chakra-ui/react"; +import { Link as LinkRouter, useLoaderData, useParams } from "react-router-dom"; +import { components } from "schema/main"; +import { SetupStepper } from "components/setupStepper"; +import { Table } from "@diamondlightsource/ui-components"; +import { createSession } from "loaders/session_clients"; +import { sessionHandshake } from "loaders/jwt"; +import { useNavigate } from "react-router-dom"; +import React, { ChangeEventHandler } from "react"; + +type Visit = components["schemas"]["Visit"]; + +const NewSession = () => { + const currentVisits = useLoaderData() as Visit[] | null; + const { isOpen, onOpen, onClose } = useDisclosure(); + const [selectedVisit, setSelectedVisit] = React.useState(""); + const [sessionReference, setSessionReference] = React.useState(""); + const navigate = useNavigate(); + + const handleChange = (event: React.ChangeEvent) => + setSessionReference(event.target.value); + + const handleVisitNameChange = ( + event: React.ChangeEvent, + ) => { + setSelectedVisit(event.target.value); + setSessionReference(event.target.value); + }; + + function selectVisit(data: Record, index: number) { + setSelectedVisit(data.name); + setSessionReference(data.name); + } + + const instrumentName = sessionStorage.getItem("instrumentName"); + + const startMurfeySession = async (iName: string) => { + const sid = await createSession(selectedVisit, sessionReference, iName); + await sessionHandshake(sid); + return sid; + }; + + return instrumentName ? ( +
+ + + + Create visit + + + + + + + + + + + + + + + + Current visits + + + + + + + + + + + + + + + + + + + + ) : ( + <> + ); +}; + +export { NewSession }; diff --git a/murfey-frontend/src/routes/ProcessingParameters.tsx b/murfey-frontend/src/routes/ProcessingParameters.tsx new file mode 100644 index 000000000..09f98dd8e --- /dev/null +++ b/murfey-frontend/src/routes/ProcessingParameters.tsx @@ -0,0 +1,184 @@ +import { + Accordion, + AccordionButton, + AccordionPanel, + AccordionItem, + AccordionIcon, + Box, + Heading, + IconButton, + HStack, + VStack, + Switch, + Text, +} from "@chakra-ui/react"; + +import { useLoaderData } from "react-router-dom"; +import { components } from "schema/main"; +import { Table } from "@diamondlightsource/ui-components"; +import { MdEditNote } from "react-icons/md"; + +import React from "react"; + +type ProcessingDetails = components["schemas"]["ProcessingDetails"]; + +type ProcessingRow = { + parameterName: string; + parameterValue?: string | number | boolean; +}; + +type ProcessingTable = { + processingRows: ProcessingRow[]; + tag: string; +}; + +const nameLabelMap: Map = new Map([ + ["pj_id", "Processing Job ID"], + ["angpix", "Pixel Size [m]"], + ["dose_per_frame", "Dose per frame [\u212B / pixel]"], + ["gain_ref", "Gain Reference"], + ["voltage", "Voltage [kV]"], + ["motion_corr_binning", "Motion correction binning factor"], + ["eer_grouping", "EER Grouping"], + ["symmetry", "Symmetry"], + ["particle_diameter", "Particle Diameter [\u212B]"], + ["downscale", "Downscaling During Extraction"], + ["do_icebreaker_jobs", "Perform IceBreaker Jobs"], + ["boxsize", "Box Size"], + ["small_boxsize", "Downscaled Box Size"], + ["mask_diameter", "Mask Diameter for Classification"], + ["estimate_particle_diameter", "Automatically Estimate Particle Diameter"], + ["hold_class2d", "2D Classification Held"], + ["rerun_class2d", "First 2D Classification Batch Needs to be Rerun"], + ["rerun_class3d", "3D Classification Needs to be Rerun"], + ["class_selection_score", "Class Selection Threshold"], + ["star_combination_job", "Job Number for Rebatching Job"], + ["initial_model", "Initial Model"], + ["next_job", "Next Job Number"], + ["picker_murfey_id", "Murfey ID of Picker for Use in ISPyB"], + ["picker_ispyb_id", "ISPyB Particle Picker ID"], +]); + +const ProcessingParameters = () => { + const procParams = useLoaderData() as ProcessingDetails[] | null; + const [showExtra, setShowExtra] = React.useState(false); + let tableRows = [] as ProcessingTable[]; + let tableRowsExtra = [] as ProcessingTable[]; + console.log(procParams); + procParams?.map((p) => { + let tr: ProcessingTable = { + processingRows: [], + tag: "", + }; + let tre: ProcessingTable = { + processingRows: [], + tag: "", + }; + Object.entries(p?.relion_params ? p?.relion_params : {}).forEach( + ([key, value]) => + tr.processingRows.push({ + parameterName: nameLabelMap.get(key) ?? key, + parameterValue: + value === true ? "True" : value === false ? "False" : value, + }), + ); + tr.tag = p?.relion_params.pj_id.toString(); + tableRows.push(tr); + Object.entries(p?.feedback_params ? p?.feedback_params : {}).forEach( + ([key, value]) => + tre.processingRows.push({ + parameterName: nameLabelMap.get(key) ?? key, + parameterValue: + value === true ? "True" : value === false ? "False" : value, + }), + ); + tre.tag = p?.feedback_params.pj_id.toString(); + tableRowsExtra.push(tre); + }); + const handleToggle = (event: React.ChangeEvent) => { + setShowExtra(!showExtra); + }; + return ( +
+ + + + + + Processing Parameters + + + + Show extra processing parameters + + + + + + {tableRows.map((tr) => { + return ( + + + + Main Processing Parameters (Processing Job ID {tr.tag}) + + + + +
+ + + ); + })} + {showExtra ? ( + tableRowsExtra.map((tre) => { + return ( + + + + Extra Processing Parameters (Processing Job ID {tre.tag}) + + + + + } + /> +
+ + + ); + }) + ) : ( + <> + )} + + + + ); +}; + +export { ProcessingParameters }; diff --git a/murfey-frontend/src/routes/Root.tsx b/murfey-frontend/src/routes/Root.tsx new file mode 100644 index 000000000..58514993e --- /dev/null +++ b/murfey-frontend/src/routes/Root.tsx @@ -0,0 +1,21 @@ +import { Box, HStack, Tag, Text, Link, Progress, Icon } from "@chakra-ui/react"; +import { Outlet, useLoaderData, Link as LinkRouter } from "react-router-dom"; +import { Navbar } from "components/navbar"; +import { MdSignalWifi4Bar } from "react-icons/md"; + +import "styles/main.css"; + +const Root = () => { + return ( +
+ + + + + + +
+ ); +}; + +export { Root }; diff --git a/murfey-frontend/src/routes/Session.tsx b/murfey-frontend/src/routes/Session.tsx new file mode 100644 index 000000000..f771ddd30 --- /dev/null +++ b/murfey-frontend/src/routes/Session.tsx @@ -0,0 +1,418 @@ +import { + Badge, + Box, + Button, + Card, + CardBody, + CardHeader, + Divider, + Flex, + GridItem, + Heading, + HStack, + IconButton, + Image, + Link, + Menu, + MenuButton, + MenuItem, + MenuList, + Modal, + ModalOverlay, + ModalContent, + ModalHeader, + ModalFooter, + ModalBody, + ModalCloseButton, + Spacer, + Spinner, + Stack, + StackDivider, + Stat, + StatHelpText, + StatLabel, + StatNumber, + Switch, + Text, + Tooltip, + VStack, + useToast, + Icon, +} from "@chakra-ui/react"; + +import { useDisclosure } from "@chakra-ui/react"; +import { ViewIcon } from "@chakra-ui/icons"; + +import { v4 as uuid4 } from "uuid"; +import { Link as LinkRouter, useLoaderData, useParams } from "react-router-dom"; +import { + MdCheck, + MdDensityMedium, + MdFileUpload, + MdOutlineWarning, + MdOutlineGridOn, +} from "react-icons/md"; +import { FiActivity } from "react-icons/fi"; +import { components } from "schema/main"; +import { getInstrumentName } from "loaders/general"; +import { + pauseRsyncer, + restartRsyncer, + removeRsyncer, + finaliseRsyncer, +} from "loaders/rsyncers"; +import { getSessionData } from "loaders/session_clients"; +import { InstrumentCard } from "components/instrumentCard"; +import { UpstreamVisitCard } from "components/upstreamVisitsCard"; +import useWebSocket from "react-use-websocket"; + +import React, { useEffect } from "react"; + +type RsyncInstance = components["schemas"]["RsyncInstance"]; +type Session = components["schemas"]["Session"]; + +const RsyncCard = (rsyncer: RsyncInstance) => { + const { isOpen, onOpen, onClose } = useDisclosure(); + const [action, setAction] = React.useState("finalise"); + + const finalise = () => { + setAction("finalise"); + onOpen(); + }; + + const remove = () => { + setAction("remove"); + onOpen(); + }; + + const handleRsyncerAction = async () => { + if (action === "finalise") + await finaliseRsyncer(rsyncer.session_id, rsyncer.source); + else if (action === "remove") + await removeRsyncer(rsyncer.session_id, rsyncer.source); + onClose(); + }; + + return ( + + + + + + Confirm RSyncer {action}: {rsyncer.source} + + + Are you sure you want to continue? + + + + + + + + + + {" "} + + {" "} + + RSync Instance + {rsyncer.transferring && } + + {rsyncer.tag} + + + + + } + /> + + {rsyncer.transferring ? ( + <> + + pauseRsyncer(rsyncer.session_id, rsyncer.source) + } + isDisabled={!rsyncer.transferring} + > + Pause + + remove()} + isDisabled={!rsyncer.transferring} + > + Remove + + { + finalise(); + }} + isDisabled={!rsyncer.transferring} + > + Finalise + + + ) : ( + <> + + restartRsyncer(rsyncer.session_id, rsyncer.source) + } + > + Start + + remove()}>Remove + + )} + + + + + + } spacing="4"> + + + Source + + + {rsyncer.source} + + + + + Destination + + + {rsyncer.destination ?? ""} + + + + + Transfer progress + + {rsyncer.files_transferred} / {rsyncer.files_counted} + + + {(rsyncer.files_transferred ?? 0) >= + (rsyncer.files_counted ?? 0) ? ( + + + Up to date + + ) : rsyncer.transferring ? ( + + + Working on it + + ) : ( + + + Broken + + )} + + + + + + + ); +}; + +const getUrl = (endpoint: string) => { + return ( + (sessionStorage.getItem("murfeyServerURL") ?? + process.env.REACT_APP_API_ENDPOINT) + endpoint + ); +}; + +const Session = () => { + const { isOpen, onOpen, onClose } = useDisclosure(); + const rsync = useLoaderData() as RsyncInstance[] | null; + const { sessid } = useParams(); + const [UUID, setUUID] = React.useState(""); + const [instrumentName, setInstrumentName] = React.useState(""); + const baseUrl = + sessionStorage.getItem("murfeyServerURL") ?? + process.env.REACT_APP_API_ENDPOINT; + const url = baseUrl ? baseUrl.replace("http", "ws") : "ws://localhost:8000"; + const toast = useToast(); + const [session, setSession] = React.useState(); + + useEffect(() => { + getSessionData(sessid).then((sess) => setSession(sess.session)); + setUUID(uuid4()); + }, []); + + const parseWebsocketMessage = (message: any) => { + let parsedMessage: any = {}; + try { + parsedMessage = JSON.parse(message); + } catch (err) { + return; + } + if (parsedMessage.message === "refresh") { + window.location.reload(); + } + if ( + parsedMessage.message === "update" && + typeof sessid !== "undefined" && + parsedMessage.session_id === parseInt(sessid) + ) { + return toast({ + title: "Update", + description: parsedMessage.payload, + isClosable: true, + duration: parsedMessage.duration ?? null, + status: parsedMessage.status ?? "info", + }); + } + }; + + useWebSocket(url + `ws/connect/${UUID}`, { + onOpen: () => { + console.log("WebSocket connection established."); + }, + onMessage: (event) => { + parseWebsocketMessage(event.data); + }, + }); + + const finaliseAll = async () => { + rsync?.map((r) => { + finaliseRsyncer(r.session_id, r.source); + }); + onClose(); + }; + + const resolveName = async () => { + const name: string = await getInstrumentName(); + setInstrumentName(name); + }; + resolveName(); + + return ( +
+ + + + Confirm Visit Completion + + + Are you sure you want to remove all data associated with this visit? + + + + + + + + + + + + + + Session {sessid}: {session ? session.visit : null} + + + + + + + + + + {/* */} + + + + + + + + {rsync && rsync.length > 0 ? ( + rsync.map((r) => { + return RsyncCard(r); + }) + ) : ( + + + No RSyncers Found + + + )} + + + + + + + + + + + + + + + +
+ ); +}; + +export { Session }; diff --git a/murfey-frontend/src/routes/SessionLinker.tsx b/murfey-frontend/src/routes/SessionLinker.tsx new file mode 100644 index 000000000..276eccdfa --- /dev/null +++ b/murfey-frontend/src/routes/SessionLinker.tsx @@ -0,0 +1,140 @@ +import { + Box, + Button, + Divider, + GridItem, + Heading, + HStack, + IconButton, + Link, + Stack, + Stat, + StatHelpText, + StatLabel, + StatNumber, + Text, + VStack, +} from "@chakra-ui/react"; + +import { MdLink } from "react-icons/md"; +import { Link as LinkRouter, useLoaderData, useParams } from "react-router-dom"; +import { components } from "schema/main"; +import { linkSessionToClient } from "loaders/session_clients"; +import { useSearchParams } from "react-router-dom"; +import React from "react"; + +type Client = components["schemas"]["ClientEnvironment"]; + +const SessionLinker = () => { + const existingClients = useLoaderData() as Client[] | null; + let [searchParams, setSearchParams] = useSearchParams(); + const [sessionId, setSessionId] = React.useState(0); + + return ( +
+ + + + + + Connect new session to client + + + + + + + + + + Existing Clients + + + + {existingClients && existingClients.length > 0 ? ( + existingClients.map((client) => { + const client_id = client.client_id!; + return ( + <> + + + + Client {client_id} + + + + } + onClick={() => { + linkSessionToClient( + client_id, + searchParams.get("session_name") ?? + "Client connection", + ).then((sid) => { + console.log(sid); + setSessionId(sid); + console.log(sessionId); + }); + }} + /> + + + + ); + }) + ) : ( + + + No Clients Found + + + )} + + + + + +
+ ); +}; + +export { SessionLinker }; diff --git a/murfey-frontend/src/routes/SessionSetup.tsx b/murfey-frontend/src/routes/SessionSetup.tsx new file mode 100644 index 000000000..f5a90a147 --- /dev/null +++ b/murfey-frontend/src/routes/SessionSetup.tsx @@ -0,0 +1,168 @@ +import { + Button, + Box, + FormControl, + FormLabel, + Input, + RadioGroup, + Radio, + Stack, + Link, + VStack, + Heading, +} from "@chakra-ui/react"; +import { getForm } from "components/forms"; +import { + Link as LinkRouter, + useParams, + useLoaderData, + useNavigate, +} from "react-router-dom"; +import { SetupStepper } from "components/setupStepper"; +import { components } from "schema/main"; +import { getProcessingParameterData } from "loaders/processingParameters"; +import { getSessionData } from "loaders/session_clients"; +import { registerProcessingParameters } from "loaders/sessionSetup"; + +import React, { useEffect } from "react"; + +type SessionClients = components["schemas"]["SessionClients"]; +type ProvidedProcessingParameters = + components["schemas"]["ProvidedProcessingParameters"]; +type Session = components["schemas"]["Session"]; + +const SessionSetup = () => { + const session = useLoaderData() as SessionClients | null; + const [expType, setExpType] = React.useState("spa"); + const [procParams, setProcParams] = React.useState(); + const { sessid } = useParams(); + const [paramsSet, setParamsSet] = React.useState(false); + + const [_session, setSession] = React.useState(); + + useEffect(() => { + getSessionData(sessid).then((sess) => setSession(sess.session)); + }, []); + + const handleSelection = (formData: any) => { + if (typeof sessid !== "undefined") { + delete formData.type; + registerProcessingParameters( + formData as ProvidedProcessingParameters, + parseInt(sessid), + ); + setParamsSet(true); + } + }; + + if (session) + getProcessingParameterData(session.session.id.toString()).then((params) => + setProcParams(params), + ); + const activeStep = session + ? procParams + ? 3 + : session.session.visit + ? 2 + : 0 + : 2; + let navigate = useNavigate(); + return ( +
+ + + + + + Processing parameters + + + + + + + + + + + + SPA + Tomography + + + + + {sessid ? getForm(expType, handleSelection) : <>} + + + + + + + + + + + +
+ ); +}; + +export { SessionSetup }; diff --git a/murfey-frontend/src/routes/UserParameters.tsx b/murfey-frontend/src/routes/UserParameters.tsx new file mode 100644 index 000000000..b52eb64dd --- /dev/null +++ b/murfey-frontend/src/routes/UserParameters.tsx @@ -0,0 +1,40 @@ +import { Box, RadioGroup, Radio, Stack } from "@chakra-ui/react"; +import { getForm } from "components/forms"; + +import React from "react"; + +const UserParameters = () => { + const [expType, setExpType] = React.useState("spa"); + const [procParams, setProcParams] = React.useState(); + return ( + + + + + SPA + Tomography + + + + + {getForm(expType, setProcParams)} + + + ); +}; + +export { UserParameters }; diff --git a/murfey-frontend/src/schema/main.ts b/murfey-frontend/src/schema/main.ts new file mode 100644 index 000000000..cec7f4c73 --- /dev/null +++ b/murfey-frontend/src/schema/main.ts @@ -0,0 +1,4335 @@ +/** + * This file was auto-generated by openapi-typescript. + * Do not make direct changes to the file. + */ + +export interface paths { + "/": { + /** Root */ + get: operations["root__get"]; + }; + "/machine": { + /** Machine Info */ + get: operations["machine_info_machine_get"]; + }; + "/instruments/{instrument_name}/machine": { + /** Machine Info By Name */ + get: operations["machine_info_by_name_instruments__instrument_name__machine_get"]; + }; + "/microscope_image/": { + /** Get Mic Image */ + get: operations["get_mic_image_microscope_image__get"]; + }; + "/mag_table/": { + /** Get Mag Table */ + get: operations["get_mag_table_mag_table__get"]; + /** Add To Mag Table */ + post: operations["add_to_mag_table_mag_table__post"]; + }; + "/mag_table/{mag}": { + /** Remove Mag Table Row */ + delete: operations["remove_mag_table_row_mag_table__mag__delete"]; + }; + "/instruments/{instrument_name}/instrument_name": { + /** Get Instrument Display Name */ + get: operations["get_instrument_display_name_instruments__instrument_name__instrument_name_get"]; + }; + "/instruments/{instrument_name}/visits/": { + /** All Visit Info */ + get: operations["all_visit_info_instruments__instrument_name__visits__get"]; + }; + "/visits/{visit_name}": { + /** Visit Info */ + get: operations["visit_info_visits__visit_name__get"]; + /** Register Client To Visit */ + post: operations["register_client_to_visit_visits__visit_name__post"]; + }; + "/num_movies": { + /** Count Number Of Movies */ + get: operations["count_number_of_movies_num_movies_get"]; + }; + "/sessions/{session_id}/rsyncer": { + /** Register Rsyncer */ + post: operations["register_rsyncer_sessions__session_id__rsyncer_post"]; + }; + "/sessions/{session_id}/rsyncer/{source}": { + /** Delete Rsyncer */ + delete: operations["delete_rsyncer_sessions__session_id__rsyncer__source__delete"]; + }; + "/sessions/{session_id}/rsyncer_stopped": { + /** Register Stopped Rsyncer */ + post: operations["register_stopped_rsyncer_sessions__session_id__rsyncer_stopped_post"]; + }; + "/sessions/{session_id}/rsyncer_started": { + /** Register Restarted Rsyncer */ + post: operations["register_restarted_rsyncer_sessions__session_id__rsyncer_started_post"]; + }; + "/clients/{client_id}/rsyncers": { + /** Get Rsyncers For Client */ + get: operations["get_rsyncers_for_client_clients__client_id__rsyncers_get"]; + }; + "/session/{session_id}": { + /** Get Session */ + get: operations["get_session_session__session_id__get"]; + }; + "/visits/{visit_name}/increment_rsync_file_count": { + /** Increment Rsync File Count */ + post: operations["increment_rsync_file_count_visits__visit_name__increment_rsync_file_count_post"]; + }; + "/visits/{visit_name}/increment_rsync_transferred_files": { + /** Increment Rsync Transferred Files */ + post: operations["increment_rsync_transferred_files_visits__visit_name__increment_rsync_transferred_files_post"]; + }; + "/visits/{visit_name}/increment_rsync_transferred_files_prometheus": { + /** Increment Rsync Transferred Files Prometheus */ + post: operations["increment_rsync_transferred_files_prometheus_visits__visit_name__increment_rsync_transferred_files_prometheus_post"]; + }; + "/sessions/{session_id}/spa_processing_parameters": { + /** Get Spa Proc Param Details */ + get: operations["get_spa_proc_param_details_sessions__session_id__spa_processing_parameters_get"]; + /** Register Spa Proc Params */ + post: operations["register_spa_proc_params_sessions__session_id__spa_processing_parameters_post"]; + }; + "/sessions/{session_id}/tomography_preprocessing_parameters": { + /** Register Tomo Preproc Params */ + post: operations["register_tomo_preproc_params_sessions__session_id__tomography_preprocessing_parameters_post"]; + }; + "/clients/{client_id}/tomography_processing_parameters": { + /** Register Tomo Proc Params */ + post: operations["register_tomo_proc_params_clients__client_id__tomography_processing_parameters_post"]; + }; + "/clients/{client_id}/spa_processing_parameters": { + /** Get Spa Proc Params */ + get: operations["get_spa_proc_params_clients__client_id__spa_processing_parameters_get"]; + }; + "/sessions/{session_id}/grid_squares": { + /** Get Grid Squares */ + get: operations["get_grid_squares_sessions__session_id__grid_squares_get"]; + }; + "/sessions/{session_id}/data_collection_groups/{dcgid}/grid_squares": { + /** Get Grid Squares From Dcg */ + get: operations["get_grid_squares_from_dcg_sessions__session_id__data_collection_groups__dcgid__grid_squares_get"]; + }; + "/sessions/{session_id}/data_collection_groups/{dcgid}/grid_squares/{gsid}/num_movies": { + /** Get Number Of Movies From Grid Square */ + get: operations["get_number_of_movies_from_grid_square_sessions__session_id__data_collection_groups__dcgid__grid_squares__gsid__num_movies_get"]; + }; + "/sessions/{session_id}/data_collection_groups/{dcgid}/grid_squares/{gsid}/foil_holes": { + /** Get Foil Holes From Grid Square */ + get: operations["get_foil_holes_from_grid_square_sessions__session_id__data_collection_groups__dcgid__grid_squares__gsid__foil_holes_get"]; + }; + "/sessions/{session_id}/data_collection_groups/{dcgid}/grid_squares/{gsid}/foil_holes/{fhid}/num_movies": { + /** Get Number Of Movies From Foil Hole */ + get: operations["get_number_of_movies_from_foil_hole_sessions__session_id__data_collection_groups__dcgid__grid_squares__gsid__foil_holes__fhid__num_movies_get"]; + }; + "/sessions/{session_id}/grid_square/{gsid}": { + /** Register Grid Square */ + post: operations["register_grid_square_sessions__session_id__grid_square__gsid__post"]; + }; + "/sessions/{session_id}/foil_hole/{fh_name}": { + /** Get Foil Hole */ + get: operations["get_foil_hole_sessions__session_id__foil_hole__fh_name__get"]; + }; + "/sessions/{session_id}/grid_square/{gs_name}/foil_hole": { + /** Register Foil Hole */ + post: operations["register_foil_hole_sessions__session_id__grid_square__gs_name__foil_hole_post"]; + }; + "/visits/{visit_name}/tilt_series": { + /** Register Tilt Series */ + post: operations["register_tilt_series_visits__visit_name__tilt_series_post"]; + }; + "/visits/{visit_name}/{client_id}/completed_tilt_series": { + /** Register Completed Tilt Series */ + post: operations["register_completed_tilt_series_visits__visit_name___client_id__completed_tilt_series_post"]; + }; + "/clients/{client_id}/tilt_series/{tilt_series_tag}/tilts": { + /** Get Tilts */ + get: operations["get_tilts_clients__client_id__tilt_series__tilt_series_tag__tilts_get"]; + }; + "/visits/{visit_name}/{client_id}/tilt": { + /** Register Tilt */ + post: operations["register_tilt_visits__visit_name___client_id__tilt_post"]; + }; + "/instruments/{instrument_name}/visits_raw": { + /** Get Current Visits */ + get: operations["get_current_visits_instruments__instrument_name__visits_raw_get"]; + }; + "/visits/{visit_name}/context": { + /** Register Context */ + post: operations["register_context_visits__visit_name__context_post"]; + }; + "/visits/{visit_name}/files": { + /** Add File */ + post: operations["add_file_visits__visit_name__files_post"]; + }; + "/feedback": { + /** Send Murfey Message */ + post: operations["send_murfey_message_feedback_post"]; + }; + "/visits/{visit_name}/spa_processing": { + /** Request Spa Processing */ + post: operations["request_spa_processing_visits__visit_name__spa_processing_post"]; + }; + "/visits/{visit_name}/{session_id}/flush_spa_processing": { + /** Flush Spa Processing */ + post: operations["flush_spa_processing_visits__visit_name___session_id__flush_spa_processing_post"]; + }; + "/visits/{visit_name}/{session_id}/spa_preprocess": { + /** Request Spa Preprocessing */ + post: operations["request_spa_preprocessing_visits__visit_name___session_id__spa_preprocess_post"]; + }; + "/visits/{visit_name}/{client_id}/flush_tomography_processing": { + /** Flush Tomography Processing */ + post: operations["flush_tomography_processing_visits__visit_name___client_id__flush_tomography_processing_post"]; + }; + "/visits/{visit_name}/{client_id}/tomography_preprocess": { + /** Request Tomography Preprocessing */ + post: operations["request_tomography_preprocessing_visits__visit_name___client_id__tomography_preprocess_post"]; + }; + "/version": { + /** Get Version */ + get: operations["get_version_version_get"]; + }; + "/visits/{visit_name}/{session_id}/suggested_path": { + /** Suggest Path */ + post: operations["suggest_path_visits__visit_name___session_id__suggested_path_post"]; + }; + "/sessions/{session_id}/data_collection_groups": { + /** Get Dc Groups */ + get: operations["get_dc_groups_sessions__session_id__data_collection_groups_get"]; + }; + "/sessions/{session_id}/data_collection_groups/{dcgid}/data_collections": { + /** Get Data Collections */ + get: operations["get_data_collections_sessions__session_id__data_collection_groups__dcgid__data_collections_get"]; + }; + "/visits/{visit_name}/{session_id}/register_data_collection_group": { + /** Register Dc Group */ + post: operations["register_dc_group_visits__visit_name___session_id__register_data_collection_group_post"]; + }; + "/visits/{visit_name}/{session_id}/start_data_collection": { + /** Start Dc */ + post: operations["start_dc_visits__visit_name___session_id__start_data_collection_post"]; + }; + "/visits/{visit_name}/{session_id}/register_processing_job": { + /** Register Proc */ + post: operations["register_proc_visits__visit_name___session_id__register_processing_job_post"]; + }; + "/sessions/{session_id}/process_gain": { + /** Process Gain */ + post: operations["process_gain_sessions__session_id__process_gain_post"]; + }; + "/new_client_id/": { + /** New Client Id */ + get: operations["new_client_id_new_client_id__get"]; + }; + "/clients": { + /** Get Clients */ + get: operations["get_clients_clients_get"]; + }; + "/sessions": { + /** Get Sessions */ + get: operations["get_sessions_sessions_get"]; + }; + "/instruments/{instrument_name}/clients/{client_id}/session": { + /** Link Client To Session */ + post: operations["link_client_to_session_instruments__instrument_name__clients__client_id__session_post"]; + }; + "/clients/{client_id}/session": { + /** Remove Session */ + delete: operations["remove_session_clients__client_id__session_delete"]; + }; + "/sessions/{session_id}/rsyncers": { + /** Get Rsyncers For Session */ + get: operations["get_rsyncers_for_session_sessions__session_id__rsyncers_get"]; + }; + "/sessions/{session_id}": { + /** Remove Session By Id */ + delete: operations["remove_session_by_id_sessions__session_id__delete"]; + }; + "/visits/{visit_name}/{session_id}/eer_fractionation_file": { + /** Write Eer Fractionation File */ + post: operations["write_eer_fractionation_file_visits__visit_name___session_id__eer_fractionation_file_post"]; + }; + "/visits/{visit_name}/monitoring/{on}": { + /** Change Monitoring Status */ + post: operations["change_monitoring_status_visits__visit_name__monitoring__on__post"]; + }; + "/sessions/{session_id}/upstream_visits": { + /** Find Upstream Visits */ + get: operations["find_upstream_visits_sessions__session_id__upstream_visits_get"]; + }; + "/visits/{visit_name}/{session_id}/upstream_tiff_paths": { + /** Gather Upstream Tiffs */ + get: operations["gather_upstream_tiffs_visits__visit_name___session_id__upstream_tiff_paths_get"]; + }; + "/visits/{visit_name}/{session_id}/upstream_tiff/{tiff_path}": { + /** Get Tiff */ + get: operations["get_tiff_visits__visit_name___session_id__upstream_tiff__tiff_path__get"]; + }; + "/failed_client_post": { + /** Failed Client Post */ + post: operations["failed_client_post_failed_client_post_post"]; + }; + "/instruments/{instrument_name}/visits/{visit}/session/{name}": { + /** Create Session */ + post: operations["create_session_instruments__instrument_name__visits__visit__session__name__post"]; + }; + "/sessions/{session_id}/current_gain_ref": { + /** Update Current Gain Ref */ + put: operations["update_current_gain_ref_sessions__session_id__current_gain_ref_put"]; + }; + "/bootstrap/": { + /** + * Get Bootstrap Instructions + * @description Return a website containing instructions for installing the Murfey client on a + * machine with no internet access. + */ + get: operations["get_bootstrap_instructions_bootstrap__get"]; + }; + "/bootstrap/pip.whl": { + /** + * Get Pip Wheel + * @description Return a static version of pip. This does not need to be the newest or best, + * but has to be compatible with all supported Python versions. + * This is only used during bootstrapping by the client to identify and then + * download the actually newest appropriate version of pip. + */ + get: operations["get_pip_wheel_bootstrap_pip_whl_get"]; + }; + "/bootstrap/murfey.whl": { + /** + * Get Murfey Wheel + * @description Return a wheel file containing the latest release version of Murfey. We should + * not have to worry about the exact Python compatibility here, as long as + * murfey.bootstrap is compatible with all relevant versions of Python. + * This also ignores yanked releases, which again should be fine. + */ + get: operations["get_murfey_wheel_bootstrap_murfey_whl_get"]; + }; + "/cygwin/setup-x86_64.exe": { + /** + * Get Cygwin Setup + * @description Obtain and pass through a Cygwin installer from an official source. + * This is used during client bootstrapping and can download and install the + * Cygwin distribution that then remains on the client machines. + */ + get: operations["get_cygwin_setup_cygwin_setup_x86_64_exe_get"]; + }; + "/cygwin/{request_path}": { + /** + * Parse Cygwin Request + * @description Forward a Cygwin setup request to an official mirror. + */ + get: operations["parse_cygwin_request_cygwin__request_path__get"]; + }; + "/pypi/": { + /** + * Get Pypi Index + * @description Obtain list of all PyPI packages via the simple API (PEP 503). + */ + get: operations["get_pypi_index_pypi__get"]; + }; + "/pypi/{package}/": { + /** + * Get Pypi Package Downloads List + * @description Obtain list of all package downloads from PyPI via the simple API (PEP 503), and + * rewrite all download URLs to point to this server, under the current directory. + */ + get: operations["get_pypi_package_downloads_list_pypi__package___get"]; + }; + "/pypi/{package}/{filename}": { + /** + * Get Pypi File + * @description Obtain and pass through a specific download for a PyPI package. + */ + get: operations["get_pypi_file_pypi__package___filename__get"]; + }; + "/plugins/instruments/{instrument_name}/{package}": { + /** Get Plugin Wheel */ + get: operations["get_plugin_wheel_plugins_instruments__instrument_name___package__get"]; + }; + "/version/": { + /** Get Version */ + get: operations["get_version_version__get"]; + }; + "/sessions/{session_id}/clem/lif_files": { + /** Register Lif File */ + post: operations["register_lif_file_sessions__session_id__clem_lif_files_post"]; + }; + "/sessions/{session_id}/clem/tiff_files": { + /** Register Tiff File */ + post: operations["register_tiff_file_sessions__session_id__clem_tiff_files_post"]; + }; + "/sessions/{session_id}/clem/metadata_files": { + /** Register Clem Metadata */ + post: operations["register_clem_metadata_sessions__session_id__clem_metadata_files_post"]; + }; + "/sessions/{session_id}/clem/image_series": { + /** Register Image Series */ + post: operations["register_image_series_sessions__session_id__clem_image_series_post"]; + }; + "/sessions/{session_id}/clem/image_stacks": { + /** Register Image Stack */ + post: operations["register_image_stack_sessions__session_id__clem_image_stacks_post"]; + }; + "/sessions/{session_id}/lif_to_stack": { + /** Lif To Stack */ + post: operations["lif_to_stack_sessions__session_id__lif_to_stack_post"]; + }; + "/sessions/{session_id}/tiff_to_stack": { + /** Tiff To Stack */ + post: operations["tiff_to_stack_sessions__session_id__tiff_to_stack_post"]; + }; + "/sessions/{session_id}/cryolo_model": { + /** Get Cryolo Model Path */ + get: operations["get_cryolo_model_path_sessions__session_id__cryolo_model_get"]; + }; + "/token": { + /** Generate Token */ + post: operations["generate_token_token_post"]; + }; + "/sessions/{session_id}/token": { + /** Mint Session Token */ + get: operations["mint_session_token_sessions__session_id__token_get"]; + }; + "/validate_token": { + /** Simple Token Validation */ + get: operations["simple_token_validation_validate_token_get"]; + }; + "/display/microscope_image/": { + /** Get Mic Image */ + get: operations["get_mic_image_display_microscope_image__get"]; + }; + "/display/sessions/{session_id}/data_collection_groups/{dcgid}/grid_squares/{grid_square_name}/image": { + /** Get Grid Square Img */ + get: operations["get_grid_square_img_display_sessions__session_id__data_collection_groups__dcgid__grid_squares__grid_square_name__image_get"]; + }; + "/display/sessions/{session_id}/data_collection_groups/{dcgid}/grid_squares/{grid_square_name}/foil_holes/{foil_hole_name}/image": { + /** Get Foil Hole Img */ + get: operations["get_foil_hole_img_display_sessions__session_id__data_collection_groups__dcgid__grid_squares__grid_square_name__foil_holes__foil_hole_name__image_get"]; + }; + "/instruments/{instrument_name}/activate_instrument_server": { + /** Activate Instrument Server */ + post: operations["activate_instrument_server_instruments__instrument_name__activate_instrument_server_post"]; + }; + "/instruments/{instrument_name}/sessions/{session_id}/activate_instrument_server": { + /** Activate Instrument Server For Session */ + post: operations["activate_instrument_server_for_session_instruments__instrument_name__sessions__session_id__activate_instrument_server_post"]; + }; + "/sessions/{session_id}/multigrid_watcher": { + /** Start Multigrid Watcher */ + post: operations["start_multigrid_watcher_sessions__session_id__multigrid_watcher_post"]; + }; + "/sessions/{session_id}/provided_processing_parameters": { + /** Pass Proc Params To Instrument Server */ + post: operations["pass_proc_params_to_instrument_server_sessions__session_id__provided_processing_parameters_post"]; + }; + "/instruments/{instrument_name}/instrument_server": { + /** Check Instrument Server */ + get: operations["check_instrument_server_instruments__instrument_name__instrument_server_get"]; + }; + "/instruments/{instrument_name}/sessions/{session_id}/possible_gain_references": { + /** Get Possible Gain References */ + get: operations["get_possible_gain_references_instruments__instrument_name__sessions__session_id__possible_gain_references_get"]; + }; + "/sessions/{session_id}/upload_gain_reference": { + /** Request Gain Reference Upload */ + post: operations["request_gain_reference_upload_sessions__session_id__upload_gain_reference_post"]; + }; + "/visits/{visit_name}/{session_id}/upstream_tiff_data_request": { + /** Request Upstream Tiff Data Download */ + post: operations["request_upstream_tiff_data_download_visits__visit_name___session_id__upstream_tiff_data_request_post"]; + }; + "/sessions/{session_id}/stop_rsyncer": { + /** Stop Rsyncer */ + post: operations["stop_rsyncer_sessions__session_id__stop_rsyncer_post"]; + }; + "/sessions/{session_id}/finalise_rsyncer": { + /** Finalise Rsyncer */ + post: operations["finalise_rsyncer_sessions__session_id__finalise_rsyncer_post"]; + }; + "/sessions/{session_id}/remove_rsyncer": { + /** Remove Rsyncer */ + post: operations["remove_rsyncer_sessions__session_id__remove_rsyncer_post"]; + }; + "/sessions/{session_id}/restart_rsyncer": { + /** Restart Rsyncer */ + post: operations["restart_rsyncer_sessions__session_id__restart_rsyncer_post"]; + }; + "/instruments": { + /** Get Instrument Info */ + get: operations["get_instrument_info_instruments_get"]; + }; + "/instrument/{instrument_name}/image": { + /** Get Instrument Image */ + get: operations["get_instrument_image_instrument__instrument_name__image_get"]; + }; + "/ws/test/{client_id}": { + /** Close Ws Connection */ + delete: operations["close_ws_connection_ws_test__client_id__delete"]; + }; + "/ws/connect/{client_id}": { + /** Close Unrecorded Ws Connection */ + delete: operations["close_unrecorded_ws_connection_ws_connect__client_id__delete"]; + }; + "/visits/{visit_name}/smartem_atlas/": { + /** Request Smartem Atlas Analysis */ + post: operations["request_smartem_atlas_analysis_visits__visit_name__smartem_atlas__post"]; + }; +} + +export type webhooks = Record; + +export interface components { + schemas: { + /** Body_generate_token_token_post */ + Body_generate_token_token_post: { + /** Grant Type */ + grant_type?: string; + /** Username */ + username: string; + /** Password */ + password: string; + /** + * Scope + * @default + */ + scope?: string; + /** Client Id */ + client_id?: string; + /** Client Secret */ + client_secret?: string; + }; + /** Body_register_clem_metadata_sessions__session_id__clem_metadata_files_post */ + Body_register_clem_metadata_sessions__session_id__clem_metadata_files_post: { + /** + * Associated Tiffs + * @default [] + */ + associated_tiffs?: string[]; + /** + * Associated Stacks + * @default [] + */ + associated_stacks?: string[]; + }; + /** Body_register_image_series_sessions__session_id__clem_image_series_post */ + Body_register_image_series_sessions__session_id__clem_image_series_post: { + /** + * Parent Tiffs + * @default [] + */ + parent_tiffs?: string[]; + /** + * Child Stacks + * @default [] + */ + child_stacks?: string[]; + }; + /** Body_register_lif_file_sessions__session_id__clem_lif_files_post */ + Body_register_lif_file_sessions__session_id__clem_lif_files_post: { + /** + * Child Metadata + * @default [] + */ + child_metadata?: string[]; + /** + * Child Series + * @default [] + */ + child_series?: string[]; + /** + * Child Stacks + * @default [] + */ + child_stacks?: string[]; + }; + /** ClientEnvironment */ + ClientEnvironment: { + /** Client Id */ + client_id?: number; + /** + * Visit + * @default + */ + visit?: string; + /** Session Id */ + session_id?: number; + /** Connected */ + connected: boolean; + }; + /** ClientInfo */ + ClientInfo: { + /** Id */ + id: number; + }; + /** ContextInfo */ + ContextInfo: { + /** Experiment Type */ + experiment_type: string; + /** Acquisition Software */ + acquisition_software: string; + }; + /** CurrentGainRef */ + CurrentGainRef: { + /** Path */ + path: string; + }; + /** DCGroupParameters */ + DCGroupParameters: { + /** Experiment Type */ + experiment_type: string; + /** Experiment Type Id */ + experiment_type_id: number; + /** Tag */ + tag: string; + /** + * Atlas + * @default + */ + atlas?: string; + /** Sample */ + sample?: number; + }; + /** DCParameters */ + DCParameters: { + /** Voltage */ + voltage: number; + /** Pixel Size On Image */ + pixel_size_on_image: string; + /** Experiment Type */ + experiment_type: string; + /** Image Size X */ + image_size_x: number; + /** Image Size Y */ + image_size_y: number; + /** File Extension */ + file_extension: string; + /** Acquisition Software */ + acquisition_software: string; + /** Image Directory */ + image_directory: string; + /** Tag */ + tag: string; + /** Source */ + source: string; + /** Magnification */ + magnification: number; + /** Total Exposed Dose */ + total_exposed_dose?: number; + /** C2Aperture */ + c2aperture?: number; + /** Exposure Time */ + exposure_time?: number; + /** Slit Width */ + slit_width?: number; + /** + * Phase Plate + * @default false + */ + phase_plate?: boolean; + /** + * Data Collection Tag + * @default + */ + data_collection_tag?: string; + }; + /** DataCollection */ + DataCollection: { + /** Id */ + id: number; + /** Tag */ + tag: string; + /** Dcg Id */ + dcg_id: number; + }; + /** DataCollectionGroup */ + DataCollectionGroup: { + /** Id */ + id: number; + /** Session Id */ + session_id: number; + /** Tag */ + tag: string; + /** + * Atlas + * @default + */ + atlas?: string; + /** Sample */ + sample?: number; + }; + /** File */ + File: { + /** Name */ + name: string; + /** Description */ + description: string; + /** Size */ + size: number; + /** + * Timestamp + * Format: date-time + */ + timestamp: string; + /** Full Path */ + full_path: string; + }; + /** FoilHole */ + FoilHole: { + /** Id */ + id?: number; + /** Grid Square Id */ + grid_square_id: number; + /** Session Id */ + session_id: number; + /** Name */ + name: number; + /** X Location */ + x_location?: number; + /** Y Location */ + y_location?: number; + /** X Stage Position */ + x_stage_position?: number; + /** Y Stage Position */ + y_stage_position?: number; + /** Readout Area X */ + readout_area_x?: number; + /** Readout Area Y */ + readout_area_y?: number; + /** Thumbnail Size X */ + thumbnail_size_x?: number; + /** Thumbnail Size Y */ + thumbnail_size_y?: number; + /** Pixel Size */ + pixel_size?: number; + /** + * Image + * @default + */ + image?: string; + }; + /** FoilHoleParameters */ + FoilHoleParameters: { + /** Tag */ + tag: string; + /** Name */ + name: number; + /** X Location */ + x_location?: number; + /** Y Location */ + y_location?: number; + /** X Stage Position */ + x_stage_position?: number; + /** Y Stage Position */ + y_stage_position?: number; + /** Readout Area X */ + readout_area_x?: number; + /** Readout Area Y */ + readout_area_y?: number; + /** Thumbnail Size X */ + thumbnail_size_x?: number; + /** Thumbnail Size Y */ + thumbnail_size_y?: number; + /** Pixel Size */ + pixel_size?: number; + /** + * Image + * @default + */ + image?: string; + }; + /** FractionationParameters */ + FractionationParameters: { + /** Fractionation */ + fractionation: number; + /** Dose Per Frame */ + dose_per_frame: number; + /** + * Num Frames + * @default 0 + */ + num_frames?: number; + /** Eer Path */ + eer_path?: string; + /** + * Fractionation File Name + * @default eer_fractionation.txt + */ + fractionation_file_name?: string; + }; + /** GainReference */ + GainReference: { + /** + * Gain Ref + * Format: path + */ + gain_ref: string; + /** + * Rescale + * @default true + */ + rescale?: boolean; + /** + * Eer + * @default false + */ + eer?: boolean; + /** + * Tag + * @default + */ + tag?: string; + }; + /** GainReferenceRequest */ + GainReferenceRequest: { + /** + * Gain Path + * Format: path + */ + gain_path: string; + }; + /** GridSquare */ + GridSquare: { + /** Id */ + id?: number; + /** Session Id */ + session_id: number; + /** Name */ + name: number; + /** Tag */ + tag: string; + /** X Location */ + x_location?: number; + /** Y Location */ + y_location?: number; + /** X Stage Position */ + x_stage_position?: number; + /** Y Stage Position */ + y_stage_position?: number; + /** Readout Area X */ + readout_area_x?: number; + /** Readout Area Y */ + readout_area_y?: number; + /** Thumbnail Size X */ + thumbnail_size_x?: number; + /** Thumbnail Size Y */ + thumbnail_size_y?: number; + /** Pixel Size */ + pixel_size?: number; + /** + * Image + * @default + */ + image?: string; + }; + /** GridSquareParameters */ + GridSquareParameters: { + /** Tag */ + tag: string; + /** X Location */ + x_location?: number; + /** Y Location */ + y_location?: number; + /** X Stage Position */ + x_stage_position?: number; + /** Y Stage Position */ + y_stage_position?: number; + /** Readout Area X */ + readout_area_x?: number; + /** Readout Area Y */ + readout_area_y?: number; + /** Thumbnail Size X */ + thumbnail_size_x?: number; + /** Thumbnail Size Y */ + thumbnail_size_y?: number; + /** Pixel Size */ + pixel_size?: number; + /** + * Image + * @default + */ + image?: string; + }; + /** HTTPValidationError */ + HTTPValidationError: { + /** Detail */ + detail?: components["schemas"]["ValidationError"][]; + }; + /** InstrumentInfo */ + InstrumentInfo: { + /** Instrument Name */ + instrument_name: string; + /** Display Name */ + display_name: string; + /** Instrument Url */ + instrument_url: string; + }; + /** LifFileInfo */ + LifFileInfo: { + /** + * Name + * Format: path + */ + name: string; + /** Size */ + size: number; + /** Timestamp */ + timestamp: number; + /** + * Description + * @default + */ + description?: string; + }; + /** MachineConfig */ + MachineConfig: { + /** Acquisition Software */ + acquisition_software: string[]; + /** Calibrations */ + calibrations: { + [key: string]: { + [key: string]: Record | number; + }; + }; + /** Data Directories */ + data_directories: string[]; + /** + * Rsync Basepath + * Format: path + */ + rsync_basepath: string; + /** + * Default Model + * Format: path + */ + default_model: string; + /** + * Display Name + * @default + */ + display_name?: string; + /** + * Instrument Name + * @default + */ + instrument_name?: string; + /** + * Image Path + * Format: path + */ + image_path?: string; + /** + * Software Versions + * @default {} + */ + software_versions?: { + [key: string]: string; + }; + /** + * External Executables + * @default {} + */ + external_executables?: { + [key: string]: string; + }; + /** + * External Executables Eer + * @default {} + */ + external_executables_eer?: { + [key: string]: string; + }; + /** + * External Environment + * @default {} + */ + external_environment?: { + [key: string]: string; + }; + /** + * Rsync Module + * @default + */ + rsync_module?: string; + /** + * Create Directories + * @default { + * "atlas": "atlas" + * } + */ + create_directories?: { + [key: string]: string; + }; + /** + * Analyse Created Directories + * @default [] + */ + analyse_created_directories?: string[]; + /** + * Gain Reference Directory + * Format: path + */ + gain_reference_directory?: string; + /** + * Processed Directory Name + * @default processed + */ + processed_directory_name?: string; + /** + * Gain Directory Name + * @default processing + */ + gain_directory_name?: string; + /** + * Feedback Queue + * @default murfey_feedback + */ + feedback_queue?: string; + /** + * Node Creator Queue + * @default node_creator + */ + node_creator_queue?: string; + /** + * Superres + * @default false + */ + superres?: boolean; + /** + * Camera + * @default FALCON + */ + camera?: string; + /** + * Data Required Substrings + * @default {} + */ + data_required_substrings?: { + [key: string]: { + [key: string]: string[]; + }; + }; + /** + * Allow Removal + * @default false + */ + allow_removal?: boolean; + /** + * Modular Spa + * @default false + */ + modular_spa?: boolean; + /** + * Processing Enabled + * @default true + */ + processing_enabled?: boolean; + /** + * Machine Override + * @default + */ + machine_override?: string; + /** + * Processed Extra Directory + * @default + */ + processed_extra_directory?: string; + /** + * Plugin Packages + * @default {} + */ + plugin_packages?: { + [key: string]: string; + }; + /** + * Software Settings Output Directories + * @default {} + */ + software_settings_output_directories?: { + [key: string]: string[]; + }; + /** + * Process By Default + * @default true + */ + process_by_default?: boolean; + /** + * Recipes + * @default { + * "em-spa-bfactor": "em-spa-bfactor", + * "em-spa-class2d": "em-spa-class2d", + * "em-spa-class3d": "em-spa-class3d", + * "em-spa-preprocess": "em-spa-preprocess", + * "em-spa-refine": "em-spa-refine", + * "em-tomo-preprocess": "em-tomo-preprocess", + * "em-tomo-align": "em-tomo-align" + * } + */ + recipes?: { + [key: string]: string; + }; + /** + * Upstream Data Directories + * @default [] + */ + upstream_data_directories?: string[]; + /** + * Upstream Data Download Directory + * Format: path + */ + upstream_data_download_directory?: string; + /** + * Upstream Data Tiff Locations + * @default [ + * "processed" + * ] + */ + upstream_data_tiff_locations?: string[]; + /** + * Model Search Directory + * @default processing + */ + model_search_directory?: string; + /** + * Initial Model Search Directory + * @default processing/initial_model + */ + initial_model_search_directory?: string; + /** + * Failure Queue + * @default + */ + failure_queue?: string; + /** + * Instrument Server Url + * @default http://localhost:8001 + */ + instrument_server_url?: string; + /** + * Frontend Url + * @default http://localhost:3000 + */ + frontend_url?: string; + /** + * Murfey Url + * @default http://localhost:8000 + */ + murfey_url?: string; + }; + /** MagnificationLookup */ + MagnificationLookup: { + /** Magnification */ + magnification: number; + /** Pixel Size */ + pixel_size: number; + }; + /** MultigridWatcherSetup */ + MultigridWatcherSetup: { + /** + * Source + * Format: path + */ + source: string; + /** + * Skip Existing Processing + * @default false + */ + skip_existing_processing?: boolean; + }; + /** PostInfo */ + PostInfo: { + /** Url */ + url: string; + /** Data */ + data: Record; + }; + /** PreprocessingParametersTomo */ + PreprocessingParametersTomo: { + /** Dose Per Frame */ + dose_per_frame: number; + /** Gain Ref */ + gain_ref?: string; + /** Experiment Type */ + experiment_type: string; + /** Voltage */ + voltage: number; + /** Image Size X */ + image_size_x: number; + /** Image Size Y */ + image_size_y: number; + /** Pixel Size On Image */ + pixel_size_on_image: string; + /** Motion Corr Binning */ + motion_corr_binning: number; + /** Manual Tilt Offset */ + manual_tilt_offset: number; + /** File Extension */ + file_extension: string; + /** Tag */ + tag: string; + /** Tilt Series Tag */ + tilt_series_tag: string; + /** Eer Fractionation File */ + eer_fractionation_file?: string; + /** Eer Fractionation */ + eer_fractionation: number; + }; + /** ProcessFile */ + ProcessFile: { + /** Path */ + path: string; + /** Description */ + description: string; + /** Tag */ + tag: string; + /** Data Collection Id */ + data_collection_id?: number; + /** Image Number */ + image_number: number; + /** Pixel Size */ + pixel_size: number; + /** Dose Per Frame */ + dose_per_frame: number; + /** Processing Job */ + processing_job?: number; + /** Autoproc Program Id */ + autoproc_program_id?: number; + /** Mc Uuid */ + mc_uuid?: number; + /** + * Voltage + * @default 300 + */ + voltage?: number; + /** + * Mc Binning + * @default 1 + */ + mc_binning?: number; + /** Gain Ref */ + gain_ref?: string; + /** + * Extract Downscale + * @default 1 + */ + extract_downscale?: number; + /** Eer Fractionation File */ + eer_fractionation_file?: string; + /** Group Tag */ + group_tag?: string; + }; + /** ProcessingDetails */ + ProcessingDetails: { + data_collection_group: components["schemas"]["DataCollectionGroup"]; + /** Data Collections */ + data_collections: components["schemas"]["DataCollection"][]; + /** Processing Jobs */ + processing_jobs: components["schemas"]["ProcessingJob"][]; + relion_params: components["schemas"]["SPARelionParameters"]; + feedback_params: components["schemas"]["SPAFeedbackParameters"]; + }; + /** ProcessingJob */ + ProcessingJob: { + /** Id */ + id: number; + /** Recipe */ + recipe: string; + /** Dc Id */ + dc_id: number; + }; + /** ProcessingJobParameters */ + ProcessingJobParameters: { + /** Tag */ + tag: string; + /** Recipe */ + recipe: string; + /** + * Parameters + * @default {} + */ + parameters?: Record; + /** + * Experiment Type + * @default spa + */ + experiment_type?: string; + }; + /** ProcessingParametersSPA */ + ProcessingParametersSPA: { + /** Tag */ + tag: string; + /** Dose Per Frame */ + dose_per_frame: number; + /** Gain Ref */ + gain_ref?: string; + /** Experiment Type */ + experiment_type: string; + /** Voltage */ + voltage: number; + /** Image Size X */ + image_size_x: number; + /** Image Size Y */ + image_size_y: number; + /** Pixel Size On Image */ + pixel_size_on_image: string; + /** Motion Corr Binning */ + motion_corr_binning: number; + /** File Extension */ + file_extension: string; + /** Acquisition Software */ + acquisition_software: string; + /** Use Cryolo */ + use_cryolo: boolean; + /** Symmetry */ + symmetry: string; + /** Mask Diameter */ + mask_diameter?: number; + /** Boxsize */ + boxsize?: number; + /** Downscale */ + downscale: boolean; + /** Small Boxsize */ + small_boxsize?: number; + /** Eer Fractionation */ + eer_fractionation: number; + /** Particle Diameter */ + particle_diameter?: number; + /** Magnification */ + magnification?: number; + /** Total Exposed Dose */ + total_exposed_dose?: number; + /** C2Aperture */ + c2aperture?: number; + /** Exposure Time */ + exposure_time?: number; + /** Slit Width */ + slit_width?: number; + /** + * Phase Plate + * @default false + */ + phase_plate?: boolean; + }; + /** ProcessingParametersTomo */ + ProcessingParametersTomo: { + /** Manual Tilt Offset */ + manual_tilt_offset: number; + /** Tag */ + tag: string; + /** Tilt Series Tag */ + tilt_series_tag: string; + }; + /** ProvidedProcessingParameters */ + ProvidedProcessingParameters: { + /** Dose Per Frame */ + dose_per_frame: number; + /** + * Extract Downscale + * @default true + */ + extract_downscale?: boolean; + /** Particle Diameter */ + particle_diameter?: number; + /** + * Symmetry + * @default C1 + */ + symmetry?: string; + /** + * Eer Fractionation + * @default 20 + */ + eer_fractionation?: number; + }; + /** RegistrationMessage */ + RegistrationMessage: { + /** Registration */ + registration: string; + /** Params */ + params?: Record; + }; + /** RsyncInstance */ + RsyncInstance: { + /** Source */ + source: string; + /** + * Destination + * @default + */ + destination?: string; + /** Session Id */ + session_id: number; + /** + * Tag + * @default + */ + tag?: string; + /** + * Files Transferred + * @default 0 + */ + files_transferred?: number; + /** + * Files Counted + * @default 0 + */ + files_counted?: number; + /** + * Transferring + * @default false + */ + transferring?: boolean; + }; + /** RsyncerInfo */ + RsyncerInfo: { + /** Source */ + source: string; + /** Destination */ + destination: string; + /** Session Id */ + session_id: number; + /** + * Transferring + * @default true + */ + transferring?: boolean; + /** + * Increment Count + * @default 1 + */ + increment_count?: number; + /** + * Bytes + * @default 0 + */ + bytes?: number; + /** + * Increment Data Count + * @default 0 + */ + increment_data_count?: number; + /** + * Data Bytes + * @default 0 + */ + data_bytes?: number; + /** + * Tag + * @default + */ + tag?: string; + }; + /** SPAFeedbackParameters */ + SPAFeedbackParameters: { + /** Pj Id */ + pj_id: number; + /** + * Estimate Particle Diameter + * @default true + */ + estimate_particle_diameter?: boolean; + /** + * Hold Class2D + * @default false + */ + hold_class2d?: boolean; + /** + * Rerun Class2D + * @default false + */ + rerun_class2d?: boolean; + /** + * Hold Class3D + * @default false + */ + hold_class3d?: boolean; + /** + * Hold Refine + * @default false + */ + hold_refine?: boolean; + /** Class Selection Score */ + class_selection_score: number; + /** Star Combination Job */ + star_combination_job: number; + /** Initial Model */ + initial_model: string; + /** Next Job */ + next_job: number; + /** Picker Murfey Id */ + picker_murfey_id?: number; + /** Picker Ispyb Id */ + picker_ispyb_id?: number; + }; + /** SPAProcessFile */ + SPAProcessFile: { + /** Tag */ + tag: string; + /** Path */ + path: string; + /** Description */ + description: string; + /** Processing Job */ + processing_job?: number; + /** Data Collection Id */ + data_collection_id?: number; + /** Image Number */ + image_number: number; + /** Autoproc Program Id */ + autoproc_program_id?: number; + /** Foil Hole Id */ + foil_hole_id?: number; + /** Pixel Size */ + pixel_size?: number; + /** Dose Per Frame */ + dose_per_frame?: number; + /** + * Mc Binning + * @default 1 + */ + mc_binning?: number; + /** Gain Ref */ + gain_ref?: string; + /** + * Extract Downscale + * @default true + */ + extract_downscale?: boolean; + /** Eer Fractionation File */ + eer_fractionation_file?: string; + /** + * Source + * @default + */ + source?: string; + }; + /** SPAProcessingParameters */ + SPAProcessingParameters: { + /** Job Id */ + job_id: number; + }; + /** SPARelionParameters */ + SPARelionParameters: { + /** Pj Id */ + pj_id: number; + /** Angpix */ + angpix: number; + /** Dose Per Frame */ + dose_per_frame: number; + /** Gain Ref */ + gain_ref?: string; + /** Voltage */ + voltage: number; + /** Motion Corr Binning */ + motion_corr_binning: number; + /** Eer Grouping */ + eer_grouping: number; + /** Symmetry */ + symmetry: string; + /** Particle Diameter */ + particle_diameter?: number; + /** Downscale */ + downscale: boolean; + /** + * Do Icebreaker Jobs + * @default true + */ + do_icebreaker_jobs?: boolean; + /** + * Boxsize + * @default 256 + */ + boxsize?: number; + /** + * Small Boxsize + * @default 64 + */ + small_boxsize?: number; + /** + * Mask Diameter + * @default 190 + */ + mask_diameter?: number; + }; + /** Session */ + Session: { + /** Id */ + id: number; + /** Name */ + name: string; + /** + * Visit + * @default + */ + visit?: string; + /** + * Started + * @default false + */ + started?: boolean; + /** + * Current Gain Ref + * @default + */ + current_gain_ref?: string; + /** + * Instrument Name + * @default + */ + instrument_name?: string; + }; + /** SessionClients */ + SessionClients: { + session: components["schemas"]["Session"]; + /** Clients */ + clients: components["schemas"]["ClientEnvironment"][]; + }; + /** SessionInfo */ + SessionInfo: { + /** Session Id */ + session_id?: number; + /** + * Session Name + * @default + */ + session_name?: string; + /** + * Rescale + * @default true + */ + rescale?: boolean; + }; + /** SmartEMAtlasRequest */ + SmartEMAtlasRequest: { + /** + * Atlas Path + * Format: path + */ + atlas_path: string; + /** + * Output Dir + * Format: path + */ + output_dir: string; + /** + * Num Preds + * @default 15 + */ + num_preds?: number; + /** + * Cpus + * @default 4 + */ + cpus?: number; + }; + /** Source */ + Source: { + /** Rsync Source */ + rsync_source: string; + }; + /** SuggestedPathParameters */ + SuggestedPathParameters: { + /** + * Base Path + * Format: path + */ + base_path: string; + /** + * Touch + * @default false + */ + touch?: boolean; + /** + * Extra Directory + * @default + */ + extra_directory?: string; + }; + /** Tag */ + Tag: { + /** Tag */ + tag: string; + }; + /** TiffSeriesInfo */ + TiffSeriesInfo: { + /** Series Name */ + series_name: string; + /** Tiff Files */ + tiff_files: string[]; + /** Tiff Sizes */ + tiff_sizes: number[]; + /** Tiff Timestamps */ + tiff_timestamps: number[]; + /** + * Series Metadata + * Format: path + */ + series_metadata: string; + /** Metadata Size */ + metadata_size: number; + /** Metadata Timestamp */ + metadata_timestamp: number; + /** + * Description + * @default + */ + description?: string; + }; + /** TiltInfo */ + TiltInfo: { + /** Tilt Series Tag */ + tilt_series_tag: string; + /** Movie Path */ + movie_path: string; + /** Source */ + source: string; + }; + /** TiltSeriesGroupInfo */ + TiltSeriesGroupInfo: { + /** Tags */ + tags: string[]; + /** Source */ + source: string; + /** Tilt Series Lengths */ + tilt_series_lengths: number[]; + }; + /** TiltSeriesInfo */ + TiltSeriesInfo: { + /** Client Id */ + client_id: number; + /** Tag */ + tag: string; + /** Source */ + source: string; + }; + /** Token */ + Token: { + /** Access Token */ + access_token: string; + /** Token Type */ + token_type: string; + }; + /** ValidationError */ + ValidationError: { + /** Location */ + loc: (string | number)[]; + /** Message */ + msg: string; + /** Error Type */ + type: string; + }; + /** Visit */ + Visit: { + /** + * Start + * Format: date-time + */ + start: string; + /** + * End + * Format: date-time + */ + end: string; + /** Session Id */ + session_id: number; + /** Name */ + name: string; + /** Beamline */ + beamline: string; + /** Proposal Title */ + proposal_title: string; + }; + /** RsyncerSource */ + murfey__server__api__instrument__RsyncerSource: { + /** Source */ + source: string; + }; + /** RsyncerSource */ + murfey__util__models__RsyncerSource: { + /** Source */ + source: string; + }; + }; + responses: never; + parameters: never; + requestBodies: never; + headers: never; + pathItems: never; +} + +export type $defs = Record; + +export type external = Record; + +export interface operations { + /** Root */ + root__get: { + responses: { + /** @description Successful Response */ + 200: { + content: { + "text/html": string; + }; + }; + }; + }; + /** Machine Info */ + machine_info_machine_get: { + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["MachineConfig"]; + }; + }; + }; + }; + /** Machine Info By Name */ + machine_info_by_name_instruments__instrument_name__machine_get: { + parameters: { + path: { + instrument_name: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["MachineConfig"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Mic Image */ + get_mic_image_microscope_image__get: { + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + }; + }; + /** Get Mag Table */ + get_mag_table_mag_table__get: { + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["MagnificationLookup"][]; + }; + }; + }; + }; + /** Add To Mag Table */ + add_to_mag_table_mag_table__post: { + requestBody: { + content: { + "application/json": components["schemas"]["MagnificationLookup"][]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Remove Mag Table Row */ + remove_mag_table_row_mag_table__mag__delete: { + parameters: { + path: { + mag: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Instrument Display Name */ + get_instrument_display_name_instruments__instrument_name__instrument_name_get: { + parameters: { + path: { + instrument_name: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": string; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** All Visit Info */ + all_visit_info_instruments__instrument_name__visits__get: { + parameters: { + path: { + instrument_name: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Visit Info */ + visit_info_visits__visit_name__get: { + parameters: { + path: { + visit_name: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Client To Visit */ + register_client_to_visit_visits__visit_name__post: { + parameters: { + path: { + visit_name: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ClientInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Count Number Of Movies */ + count_number_of_movies_num_movies_get: { + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": { + [key: string]: number; + }; + }; + }; + }; + }; + /** Register Rsyncer */ + register_rsyncer_sessions__session_id__rsyncer_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["RsyncerInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Delete Rsyncer */ + delete_rsyncer_sessions__session_id__rsyncer__source__delete: { + parameters: { + path: { + session_id: number; + source: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Stopped Rsyncer */ + register_stopped_rsyncer_sessions__session_id__rsyncer_stopped_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["murfey__util__models__RsyncerSource"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Restarted Rsyncer */ + register_restarted_rsyncer_sessions__session_id__rsyncer_started_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["murfey__util__models__RsyncerSource"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Rsyncers For Client */ + get_rsyncers_for_client_clients__client_id__rsyncers_get: { + parameters: { + path: { + client_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Session */ + get_session_session__session_id__get: { + parameters: { + path: { + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["SessionClients"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Increment Rsync File Count */ + increment_rsync_file_count_visits__visit_name__increment_rsync_file_count_post: { + parameters: { + path: { + visit_name: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["RsyncerInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Increment Rsync Transferred Files */ + increment_rsync_transferred_files_visits__visit_name__increment_rsync_transferred_files_post: { + parameters: { + path: { + visit_name: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["RsyncerInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Increment Rsync Transferred Files Prometheus */ + increment_rsync_transferred_files_prometheus_visits__visit_name__increment_rsync_transferred_files_prometheus_post: { + parameters: { + path: { + visit_name: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["RsyncerInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Spa Proc Param Details */ + get_spa_proc_param_details_sessions__session_id__spa_processing_parameters_get: { + parameters: { + path: { + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["ProcessingDetails"][]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Spa Proc Params */ + register_spa_proc_params_sessions__session_id__spa_processing_parameters_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ProcessingParametersSPA"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Tomo Preproc Params */ + register_tomo_preproc_params_sessions__session_id__tomography_preprocessing_parameters_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["PreprocessingParametersTomo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Tomo Proc Params */ + register_tomo_proc_params_clients__client_id__tomography_processing_parameters_post: { + parameters: { + path: { + client_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ProcessingParametersTomo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Spa Proc Params */ + get_spa_proc_params_clients__client_id__spa_processing_parameters_get: { + parameters: { + path: { + client_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record[]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Grid Squares */ + get_grid_squares_sessions__session_id__grid_squares_get: { + parameters: { + path: { + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Grid Squares From Dcg */ + get_grid_squares_from_dcg_sessions__session_id__data_collection_groups__dcgid__grid_squares_get: { + parameters: { + path: { + session_id: number; + dcgid: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["GridSquare"][]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Number Of Movies From Grid Square */ + get_number_of_movies_from_grid_square_sessions__session_id__data_collection_groups__dcgid__grid_squares__gsid__num_movies_get: { + parameters: { + path: { + session_id: number; + dcgid: number; + gsid: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": number; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Foil Holes From Grid Square */ + get_foil_holes_from_grid_square_sessions__session_id__data_collection_groups__dcgid__grid_squares__gsid__foil_holes_get: { + parameters: { + path: { + session_id: number; + dcgid: number; + gsid: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["FoilHole"][]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Number Of Movies From Foil Hole */ + get_number_of_movies_from_foil_hole_sessions__session_id__data_collection_groups__dcgid__grid_squares__gsid__foil_holes__fhid__num_movies_get: { + parameters: { + path: { + session_id: number; + dcgid: number; + gsid: number; + fhid: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": number; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Grid Square */ + register_grid_square_sessions__session_id__grid_square__gsid__post: { + parameters: { + path: { + session_id: number; + gsid: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["GridSquareParameters"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Foil Hole */ + get_foil_hole_sessions__session_id__foil_hole__fh_name__get: { + parameters: { + path: { + fh_name: number; + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": { + [key: string]: number; + }; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Foil Hole */ + register_foil_hole_sessions__session_id__grid_square__gs_name__foil_hole_post: { + parameters: { + path: { + gs_name: number; + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["FoilHoleParameters"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Tilt Series */ + register_tilt_series_visits__visit_name__tilt_series_post: { + parameters: { + path: { + visit_name: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["TiltSeriesInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Completed Tilt Series */ + register_completed_tilt_series_visits__visit_name___client_id__completed_tilt_series_post: { + parameters: { + path: { + visit_name: string; + client_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["TiltSeriesGroupInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Tilts */ + get_tilts_clients__client_id__tilt_series__tilt_series_tag__tilts_get: { + parameters: { + path: { + client_id: number; + tilt_series_tag: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Tilt */ + register_tilt_visits__visit_name___client_id__tilt_post: { + parameters: { + path: { + visit_name: string; + client_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["TiltInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Current Visits */ + get_current_visits_instruments__instrument_name__visits_raw_get: { + parameters: { + path: { + instrument_name: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["Visit"][]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Context */ + register_context_visits__visit_name__context_post: { + requestBody: { + content: { + "application/json": components["schemas"]["ContextInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Add File */ + add_file_visits__visit_name__files_post: { + requestBody: { + content: { + "application/json": components["schemas"]["File"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Send Murfey Message */ + send_murfey_message_feedback_post: { + requestBody: { + content: { + "application/json": components["schemas"]["RegistrationMessage"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Request Spa Processing */ + request_spa_processing_visits__visit_name__spa_processing_post: { + parameters: { + path: { + visit_name: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["SPAProcessingParameters"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Flush Spa Processing */ + flush_spa_processing_visits__visit_name___session_id__flush_spa_processing_post: { + parameters: { + path: { + visit_name: string; + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["Tag"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Request Spa Preprocessing */ + request_spa_preprocessing_visits__visit_name___session_id__spa_preprocess_post: { + parameters: { + path: { + visit_name: string; + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["SPAProcessFile"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Flush Tomography Processing */ + flush_tomography_processing_visits__visit_name___client_id__flush_tomography_processing_post: { + parameters: { + path: { + visit_name: string; + client_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["Source"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Request Tomography Preprocessing */ + request_tomography_preprocessing_visits__visit_name___client_id__tomography_preprocess_post: { + parameters: { + path: { + visit_name: string; + client_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ProcessFile"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Version */ + get_version_version_get: { + parameters: { + query?: { + client_version?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Suggest Path */ + suggest_path_visits__visit_name___session_id__suggested_path_post: { + parameters: { + path: { + visit_name: string; + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["SuggestedPathParameters"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Dc Groups */ + get_dc_groups_sessions__session_id__data_collection_groups_get: { + parameters: { + path: { + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": { + [key: string]: components["schemas"]["DataCollectionGroup"]; + }; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Data Collections */ + get_data_collections_sessions__session_id__data_collection_groups__dcgid__data_collections_get: { + parameters: { + path: { + dcgid: number; + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["DataCollection"][]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Dc Group */ + register_dc_group_visits__visit_name___session_id__register_data_collection_group_post: { + parameters: { + path: { + visit_name: string; + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["DCGroupParameters"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Start Dc */ + start_dc_visits__visit_name___session_id__start_data_collection_post: { + parameters: { + path: { + visit_name: string; + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["DCParameters"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["DCParameters"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Proc */ + register_proc_visits__visit_name___session_id__register_processing_job_post: { + parameters: { + path: { + visit_name: unknown; + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ProcessingJobParameters"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Process Gain */ + process_gain_sessions__session_id__process_gain_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["GainReference"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** New Client Id */ + new_client_id_new_client_id__get: { + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + }; + }; + /** Get Clients */ + get_clients_clients_get: { + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + }; + }; + /** Get Sessions */ + get_sessions_sessions_get: { + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + }; + }; + /** Link Client To Session */ + link_client_to_session_instruments__instrument_name__clients__client_id__session_post: { + parameters: { + path: { + instrument_name: string; + client_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["SessionInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Remove Session */ + remove_session_clients__client_id__session_delete: { + parameters: { + path: { + client_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Rsyncers For Session */ + get_rsyncers_for_session_sessions__session_id__rsyncers_get: { + parameters: { + path: { + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["RsyncInstance"][]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Remove Session By Id */ + remove_session_by_id_sessions__session_id__delete: { + parameters: { + path: { + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Write Eer Fractionation File */ + write_eer_fractionation_file_visits__visit_name___session_id__eer_fractionation_file_post: { + parameters: { + path: { + visit_name: string; + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["FractionationParameters"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": Record; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Change Monitoring Status */ + change_monitoring_status_visits__visit_name__monitoring__on__post: { + parameters: { + path: { + visit_name: string; + on: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Find Upstream Visits */ + find_upstream_visits_sessions__session_id__upstream_visits_get: { + parameters: { + path: { + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Gather Upstream Tiffs */ + gather_upstream_tiffs_visits__visit_name___session_id__upstream_tiff_paths_get: { + parameters: { + path: { + visit_name: string; + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Tiff */ + get_tiff_visits__visit_name___session_id__upstream_tiff__tiff_path__get: { + parameters: { + path: { + visit_name: string; + session_id: number; + tiff_path: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Failed Client Post */ + failed_client_post_failed_client_post_post: { + requestBody: { + content: { + "application/json": components["schemas"]["PostInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Create Session */ + create_session_instruments__instrument_name__visits__visit__session__name__post: { + parameters: { + path: { + instrument_name: string; + visit: string; + name: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": number; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Update Current Gain Ref */ + update_current_gain_ref_sessions__session_id__current_gain_ref_put: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["CurrentGainRef"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** + * Get Bootstrap Instructions + * @description Return a website containing instructions for installing the Murfey client on a + * machine with no internet access. + */ + get_bootstrap_instructions_bootstrap__get: { + responses: { + /** @description Successful Response */ + 200: { + content: { + "text/html": string; + }; + }; + }; + }; + /** + * Get Pip Wheel + * @description Return a static version of pip. This does not need to be the newest or best, + * but has to be compatible with all supported Python versions. + * This is only used during bootstrapping by the client to identify and then + * download the actually newest appropriate version of pip. + */ + get_pip_wheel_bootstrap_pip_whl_get: { + responses: { + /** @description Successful Response */ + 200: { + content: never; + }; + }; + }; + /** + * Get Murfey Wheel + * @description Return a wheel file containing the latest release version of Murfey. We should + * not have to worry about the exact Python compatibility here, as long as + * murfey.bootstrap is compatible with all relevant versions of Python. + * This also ignores yanked releases, which again should be fine. + */ + get_murfey_wheel_bootstrap_murfey_whl_get: { + responses: { + /** @description Successful Response */ + 200: { + content: never; + }; + }; + }; + /** + * Get Cygwin Setup + * @description Obtain and pass through a Cygwin installer from an official source. + * This is used during client bootstrapping and can download and install the + * Cygwin distribution that then remains on the client machines. + */ + get_cygwin_setup_cygwin_setup_x86_64_exe_get: { + responses: { + /** @description Successful Response */ + 200: { + content: never; + }; + }; + }; + /** + * Parse Cygwin Request + * @description Forward a Cygwin setup request to an official mirror. + */ + parse_cygwin_request_cygwin__request_path__get: { + parameters: { + path: { + request_path: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: never; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** + * Get Pypi Index + * @description Obtain list of all PyPI packages via the simple API (PEP 503). + */ + get_pypi_index_pypi__get: { + responses: { + /** @description Successful Response */ + 200: { + content: never; + }; + }; + }; + /** + * Get Pypi Package Downloads List + * @description Obtain list of all package downloads from PyPI via the simple API (PEP 503), and + * rewrite all download URLs to point to this server, under the current directory. + */ + get_pypi_package_downloads_list_pypi__package___get: { + parameters: { + path: { + package: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: never; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** + * Get Pypi File + * @description Obtain and pass through a specific download for a PyPI package. + */ + get_pypi_file_pypi__package___filename__get: { + parameters: { + path: { + package: string; + filename: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: never; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Plugin Wheel */ + get_plugin_wheel_plugins_instruments__instrument_name___package__get: { + parameters: { + path: { + instrument_name: string; + package: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: never; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Version */ + get_version_version__get: { + parameters: { + query?: { + client_version?: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Lif File */ + register_lif_file_sessions__session_id__clem_lif_files_post: { + parameters: { + query: { + lif_file: string; + master_metadata?: string; + }; + path: { + session_id: number; + }; + }; + requestBody?: { + content: { + "application/json": components["schemas"]["Body_register_lif_file_sessions__session_id__clem_lif_files_post"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Tiff File */ + register_tiff_file_sessions__session_id__clem_tiff_files_post: { + parameters: { + query: { + tiff_file: string; + associated_metadata?: string; + associated_series?: string; + associated_stack?: string; + }; + path: { + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Clem Metadata */ + register_clem_metadata_sessions__session_id__clem_metadata_files_post: { + parameters: { + query: { + metadata_file: string; + parent_lif?: string; + associated_series?: string; + }; + path: { + session_id: number; + }; + }; + requestBody?: { + content: { + "application/json": components["schemas"]["Body_register_clem_metadata_sessions__session_id__clem_metadata_files_post"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Image Series */ + register_image_series_sessions__session_id__clem_image_series_post: { + parameters: { + query: { + series_name: string; + parent_lif?: string; + associated_metadata?: string; + }; + path: { + session_id: number; + }; + }; + requestBody?: { + content: { + "application/json": components["schemas"]["Body_register_image_series_sessions__session_id__clem_image_series_post"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Register Image Stack */ + register_image_stack_sessions__session_id__clem_image_stacks_post: { + parameters: { + query: { + image_stack: string; + channel?: string; + parent_lif?: string; + associated_metadata?: string; + parent_series?: string; + }; + path: { + session_id: number; + }; + }; + requestBody?: { + content: { + "application/json": string[]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Lif To Stack */ + lif_to_stack_sessions__session_id__lif_to_stack_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["LifFileInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Tiff To Stack */ + tiff_to_stack_sessions__session_id__tiff_to_stack_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["TiffSeriesInfo"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Cryolo Model Path */ + get_cryolo_model_path_sessions__session_id__cryolo_model_get: { + parameters: { + path: { + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Generate Token */ + generate_token_token_post: { + requestBody: { + content: { + "application/x-www-form-urlencoded": components["schemas"]["Body_generate_token_token_post"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["Token"]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Mint Session Token */ + mint_session_token_sessions__session_id__token_get: { + parameters: { + path: { + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Simple Token Validation */ + simple_token_validation_validate_token_get: { + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + }; + }; + /** Get Mic Image */ + get_mic_image_display_microscope_image__get: { + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + }; + }; + /** Get Grid Square Img */ + get_grid_square_img_display_sessions__session_id__data_collection_groups__dcgid__grid_squares__grid_square_name__image_get: { + parameters: { + path: { + session_id: number; + dcgid: number; + grid_square_name: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Foil Hole Img */ + get_foil_hole_img_display_sessions__session_id__data_collection_groups__dcgid__grid_squares__grid_square_name__foil_holes__foil_hole_name__image_get: { + parameters: { + path: { + session_id: number; + dcgid: number; + grid_square_name: number; + foil_hole_name: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Activate Instrument Server */ + activate_instrument_server_instruments__instrument_name__activate_instrument_server_post: { + parameters: { + path: { + instrument_name: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Activate Instrument Server For Session */ + activate_instrument_server_for_session_instruments__instrument_name__sessions__session_id__activate_instrument_server_post: { + parameters: { + path: { + instrument_name: string; + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Start Multigrid Watcher */ + start_multigrid_watcher_sessions__session_id__multigrid_watcher_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["MultigridWatcherSetup"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Pass Proc Params To Instrument Server */ + pass_proc_params_to_instrument_server_sessions__session_id__provided_processing_parameters_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["ProvidedProcessingParameters"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Check Instrument Server */ + check_instrument_server_instruments__instrument_name__instrument_server_get: { + parameters: { + path: { + instrument_name: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Possible Gain References */ + get_possible_gain_references_instruments__instrument_name__sessions__session_id__possible_gain_references_get: { + parameters: { + path: { + instrument_name: string; + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["File"][]; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Request Gain Reference Upload */ + request_gain_reference_upload_sessions__session_id__upload_gain_reference_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["GainReferenceRequest"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Request Upstream Tiff Data Download */ + request_upstream_tiff_data_download_visits__visit_name___session_id__upstream_tiff_data_request_post: { + parameters: { + path: { + visit_name: string; + session_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Stop Rsyncer */ + stop_rsyncer_sessions__session_id__stop_rsyncer_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["murfey__server__api__instrument__RsyncerSource"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Finalise Rsyncer */ + finalise_rsyncer_sessions__session_id__finalise_rsyncer_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["murfey__server__api__instrument__RsyncerSource"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Remove Rsyncer */ + remove_rsyncer_sessions__session_id__remove_rsyncer_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["murfey__server__api__instrument__RsyncerSource"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Restart Rsyncer */ + restart_rsyncer_sessions__session_id__restart_rsyncer_post: { + parameters: { + path: { + session_id: number; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["murfey__server__api__instrument__RsyncerSource"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Get Instrument Info */ + get_instrument_info_instruments_get: { + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": components["schemas"]["InstrumentInfo"][]; + }; + }; + }; + }; + /** Get Instrument Image */ + get_instrument_image_instrument__instrument_name__image_get: { + parameters: { + path: { + instrument_name: string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Close Ws Connection */ + close_ws_connection_ws_test__client_id__delete: { + parameters: { + path: { + client_id: number; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Close Unrecorded Ws Connection */ + close_unrecorded_ws_connection_ws_connect__client_id__delete: { + parameters: { + path: { + client_id: number | string; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; + /** Request Smartem Atlas Analysis */ + request_smartem_atlas_analysis_visits__visit_name__smartem_atlas__post: { + parameters: { + path: { + visit_name: string; + }; + }; + requestBody: { + content: { + "application/json": components["schemas"]["SmartEMAtlasRequest"]; + }; + }; + responses: { + /** @description Successful Response */ + 200: { + content: { + "application/json": unknown; + }; + }; + /** @description Validation Error */ + 422: { + content: { + "application/json": components["schemas"]["HTTPValidationError"]; + }; + }; + }; + }; +} diff --git a/murfey-frontend/src/setupTests.js b/murfey-frontend/src/setupTests.js new file mode 100644 index 000000000..1dd407a63 --- /dev/null +++ b/murfey-frontend/src/setupTests.js @@ -0,0 +1,5 @@ +// jest-dom adds custom jest matchers for asserting on DOM nodes. +// allows you to do things like: +// expect(element).toHaveTextContent(/react/i) +// learn more: https://github.com/testing-library/jest-dom +import "@testing-library/jest-dom"; diff --git a/murfey-frontend/src/styles/colours.tsx b/murfey-frontend/src/styles/colours.tsx new file mode 100644 index 000000000..1cc89cc1c --- /dev/null +++ b/murfey-frontend/src/styles/colours.tsx @@ -0,0 +1,16 @@ +const colours = { + murfey: { + 50: { default: "#FBFBFB", _dark: "#525151" }, + 75: { derfault: "#F7F7F7", _dark: "#080808" }, + 100: { default: "#E7ECEF", _dark: "#383838" }, + 200: { default: "#CBD5E0", _dark: "#030303" }, + 300: { default: "#39435E", _dark: "#5f709e" }, + 400: { default: "#ACACF9", _dark: "#030405" }, + 500: { default: "#FC6321", _dark: "#050401" }, + 600: { default: "#5738BD", _dark: "#101a36" }, + 700: { default: "#2910A1", _dark: "#071d4a" }, + 800: { default: "#0E0055", _dark: "#023496" }, + }, +}; + +export { colours }; diff --git a/murfey-frontend/src/styles/components.ts b/murfey-frontend/src/styles/components.ts new file mode 100644 index 000000000..daf1da12f --- /dev/null +++ b/murfey-frontend/src/styles/components.ts @@ -0,0 +1,325 @@ +import { + defineStyleConfig, + defineStyle, + createMultiStyleConfigHelpers, + UseToastOptions, +} from "@chakra-ui/react"; +import { + cardAnatomy, + tabsAnatomy, + inputAnatomy, + numberInputAnatomy, + selectAnatomy, +} from "@chakra-ui/anatomy"; + +const baseToast: UseToastOptions = { + id: "main-toast", + status: "success", + duration: 6000, + isClosable: true, +}; + +const baseInput = { + field: { + bg: "white", + border: "solid 1px", + borderColor: "murfey.200", + borderRadius: 0, + }, +}; + +const Accordion = defineStyleConfig({ + baseStyle: { + container: { + border: "1px solid var(--chakra-colors-murfey-100)", + }, + }, +}); + +const Text = defineStyleConfig({ + variants: { + infoGroupText: { + wordBreak: "break-all", + display: "inline", + fontSize: "xs", + }, + }, +}); + +const Checkbox = defineStyleConfig({ + sizes: { + sm: { + control: { + height: "16px", + width: "16px", + }, + icon: { + height: "16px", + fontSize: "10px", + }, + label: { + fontSize: "14px", + height: "16px", + }, + }, + }, + baseStyle: { + control: { + borderColor: "murfey.600", + backgroundColor: "#FFF", + _checked: { + backgroundColor: "murfey.600", + borderColor: "murfey.600", + }, + }, + }, +}); + +const Table = defineStyleConfig({ + variants: { + diamondStriped: { + tbody: { + tr: { + _odd: { + bg: "murfey.100", + }, + _even: { + bg: "murfey.50", + }, + _hover: { + bg: "murfey.200", + }, + }, + }, + }, + }, +}); + +const CardHeader = defineStyleConfig({ + baseStyle: { + p: "10px !important", + h: "10%", + }, +}); + +const CardBody = defineStyleConfig({ + baseStyle: { + p: 2, + h: "90%", + }, +}); + +const { definePartsStyle, defineMultiStyleConfig } = + createMultiStyleConfigHelpers(cardAnatomy.keys); + +const baseCardStyle = definePartsStyle({ + container: { + p: 1, + borderWidth: "1px", + borderRadius: "lg", + borderColor: "murfey.200", + _hover: { + borderColor: "murfey.400", + cursor: "pointer", + }, + _selected: { + bg: "murfey.100", + fontWeight: "600", + borderBottomWidth: "3px", + }, + }, + header: { + p: 2, + cursor: "pointer", + _hover: { + color: "murfey.300", + }, + }, + body: { + px: 2, + height: "90%", + }, +}); + +const Card = defineMultiStyleConfig({ + baseStyle: baseCardStyle, + defaultProps: { variant: "outline" }, +}); + +const Button = defineStyleConfig({ + defaultProps: { + variant: "default", + }, + baseStyle: { + borderBottom: "2px solid rgba(0,0,0,0.2)", + }, + variants: { + default: { + color: "murfey.50", + bg: "murfey.600", + _hover: { + bgImage: "linear-gradient(rgb(0 0 0/30%) 0 0)", + _disabled: { + bg: "murfey.600", + }, + }, + }, + pgSelected: { + bg: "murfey.600", + color: "murfey.50", + cursor: "default", + }, + pgNotSelected: { + bg: "gray.200", + color: "charcoal", + fontSize: "sm", + _hover: { + bg: "murfey.200", + }, + }, + onBlue: { + color: "murfey.500", + borderColor: "murfey.500", + border: "1px solid", + fontSize: "sm", + _hover: { + color: "murfey.300", + bg: "murfey.500", + }, + }, + }, +}); + +const notFound = defineStyle({ + textAlign: "center", + color: "murfey.300", +}); + +const Heading = defineStyleConfig({ + variants: { + collection: { + fontSize: 20, + py: "4px", + }, + notFound, + notFoundSubtitle: { + ...notFound, + fontWeight: 200, + fontSize: 20, + paddingBottom: 10, + }, + }, +}); + +const { + definePartsStyle: defineInputStyle, + defineMultiStyleConfig: defineInputConfig, +} = createMultiStyleConfigHelpers(inputAnatomy.keys); + +const hiContrastInput = defineInputStyle({ + field: { + borderWidth: "1px", + borderColor: "murfey.800", + borderRadius: 0, + _invalid: { + borderColor: "red.500", + }, + }, +}); + +const baseInputStyle = defineInputStyle({ + ...baseInput, + addon: { + border: "solid 1px", + borderColor: "murfey.200", + background: "murfey.100", + }, +}); + +const Input = defineInputConfig({ + baseStyle: baseInputStyle, + variants: { "hi-contrast": hiContrastInput, default: baseInputStyle }, + defaultProps: { variant: "default" }, +}); + +const { defineMultiStyleConfig: defineNumberInputConfig } = + createMultiStyleConfigHelpers(numberInputAnatomy.keys); + +const NumberInput = defineNumberInputConfig({ + defaultProps: { variant: "default" }, + variants: { default: baseInput }, +}); + +const { defineMultiStyleConfig: defineSelectConfig } = + createMultiStyleConfigHelpers(selectAnatomy.keys); + +const Select = defineSelectConfig({ + defaultProps: { variant: "default" }, + variants: { default: baseInput, "hi-contrast": hiContrastInput }, +}); + +const { + definePartsStyle: defineTabsStyle, + defineMultiStyleConfig: defineTabsConfig, +} = createMultiStyleConfigHelpers(tabsAnatomy.keys); + +const baseTabsStyle = defineTabsStyle({ + tab: { + border: "1px solid", + borderColor: "murfey.200", + bg: "murfey.75", + borderBottom: "none", + _selected: { + bg: "murfey.50", + color: "murfey.700", + borderColor: "inherit", + borderBottom: "none", + borderTopColor: "murfey.700", + mb: "-2px", + }, + }, + tablist: { + borderBottom: "none", + }, + tabpanel: { + p: "2", + bg: "murfey.50", + border: "1px solid", + borderColor: "inherit", + }, +}); + +const Tabs = defineTabsConfig({ + baseStyle: baseTabsStyle, + defaultProps: { variant: "none" }, +}); + +const Code = defineStyleConfig({ + baseStyle: { + backgroundColor: "murfey.100", + color: "murfey.800", + }, +}); + +const Textarea = defineStyleConfig({ + variants: { "hi-contrast": hiContrastInput.field }, +}); + +export { + Accordion, + Button, + Table, + Text, + Heading, + Card, + CardHeader, + CardBody, + Tabs, + baseToast, + Checkbox, + Code, + Input, + Textarea, + NumberInput, + Select, +}; diff --git a/murfey-frontend/src/styles/main.css b/murfey-frontend/src/styles/main.css new file mode 100644 index 000000000..ad6ec7d8b --- /dev/null +++ b/murfey-frontend/src/styles/main.css @@ -0,0 +1,29 @@ +.rootContainer { + display: flex; + flex-direction: column; + height: 100%; + width: 100%; +} + +.footer { + flex-shrink: 0; +} + +.main { + margin: 0.3em 7.3vw !important; + flex: 1 0 auto; +} + +html, +body, +#root { + height: 100%; + background-color: var(--chakra-colors-murfey-50); +} + +.homeRoot > * { + padding: 4vh 10vw; + width: 100%; + justify-content: start; + align-items: start; +} diff --git a/murfey-frontend/src/styles/theme.tsx b/murfey-frontend/src/styles/theme.tsx new file mode 100644 index 000000000..500247036 --- /dev/null +++ b/murfey-frontend/src/styles/theme.tsx @@ -0,0 +1,49 @@ +import { ThemeConfig, extendTheme } from "@chakra-ui/react"; +import { colours } from "styles/colours"; +import { + Accordion, + Button, + Checkbox, + Heading, + Table, + Card, + Tabs, + Code, + Text, + Input, + Textarea, + NumberInput, + Select, +} from "./components"; + +const config: ThemeConfig = { + initialColorMode: "light", + useSystemColorMode: false, +}; + +export const theme = extendTheme({ + semanticTokens: { colors: colours }, + components: { + Accordion, + Checkbox, + Button, + Text, + Heading, + Table, + Card, + Tabs, + Code, + Input, + Textarea, + NumberInput, + Select, + }, + breakpoints: { + sm: "30em", + md: "48em", + lg: "62em", + xl: "80em", + "2xl": "150em", + }, + config, +}); diff --git a/murfey-frontend/src/utils/api/client.tsx b/murfey-frontend/src/utils/api/client.tsx new file mode 100644 index 000000000..7dd33767d --- /dev/null +++ b/murfey-frontend/src/utils/api/client.tsx @@ -0,0 +1,162 @@ +import { createStandaloneToast } from "@chakra-ui/toast"; +import { baseToast } from "@diamondlightsource/ui-components"; +const { toast } = createStandaloneToast(); + +const controller = new AbortController(); + +const defaultSettings: Partial = { + credentials: + process.env.NODE_ENV === "development" ? "include" : "same-origin", +}; + +interface RequestConfig { + method: string; + headers: Record; + body?: string | FormData; + [k: string]: any; +} + +export interface Response { + status: number; + data: any; + headers: Record; + url: string; +} + +export const getPrefix = (prefix: string = "/api/") => { + if (prefix.substring(0, 1) === "/") { + return window.location.origin + prefix; + } + + return prefix; +}; + +export const client = async ( + endpoint: string, + customConfig: Record = {}, + body?: Record | FormData | null, + method: string | null = null, + errToast: boolean = true, + prefix: string = getPrefix( + sessionStorage.getItem("murfeyServerURL") ?? + process.env.REACT_APP_API_ENDPOINT, + ), +): Promise => { + const config: RequestConfig = { + method: method ? method : body != null ? "POST" : "GET", + ...customConfig, + headers: { + ...customConfig.headers, + }, + signal: controller.signal, + body: undefined, + ...defaultSettings, + }; + console.log(endpoint); + + if (body != null) { + if (!(body instanceof FormData)) { + config.body = JSON.stringify(body); + config.headers = { + ...config.headers, + Accept: "application/json", + "Content-Type": "application/json", + }; + } else { + config.body = body; + } + } + + try { + const token = sessionStorage.getItem("token"); + config.headers = { ...config.headers, Authorization: `Bearer ${token}` }; + const response = await fetch(prefix + endpoint, config); + const isJson = response.headers.get("content-type") === "application/json"; + + if (!isJson) console.log(endpoint); + + return { + status: response.status, + data: isJson ? await response.json() : await response.arrayBuffer(), + headers: response.headers, + url: response.url, + }; + } catch (err) { + if (!toast.isActive("main-toast") && errToast) { + toast({ + ...baseToast, + title: + "An error has occurred while fetching data, please try again later.", + status: "error", + }); + } + + throw err; + } +}; + +client.get = async ( + endpoint: string, + customConfig = {}, + errToast: boolean = true, +) => { + return await client( + endpoint, + (customConfig = { + ...customConfig, + }), + null, + "GET", + (errToast = errToast), + ); +}; + +client.hub_get = async ( + endpoint: string, + customConfig = {}, + errToast: boolean = true, +) => { + return await client( + endpoint, + (customConfig = { + ...customConfig, + }), + null, + "GET", + (errToast = errToast), + getPrefix(process.env.REACT_APP_HUB_ENDPOINT), + ); +}; + +client.delete = async (endpoint: string, customConfig = {}) => { + return await client( + endpoint, + (customConfig = { + ...customConfig, + }), + null, + "DELETE", + ); +}; + +client.post = async ( + endpoint: string, + body: Record | FormData, + customConfig = {}, +) => { + return await client(endpoint, { ...customConfig }, body); +}; + +client.put = async ( + endpoint: string, + body: Record | FormData, + customConfig = {}, +) => { + return await client(endpoint, { ...customConfig }, body, "PUT"); +}; + +export const prependApiUrl = (url: string) => + `${getPrefix( + sessionStorage.getItem("murfeyServerURL") ?? + process.env.REACT_APP_API_ENDPOINT, + )}${url}`; diff --git a/murfey-frontend/src/utils/generic.tsx b/murfey-frontend/src/utils/generic.tsx new file mode 100644 index 000000000..dd06c16ea --- /dev/null +++ b/murfey-frontend/src/utils/generic.tsx @@ -0,0 +1,15 @@ +const timeFormatter = new Intl.DateTimeFormat("en-GB", { + dateStyle: "short", + timeStyle: "short", +}); + +export const parseDate = (dateString: string | undefined) => { + const safeDate = dateString ?? ""; + const date = Date.parse(safeDate); + + if (isNaN(date)) { + return safeDate; + } + + return timeFormatter.format(date); +}; diff --git a/murfey-frontend/tsconfig.json b/murfey-frontend/tsconfig.json new file mode 100644 index 000000000..faea932dd --- /dev/null +++ b/murfey-frontend/tsconfig.json @@ -0,0 +1,21 @@ +{ + "compilerOptions": { + "target": "es2017", + "lib": ["dom", "dom.iterable", "esnext"], + "allowJs": true, + "skipLibCheck": true, + "esModuleInterop": true, + "allowSyntheticDefaultImports": true, + "strict": true, + "forceConsistentCasingInFileNames": true, + "noFallthroughCasesInSwitch": true, + "module": "esnext", + "moduleResolution": "node", + "resolveJsonModule": true, + "isolatedModules": true, + "noEmit": true, + "jsx": "react-jsx", + "baseUrl": "src" + }, + "include": ["src"] +} diff --git a/murfey-frontend/yarn.lock b/murfey-frontend/yarn.lock new file mode 100644 index 000000000..3d8fd8c14 --- /dev/null +++ b/murfey-frontend/yarn.lock @@ -0,0 +1,11673 @@ +# THIS IS AN AUTOGENERATED FILE. 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murfey-frontend/public/favicon.ico | Bin 3870 -> 0 bytes murfey-frontend/public/images/diamondgs.png | Bin 1931 -> 0 bytes murfey-frontend/public/index.html | 43 - murfey-frontend/public/logo192.png | Bin 5347 -> 0 bytes murfey-frontend/public/logo512.png | Bin 9664 -> 0 bytes murfey-frontend/public/manifest.json | 25 - murfey-frontend/public/robots.txt | 3 - murfey-frontend/src/components/forms.tsx | 195 - .../src/components/gridSquareCard.tsx | 147 - .../src/components/instrumentCard.tsx | 58 - murfey-frontend/src/components/navbar.tsx | 170 - .../src/components/protectedRoutes.tsx | 20 - .../src/components/setupStepper.tsx | 65 - .../src/components/upstreamVisitsCard.tsx | 48 - murfey-frontend/src/index.css | 13 - murfey-frontend/src/index.tsx | 149 - .../src/loaders/dataCollectionGroups.tsx | 33 - murfey-frontend/src/loaders/general.tsx | 49 - murfey-frontend/src/loaders/gridSquares.tsx | 80 - murfey-frontend/src/loaders/hub.tsx | 22 - murfey-frontend/src/loaders/jwt.tsx | 43 - murfey-frontend/src/loaders/machineConfig.tsx | 27 - murfey-frontend/src/loaders/magTable.tsx | 46 - .../src/loaders/multigridSetup.tsx | 21 - .../src/loaders/possibleGainRefs.tsx | 84 - .../src/loaders/processingParameters.tsx | 34 - murfey-frontend/src/loaders/rsyncers.tsx | 94 - murfey-frontend/src/loaders/sessionSetup.tsx | 22 - .../src/loaders/session_clients.tsx | 116 - murfey-frontend/src/loaders/visits.tsx | 33 - murfey-frontend/src/logo.svg | 1 - murfey-frontend/src/reportWebVitals.js | 13 - .../src/routes/DataCollectionGroups.tsx | 87 - murfey-frontend/src/routes/Error.tsx | 59 - .../src/routes/GainRefTransfer.tsx | 158 - murfey-frontend/src/routes/GridSquares.tsx | 75 - murfey-frontend/src/routes/Home.tsx | 206 - murfey-frontend/src/routes/Hub.tsx | 97 - murfey-frontend/src/routes/Login.tsx | 75 - murfey-frontend/src/routes/MagTable.tsx | 168 - murfey-frontend/src/routes/MultigridSetup.tsx | 166 - murfey-frontend/src/routes/NewSession.tsx | 185 - .../src/routes/ProcessingParameters.tsx | 184 - murfey-frontend/src/routes/Root.tsx | 21 - murfey-frontend/src/routes/Session.tsx | 418 - murfey-frontend/src/routes/SessionLinker.tsx | 140 - murfey-frontend/src/routes/SessionSetup.tsx | 168 - murfey-frontend/src/routes/UserParameters.tsx | 40 - murfey-frontend/src/schema/main.ts | 4335 ------ murfey-frontend/src/setupTests.js | 5 - murfey-frontend/src/styles/colours.tsx | 16 - murfey-frontend/src/styles/components.ts | 325 - murfey-frontend/src/styles/main.css | 29 - murfey-frontend/src/styles/theme.tsx | 49 - murfey-frontend/src/utils/api/client.tsx | 162 - murfey-frontend/src/utils/generic.tsx | 15 - murfey-frontend/tsconfig.json | 21 - murfey-frontend/yarn.lock | 11673 ---------------- 64 files changed, 22702 deletions(-) delete mode 100644 Dockerfiles/murfey-frontend delete mode 100644 murfey-frontend/README.md delete mode 100644 murfey-frontend/mime.types delete mode 100644 murfey-frontend/nginx/conf.d delete mode 100644 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murfey-frontend/src/routes/UserParameters.tsx delete mode 100644 murfey-frontend/src/schema/main.ts delete mode 100644 murfey-frontend/src/setupTests.js delete mode 100644 murfey-frontend/src/styles/colours.tsx delete mode 100644 murfey-frontend/src/styles/components.ts delete mode 100644 murfey-frontend/src/styles/main.css delete mode 100644 murfey-frontend/src/styles/theme.tsx delete mode 100644 murfey-frontend/src/utils/api/client.tsx delete mode 100644 murfey-frontend/src/utils/generic.tsx delete mode 100644 murfey-frontend/tsconfig.json delete mode 100644 murfey-frontend/yarn.lock diff --git a/Dockerfiles/murfey-frontend b/Dockerfiles/murfey-frontend deleted file mode 100644 index dec866090..000000000 --- a/Dockerfiles/murfey-frontend +++ /dev/null @@ -1,47 +0,0 @@ -# Build commmand template: -# podman build --build-arg API_ENDPOINT= ... --no-cache -t murfey-frontend: -f /path/to/Dockerfiles/murfey-frontend path/to/murfey-frontend - -FROM docker.io/library/node:22.13.0-alpine3.20 as build -# FROM docker.io/library/node:20.11.0-alpine3.19 as build - -# Set arguments and environment variables -ARG DEPLOY_TYPE="production" -ARG API_ENDPOINT="http://localhost:8000/" -ARG DEV_CONTACT="daniel.hatton@diamond.ac.uk" -ARG VERSION=0.0.1 -ARG FEEDBACK_URL="http://localhost:8080/" - -ENV REACT_APP_DEPLOY_TYPE=${DEPLOY_TYPE} -ENV REACT_APP_HUB_ENDPOINT=${API_ENDPOINT} -ENV REACT_APP_VERSION=${VERSION} -ENV REACT_APP_DEV_CONTACT=${DEV_CONTACT} -ENV REACT_APP_AUTH_TYPE="oidc" -ENV REACT_APP_FEEDBACK_URL=${FEEDBACK_URL} - -# Set working directory to build installation in -WORKDIR /usr/src/app - -# Install all Yarn dependencies listed in package.json using versions listed in -# .lock file as unless they are not sufficient to satisfy package requirements -COPY ./package.json ./yarn.lock ./ -RUN yarn install --immutable --check-cache - -# Copy across files needed to build the app and build it -COPY ./ ./ -RUN yarn build - -# Start second stage of build(?) -FROM docker.io/nginxinc/nginx-unprivileged:alpine3.20-slim -# FROM docker.io/nginxinc/nginx-unprivileged:alpine3.18-slim -COPY --from=build --chown=nginx /usr/src/app/build /usr/share/nginx/html -COPY --chown=nginx nginx/conf.d /tmp/nginx/nginx.conf -COPY --chown=nginx mime.types /tmp/nginx/mime.types - -EXPOSE 8080 -CMD [ \ - "nginx", \ - "-c", \ - "/tmp/nginx/nginx.conf", \ - "-g", \ - "daemon off;" \ -] diff --git a/murfey-frontend/README.md b/murfey-frontend/README.md deleted file mode 100644 index c0541f9c0..000000000 --- a/murfey-frontend/README.md +++ /dev/null @@ -1,70 +0,0 @@ -# Getting Started with Create React App - -This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app). - -## Available Scripts - -In the project directory, you can run: - -### `yarn start` - -Runs the app in the development mode.\ -Open [http://localhost:3000](http://localhost:3000) to view it in your browser. - -The page will reload when you make changes.\ -You may also see any lint errors in the console. - -### `yarn test` - -Launches the test runner in the interactive watch mode.\ -See the section about [running tests](https://facebook.github.io/create-react-app/docs/running-tests) for more information. - -### `yarn build` - -Builds the app for production to the `build` folder.\ -It correctly bundles React in production mode and optimizes the build for the best performance. - -The build is minified and the filenames include the hashes.\ -Your app is ready to be deployed! - -See the section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information. - -### `yarn eject` - -**Note: this is a one-way operation. Once you `eject`, you can't go back!** - -If you aren't satisfied with the build tool and configuration choices, you can `eject` at any time. This command will remove the single build dependency from your project. - -Instead, it will copy all the configuration files and the transitive dependencies (webpack, Babel, ESLint, etc) right into your project so you have full control over them. All of the commands except `eject` will still work, but they will point to the copied scripts so you can tweak them. At this point you're on your own. - -You don't have to ever use `eject`. The curated feature set is suitable for small and middle deployments, and you shouldn't feel obligated to use this feature. However we understand that this tool wouldn't be useful if you couldn't customize it when you are ready for it. - -## Learn More - -You can learn more in the [Create React App documentation](https://facebook.github.io/create-react-app/docs/getting-started). - -To learn React, check out the [React documentation](https://reactjs.org/). - -### Code Splitting - -This section has moved here: [https://facebook.github.io/create-react-app/docs/code-splitting](https://facebook.github.io/create-react-app/docs/code-splitting) - -### Analyzing the Bundle Size - -This section has moved here: [https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size](https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size) - -### Making a Progressive Web App - -This section has moved here: [https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app](https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app) - -### Advanced Configuration - -This section has moved here: [https://facebook.github.io/create-react-app/docs/advanced-configuration](https://facebook.github.io/create-react-app/docs/advanced-configuration) - -### Deployment - -This section has moved here: [https://facebook.github.io/create-react-app/docs/deployment](https://facebook.github.io/create-react-app/docs/deployment) - -### `yarn build` fails to minify - -This section has moved here: [https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify](https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify) diff --git a/murfey-frontend/mime.types b/murfey-frontend/mime.types deleted file mode 100644 index d77e2680c..000000000 --- a/murfey-frontend/mime.types +++ /dev/null @@ -1,99 +0,0 @@ -types { - text/html html htm shtml; - text/css css; - text/xml xml; - image/gif gif; - image/jpeg jpeg jpg; - application/javascript js; - application/atom+xml atom; - application/rss+xml rss; - - text/mathml mml; - text/plain txt; - text/vnd.sun.j2me.app-descriptor jad; - text/vnd.wap.wml wml; - text/x-component htc; - - image/avif avif; - image/png png; - image/svg+xml svg svgz; - image/tiff tif tiff; - image/vnd.wap.wbmp wbmp; - image/webp webp; - image/x-icon ico; - image/x-jng jng; - image/x-ms-bmp bmp; - - font/woff woff; - font/woff2 woff2; - - application/java-archive jar war ear; - application/json json; - application/mac-binhex40 hqx; - application/msword doc; - application/pdf pdf; - application/postscript ps eps ai; - application/rtf rtf; - application/vnd.apple.mpegurl m3u8; - application/vnd.google-earth.kml+xml kml; - application/vnd.google-earth.kmz kmz; - application/vnd.ms-excel xls; - application/vnd.ms-fontobject eot; - application/vnd.ms-powerpoint ppt; - application/vnd.oasis.opendocument.graphics odg; - application/vnd.oasis.opendocument.presentation odp; - application/vnd.oasis.opendocument.spreadsheet ods; - application/vnd.oasis.opendocument.text odt; - application/vnd.openxmlformats-officedocument.presentationml.presentation - pptx; - application/vnd.openxmlformats-officedocument.spreadsheetml.sheet - xlsx; - application/vnd.openxmlformats-officedocument.wordprocessingml.document - docx; - application/vnd.wap.wmlc wmlc; - application/wasm wasm; - application/x-7z-compressed 7z; - application/x-cocoa cco; - application/x-java-archive-diff jardiff; - application/x-java-jnlp-file jnlp; - application/x-makeself run; - application/x-perl pl pm; - application/x-pilot prc pdb; - application/x-rar-compressed rar; - application/x-redhat-package-manager rpm; - application/x-sea sea; - application/x-shockwave-flash swf; - application/x-stuffit sit; - application/x-tcl tcl tk; - application/x-x509-ca-cert der pem crt; - application/x-xpinstall xpi; - application/xhtml+xml xhtml; - application/xspf+xml xspf; - application/zip zip; - - application/octet-stream bin exe dll; - application/octet-stream deb; - application/octet-stream dmg; - application/octet-stream iso img; - application/octet-stream msi msp msm; - - audio/midi mid midi kar; - audio/mpeg mp3; - audio/ogg ogg; - audio/x-m4a m4a; - audio/x-realaudio ra; - - video/3gpp 3gpp 3gp; - video/mp2t ts; - video/mp4 mp4; - video/mpeg mpeg mpg; - video/quicktime mov; - video/webm webm; - video/x-flv flv; - video/x-m4v m4v; - video/x-mng mng; - video/x-ms-asf asx asf; - video/x-ms-wmv wmv; - video/x-msvideo avi; -} - diff --git a/murfey-frontend/nginx/conf.d b/murfey-frontend/nginx/conf.d deleted file mode 100644 index cd28dd198..000000000 --- a/murfey-frontend/nginx/conf.d +++ /dev/null @@ -1,28 +0,0 @@ -worker_processes 3; -pid /tmp/nginx.pid; # Changed from /var/run/nginx.pid -error_log /var/log/nginx/error.log; -events { - worker_connections 10240; -} - -http { - include mime.types; - client_body_temp_path /tmp/client_temp; - proxy_temp_path /tmp/proxy_temp_path; - fastcgi_temp_path /tmp/fastcgi_temp; - uwsgi_temp_path /tmp/uwsgi_temp; - scgi_temp_path /tmp/scgi_temp; - server { - listen 8080; - location / { - root /usr/share/nginx/html; - index index.html index.htm; - try_files $uri $uri/ /index.html; - } - error_page 500 502 503 504 /50x.html; - location = /50x.html { - root /usr/share/nginx/html; - } - } -} - diff --git a/murfey-frontend/openapi.yaml b/murfey-frontend/openapi.yaml deleted file mode 100644 index c4b3b6e5f..000000000 --- a/murfey-frontend/openapi.yaml +++ /dev/null @@ -1,1869 +0,0 @@ -components: - schemas: - ClientInfo: - properties: - id: - title: Id - type: integer - required: - - id - title: ClientInfo - type: object - CompletedTiltSeries: - properties: - rsync_source: - title: Rsync Source - type: string - tilt_series: - items: - type: string - title: Tilt Series - type: array - required: - - tilt_series - - rsync_source - title: CompletedTiltSeries - type: object - ConnectionFileParameters: - properties: - destinations: - items: - type: string - title: Destinations - type: array - filename: - title: Filename - type: string - required: - - filename - - destinations - title: ConnectionFileParameters - type: object - ContextInfo: - properties: - acquisition_software: - title: Acquisition Software - type: string - experiment_type: - title: Experiment Type - type: string - required: - - experiment_type - - acquisition_software - title: ContextInfo - type: object - DCGroupParameters: - properties: - experiment_type: - title: Experiment Type - type: string - experiment_type_id: - title: Experiment Type Id - type: integer - tag: - title: Tag - type: string - required: - - experiment_type - - experiment_type_id - - tag - title: DCGroupParameters - type: object - DCParameters: - properties: - acquisition_software: - title: Acquisition Software - type: string - c2aperture: - title: C2Aperture - type: number - experiment_type: - title: Experiment Type - type: string - exposure_time: - title: Exposure Time - type: number - file_extension: - title: File Extension - type: string - image_directory: - title: Image Directory - type: string - image_size_x: - title: Image Size X - type: integer - image_size_y: - title: Image Size Y - type: integer - magnification: - title: Magnification - type: number - phase_plate: - default: false - title: Phase Plate - type: boolean - pixel_size_on_image: - title: Pixel Size On Image - type: string - slit_width: - title: Slit Width - type: number - source: - title: Source - type: string - tag: - title: Tag - type: string - total_exposed_dose: - title: Total Exposed Dose - type: number - voltage: - title: Voltage - type: number - required: - - voltage - - pixel_size_on_image - - experiment_type - - image_size_x - - image_size_y - - file_extension - - acquisition_software - - image_directory - - tag - - source - - magnification - title: DCParameters - type: object - File: - properties: - description: - title: Description - type: string - name: - title: Name - type: string - size: - title: Size - type: integer - timestamp: - title: Timestamp - type: number - required: - - name - - description - - size - - timestamp - title: File - type: object - FractionationParameters: - properties: - dose_per_frame: - title: Dose Per Frame - type: number - fractionation: - title: Fractionation - type: integer - fractionation_file_name: - default: eer_fractionation.txt - title: Fractionation File Name - type: string - num_frames: - title: Num Frames - type: integer - required: - - num_frames - - fractionation - - dose_per_frame - title: FractionationParameters - type: object - GainReference: - properties: - gain_ref: - format: path - title: Gain Ref - type: string - rescale: - default: true - title: Rescale - type: boolean - required: - - gain_ref - title: GainReference - type: object - HTTPValidationError: - properties: - detail: - items: - $ref: "#/components/schemas/ValidationError" - title: Detail - type: array - title: HTTPValidationError - type: object - ProcessFile: - properties: - autoproc_program_id: - title: Autoproc Program Id - type: integer - data_collection_id: - title: Data Collection Id - type: integer - description: - title: Description - type: string - dose_per_frame: - title: Dose Per Frame - type: number - eer_fractionation_file: - title: Eer Fractionation File - type: string - extract_downscale: - default: 1 - title: Extract Downscale - type: integer - gain_ref: - title: Gain Ref - type: string - image_number: - title: Image Number - type: integer - mc_binning: - default: 1 - title: Mc Binning - type: integer - mc_uuid: - title: Mc Uuid - type: integer - path: - title: Path - type: string - pixel_size: - title: Pixel Size - type: number - processing_job: - title: Processing Job - type: integer - size: - title: Size - type: integer - timestamp: - title: Timestamp - type: number - voltage: - default: 300 - title: Voltage - type: number - required: - - path - - description - - size - - timestamp - - image_number - - mc_uuid - - pixel_size - - dose_per_frame - title: ProcessFile - type: object - ProcessingJobParameters: - properties: - experiment_type: - default: spa - title: Experiment Type - type: string - parameters: - default: {} - title: Parameters - type: object - recipe: - title: Recipe - type: string - tag: - title: Tag - type: string - required: - - tag - - recipe - title: ProcessingJobParameters - type: object - ProcessingParametersSPA: - properties: - acquisition_software: - title: Acquisition Software - type: string - boxsize: - title: Boxsize - type: integer - c2aperture: - title: C2Aperture - type: number - dose_per_frame: - title: Dose Per Frame - type: number - downscale: - title: Downscale - type: boolean - eer_fractionation: - title: Eer Fractionation - type: integer - experiment_type: - title: Experiment Type - type: string - exposure_time: - title: Exposure Time - type: number - file_extension: - title: File Extension - type: string - gain_ref: - title: Gain Ref - type: string - image_size_x: - title: Image Size X - type: integer - image_size_y: - title: Image Size Y - type: integer - magnification: - title: Magnification - type: integer - mask_diameter: - title: Mask Diameter - type: integer - motion_corr_binning: - title: Motion Corr Binning - type: integer - particle_diameter: - title: Particle Diameter - type: number - phase_plate: - default: false - title: Phase Plate - type: boolean - pixel_size_on_image: - title: Pixel Size On Image - type: string - slit_width: - title: Slit Width - type: number - small_boxsize: - title: Small Boxsize - type: integer - symmetry: - title: Symmetry - type: string - tag: - title: Tag - type: string - total_exposed_dose: - title: Total Exposed Dose - type: number - use_cryolo: - title: Use Cryolo - type: boolean - voltage: - title: Voltage - type: number - required: - - tag - - dose_per_frame - - experiment_type - - voltage - - image_size_x - - image_size_y - - pixel_size_on_image - - motion_corr_binning - - file_extension - - acquisition_software - - use_cryolo - - symmetry - - downscale - - eer_fractionation - title: ProcessingParametersSPA - type: object - RegistrationMessage: - properties: - params: - title: Params - type: object - registration: - title: Registration - type: string - required: - - registration - title: RegistrationMessage - type: object - RsyncerInfo: - properties: - bytes: - default: 0 - title: Bytes - type: integer - client_id: - title: Client Id - type: integer - data_bytes: - default: 0 - title: Data Bytes - type: integer - destination: - title: Destination - type: string - increment_count: - default: 1 - title: Increment Count - type: integer - increment_data_count: - default: 0 - title: Increment Data Count - type: integer - source: - title: Source - type: string - transferring: - default: true - title: Transferring - type: boolean - required: - - source - - destination - - client_id - title: RsyncerInfo - type: object - SPAProcessFile: - properties: - autoproc_program_id: - title: Autoproc Program Id - type: integer - data_collection_id: - title: Data Collection Id - type: integer - description: - title: Description - type: string - dose_per_frame: - title: Dose Per Frame - type: number - eer_fractionation_file: - title: Eer Fractionation File - type: string - extract_downscale: - default: true - title: Extract Downscale - type: boolean - gain_ref: - title: Gain Ref - type: string - image_number: - title: Image Number - type: integer - mc_binning: - default: 1 - title: Mc Binning - type: integer - path: - title: Path - type: string - pixel_size: - title: Pixel Size - type: number - processing_job: - title: Processing Job - type: integer - source: - default: "" - title: Source - type: string - tag: - title: Tag - type: string - required: - - tag - - path - - description - - image_number - title: SPAProcessFile - type: object - SPAProcessingParameters: - properties: - job_id: - title: Job Id - type: integer - required: - - job_id - title: SPAProcessingParameters - type: object - SessionInfo: - properties: - rescale: - default: true - title: Rescale - type: boolean - session_id: - title: Session Id - type: integer - session_name: - default: "" - title: Session Name - type: string - title: SessionInfo - type: object - SmartEMAtlasRequest: - properties: - atlas_path: - format: path - title: Atlas Path - type: string - num_preds: - default: 15 - title: Num Preds - type: integer - output_dir: - format: path - title: Output Dir - type: string - required: - - atlas_path - - output_dir - title: SmartEMAtlasRequest - type: object - SuggestedPathParameters: - properties: - base_path: - format: path - title: Base Path - type: string - touch: - default: false - title: Touch - type: boolean - required: - - base_path - title: SuggestedPathParameters - type: object - TiltInfo: - properties: - movie_path: - title: Movie Path - type: string - rsync_source: - title: Rsync Source - type: string - tilt_series_tag: - title: Tilt Series Tag - type: string - required: - - tilt_series_tag - - movie_path - - rsync_source - title: TiltInfo - type: object - TiltSeriesInfo: - properties: - client_id: - title: Client Id - type: integer - rsync_source: - title: Rsync Source - type: string - tag: - title: Tag - type: string - required: - - client_id - - tag - - rsync_source - title: TiltSeriesInfo - type: object - TiltSeriesProcessingDetails: - properties: - autoproc_program_id: - title: Autoproc Program Id - type: integer - dcid: - title: Dcid - type: integer - file_tilt_list: - title: File Tilt List - type: string - manual_tilt_offset: - title: Manual Tilt Offset - type: integer - motion_corrected_path: - title: Motion Corrected Path - type: string - movie_id: - title: Movie Id - type: integer - name: - title: Name - type: string - pixel_size: - title: Pixel Size - type: number - processing_job: - title: Processing Job - type: integer - required: - - name - - file_tilt_list - - dcid - - processing_job - - autoproc_program_id - - motion_corrected_path - - movie_id - - pixel_size - - manual_tilt_offset - title: TiltSeriesProcessingDetails - type: object - ValidationError: - properties: - loc: - items: - anyOf: - - type: string - - type: integer - title: Location - type: array - msg: - title: Message - type: string - type: - title: Error Type - type: string - required: - - loc - - msg - - type - title: ValidationError - type: object - Visit: - properties: - beamline: - title: Beamline - type: string - end: - format: date-time - title: End - type: string - name: - title: Name - type: string - proposal_title: - title: Proposal Title - type: string - session_id: - title: Session Id - type: integer - start: - format: date-time - title: Start - type: string - required: - - start - - end - - session_id - - name - - beamline - - proposal_title - title: Visit - type: object -info: - title: Murfey server - version: 0.1.0 -openapi: 3.1.0 -paths: - /: - get: - operationId: root__get - responses: - "200": - content: - text/html: - schema: - type: string - description: Successful Response - summary: Root - /bootstrap/: - get: - description: - "Return a website containing instructions for installing the Murfey - client on a - - machine with no internet access." - operationId: get_bootstrap_instructions_bootstrap__get - responses: - "200": - content: - text/html: - schema: - type: string - description: Successful Response - summary: Get Bootstrap Instructions - tags: - - bootstrap - /bootstrap/murfey.whl: - get: - description: - "Return a wheel file containing the latest release version of Murfey. - We should - - not have to worry about the exact Python compatibility here, as long as - - murfey.bootstrap is compatible with all relevant versions of Python. - - This also ignores yanked releases, which again should be fine." - operationId: get_murfey_wheel_bootstrap_murfey_whl_get - responses: - "200": - description: Successful Response - summary: Get Murfey Wheel - tags: - - bootstrap - /bootstrap/pip.whl: - get: - description: - "Return a static version of pip. This does not need to be the newest - or best, - - but has to be compatible with all supported Python versions. - - This is only used during bootstrapping by the client to identify and then - - download the actually newest appropriate version of pip." - operationId: get_pip_wheel_bootstrap_pip_whl_get - responses: - "200": - description: Successful Response - summary: Get Pip Wheel - tags: - - bootstrap - /clients: - get: - operationId: get_clients_clients_get - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - summary: Get Clients - /clients/{client_id}/rsyncers: - get: - operationId: get_rsyncers_for_client_clients__client_id__rsyncers_get - parameters: - - in: path - name: client_id - required: true - schema: - title: Client Id - type: integer - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Get Rsyncers For Client - /clients/{client_id}/session: - delete: - operationId: remove_session_clients__client_id__session_delete - parameters: - - in: path - name: client_id - required: true - schema: - title: Client Id - type: integer - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Remove Session - post: - operationId: link_client_to_session_clients__client_id__session_post - parameters: - - in: path - name: client_id - required: true - schema: - title: Client Id - type: integer - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/SessionInfo" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Link Client To Session - /clients/{client_id}/spa_processing_parameters: - get: - operationId: get_spa_proc_params_clients__client_id__spa_processing_parameters_get - parameters: - - in: path - name: client_id - required: true - schema: - title: Client Id - type: integer - responses: - "200": - content: - application/json: - schema: - items: - type: object - title: - Response Get Spa Proc Params Clients Client Id Spa Processing - Parameters Get - type: array - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Get Spa Proc Params - post: - operationId: register_spa_proc_params_clients__client_id__spa_processing_parameters_post - parameters: - - in: path - name: client_id - required: true - schema: - title: Client Id - type: integer - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/ProcessingParametersSPA" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Register Spa Proc Params - /cygwin/setup-x86_64.exe: - get: - description: - "Obtain and past though a Cygwin installer from an official source. - - This is used during client bootstrapping and can download and install the - - Cygwin distribution that then remains on the client machines." - operationId: get_cygwin_setup_cygwin_setup_x86_64_exe_get - responses: - "200": - description: Successful Response - summary: Get Cygwin Setup - tags: - - bootstrap - /cygwin/{request_path}: - get: - description: Forward a Cygwin setup request to an official mirror. - operationId: parse_cygwin_request_cygwin__request_path__get - parameters: - - in: path - name: request_path - required: true - schema: - title: Request Path - type: string - responses: - "200": - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Parse Cygwin Request - tags: - - bootstrap - /feedback: - post: - operationId: send_murfey_message_feedback_post - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/RegistrationMessage" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Send Murfey Message - /machine/: - get: - operationId: machine_info_machine__get - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - summary: Machine Info - /microscope/: - get: - operationId: get_mic_microscope__get - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - summary: Get Mic - /microscope_image/: - get: - operationId: get_mic_image_microscope_image__get - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - summary: Get Mic Image - /new_client_id/: - get: - operationId: new_client_id_new_client_id__get - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - summary: New Client Id - /plugins/{package}: - get: - operationId: get_plugin_wheel_plugins__package__get - parameters: - - in: path - name: package - required: true - schema: - title: Package - type: string - responses: - "200": - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Get Plugin Wheel - tags: - - bootstrap - /pypi/: - get: - description: Obtain list of all PyPI packages via the simple API (PEP 503). - operationId: get_pypi_index_pypi__get - responses: - "200": - description: Successful Response - summary: Get Pypi Index - tags: - - bootstrap - /pypi/{package}/: - get: - description: - "Obtain list of all package downloads from PyPI via the simple - API (PEP 503), - - and rewrite all download URLs to point to this server, - - underneath the current directory." - operationId: get_pypi_package_downloads_list_pypi__package___get - parameters: - - in: path - name: package - required: true - schema: - title: Package - type: string - responses: - "200": - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Get Pypi Package Downloads List - tags: - - bootstrap - /pypi/{package}/{filename}: - get: - description: Obtain and pass through a specific download for a PyPI package. - operationId: get_pypi_file_pypi__package___filename__get - parameters: - - in: path - name: package - required: true - schema: - title: Package - type: string - - in: path - name: filename - required: true - schema: - title: Filename - type: string - responses: - "200": - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Get Pypi File - tags: - - bootstrap - /sessions: - get: - operationId: get_sessions_sessions_get - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - summary: Get Sessions - /sessions/{session_id}: - delete: - operationId: remove_session_by_id_sessions__session_id__delete - parameters: - - in: path - name: session_id - required: true - schema: - title: Session Id - type: integer - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Remove Session By Id - /version: - get: - operationId: get_version_version_get - parameters: - - in: query - name: client_version - required: false - schema: - default: "" - title: Client Version - type: string - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Get Version - /visits/: - get: - operationId: all_visit_info_visits__get - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - summary: All Visit Info - /visits/{visit_name}: - get: - operationId: visit_info_visits__visit_name__get - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Visit Info - post: - operationId: register_client_to_visit_visits__visit_name__post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/ClientInfo" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Register Client To Visit - /visits/{visit_name}/align: - post: - operationId: request_tilt_series_alignment_visits__visit_name__align_post - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/TiltSeriesProcessingDetails" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Request Tilt Series Alignment - /visits/{visit_name}/context: - post: - operationId: register_context_visits__visit_name__context_post - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/ContextInfo" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Register Context - /visits/{visit_name}/eer_fractionation_file: - post: - operationId: write_eer_fractionation_file_visits__visit_name__eer_fractionation_file_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/FractionationParameters" - required: true - responses: - "200": - content: - application/json: - schema: - title: - Response Write Eer Fractionation File Visits Visit Name Eer - Fractionation File Post - type: object - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Write Eer Fractionation File - /visits/{visit_name}/files: - post: - operationId: add_file_visits__visit_name__files_post - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/File" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Add File - /visits/{visit_name}/increment_rsync_file_count: - post: - operationId: increment_rsync_file_count_visits__visit_name__increment_rsync_file_count_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/RsyncerInfo" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Increment Rsync File Count - /visits/{visit_name}/increment_rsync_transferred_files: - post: - operationId: increment_rsync_transferred_files_visits__visit_name__increment_rsync_transferred_files_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/RsyncerInfo" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Increment Rsync Transferred Files - /visits/{visit_name}/process_gain: - post: - operationId: process_gain_visits__visit_name__process_gain_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/GainReference" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Process Gain - /visits/{visit_name}/rsyncer: - post: - operationId: register_rsyncer_visits__visit_name__rsyncer_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/RsyncerInfo" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Register Rsyncer - /visits/{visit_name}/smartem_atlas/: - post: - operationId: request_smartem_atlas_analysis_visits__visit_name__smartem_atlas__post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/SmartEMAtlasRequest" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Request Smartem Atlas Analysis - /visits/{visit_name}/spa_processing: - post: - operationId: request_spa_processing_visits__visit_name__spa_processing_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/SPAProcessingParameters" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Request Spa Processing - /visits/{visit_name}/suggested_path: - post: - operationId: suggest_path_visits__visit_name__suggested_path_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/SuggestedPathParameters" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Suggest Path - /visits/{visit_name}/tilt: - post: - operationId: register_tilt_visits__visit_name__tilt_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/TiltInfo" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Register Tilt - /visits/{visit_name}/tilt_series: - post: - operationId: register_tilt_series_visits__visit_name__tilt_series_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/TiltSeriesInfo" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Register Tilt Series - /visits/{visit_name}/tomography_preprocess: - post: - operationId: request_tomography_preprocessing_visits__visit_name__tomography_preprocess_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/ProcessFile" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Request Tomography Preprocessing - /visits/{visit_name}/write_connections_file: - post: - operationId: write_conn_file_visits__visit_name__write_connections_file_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/ConnectionFileParameters" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Write Conn File - /visits/{visit_name}/{client_id}/completed_tilt_series: - post: - operationId: register_completed_tilt_series_visits__visit_name___client_id__completed_tilt_series_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - - in: path - name: client_id - required: true - schema: - title: Client Id - type: integer - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/CompletedTiltSeries" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Register Completed Tilt Series - /visits/{visit_name}/{client_id}/flush_spa_processing: - post: - operationId: flush_spa_processing_visits__visit_name___client_id__flush_spa_processing_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - - in: path - name: client_id - required: true - schema: - title: Client Id - type: integer - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Flush Spa Processing - /visits/{visit_name}/{client_id}/register_data_collection_group: - post: - operationId: register_dc_group_visits__visit_name___client_id__register_data_collection_group_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - - in: path - name: client_id - required: true - schema: - title: Client Id - type: integer - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/DCGroupParameters" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Register Dc Group - /visits/{visit_name}/{client_id}/register_processing_job: - post: - operationId: register_proc_visits__visit_name___client_id__register_processing_job_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - - in: path - name: client_id - required: true - schema: - title: Client Id - type: integer - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/ProcessingJobParameters" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Register Proc - /visits/{visit_name}/{client_id}/spa_preprocess: - post: - operationId: request_spa_preprocessing_visits__visit_name___client_id__spa_preprocess_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - type: string - - in: path - name: client_id - required: true - schema: - title: Client Id - type: integer - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/SPAProcessFile" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Request Spa Preprocessing - /visits/{visit_name}/{client_id}/start_data_collection: - post: - operationId: start_dc_visits__visit_name___client_id__start_data_collection_post - parameters: - - in: path - name: visit_name - required: true - schema: - title: Visit Name - - in: path - name: client_id - required: true - schema: - title: Client Id - type: integer - requestBody: - content: - application/json: - schema: - $ref: "#/components/schemas/DCParameters" - required: true - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Start Dc - /visits_raw: - get: - operationId: get_current_visits_visits_raw_get - responses: - "200": - content: - application/json: - schema: - items: - $ref: "#/components/schemas/Visit" - title: Response Get Current Visits Visits Raw Get - type: array - description: Successful Response - summary: Get Current Visits - /ws/test/{client_id}: - delete: - operationId: close_ws_connection_ws_test__client_id__delete - parameters: - - in: path - name: client_id - required: true - schema: - title: Client Id - type: integer - responses: - "200": - content: - application/json: - schema: {} - description: Successful Response - "422": - content: - application/json: - schema: - $ref: "#/components/schemas/HTTPValidationError" - description: Validation Error - summary: Close Ws Connection - tags: - - websocket -tags: - - description: " - - API endpoints related to installing Murfey on a client. - - - Client machines may not have a direct internet connection, so Murfey allows - - passing through requests to PyPI using the PEP 503 simple API, and download - - requests to the Cygwin website and mirrors. - - - A static HTML page gives instructions on how to install on a network-isolated - - system that has Python already installed. A previously set up system does not - - need to have pip installed in order to bootstrap Murfey. Python and rsync are - - required. - - " - externalDocs: - description: PEP 503 - url: https://www.python.org/dev/peps/pep-0503/ - name: bootstrap diff --git a/murfey-frontend/package.json b/murfey-frontend/package.json deleted file mode 100644 index 37f5b1531..000000000 --- a/murfey-frontend/package.json +++ /dev/null @@ -1,58 +0,0 @@ -{ - "name": "murfey-frontend", - "version": "0.1.0", - "private": true, - "dependencies": { - "@chakra-ui/icons": "^2.1.1", - "@chakra-ui/react": "^2.8.2", - "@diamondlightsource/ui-components": "^1.0.3", - "@emotion/react": "^11.11.1", - "@emotion/styled": "^11.11.0", - "@tanstack/react-query": "^5.12.2", - "@tanstack/react-query-devtools": "^5.12.2", - "@testing-library/jest-dom": "^5.14.1", - "@testing-library/react": "^13.0.0", - "@testing-library/user-event": "^13.2.1", - "@types/uuid": "^10.0.0", - "framer-motion": "^10.16.12", - "react": "^18.2.0", - "react-collapsible": "^2.10.0", - "react-dom": "^18.2.0", - "react-query": "^3.39.3", - "react-query-devtools": "^2.6.3", - "react-router-dom": "^6.20.1", - "react-scripts": "5.0.1", - "react-use-websocket": "^4.5.0", - "typescript": "^5.3.2", - "uuid": "^10.0.0", - "web-vitals": "^2.1.0" - }, - "scripts": { - "start": "react-scripts start", - "build": "react-scripts build", - "test": "react-scripts test", - "eject": "react-scripts eject" - }, - "eslintConfig": { - "extends": [ - "react-app", - "react-app/jest" - ] - }, - "browserslist": { - "production": [ - ">0.2%", - "not dead", - "not op_mini all" - ], - "development": [ - "last 1 chrome version", - "last 1 firefox version", - "last 1 safari version" - ] - }, - "devDependencies": { - "openapi-typescript": "^6.7.2", - "prettier": "3.3.1" - } -} diff --git a/murfey-frontend/public/favicon.ico b/murfey-frontend/public/favicon.ico deleted file mode 100644 index a11777cc471a4344702741ab1c8a588998b1311a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3870 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a/murfey-frontend/public/manifest.json b/murfey-frontend/public/manifest.json deleted file mode 100644 index 080d6c77a..000000000 --- a/murfey-frontend/public/manifest.json +++ /dev/null @@ -1,25 +0,0 @@ -{ - "short_name": "React App", - "name": "Create React App Sample", - "icons": [ - { - "src": "favicon.ico", - "sizes": "64x64 32x32 24x24 16x16", - "type": "image/x-icon" - }, - { - "src": "logo192.png", - "type": "image/png", - "sizes": "192x192" - }, - { - "src": "logo512.png", - "type": "image/png", - "sizes": "512x512" - } - ], - "start_url": ".", - "display": "standalone", - "theme_color": "#000000", - "background_color": "#ffffff" -} diff --git a/murfey-frontend/public/robots.txt b/murfey-frontend/public/robots.txt deleted file mode 100644 index e9e57dc4d..000000000 --- a/murfey-frontend/public/robots.txt +++ /dev/null @@ -1,3 +0,0 @@ -# https://www.robotstxt.org/robotstxt.html -User-agent: * -Disallow: diff --git a/murfey-frontend/src/components/forms.tsx b/murfey-frontend/src/components/forms.tsx deleted file mode 100644 index e654a9ce3..000000000 --- a/murfey-frontend/src/components/forms.tsx +++ /dev/null @@ -1,195 +0,0 @@ -import { - Button, - Divider, - Text, - FormControl, - FormLabel, - Input, - NumberInput, - NumberInputField, - NumberInputStepper, - NumberIncrementStepper, - NumberDecrementStepper, - RadioGroup, - Radio, - HStack, - VStack, - Select, - Switch, - Link, -} from "@chakra-ui/react"; -import { Link as LinkRouter } from "react-router-dom"; - -import React, { ReactElement } from "react"; - -const formDataSPA: { [key: string]: any } = { - type: "SPA", - dose_per_frame: 1, - symmetry: "C1", - particle_diameter: null, - extract_downscale: true, - eer_fractionation: 20, -}; - -const formDataTomo: { [key: string]: any } = { - type: "tomo", - dose_per_frame: 0.5, - eer_fractionation: 20, -}; - -const SpaForm = (submissionCallback: (arg0: any) => void) => { - const validateInt = (char: string) => { - return /\d/.test(char); - }; - const validateFloat = (char: string) => { - return /^\d*\.?\d*$/.test(char); - }; - const [symmetryType, setSymmetryType] = React.useState("C"); - const [particleDetection, setParticleDetection] = React.useState(true); - const handleChange = (event: React.ChangeEvent) => { - setSymmetryType(event.target.value); - }; - const handleSwitchChange = (event: React.ChangeEvent) => { - setParticleDetection(!particleDetection); - }; - const setFormElement = ( - event: React.FormEvent, - callback: (arg0: any) => void, - ) => { - event.preventDefault(); - const formData = new FormData(event.currentTarget); - formDataSPA.dose_per_frame = formData.get("dose"); - formDataSPA.symmetry = ((formData.get("symmetry1") as string) + - formData.get("symmetry2")) as string; - formDataSPA.particle_diameter = formData.get("detect-particle-size") - ? null - : formData.get("particle-diameter"); - formDataSPA.eer_fractionation = formData.get("eer-grouping"); - callback(formDataSPA); - }; - - return ( -
setFormElement(e, submissionCallback)}> - - - - - {"Dose per frame [\u212B / pixel]"} - - - - Symmetry - - - - - - - - - - - - - - {"EER grouping (number of EER frames in each fraction)"} - - - - - - Automatically detect particle size - - - - {!particleDetection ? ( - - {"Particle diameter [\u212B]"} - - - ) : ( - <> - )} - - - Downscale in extraction - - - - - - - - - ); -}; - -const TomoForm = (submissionCallback: (arg0: any) => void) => { - const setFormElement = ( - event: React.FormEvent, - callback: (arg0: any) => void, - ) => { - event.preventDefault(); - const formData = new FormData(event.currentTarget); - formDataSPA.dose_per_frame = formData.get("dose"); - formDataSPA.eer_fractionation = formData.get("eer-grouping"); - callback(formDataSPA); - }; - return ( -
setFormElement(e, submissionCallback)}> - - - - - {"Dose per frame [\u212B / pixel]"} - - - - - {"EER grouping (number of EER frames in each fraction)"} - - - - - - - - - ); -}; - -interface Forms { - [expType: string]: ReactElement; -} - -export const getForm = ( - expType: string, - submissionCallback: (arg0: any) => void, -) => { - let forms = { - spa: SpaForm(submissionCallback), - tomography: TomoForm(submissionCallback), - } as Forms; - return forms[expType]; -}; diff --git a/murfey-frontend/src/components/gridSquareCard.tsx b/murfey-frontend/src/components/gridSquareCard.tsx deleted file mode 100644 index 17fc868d7..000000000 --- a/murfey-frontend/src/components/gridSquareCard.tsx +++ /dev/null @@ -1,147 +0,0 @@ -import { - CardBody, - Card, - CardHeader, - Image, - Text, - Box, - Tooltip, - VStack, - Slider, - SliderTrack, - SliderFilledTrack, - SliderThumb, -} from "@chakra-ui/react"; - -import { components } from "schema/main"; -import { getFoilHoles, getNumMovies } from "loaders/gridSquares"; - -import { useState, useEffect } from "react"; - -type GridSquare = components["schemas"]["GridSquare"]; -type FoilHole = components["schemas"]["FoilHole"]; - -const getUrl = (endpoint: string) => { - return ( - (sessionStorage.getItem("murfeyServerURL") ?? - process.env.REACT_APP_API_ENDPOINT) + endpoint - ); -}; - -const GridSquareCard = ( - gs: GridSquare, - sessid: string | undefined, - dcgid: string | undefined, -) => { - const [numFoilHoles, setNumFoilHoles] = useState(0); - const [numMovies, setNumMovies] = useState(0); - const [foilHoleXPositions, setFoilHoleXPositions] = useState([]); - const [foilHoleYPositions, setFoilHoleYPositions] = useState([]); - const [foilHoleNames, setFoilHoleNames] = useState([]); - const [foilHoleImages, setFoilHoleImages] = useState<(string | null)[]>([]); - const [sliderValue, setSliderValue] = useState(10); - const foilHoleSetup = (foilHoles: FoilHole[]) => { - let xpositions: number[] = []; - let ypositions = []; - let names: number[] = []; - let images: (string | null)[] = []; - for (let i = 0; i < foilHoles.length; i++) { - const unscaledx = foilHoles[i].x_location; - const x = - gs.thumbnail_size_x && gs.readout_area_x && unscaledx - ? unscaledx * (gs.thumbnail_size_x / gs.readout_area_x) - : unscaledx; - const unscaledy = foilHoles[i].y_location; - const y = - gs.thumbnail_size_y && gs.readout_area_y && unscaledy - ? unscaledy * (gs.thumbnail_size_y / gs.readout_area_y) - : unscaledy; - if (x) xpositions.push(Math.floor(x)); - if (y) ypositions.push(Math.floor(y)); - if (x) names.push(foilHoles[i].name); - const image = foilHoles[i].image; - if (x) image ? images.push(image) : images.push(null); - } - setFoilHoleXPositions(xpositions); - setFoilHoleYPositions(ypositions); - setFoilHoleNames(names); - setFoilHoleImages(images); - setNumFoilHoles(foilHoles.length); - }; - useEffect(() => { - getFoilHoles(sessid ?? "0", dcgid ?? "0", gs.name).then((fhs) => - foilHoleSetup(fhs), - ); - getNumMovies(sessid ?? "0", dcgid ?? "0", gs.name).then((nm) => - setNumMovies(nm), - ); - }, []); - - const zip = (a: number[], b: number[]) => a.map((k, i) => [k, b[i]]); - - const foilHoleTooltip = (fhName: number, fhImage: string | null) => { - const fhImageUrl = getUrl( - `display/sessions/${sessid}/data_collection_groups/${dcgid}/grid_squares/${gs.name}/foil_holes/${fhName}/image`, - ); - return ( - - {fhName} - {fhImage ? : <>} - - ); - }; - - return ( - - {gs.name} - - - - - {zip(foilHoleXPositions, foilHoleYPositions).map((pos, index) => ( - - - - ))} - - - {numFoilHoles} foil holes - {numMovies} movies - setSliderValue(val)} - > - - - - - - - - ); -}; - -export { GridSquareCard }; diff --git a/murfey-frontend/src/components/instrumentCard.tsx b/murfey-frontend/src/components/instrumentCard.tsx deleted file mode 100644 index ee4e95a64..000000000 --- a/murfey-frontend/src/components/instrumentCard.tsx +++ /dev/null @@ -1,58 +0,0 @@ -import { - Card, - CardBody, - CardHeader, - Image, - Link, - Text, -} from "@chakra-ui/react"; - -import { Link as LinkRouter } from "react-router-dom"; -import { getInstrumentName } from "loaders/general"; - -import React, { useEffect } from "react"; - -const getUrl = (endpoint: string) => { - return ( - (sessionStorage.getItem("murfeyServerURL") ?? - process.env.REACT_APP_API_ENDPOINT) + endpoint - ); -}; - -const InstrumentCard = () => { - const [instrumentName, setInstrumentName] = React.useState(""); - - const resolveName = async () => { - const name: string = await getInstrumentName(); - setInstrumentName(name); - }; - useEffect(() => { - resolveName(); - }, []); - - return ( - - - - - - - {instrumentName} - - - - ); -}; - -export { InstrumentCard }; diff --git a/murfey-frontend/src/components/navbar.tsx b/murfey-frontend/src/components/navbar.tsx deleted file mode 100644 index 178dc0cda..000000000 --- a/murfey-frontend/src/components/navbar.tsx +++ /dev/null @@ -1,170 +0,0 @@ -import { - Box, - Flex, - HStack, - Link, - IconButton, - useDisclosure, - Image, - Tooltip, - VStack, - BoxProps, - Icon, -} from "@chakra-ui/react"; -import { - MdMenu, - MdClose, - MdSignalWifi4Bar, - MdOutlineSignalWifiBad, -} from "react-icons/md"; -import { TbMicroscope, TbSnowflake } from "react-icons/tb"; -import { getInstrumentConnectionStatus } from "loaders/general"; -import { Link as LinkRouter } from "react-router-dom"; -import React from "react"; - -export interface LinkDescriptor { - label: string; - route: string; -} - -interface BaseLinkProps { - links?: LinkDescriptor[]; - as?: React.ElementType; -} - -export interface NavbarProps extends BaseLinkProps, BoxProps { - logo?: string | null; - children?: React.ReactElement; -} - -const NavLinks = ({ links, as }: BaseLinkProps) => ( - <> - {links - ? links.map((link) => ( - - {link.label} - - )) - : null} - -); - -const Navbar = ({ links, as, children, logo, ...props }: NavbarProps) => { - const { isOpen, onOpen, onClose } = useDisclosure(); - const [instrumentConnectionStatus, setInsrumentConnectionStatus] = - React.useState(false); - - const resolveConnectionStatus = async () => { - const status: boolean = await getInstrumentConnectionStatus(); - setInsrumentConnectionStatus(status); - }; - resolveConnectionStatus(); - - return ( - - - : } - aria-label={"Open Menu"} - display={{ md: "none" }} - bg="transparent" - border="none" - _hover={{ background: "transparent", color: "murfey.500" }} - onClick={isOpen ? onClose : onOpen} - /> - - {logo ? ( - - - - - - ) : null} - - - - - - - } - aria-label={"Back to the Hub"} - _hover={{ background: "transparent", color: "murfey.500" }} - /> - - - - - - - - - - {children} - - {isOpen && ( - - - - )} - - ); -}; - -export { Navbar }; diff --git a/murfey-frontend/src/components/protectedRoutes.tsx b/murfey-frontend/src/components/protectedRoutes.tsx deleted file mode 100644 index 75cd228b0..000000000 --- a/murfey-frontend/src/components/protectedRoutes.tsx +++ /dev/null @@ -1,20 +0,0 @@ -import { Navigate, Outlet } from "react-router-dom"; -import { Box } from "@chakra-ui/react"; -import { Navbar } from "components/navbar"; - -const ProtectedRoutes = () => { - const sessionToken = sessionStorage.getItem("token"); - const standard = ( -
- - - - - - -
- ); - return sessionToken ? standard : ; -}; - -export { ProtectedRoutes }; diff --git a/murfey-frontend/src/components/setupStepper.tsx b/murfey-frontend/src/components/setupStepper.tsx deleted file mode 100644 index 18c9f4f60..000000000 --- a/murfey-frontend/src/components/setupStepper.tsx +++ /dev/null @@ -1,65 +0,0 @@ -import { - Box, - Step, - StepDescription, - StepIcon, - StepIndicator, - StepNumber, - StepSeparator, - StepStatus, - StepTitle, - Stepper, - useSteps, -} from "@chakra-ui/react"; - -import React from "react"; - -const getUrl = (endpoint: string) => { - return ( - (sessionStorage.getItem("murfeyServerURL") ?? - process.env.REACT_APP_API_ENDPOINT) + endpoint - ); -}; - -interface StepperStartConditions { - activeStepIndex: number; -} - -const SetupStepper = ({ activeStepIndex }: StepperStartConditions) => { - const steps = [ - { title: "Visit", description: "Select visit" }, - { title: "Gain reference", description: "Transfer and transform" }, - { title: "Parameters", description: "For processing" }, - { title: "Confirm", description: "Start data transfer" }, - ]; - - const { activeStep } = useSteps({ - index: activeStepIndex, - count: steps.length, - }); - - return ( - - {steps.map((step, index) => ( - - - } - incomplete={} - active={} - /> - - - - {step.title} - {step.description} - - - - - ))} - - ); -}; - -export { SetupStepper }; diff --git a/murfey-frontend/src/components/upstreamVisitsCard.tsx b/murfey-frontend/src/components/upstreamVisitsCard.tsx deleted file mode 100644 index a5b802334..000000000 --- a/murfey-frontend/src/components/upstreamVisitsCard.tsx +++ /dev/null @@ -1,48 +0,0 @@ -import { Card, CardBody, Button, CardHeader } from "@chakra-ui/react"; - -import { - getUpstreamVisits, - upstreamDataDownloadRequest, -} from "loaders/general"; -import { MdFileDownload } from "react-icons/md"; - -import React, { useEffect } from "react"; - -interface SessionId { - sessid: number; -} - -const UpstreamVisitCard = ({ sessid }: SessionId) => { - const [upstreamVisits, setUpstreamVisits] = React.useState({}); - - const resolveVisits = async () => { - const visits = await getUpstreamVisits(sessid); - setUpstreamVisits(visits); - console.log(upstreamVisits); - }; - useEffect(() => { - resolveVisits(); - }, []); - - return upstreamVisits ? ( - - Upstream Visit Data Download - {Object.keys(upstreamVisits).map((k) => { - return ( - - - - ); - })} - - ) : ( - <> - ); -}; - -export { UpstreamVisitCard }; diff --git a/murfey-frontend/src/index.css b/murfey-frontend/src/index.css deleted file mode 100644 index 4a1df4db7..000000000 --- a/murfey-frontend/src/index.css +++ /dev/null @@ -1,13 +0,0 @@ -body { - margin: 0; - font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", "Roboto", "Oxygen", - "Ubuntu", "Cantarell", "Fira Sans", "Droid Sans", "Helvetica Neue", - sans-serif; - -webkit-font-smoothing: antialiased; - -moz-osx-font-smoothing: grayscale; -} - -code { - font-family: source-code-pro, Menlo, Monaco, Consolas, "Courier New", - monospace; -} diff --git a/murfey-frontend/src/index.tsx b/murfey-frontend/src/index.tsx deleted file mode 100644 index 17a01add8..000000000 --- a/murfey-frontend/src/index.tsx +++ /dev/null @@ -1,149 +0,0 @@ -import React, { Suspense } from "react"; -import { createRoot } from "react-dom/client"; -import { ChakraProvider, createStandaloneToast } from "@chakra-ui/react"; -import { - createBrowserRouter, - Navigate, - RouterProvider, -} from "react-router-dom"; -import { Root } from "routes/Root"; -import { DataCollectionGroups } from "routes/DataCollectionGroups"; -import { GridSquares } from "routes/GridSquares"; -import { Home } from "routes/Home"; -import { Hub } from "routes/Hub"; -import { Session } from "routes/Session"; -import { NewSession } from "routes/NewSession"; -import { SessionLinker } from "routes/SessionLinker"; -import { GainRefTransfer } from "routes/GainRefTransfer"; -import { SessionSetup } from "routes/SessionSetup"; -import { MagTable } from "routes/MagTable"; -import { ProcessingParameters } from "routes/ProcessingParameters"; -import { Error } from "routes/Error"; -import { - clientsLoader, - sessionsLoader, - sessionLoader, -} from "loaders/session_clients"; -import { rsyncerLoader } from "loaders/rsyncers"; -import { visitLoader } from "loaders/visits"; -import { gainRefLoader } from "loaders/possibleGainRefs"; -import { instrumentInfoLoader } from "loaders/hub"; -import { magTableLoader } from "loaders/magTable"; -import { processingParametersLoader } from "loaders/processingParameters"; -import { dataCollectionGroupsLoader } from "loaders/dataCollectionGroups"; -import { theme } from "styles/theme"; -import { QueryClient, QueryClientProvider } from "@tanstack/react-query"; -import { ReactQueryDevtools } from "@tanstack/react-query-devtools"; -import { MultigridSetup } from "routes/MultigridSetup"; -import { machineConfigLoader } from "loaders/machineConfig"; -import { ProtectedRoutes } from "components/protectedRoutes"; -import { Login } from "routes/Login"; -import { gridSquaresLoader } from "loaders/gridSquares"; - -const { ToastContainer } = createStandaloneToast(); -const container = document.getElementById("root")!; -const root = createRoot(container); -const queryClient = new QueryClient({ - defaultOptions: { queries: { staleTime: 1.08e7 } }, -}); - -const router = createBrowserRouter([ - { - path: "/hub", - element: , - errorElement: , - loader: instrumentInfoLoader(queryClient), - }, - { - path: "/login", - element: , - errorElement: , - }, - { - path: "/", - element: , - errorElement: , - children: [ - { - path: "/home", - element: , - errorElement: , - loader: sessionsLoader(queryClient), - }, - { - path: "/sessions/:sessid", - element: , - errorElement: , - loader: ({ params }) => rsyncerLoader(queryClient)(params), - }, - { - path: "/instruments/:instrumentName/new_session", - element: , - errorElement: , - loader: ({ params }) => visitLoader(queryClient)(params), - }, - { - path: "/new_session/setup/:sessid", - element: , - errorElement: , - loader: machineConfigLoader(queryClient), - }, - { - path: "/link_session", - element: , - errorElement: , - loader: clientsLoader(queryClient), - }, - { - path: "/sessions/:sessid/gain_ref_transfer", - element: , - errorElement: , - loader: ({ params }) => gainRefLoader(queryClient)(params), - }, - { - path: "/new_session/parameters/:sessid", - element: , - errorElement: , - loader: ({ params }) => sessionLoader(queryClient)(params), - }, - { - path: "/sessions/:sessid/processing_parameters", - element: , - errorElement: , - loader: ({ params }) => processingParametersLoader(queryClient)(params), - }, - { - path: "/mag_table", - element: , - errorElement: , - loader: magTableLoader(queryClient), - }, - { - path: "/sessions/:sessid/data_collection_groups", - element: , - errorElement: , - loader: ({ params }) => dataCollectionGroupsLoader(queryClient)(params), - }, - { - path: "/sessions/:sessid/data_collection_groups/:dcgid/grid_squares", - element: , - errorElement: , - loader: ({ params }) => gridSquaresLoader(queryClient)(params), - }, - ], - }, -]); - -root.render( - - - - - {process.env.NODE_ENV === "development" && ( - - )} - - , -); - -// loader: ({ params }) => gridSquaresLoader(queryClient)(params), diff --git a/murfey-frontend/src/loaders/dataCollectionGroups.tsx b/murfey-frontend/src/loaders/dataCollectionGroups.tsx deleted file mode 100644 index 93af47b6c..000000000 --- a/murfey-frontend/src/loaders/dataCollectionGroups.tsx +++ /dev/null @@ -1,33 +0,0 @@ -import { QueryClient } from "@tanstack/react-query"; -import { client } from "utils/api/client"; -import { Params } from "react-router-dom"; - -const getDataCollectionGroups = async (sessid: string = "0") => { - console.log("data collection groups gather"); - const response = await client.get( - `sessions/${sessid}/data_collection_groups`, - ); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -const queryBuilder = (sessid: string = "0") => { - return { - queryKey: ["sessionId", sessid], - queryFn: () => getDataCollectionGroups(sessid), - staleTime: 60000, - }; -}; - -export const dataCollectionGroupsLoader = - (queryClient: QueryClient) => async (params: Params) => { - const singleQuery = queryBuilder(params.sessid); - return ( - (await queryClient.getQueryData(singleQuery.queryKey)) ?? - (await queryClient.fetchQuery(singleQuery)) - ); - }; diff --git a/murfey-frontend/src/loaders/general.tsx b/murfey-frontend/src/loaders/general.tsx deleted file mode 100644 index cf628b1d9..000000000 --- a/murfey-frontend/src/loaders/general.tsx +++ /dev/null @@ -1,49 +0,0 @@ -import { client } from "utils/api/client"; - -export const getInstrumentName = async () => { - const response = await client.get( - `instruments/${sessionStorage.getItem("instrumentName")}/instrument_name`, - ); - - if (response.status !== 200) { - return null; - } - return response.data; -}; - -export const getInstrumentConnectionStatus = async () => { - const response = await client.get( - `instruments/${sessionStorage.getItem("instrumentName")}/instrument_server`, - {}, - false, - ); - - if (response.status !== 200) { - return false; - } - - return response.data; -}; - -export const getUpstreamVisits = async (sessid: number) => { - const response = await client.get(`sessions/${sessid}/upstream_visits`); - - if (response.status !== 200) { - return null; - } - return response.data; -}; - -export const upstreamDataDownloadRequest = async ( - visitName: string, - sessid: number, -) => { - const response = await client.get( - `visits/${visitName}/${sessid}/upstream_tiff_data_request`, - ); - - if (response.status !== 200) { - return null; - } - return response.data; -}; diff --git a/murfey-frontend/src/loaders/gridSquares.tsx b/murfey-frontend/src/loaders/gridSquares.tsx deleted file mode 100644 index 2c5a00d82..000000000 --- a/murfey-frontend/src/loaders/gridSquares.tsx +++ /dev/null @@ -1,80 +0,0 @@ -import { QueryClient } from "@tanstack/react-query"; -import { client } from "utils/api/client"; -import { Params } from "react-router-dom"; - -const getGridSquares = async ( - sessid: string = "0", - dataCollectionGroupId: string = "0", -) => { - console.log("getting grid squares"); - const response = await client.get( - `sessions/${sessid}/data_collection_groups/${dataCollectionGroupId}/grid_squares`, - ); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -const getNumMovies = async ( - sessid: string, - dataCollectionGroupId: string, - gridSquareId: number, -) => { - const response = await client.get( - `sessions/${sessid}/data_collection_groups/${dataCollectionGroupId}/grid_squares/${gridSquareId}/num_movies`, - ); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -const getFoilHoles = async ( - sessid: string, - dataCollectionGroupId: string, - gridSquareId: number, -) => { - const response = await client.get( - `sessions/${sessid}/data_collection_groups/${dataCollectionGroupId}/grid_squares/${gridSquareId}/foil_holes`, - ); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -const queryBuilder = ( - sessid: string = "0", - dataCollectionGroupId: string = "0", -) => { - return { - queryKey: [ - "gridSquares", - "sessionId", - sessid, - "dataCollectionGroup", - dataCollectionGroupId, - ], - queryFn: () => getGridSquares(sessid, dataCollectionGroupId), - staleTime: 60000, - }; -}; - -export const gridSquaresLoader = - (queryClient: QueryClient) => async (params: Params) => { - // const singleQuery = queryBuilder(params.sessid, params.dcgid); - const singleQuery = queryBuilder(params.sessid); - return ( - (await queryClient.getQueryData(singleQuery.queryKey)) ?? - (await queryClient.fetchQuery(singleQuery)) - ); - }; - -export { getFoilHoles, getNumMovies }; diff --git a/murfey-frontend/src/loaders/hub.tsx b/murfey-frontend/src/loaders/hub.tsx deleted file mode 100644 index a4fa20d45..000000000 --- a/murfey-frontend/src/loaders/hub.tsx +++ /dev/null @@ -1,22 +0,0 @@ -import { QueryClient } from "@tanstack/react-query"; -import { client, getPrefix } from "utils/api/client"; - -const getInstrumentInfo = async () => { - const response = await client.hub_get(`instruments`); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -const query = { - queryKey: ["instrumentInfo"], - queryFn: getInstrumentInfo, - staleTime: 60000, -}; - -export const instrumentInfoLoader = (queryClient: QueryClient) => async () => - (await queryClient.getQueryData(query.queryKey)) ?? - (await queryClient.fetchQuery(query)); diff --git a/murfey-frontend/src/loaders/jwt.tsx b/murfey-frontend/src/loaders/jwt.tsx deleted file mode 100644 index 0532a0087..000000000 --- a/murfey-frontend/src/loaders/jwt.tsx +++ /dev/null @@ -1,43 +0,0 @@ -import { client } from "utils/api/client"; - -type LoginDetails = { - username: string; - password: string; -}; - -export const getJWT = async (loginDetails: LoginDetails) => { - const formData = new FormData(); - formData.append("username", loginDetails.username); - formData.append("password", loginDetails.password); - - const response = await client.post(`token`, formData); - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -export const handshake = async () => { - const response = await client.post( - `instruments/${sessionStorage.getItem( - "instrumentName", - )}/activate_instrument_server`, - {}, - ); - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -export const sessionHandshake = async (sessid: number) => { - const response = await client.post( - `instruments/${sessionStorage.getItem( - "instrumentName", - )}/sessions/${sessid}/activate_instrument_server`, - {}, - ); - return response.data; -}; diff --git a/murfey-frontend/src/loaders/machineConfig.tsx b/murfey-frontend/src/loaders/machineConfig.tsx deleted file mode 100644 index 458bd31d3..000000000 --- a/murfey-frontend/src/loaders/machineConfig.tsx +++ /dev/null @@ -1,27 +0,0 @@ -import { QueryClient } from "@tanstack/react-query"; -import { components } from "schema/main"; -import { client } from "utils/api/client"; -import { Params } from "react-router-dom"; -import { parseDate } from "utils/generic"; - -export const getMachineConfigData = async () => { - const response = await client.get( - `instruments/${sessionStorage.getItem("instrumentName")}/machine`, - ); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -const query = { - queryKey: ["machineConfig"], - queryFn: getMachineConfigData, - staleTime: 60000, -}; - -export const machineConfigLoader = (queryClient: QueryClient) => async () => - (await queryClient.getQueryData(query.queryKey)) ?? - (await queryClient.fetchQuery(query)); diff --git a/murfey-frontend/src/loaders/magTable.tsx b/murfey-frontend/src/loaders/magTable.tsx deleted file mode 100644 index 4a26ff4b8..000000000 --- a/murfey-frontend/src/loaders/magTable.tsx +++ /dev/null @@ -1,46 +0,0 @@ -import { QueryClient } from "@tanstack/react-query"; -import { client } from "utils/api/client"; - -const getMagTableData = async () => { - const response = await client.get(`mag_table`); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -export const addMagTableRow = async ( - magnification: number, - pixelSize: number, -) => { - const response = await client.post(`mag_table/`, [ - { - magnification: magnification, - pixel_size: pixelSize, - }, - ]); - if (response.status !== 200) { - return null; - } - return response.data; -}; - -export const removeMagTableRow = async (magnification: number) => { - const response = await client.delete(`mag_table/${magnification}`); - if (response.status !== 200) { - return null; - } - return response.data; -}; - -const query = { - queryKey: ["magTable"], - queryFn: getMagTableData, - staleTime: 60000, -}; - -export const magTableLoader = (queryClient: QueryClient) => async () => - (await queryClient.getQueryData(query.queryKey)) ?? - (await queryClient.fetchQuery(query)); diff --git a/murfey-frontend/src/loaders/multigridSetup.tsx b/murfey-frontend/src/loaders/multigridSetup.tsx deleted file mode 100644 index 51434a3b1..000000000 --- a/murfey-frontend/src/loaders/multigridSetup.tsx +++ /dev/null @@ -1,21 +0,0 @@ -import { QueryClient } from "@tanstack/react-query"; -import { client } from "utils/api/client"; -import { components } from "schema/main"; - -type MultigridWatcherSpec = components["schemas"]["MultigridWatcherSetup"]; - -export const startMultigridWatcher = async ( - multigridWatcher: MultigridWatcherSpec, - sessionId: number, -) => { - const response = await client.post( - `sessions/${sessionId}/multigrid_watcher`, - multigridWatcher, - ); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; diff --git a/murfey-frontend/src/loaders/possibleGainRefs.tsx b/murfey-frontend/src/loaders/possibleGainRefs.tsx deleted file mode 100644 index 70105a708..000000000 --- a/murfey-frontend/src/loaders/possibleGainRefs.tsx +++ /dev/null @@ -1,84 +0,0 @@ -import { QueryClient } from "@tanstack/react-query"; -import { client } from "utils/api/client"; -import { Params } from "react-router-dom"; - -const getGainRefData = async (sessionId: string) => { - const response = await client.get( - `instruments/${sessionStorage.getItem( - "instrumentName", - )}/sessions/${sessionId}/possible_gain_references`, - ); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -export const transferGainReference = async ( - sessionId: number, - gainRef: string, -) => { - const response = await client.post( - `sessions/${sessionId}/upload_gain_reference`, - { - gain_path: gainRef, - }, - ); - if (response.status !== 200) { - return null; - } - return response.data; -}; - -export const prepareGainReference = async ( - sessionId: number, - gainRef: string, - rescale: boolean = false, - eer: boolean = false, - tag: string = "", -) => { - const response = await client.post(`sessions/${sessionId}/process_gain`, { - gain_ref: gainRef, - rescale: rescale, - eer: eer, - tag: tag, - }); - if (response.status !== 200) { - return null; - } - return response.data; -}; - -export const updateCurrentGainReference = async ( - sessionId: number, - gainRef: string, -) => { - const response = await client.put(`sessions/${sessionId}/current_gain_ref`, { - path: gainRef, - }); - if (response.status !== 200) { - return null; - } - return response.data; -}; - -const query = (sessid: string) => { - return { - queryKey: ["gainRefs"], - queryFn: () => getGainRefData(sessid), - staleTime: 60000, - }; -}; - -export const gainRefLoader = - (queryClient: QueryClient) => async (params: Params) => { - if (params.sessid) { - const singleQuery = query(params.sessid); - return ( - (await queryClient.getQueryData(singleQuery.queryKey)) ?? - (await queryClient.fetchQuery(singleQuery)) - ); - } - }; diff --git a/murfey-frontend/src/loaders/processingParameters.tsx b/murfey-frontend/src/loaders/processingParameters.tsx deleted file mode 100644 index 78d71e14f..000000000 --- a/murfey-frontend/src/loaders/processingParameters.tsx +++ /dev/null @@ -1,34 +0,0 @@ -import { QueryClient } from "@tanstack/react-query"; -import { client } from "utils/api/client"; -import { Params } from "react-router-dom"; - -const getProcessingParameterData = async (sessid: string = "0") => { - const response = await client.get( - `sessions/${sessid}/spa_processing_parameters`, - ); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -const queryBuilder = (sessid: string = "0") => { - return { - queryKey: ["sessionId", sessid], - queryFn: () => getProcessingParameterData(sessid), - staleTime: 60000, - }; -}; - -export const processingParametersLoader = - (queryClient: QueryClient) => async (params: Params) => { - const singleQuery = queryBuilder(params.sessid); - return ( - (await queryClient.getQueryData(singleQuery.queryKey)) ?? - (await queryClient.fetchQuery(singleQuery)) - ); - }; - -export { getProcessingParameterData }; diff --git a/murfey-frontend/src/loaders/rsyncers.tsx b/murfey-frontend/src/loaders/rsyncers.tsx deleted file mode 100644 index 3d0a81eb0..000000000 --- a/murfey-frontend/src/loaders/rsyncers.tsx +++ /dev/null @@ -1,94 +0,0 @@ -import { QueryClient } from "@tanstack/react-query"; -import { components } from "schema/main"; -import { client } from "utils/api/client"; -import { Params } from "react-router-dom"; -import { parseDate } from "utils/generic"; - -const getRsyncerData = async (sessionId: string) => { - const response = await client.get(`sessions/${sessionId}/rsyncers`); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -export const pauseRsyncer = async (sessionId: number, source: string) => { - console.log("stopping rsyncer"); - - const response = await client.post(`sessions/${sessionId}/stop_rsyncer`, { - source: source, - }); - - if (response.status !== 200) { - return null; - } - - console.log(response.data); - - return response.data; -}; - -export const restartRsyncer = async (sessionId: number, source: string) => { - console.log("stopping rsyncer"); - - const response = await client.post(`sessions/${sessionId}/restart_rsyncer`, { - source: source, - }); - - if (response.status !== 200) { - return null; - } - - console.log(response.data); - - return response.data; -}; - -export const finaliseRsyncer = async (sessionId: number, source: string) => { - const response = await client.post(`sessions/${sessionId}/finalise_rsyncer`, { - source: source, - }); - - if (response.status !== 200) { - return null; - } - - console.log(response.data); - - return response.data; -}; - -export const removeRsyncer = async (sessionId: number, source: string) => { - console.log("removing rsyncer"); - - const response = await client.post(`sessions/${sessionId}/remove_rsyncer`, { - source: source, - }); - - if (response.status !== 200) { - return null; - } - - console.log(response.data); - - return response.data; -}; - -const queryBuilder = (sessionId: string = "0") => { - return { - queryKey: ["sessid", sessionId], - queryFn: () => getRsyncerData(sessionId), - staleTime: 60000, - }; -}; - -export const rsyncerLoader = - (queryClient: QueryClient) => async (params: Params) => { - const singleQuery = queryBuilder(params.sessid); - return ( - (await queryClient.getQueryData(singleQuery.queryKey)) ?? - (await queryClient.fetchQuery(singleQuery)) - ); - }; diff --git a/murfey-frontend/src/loaders/sessionSetup.tsx b/murfey-frontend/src/loaders/sessionSetup.tsx deleted file mode 100644 index b5eb257bb..000000000 --- a/murfey-frontend/src/loaders/sessionSetup.tsx +++ /dev/null @@ -1,22 +0,0 @@ -import { QueryClient } from "@tanstack/react-query"; -import { client } from "utils/api/client"; -import { components } from "schema/main"; - -type ProvidedProcessingParameters = - components["schemas"]["ProvidedProcessingParameters"]; - -export const registerProcessingParameters = async ( - processingParameters: ProvidedProcessingParameters, - sessionId: number, -) => { - const response = await client.post( - `sessions/${sessionId}/provided_processing_parameters`, - processingParameters, - ); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; diff --git a/murfey-frontend/src/loaders/session_clients.tsx b/murfey-frontend/src/loaders/session_clients.tsx deleted file mode 100644 index f7af42db4..000000000 --- a/murfey-frontend/src/loaders/session_clients.tsx +++ /dev/null @@ -1,116 +0,0 @@ -import { QueryClient } from "@tanstack/react-query"; -import { components } from "schema/main"; -import { client } from "utils/api/client"; -import { Params } from "react-router-dom"; - -export const includePage = (endpoint: string, limit: number, page: number) => - `${endpoint}${endpoint.includes("?") ? "&" : "?"}page=${ - page - 1 - }&limit=${limit}`; - -const getSessionsData = async () => { - const response = await client.get(`sessions`); - - if (response.status !== 200) { - return null; - } - - return { - current: response.data, - }; -}; - -const getClientData = async () => { - const response = await client.get(`clients`); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -const getSessionData = async (sessid: string = "0") => { - const response = await client.get(`session/${sessid}`); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -export const linkSessionToClient = async ( - client_id: number, - sessionName: string, -) => { - const response = await client.post(`clients/${client_id}/session`, { - session_name: sessionName, - }); - if (response.status !== 200) { - return null; - } - return response.data; -}; - -export const createSession = async ( - visit: string, - sessionName: string, - instrumentName: string, -) => { - const response = await client.post( - `instruments/${instrumentName}/visits/${visit}/session/${sessionName}`, - {}, - ); - if (response.status !== 200) { - return null; - } - return response.data; -}; - -export const deleteSessionData = async (sessid: number) => { - const response = await client.delete(`sessions/${sessid}`); - if (response.status !== 200) { - return null; - } - return response.data; -}; - -const query = { - queryKey: ["homepageSessions", sessionStorage.getItem("instrumentName")], - queryFn: getSessionsData, - staleTime: 60000, -}; - -const clientQuery = { - queryKey: ["homepageClients", sessionStorage.getItem("instrumentName")], - queryFn: getClientData, - staleTime: 60000, -}; - -export const sessionsLoader = (queryClient: QueryClient) => async () => - (await queryClient.getQueryData(query.queryKey)) ?? - (await queryClient.fetchQuery(query)); - -export const clientsLoader = (queryClient: QueryClient) => async () => - (await queryClient.getQueryData(clientQuery.queryKey)) ?? - (await queryClient.fetchQuery(clientQuery)); - -const queryBuilder = (sessid: string = "0") => { - return { - queryKey: ["sessionId", sessid], - queryFn: () => getSessionData(sessid), - staleTime: 60000, - }; -}; - -export const sessionLoader = - (queryClient: QueryClient) => async (params: Params) => { - const singleQuery = queryBuilder(params.sessid); - return ( - (await queryClient.getQueryData(singleQuery.queryKey)) ?? - (await queryClient.fetchQuery(singleQuery)) - ); - }; - -export { getSessionData }; diff --git a/murfey-frontend/src/loaders/visits.tsx b/murfey-frontend/src/loaders/visits.tsx deleted file mode 100644 index 8be762354..000000000 --- a/murfey-frontend/src/loaders/visits.tsx +++ /dev/null @@ -1,33 +0,0 @@ -import { QueryClient } from "@tanstack/react-query"; -import { client } from "utils/api/client"; -import { Params } from "react-router-dom"; - -const getVisitData = async (instrumentName: string) => { - const response = await client.get(`instruments/${instrumentName}/visits_raw`); - - if (response.status !== 200) { - return null; - } - - return response.data; -}; - -const query = (instrumentName: string) => { - return { - queryKey: ["visits", instrumentName], - queryFn: () => getVisitData(instrumentName), - staleTime: 60000, - }; -}; - -export const visitLoader = - (queryClient: QueryClient) => async (params: Params) => { - if (params.instrumentName) { - const singleQuery = query(params.instrumentName); - return ( - (await queryClient.getQueryData(singleQuery.queryKey)) ?? - (await queryClient.fetchQuery(singleQuery)) - ); - } - return null; - }; diff --git a/murfey-frontend/src/logo.svg b/murfey-frontend/src/logo.svg deleted file mode 100644 index 9dfc1c058..000000000 --- a/murfey-frontend/src/logo.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/murfey-frontend/src/reportWebVitals.js b/murfey-frontend/src/reportWebVitals.js deleted file mode 100644 index 9ecd33f9c..000000000 --- a/murfey-frontend/src/reportWebVitals.js +++ /dev/null @@ -1,13 +0,0 @@ -const reportWebVitals = (onPerfEntry) => { - if (onPerfEntry && onPerfEntry instanceof Function) { - import("web-vitals").then(({ getCLS, getFID, getFCP, getLCP, getTTFB }) => { - getCLS(onPerfEntry); - getFID(onPerfEntry); - getFCP(onPerfEntry); - getLCP(onPerfEntry); - getTTFB(onPerfEntry); - }); - } -}; - -export default reportWebVitals; diff --git a/murfey-frontend/src/routes/DataCollectionGroups.tsx b/murfey-frontend/src/routes/DataCollectionGroups.tsx deleted file mode 100644 index 9f8dadbcd..000000000 --- a/murfey-frontend/src/routes/DataCollectionGroups.tsx +++ /dev/null @@ -1,87 +0,0 @@ -import { Box, Button, Heading, HStack, VStack, Link } from "@chakra-ui/react"; - -import { - useNavigate, - useLoaderData, - useParams, - Link as LinkRouter, -} from "react-router-dom"; -import { components } from "schema/main"; -import { Table } from "@diamondlightsource/ui-components"; -import { SetupStepper } from "components/setupStepper"; -import { - prepareGainReference, - transferGainReference, - updateCurrentGainReference, -} from "loaders/possibleGainRefs"; -import { getMachineConfigData } from "loaders/machineConfig"; - -import { useState } from "react"; - -type DataCollectionGroup = components["schemas"]["DataCollectionGroup"]; - -const DataCollectionGroups = () => { - const dataCollectionGroups = useLoaderData() as { - [key: string]: DataCollectionGroup; - }; - const { sessid } = useParams(); - const navigate = useNavigate(); - - const SelectDataCollectionGroup = async ( - data: Record, - index: number, - ) => { - navigate( - `/sessions/${sessid}/data_collection_groups/${data["id"]}/grid_squares`, - ); - }; - - return ( -
- - - - - - Data Collection Groups - - - - - - {dataCollectionGroups ? ( -
- ) : ( - <> - )} - - - - ); -}; - -export { DataCollectionGroups }; diff --git a/murfey-frontend/src/routes/Error.tsx b/murfey-frontend/src/routes/Error.tsx deleted file mode 100644 index 61bc62503..000000000 --- a/murfey-frontend/src/routes/Error.tsx +++ /dev/null @@ -1,59 +0,0 @@ -import { Heading, Link, VStack, Box, Text, Code } from "@chakra-ui/react"; -import { useEffect, useState } from "react"; -import { useRouteError } from "react-router-dom"; -import { Navbar } from "@diamondlightsource/ui-components"; - -interface ErrorType { - status: number; - statusText: string; - data?: string; -} - -const Error = () => { - const [heading, setHeading] = useState(""); - const [message, setMessage] = useState(""); - const [details, setDetails] = useState(""); - const error = useRouteError() as ErrorType; - - useEffect(() => { - console.error(error); - if (error.status === 404) { - setHeading("Page not found"); - setMessage("This page does not exist."); - } else { - setHeading("An error has occurred"); - setMessage( - "An unexpected error has occurred. If this persists, please contact the developers. Details:", - ); - setDetails(error.toString()); - } - }, [error]); - - return ( -
- - - - {heading} - {message} - {details && ( - - {details} - - )} - - Go home - - - -
- ); -}; - -export { Error }; diff --git a/murfey-frontend/src/routes/GainRefTransfer.tsx b/murfey-frontend/src/routes/GainRefTransfer.tsx deleted file mode 100644 index 373442593..000000000 --- a/murfey-frontend/src/routes/GainRefTransfer.tsx +++ /dev/null @@ -1,158 +0,0 @@ -import { - Box, - Heading, - HStack, - VStack, - Input, - Checkbox, - Modal, - ModalOverlay, - ModalContent, - ModalBody, - ModalHeader, - Spinner, - Tooltip, -} from "@chakra-ui/react"; - -import { useNavigate, useLoaderData, useSearchParams } from "react-router-dom"; -import { components } from "schema/main"; -import { Table } from "@diamondlightsource/ui-components"; -import { SetupStepper } from "components/setupStepper"; -import { - prepareGainReference, - transferGainReference, - updateCurrentGainReference, -} from "loaders/possibleGainRefs"; -import { getMachineConfigData } from "loaders/machineConfig"; - -import React from "react"; - -type File = components["schemas"]["File"]; - -const GainRefTransfer = () => { - const possibleGainRefs = useLoaderData() as File[] | null; - let [searchParams, setSearchParams] = useSearchParams(); - const navigate = useNavigate(); - const [processing, setProcessing] = React.useState(false); - const [tag, setTag] = React.useState(""); - const [falcon, setFalcon] = React.useState(false); - const [falconPreset, setFalconPreset] = React.useState(false); - - const SelectGainRef = async (data: Record, index: number) => { - setProcessing(true); - const sessid = searchParams.get("sessid"); - const setup = searchParams.get("setup"); - if (sessid) { - const transferStatus = await transferGainReference( - parseInt(sessid), - data["full_path"], - ); - if (true) { - const preparedGainReference = await prepareGainReference( - parseInt(sessid), - data["full_path"], - !falcon, - falcon, - tag, - ); - await updateCurrentGainReference( - parseInt(sessid), - preparedGainReference.gain_ref, - ); - } - } - if (setup) - sessid ? navigate(`/new_session/parameters/${sessid}`) : navigate("/"); - else sessid ? navigate(`/sessions/${sessid}`) : navigate("/"); - setProcessing(false); - }; - - if (!falconPreset) { - setFalconPreset(true); - getMachineConfigData().then((cfg) => setFalcon(cfg.camera === "FALCON")); - } - - return ( -
- - - - - - Possible Gain Reference Files - - - - - void 0}> - - - Processing gain reference - - - - - - - {searchParams.get("setup") ? ( - - ) : null} - - - - -
- - setTag(e.target.value)} - /> - - setFalcon(e.target.checked)} - > - Falcon - - - - - - - ); -}; - -export { GainRefTransfer }; diff --git a/murfey-frontend/src/routes/GridSquares.tsx b/murfey-frontend/src/routes/GridSquares.tsx deleted file mode 100644 index 431381e8c..000000000 --- a/murfey-frontend/src/routes/GridSquares.tsx +++ /dev/null @@ -1,75 +0,0 @@ -import { - Box, - Heading, - HStack, - VStack, - CardBody, - Card, - CardHeader, - Image, -} from "@chakra-ui/react"; - -import { useNavigate, useLoaderData, useParams } from "react-router-dom"; -import { components } from "schema/main"; -import { GridSquareCard } from "components/gridSquareCard"; - -type GridSquare = components["schemas"]["GridSquare"]; - -const GridSquares = () => { - console.log("gather grid squares"); - const gridSquares = useLoaderData() as GridSquare[]; - console.log( - "grid squares", - gridSquares, - typeof gridSquares, - gridSquares.length, - ); - const { sessid, dcgid } = useParams(); - - const getUrl = (endpoint: string) => { - return ( - (sessionStorage.getItem("murfeyServerURL") ?? - process.env.REACT_APP_API_ENDPOINT) + endpoint - ); - }; - - const res = ( -
- - - - - - Grid Squares - - - - - - {gridSquares && gridSquares.length > 0 ? ( - gridSquares.map((gs) => GridSquareCard(gs, sessid, dcgid)) - ) : ( - <> - )} - - -
- ); - return res; -}; - -export { GridSquares }; diff --git a/murfey-frontend/src/routes/Home.tsx b/murfey-frontend/src/routes/Home.tsx deleted file mode 100644 index 5859c0191..000000000 --- a/murfey-frontend/src/routes/Home.tsx +++ /dev/null @@ -1,206 +0,0 @@ -import { - Box, - Button, - Divider, - GridItem, - Heading, - HStack, - IconButton, - Link, - Stack, - Stat, - StatLabel, - Tooltip, - VStack, -} from "@chakra-ui/react"; - -import { v4 as uuid4 } from "uuid"; -import { Link as LinkRouter, useLoaderData } from "react-router-dom"; -import { components } from "schema/main"; -import { MdDelete } from "react-icons/md"; -import { deleteSessionData } from "loaders/session_clients"; -import { InstrumentCard } from "components/instrumentCard"; -import useWebSocket from "react-use-websocket"; - -import React, { useEffect } from "react"; - -type SessionClients = components["schemas"]["SessionClients"]; - -interface SessionRowProps { - session_clients: SessionClients[]; - title: string; -} - -const SessionRow = ({ session_clients, title }: SessionRowProps) => { - return ( - - - {title} - - - - {session_clients && session_clients.length > 0 ? ( - session_clients.map((session_client) => { - const session_id = session_client["session"]["id"]; - return ( - <> - - c.connected) - ? "Active (live connections)" - : "Inactive" - } - > - - c.connected) - ? "murfey.500" - : "murfey.400" - } - overflow="auto" - w="calc(100%)" - p={2} - border="1px solid grey" - borderRadius={5} - display={"flex"} - > - - {session_client.session.name}:{" "} - {session_client.session.id} - - - - - } - onClick={() => { - deleteSessionData(session_id); - window.location.reload(); - }} - /> - - - ); - }) - ) : ( - - - No {title} Found - - - )} - - - ); -}; - -const Home = () => { - const sessions = useLoaderData() as { - current: SessionClients[]; - } | null; - const [UUID, setUUID] = React.useState(""); - const baseUrl = - sessionStorage.getItem("murfeyServerURL") ?? - process.env.REACT_APP_API_ENDPOINT; - const url = baseUrl ? baseUrl.replace("http", "ws") : "ws://localhost:8000"; - const parseWebsocketMessage = (message: any) => { - let parsedMessage: any = {}; - try { - parsedMessage = JSON.parse(message); - } catch (err) { - return; - } - if (parsedMessage.message === "refresh") { - window.location.reload(); - } - }; - - //const wsid = uuid1(); - useEffect(() => { - setUUID(uuid4()); - }, []); - useWebSocket(url + `ws/connect/${UUID}`, { - onOpen: () => { - console.log("WebSocket connection established."); - }, - onMessage: (event) => { - parseWebsocketMessage(event.data); - }, - }); - - return ( -
- Murfey - - - - - - Murfey Sessions - - - Microscope Data Transfer Control System - - - - - - - - - {sessions ? ( - - - - ) : ( - - - No sessions found - - - )} - - - - - - -
- ); -}; - -export { Home }; diff --git a/murfey-frontend/src/routes/Hub.tsx b/murfey-frontend/src/routes/Hub.tsx deleted file mode 100644 index 7358e840b..000000000 --- a/murfey-frontend/src/routes/Hub.tsx +++ /dev/null @@ -1,97 +0,0 @@ -import { - Card, - CardBody, - CardHeader, - Image, - Link, - Text, - HStack, - Heading, - VStack, - Box, - SimpleGrid, -} from "@chakra-ui/react"; - -import { TbMicroscope, TbSnowflake } from "react-icons/tb"; -import { Link as LinkRouter, useLoaderData } from "react-router-dom"; -import { getInstrumentName } from "loaders/general"; - -import React from "react"; - -const getUrl = (endpoint: string) => { - return process.env.REACT_APP_HUB_ENDPOINT + endpoint; -}; - -type InstrumentInfo = { - instrument_name: string; - display_name: string; - instrument_url: string; -}; - -const Hub = () => { - const instrumentInfo = useLoaderData() as InstrumentInfo[]; - - const sessionStorageSetup = (ininfo: InstrumentInfo) => { - sessionStorage.setItem("murfeyServerURL", ininfo.instrument_url + "/"); - sessionStorage.setItem("instrumentName", ininfo.instrument_name); - }; - - return ( - - - - - {" "} - {" "} - {" "} - Murfey Hub - - - - {instrumentInfo ? ( - instrumentInfo.map((ini) => { - return ( - - sessionStorageSetup(ini)}> - - - - - {ini.display_name} - - - - ); - }) - ) : ( - <> - )} - - - ); -}; - -export { Hub }; diff --git a/murfey-frontend/src/routes/Login.tsx b/murfey-frontend/src/routes/Login.tsx deleted file mode 100644 index 9f62d5b5b..000000000 --- a/murfey-frontend/src/routes/Login.tsx +++ /dev/null @@ -1,75 +0,0 @@ -import { - Button, - Input, - VStack, - Link, - FormControl, - Card, - CardBody, - Heading, - HStack, -} from "@chakra-ui/react"; -import { Link as LinkRouter, useNavigate, Navigate } from "react-router-dom"; -import { TbMicroscope, TbSnowflake } from "react-icons/tb"; - -import { getJWT, handshake } from "loaders/jwt"; - -import React from "react"; - -const Login = () => { - const [username, setUsername] = React.useState(""); - const handleUsername = (event: React.ChangeEvent) => - setUsername(event.target.value); - const [password, setPassword] = React.useState(""); - const handlePassword = (event: React.ChangeEvent) => - setPassword(event.target.value); - - const navigate = useNavigate(); - - return sessionStorage.getItem("murfeyServerURL") ? ( - - - - {" "} - {" "} - {" "} - Murfey Login - - - - - - - - - - - - ) : ( - - ); -}; - -export { Login }; diff --git a/murfey-frontend/src/routes/MagTable.tsx b/murfey-frontend/src/routes/MagTable.tsx deleted file mode 100644 index a120aeae2..000000000 --- a/murfey-frontend/src/routes/MagTable.tsx +++ /dev/null @@ -1,168 +0,0 @@ -import { - Button, - Box, - Heading, - HStack, - IconButton, - Input, - VStack, - TableContainer, - Table, - Thead, - Tbody, - Tfoot, - Tr, - Th, - Td, - Text, - TableCaption, - Modal, - ModalOverlay, - ModalHeader, - ModalFooter, - ModalContent, - ModalBody, - ModalCloseButton, - FormControl, - useDisclosure, -} from "@chakra-ui/react"; - -import { CheckIcon, EditIcon } from "@chakra-ui/icons"; - -import { Link as LinkRouter, useLoaderData } from "react-router-dom"; -import { components } from "schema/main"; -import { MdAdd, MdHorizontalRule } from "react-icons/md"; -import { addMagTableRow, removeMagTableRow } from "loaders/magTable"; - -import React from "react"; - -type MagTableRow = components["schemas"]["MagnificationLookup"]; - -const MagTable = () => { - const magTable = useLoaderData() as MagTableRow[] | null; - const { isOpen, onOpen, onClose } = useDisclosure(); - const [numNewRows, setNumNewRows] = React.useState(0); - - const handleRemoveRow = (mag: number) => { - removeMagTableRow(mag); - window.location.reload(); - }; - - const handleForm = (event: React.FormEvent) => { - event.preventDefault(); - const formData = new FormData(event.currentTarget); - const mag = parseInt(formData.get("magnification") as string); - const pixelSize = parseFloat(formData.get("pixelSize") as string); - addMagTableRow(mag, pixelSize); - window.location.reload(); - }; - - return ( -
- Murfey - - - - - - Magnification Table - - - - - -
- Magnification Table - - - - - - - - - - - Add Mag Table Row - - -
- - - - - - - - - - - - - {magTable && magTable.length > 0 ? ( - magTable.map((row) => { - return ( - - - - - - ); - }) - ) : ( - <> - )} - - - - } - size="m" - onClick={onOpen} - > - - -
MagnificationPixel SizeRemove
- {row.magnification} - - {row.pixel_size} - - } - onClick={() => - handleRemoveRow(row.magnification) - } - > -
- - - - - -
- ); -}; - -export { MagTable }; diff --git a/murfey-frontend/src/routes/MultigridSetup.tsx b/murfey-frontend/src/routes/MultigridSetup.tsx deleted file mode 100644 index e2857e3a4..000000000 --- a/murfey-frontend/src/routes/MultigridSetup.tsx +++ /dev/null @@ -1,166 +0,0 @@ -import { - Box, - FormControl, - FormLabel, - GridItem, - Heading, - HStack, - IconButton, - Link, - Select, - Stack, - Switch, - VStack, -} from "@chakra-ui/react"; -import { ArrowForwardIcon } from "@chakra-ui/icons"; - -import { Link as LinkRouter, useLoaderData, useParams } from "react-router-dom"; -import { components } from "schema/main"; -import { startMultigridWatcher } from "loaders/multigridSetup"; -import { getSessionData } from "loaders/session_clients"; -import { SetupStepper } from "components/setupStepper"; -import React, { useEffect } from "react"; - -type MachineConfig = components["schemas"]["MachineConfig"]; -type MultigridWatcherSpec = components["schemas"]["MultigridWatcherSetup"]; -type Session = components["schemas"]["Session"]; - -const MultigridSetup = () => { - const machineConfig = useLoaderData() as MachineConfig | null; - const { sessid } = useParams(); - let initialDirectory = ""; - if (machineConfig) { - initialDirectory = machineConfig.data_directories[0]; - } - const [selectedDirectory, setSelectedDirectory] = - React.useState(initialDirectory); - const processByDefault = machineConfig - ? machineConfig.process_by_default - : true; - const [skipExistingProcessing, setSkipExistingProcessing] = - React.useState(!processByDefault); - const [session, setSession] = React.useState(); - - useEffect(() => { - getSessionData(sessid).then((sess) => setSession(sess.session)); - }, []); - const activeStep = session != null ? (session.started ? 4 : 3) : 3; - - const handleDirectorySelection = (e: React.ChangeEvent) => - setSelectedDirectory(e.target.value); - - const handleSelection = () => { - if (typeof sessid !== "undefined") { - console.log(sessid); - startMultigridWatcher( - { - source: selectedDirectory, - skip_existing_processing: skipExistingProcessing, - } as MultigridWatcherSpec, - parseInt(sessid), - ); - } - }; - - return ( -
- - - - - - Select data directory - - - - - - - - - - - - - - Do not process existing data - { - setSkipExistingProcessing(!skipExistingProcessing); - }} - /> - - - - - } - onClick={handleSelection} - /> - - - - - - - -
- ); -}; - -export { MultigridSetup }; diff --git a/murfey-frontend/src/routes/NewSession.tsx b/murfey-frontend/src/routes/NewSession.tsx deleted file mode 100644 index d7c3db10a..000000000 --- a/murfey-frontend/src/routes/NewSession.tsx +++ /dev/null @@ -1,185 +0,0 @@ -import { - Box, - Button, - Divider, - GridItem, - Input, - Heading, - HStack, - Link, - Stack, - Stat, - StatHelpText, - StatLabel, - StatNumber, - Text, - VStack, - Modal, - ModalOverlay, - ModalHeader, - ModalContent, - ModalFooter, - ModalCloseButton, - ModalBody, -} from "@chakra-ui/react"; - -import { useDisclosure } from "@chakra-ui/react"; -import { Link as LinkRouter, useLoaderData, useParams } from "react-router-dom"; -import { components } from "schema/main"; -import { SetupStepper } from "components/setupStepper"; -import { Table } from "@diamondlightsource/ui-components"; -import { createSession } from "loaders/session_clients"; -import { sessionHandshake } from "loaders/jwt"; -import { useNavigate } from "react-router-dom"; -import React, { ChangeEventHandler } from "react"; - -type Visit = components["schemas"]["Visit"]; - -const NewSession = () => { - const currentVisits = useLoaderData() as Visit[] | null; - const { isOpen, onOpen, onClose } = useDisclosure(); - const [selectedVisit, setSelectedVisit] = React.useState(""); - const [sessionReference, setSessionReference] = React.useState(""); - const navigate = useNavigate(); - - const handleChange = (event: React.ChangeEvent) => - setSessionReference(event.target.value); - - const handleVisitNameChange = ( - event: React.ChangeEvent, - ) => { - setSelectedVisit(event.target.value); - setSessionReference(event.target.value); - }; - - function selectVisit(data: Record, index: number) { - setSelectedVisit(data.name); - setSessionReference(data.name); - } - - const instrumentName = sessionStorage.getItem("instrumentName"); - - const startMurfeySession = async (iName: string) => { - const sid = await createSession(selectedVisit, sessionReference, iName); - await sessionHandshake(sid); - return sid; - }; - - return instrumentName ? ( -
- - - - Create visit - - - - - - - - - - - - - - - - Current visits - - - - - - - - - - - - - - - - - - - - ) : ( - <> - ); -}; - -export { NewSession }; diff --git a/murfey-frontend/src/routes/ProcessingParameters.tsx b/murfey-frontend/src/routes/ProcessingParameters.tsx deleted file mode 100644 index 09f98dd8e..000000000 --- a/murfey-frontend/src/routes/ProcessingParameters.tsx +++ /dev/null @@ -1,184 +0,0 @@ -import { - Accordion, - AccordionButton, - AccordionPanel, - AccordionItem, - AccordionIcon, - Box, - Heading, - IconButton, - HStack, - VStack, - Switch, - Text, -} from "@chakra-ui/react"; - -import { useLoaderData } from "react-router-dom"; -import { components } from "schema/main"; -import { Table } from "@diamondlightsource/ui-components"; -import { MdEditNote } from "react-icons/md"; - -import React from "react"; - -type ProcessingDetails = components["schemas"]["ProcessingDetails"]; - -type ProcessingRow = { - parameterName: string; - parameterValue?: string | number | boolean; -}; - -type ProcessingTable = { - processingRows: ProcessingRow[]; - tag: string; -}; - -const nameLabelMap: Map = new Map([ - ["pj_id", "Processing Job ID"], - ["angpix", "Pixel Size [m]"], - ["dose_per_frame", "Dose per frame [\u212B / pixel]"], - ["gain_ref", "Gain Reference"], - ["voltage", "Voltage [kV]"], - ["motion_corr_binning", "Motion correction binning factor"], - ["eer_grouping", "EER Grouping"], - ["symmetry", "Symmetry"], - ["particle_diameter", "Particle Diameter [\u212B]"], - ["downscale", "Downscaling During Extraction"], - ["do_icebreaker_jobs", "Perform IceBreaker Jobs"], - ["boxsize", "Box Size"], - ["small_boxsize", "Downscaled Box Size"], - ["mask_diameter", "Mask Diameter for Classification"], - ["estimate_particle_diameter", "Automatically Estimate Particle Diameter"], - ["hold_class2d", "2D Classification Held"], - ["rerun_class2d", "First 2D Classification Batch Needs to be Rerun"], - ["rerun_class3d", "3D Classification Needs to be Rerun"], - ["class_selection_score", "Class Selection Threshold"], - ["star_combination_job", "Job Number for Rebatching Job"], - ["initial_model", "Initial Model"], - ["next_job", "Next Job Number"], - ["picker_murfey_id", "Murfey ID of Picker for Use in ISPyB"], - ["picker_ispyb_id", "ISPyB Particle Picker ID"], -]); - -const ProcessingParameters = () => { - const procParams = useLoaderData() as ProcessingDetails[] | null; - const [showExtra, setShowExtra] = React.useState(false); - let tableRows = [] as ProcessingTable[]; - let tableRowsExtra = [] as ProcessingTable[]; - console.log(procParams); - procParams?.map((p) => { - let tr: ProcessingTable = { - processingRows: [], - tag: "", - }; - let tre: ProcessingTable = { - processingRows: [], - tag: "", - }; - Object.entries(p?.relion_params ? p?.relion_params : {}).forEach( - ([key, value]) => - tr.processingRows.push({ - parameterName: nameLabelMap.get(key) ?? key, - parameterValue: - value === true ? "True" : value === false ? "False" : value, - }), - ); - tr.tag = p?.relion_params.pj_id.toString(); - tableRows.push(tr); - Object.entries(p?.feedback_params ? p?.feedback_params : {}).forEach( - ([key, value]) => - tre.processingRows.push({ - parameterName: nameLabelMap.get(key) ?? key, - parameterValue: - value === true ? "True" : value === false ? "False" : value, - }), - ); - tre.tag = p?.feedback_params.pj_id.toString(); - tableRowsExtra.push(tre); - }); - const handleToggle = (event: React.ChangeEvent) => { - setShowExtra(!showExtra); - }; - return ( -
- - - - - - Processing Parameters - - - - Show extra processing parameters - - - - - - {tableRows.map((tr) => { - return ( - - - - Main Processing Parameters (Processing Job ID {tr.tag}) - - - - -
- - - ); - })} - {showExtra ? ( - tableRowsExtra.map((tre) => { - return ( - - - - Extra Processing Parameters (Processing Job ID {tre.tag}) - - - - - } - /> -
- - - ); - }) - ) : ( - <> - )} - - - - ); -}; - -export { ProcessingParameters }; diff --git a/murfey-frontend/src/routes/Root.tsx b/murfey-frontend/src/routes/Root.tsx deleted file mode 100644 index 58514993e..000000000 --- a/murfey-frontend/src/routes/Root.tsx +++ /dev/null @@ -1,21 +0,0 @@ -import { Box, HStack, Tag, Text, Link, Progress, Icon } from "@chakra-ui/react"; -import { Outlet, useLoaderData, Link as LinkRouter } from "react-router-dom"; -import { Navbar } from "components/navbar"; -import { MdSignalWifi4Bar } from "react-icons/md"; - -import "styles/main.css"; - -const Root = () => { - return ( -
- - - - - - -
- ); -}; - -export { Root }; diff --git a/murfey-frontend/src/routes/Session.tsx b/murfey-frontend/src/routes/Session.tsx deleted file mode 100644 index f771ddd30..000000000 --- a/murfey-frontend/src/routes/Session.tsx +++ /dev/null @@ -1,418 +0,0 @@ -import { - Badge, - Box, - Button, - Card, - CardBody, - CardHeader, - Divider, - Flex, - GridItem, - Heading, - HStack, - IconButton, - Image, - Link, - Menu, - MenuButton, - MenuItem, - MenuList, - Modal, - ModalOverlay, - ModalContent, - ModalHeader, - ModalFooter, - ModalBody, - ModalCloseButton, - Spacer, - Spinner, - Stack, - StackDivider, - Stat, - StatHelpText, - StatLabel, - StatNumber, - Switch, - Text, - Tooltip, - VStack, - useToast, - Icon, -} from "@chakra-ui/react"; - -import { useDisclosure } from "@chakra-ui/react"; -import { ViewIcon } from "@chakra-ui/icons"; - -import { v4 as uuid4 } from "uuid"; -import { Link as LinkRouter, useLoaderData, useParams } from "react-router-dom"; -import { - MdCheck, - MdDensityMedium, - MdFileUpload, - MdOutlineWarning, - MdOutlineGridOn, -} from "react-icons/md"; -import { FiActivity } from "react-icons/fi"; -import { components } from "schema/main"; -import { getInstrumentName } from "loaders/general"; -import { - pauseRsyncer, - restartRsyncer, - removeRsyncer, - finaliseRsyncer, -} from "loaders/rsyncers"; -import { getSessionData } from "loaders/session_clients"; -import { InstrumentCard } from "components/instrumentCard"; -import { UpstreamVisitCard } from "components/upstreamVisitsCard"; -import useWebSocket from "react-use-websocket"; - -import React, { useEffect } from "react"; - -type RsyncInstance = components["schemas"]["RsyncInstance"]; -type Session = components["schemas"]["Session"]; - -const RsyncCard = (rsyncer: RsyncInstance) => { - const { isOpen, onOpen, onClose } = useDisclosure(); - const [action, setAction] = React.useState("finalise"); - - const finalise = () => { - setAction("finalise"); - onOpen(); - }; - - const remove = () => { - setAction("remove"); - onOpen(); - }; - - const handleRsyncerAction = async () => { - if (action === "finalise") - await finaliseRsyncer(rsyncer.session_id, rsyncer.source); - else if (action === "remove") - await removeRsyncer(rsyncer.session_id, rsyncer.source); - onClose(); - }; - - return ( - - - - - - Confirm RSyncer {action}: {rsyncer.source} - - - Are you sure you want to continue? - - - - - - - - - - {" "} - - {" "} - - RSync Instance - {rsyncer.transferring && } - - {rsyncer.tag} - - - - - } - /> - - {rsyncer.transferring ? ( - <> - - pauseRsyncer(rsyncer.session_id, rsyncer.source) - } - isDisabled={!rsyncer.transferring} - > - Pause - - remove()} - isDisabled={!rsyncer.transferring} - > - Remove - - { - finalise(); - }} - isDisabled={!rsyncer.transferring} - > - Finalise - - - ) : ( - <> - - restartRsyncer(rsyncer.session_id, rsyncer.source) - } - > - Start - - remove()}>Remove - - )} - - - - - - } spacing="4"> - - - Source - - - {rsyncer.source} - - - - - Destination - - - {rsyncer.destination ?? ""} - - - - - Transfer progress - - {rsyncer.files_transferred} / {rsyncer.files_counted} - - - {(rsyncer.files_transferred ?? 0) >= - (rsyncer.files_counted ?? 0) ? ( - - - Up to date - - ) : rsyncer.transferring ? ( - - - Working on it - - ) : ( - - - Broken - - )} - - - - - - - ); -}; - -const getUrl = (endpoint: string) => { - return ( - (sessionStorage.getItem("murfeyServerURL") ?? - process.env.REACT_APP_API_ENDPOINT) + endpoint - ); -}; - -const Session = () => { - const { isOpen, onOpen, onClose } = useDisclosure(); - const rsync = useLoaderData() as RsyncInstance[] | null; - const { sessid } = useParams(); - const [UUID, setUUID] = React.useState(""); - const [instrumentName, setInstrumentName] = React.useState(""); - const baseUrl = - sessionStorage.getItem("murfeyServerURL") ?? - process.env.REACT_APP_API_ENDPOINT; - const url = baseUrl ? baseUrl.replace("http", "ws") : "ws://localhost:8000"; - const toast = useToast(); - const [session, setSession] = React.useState(); - - useEffect(() => { - getSessionData(sessid).then((sess) => setSession(sess.session)); - setUUID(uuid4()); - }, []); - - const parseWebsocketMessage = (message: any) => { - let parsedMessage: any = {}; - try { - parsedMessage = JSON.parse(message); - } catch (err) { - return; - } - if (parsedMessage.message === "refresh") { - window.location.reload(); - } - if ( - parsedMessage.message === "update" && - typeof sessid !== "undefined" && - parsedMessage.session_id === parseInt(sessid) - ) { - return toast({ - title: "Update", - description: parsedMessage.payload, - isClosable: true, - duration: parsedMessage.duration ?? null, - status: parsedMessage.status ?? "info", - }); - } - }; - - useWebSocket(url + `ws/connect/${UUID}`, { - onOpen: () => { - console.log("WebSocket connection established."); - }, - onMessage: (event) => { - parseWebsocketMessage(event.data); - }, - }); - - const finaliseAll = async () => { - rsync?.map((r) => { - finaliseRsyncer(r.session_id, r.source); - }); - onClose(); - }; - - const resolveName = async () => { - const name: string = await getInstrumentName(); - setInstrumentName(name); - }; - resolveName(); - - return ( -
- - - - Confirm Visit Completion - - - Are you sure you want to remove all data associated with this visit? - - - - - - - - - - - - - - Session {sessid}: {session ? session.visit : null} - - - - - - - - - - {/* */} - - - - - - - - {rsync && rsync.length > 0 ? ( - rsync.map((r) => { - return RsyncCard(r); - }) - ) : ( - - - No RSyncers Found - - - )} - - - - - - - - - - - - - - - -
- ); -}; - -export { Session }; diff --git a/murfey-frontend/src/routes/SessionLinker.tsx b/murfey-frontend/src/routes/SessionLinker.tsx deleted file mode 100644 index 276eccdfa..000000000 --- a/murfey-frontend/src/routes/SessionLinker.tsx +++ /dev/null @@ -1,140 +0,0 @@ -import { - Box, - Button, - Divider, - GridItem, - Heading, - HStack, - IconButton, - Link, - Stack, - Stat, - StatHelpText, - StatLabel, - StatNumber, - Text, - VStack, -} from "@chakra-ui/react"; - -import { MdLink } from "react-icons/md"; -import { Link as LinkRouter, useLoaderData, useParams } from "react-router-dom"; -import { components } from "schema/main"; -import { linkSessionToClient } from "loaders/session_clients"; -import { useSearchParams } from "react-router-dom"; -import React from "react"; - -type Client = components["schemas"]["ClientEnvironment"]; - -const SessionLinker = () => { - const existingClients = useLoaderData() as Client[] | null; - let [searchParams, setSearchParams] = useSearchParams(); - const [sessionId, setSessionId] = React.useState(0); - - return ( -
- - - - - - Connect new session to client - - - - - - - - - - Existing Clients - - - - {existingClients && existingClients.length > 0 ? ( - existingClients.map((client) => { - const client_id = client.client_id!; - return ( - <> - - - - Client {client_id} - - - - } - onClick={() => { - linkSessionToClient( - client_id, - searchParams.get("session_name") ?? - "Client connection", - ).then((sid) => { - console.log(sid); - setSessionId(sid); - console.log(sessionId); - }); - }} - /> - - - - ); - }) - ) : ( - - - No Clients Found - - - )} - - - - - -
- ); -}; - -export { SessionLinker }; diff --git a/murfey-frontend/src/routes/SessionSetup.tsx b/murfey-frontend/src/routes/SessionSetup.tsx deleted file mode 100644 index f5a90a147..000000000 --- a/murfey-frontend/src/routes/SessionSetup.tsx +++ /dev/null @@ -1,168 +0,0 @@ -import { - Button, - Box, - FormControl, - FormLabel, - Input, - RadioGroup, - Radio, - Stack, - Link, - VStack, - Heading, -} from "@chakra-ui/react"; -import { getForm } from "components/forms"; -import { - Link as LinkRouter, - useParams, - useLoaderData, - useNavigate, -} from "react-router-dom"; -import { SetupStepper } from "components/setupStepper"; -import { components } from "schema/main"; -import { getProcessingParameterData } from "loaders/processingParameters"; -import { getSessionData } from "loaders/session_clients"; -import { registerProcessingParameters } from "loaders/sessionSetup"; - -import React, { useEffect } from "react"; - -type SessionClients = components["schemas"]["SessionClients"]; -type ProvidedProcessingParameters = - components["schemas"]["ProvidedProcessingParameters"]; -type Session = components["schemas"]["Session"]; - -const SessionSetup = () => { - const session = useLoaderData() as SessionClients | null; - const [expType, setExpType] = React.useState("spa"); - const [procParams, setProcParams] = React.useState(); - const { sessid } = useParams(); - const [paramsSet, setParamsSet] = React.useState(false); - - const [_session, setSession] = React.useState(); - - useEffect(() => { - getSessionData(sessid).then((sess) => setSession(sess.session)); - }, []); - - const handleSelection = (formData: any) => { - if (typeof sessid !== "undefined") { - delete formData.type; - registerProcessingParameters( - formData as ProvidedProcessingParameters, - parseInt(sessid), - ); - setParamsSet(true); - } - }; - - if (session) - getProcessingParameterData(session.session.id.toString()).then((params) => - setProcParams(params), - ); - const activeStep = session - ? procParams - ? 3 - : session.session.visit - ? 2 - : 0 - : 2; - let navigate = useNavigate(); - return ( -
- - - - - - Processing parameters - - - - - - - - - - - - SPA - Tomography - - - - - {sessid ? getForm(expType, handleSelection) : <>} - - - - - - - - - - - -
- ); -}; - -export { SessionSetup }; diff --git a/murfey-frontend/src/routes/UserParameters.tsx b/murfey-frontend/src/routes/UserParameters.tsx deleted file mode 100644 index b52eb64dd..000000000 --- a/murfey-frontend/src/routes/UserParameters.tsx +++ /dev/null @@ -1,40 +0,0 @@ -import { Box, RadioGroup, Radio, Stack } from "@chakra-ui/react"; -import { getForm } from "components/forms"; - -import React from "react"; - -const UserParameters = () => { - const [expType, setExpType] = React.useState("spa"); - const [procParams, setProcParams] = React.useState(); - return ( - - - - - SPA - Tomography - - - - - {getForm(expType, setProcParams)} - - - ); -}; - -export { UserParameters }; diff --git a/murfey-frontend/src/schema/main.ts b/murfey-frontend/src/schema/main.ts deleted file mode 100644 index cec7f4c73..000000000 --- a/murfey-frontend/src/schema/main.ts +++ /dev/null @@ -1,4335 +0,0 @@ -/** - * This file was auto-generated by openapi-typescript. - * Do not make direct changes to the file. - */ - -export interface paths { - "/": { - /** Root */ - get: operations["root__get"]; - }; - "/machine": { - /** Machine Info */ - get: operations["machine_info_machine_get"]; - }; - "/instruments/{instrument_name}/machine": { - /** Machine Info By Name */ - get: operations["machine_info_by_name_instruments__instrument_name__machine_get"]; - }; - "/microscope_image/": { - /** Get Mic Image */ - get: operations["get_mic_image_microscope_image__get"]; - }; - "/mag_table/": { - /** Get Mag Table */ - get: operations["get_mag_table_mag_table__get"]; - /** Add To Mag Table */ - post: operations["add_to_mag_table_mag_table__post"]; - }; - "/mag_table/{mag}": { - /** Remove Mag Table Row */ - delete: operations["remove_mag_table_row_mag_table__mag__delete"]; - }; - "/instruments/{instrument_name}/instrument_name": { - /** Get Instrument Display Name */ - get: operations["get_instrument_display_name_instruments__instrument_name__instrument_name_get"]; - }; - "/instruments/{instrument_name}/visits/": { - /** All Visit Info */ - get: operations["all_visit_info_instruments__instrument_name__visits__get"]; - }; - "/visits/{visit_name}": { - /** Visit Info */ - get: operations["visit_info_visits__visit_name__get"]; - /** Register Client To Visit */ - post: operations["register_client_to_visit_visits__visit_name__post"]; - }; - "/num_movies": { - /** Count Number Of Movies */ - get: operations["count_number_of_movies_num_movies_get"]; - }; - "/sessions/{session_id}/rsyncer": { - /** Register Rsyncer */ - post: operations["register_rsyncer_sessions__session_id__rsyncer_post"]; - }; - "/sessions/{session_id}/rsyncer/{source}": { - /** Delete Rsyncer */ - delete: operations["delete_rsyncer_sessions__session_id__rsyncer__source__delete"]; - }; - "/sessions/{session_id}/rsyncer_stopped": { - /** Register Stopped Rsyncer */ - post: operations["register_stopped_rsyncer_sessions__session_id__rsyncer_stopped_post"]; - }; - "/sessions/{session_id}/rsyncer_started": { - /** Register Restarted Rsyncer */ - post: operations["register_restarted_rsyncer_sessions__session_id__rsyncer_started_post"]; - }; - "/clients/{client_id}/rsyncers": { - /** Get Rsyncers For Client */ - get: operations["get_rsyncers_for_client_clients__client_id__rsyncers_get"]; - }; - "/session/{session_id}": { - /** Get Session */ - get: operations["get_session_session__session_id__get"]; - }; - "/visits/{visit_name}/increment_rsync_file_count": { - /** Increment Rsync File Count */ - post: operations["increment_rsync_file_count_visits__visit_name__increment_rsync_file_count_post"]; - }; - "/visits/{visit_name}/increment_rsync_transferred_files": { - /** Increment Rsync Transferred Files */ - post: operations["increment_rsync_transferred_files_visits__visit_name__increment_rsync_transferred_files_post"]; - }; - "/visits/{visit_name}/increment_rsync_transferred_files_prometheus": { - /** Increment Rsync Transferred Files Prometheus */ - post: operations["increment_rsync_transferred_files_prometheus_visits__visit_name__increment_rsync_transferred_files_prometheus_post"]; - }; - "/sessions/{session_id}/spa_processing_parameters": { - /** Get Spa Proc Param Details */ - get: operations["get_spa_proc_param_details_sessions__session_id__spa_processing_parameters_get"]; - /** Register Spa Proc Params */ - post: operations["register_spa_proc_params_sessions__session_id__spa_processing_parameters_post"]; - }; - "/sessions/{session_id}/tomography_preprocessing_parameters": { - /** Register Tomo Preproc Params */ - post: operations["register_tomo_preproc_params_sessions__session_id__tomography_preprocessing_parameters_post"]; - }; - "/clients/{client_id}/tomography_processing_parameters": { - /** Register Tomo Proc Params */ - post: operations["register_tomo_proc_params_clients__client_id__tomography_processing_parameters_post"]; - }; - "/clients/{client_id}/spa_processing_parameters": { - /** Get Spa Proc Params */ - get: operations["get_spa_proc_params_clients__client_id__spa_processing_parameters_get"]; - }; - "/sessions/{session_id}/grid_squares": { - /** Get Grid Squares */ - get: operations["get_grid_squares_sessions__session_id__grid_squares_get"]; - }; - "/sessions/{session_id}/data_collection_groups/{dcgid}/grid_squares": { - /** Get Grid Squares From Dcg */ - get: operations["get_grid_squares_from_dcg_sessions__session_id__data_collection_groups__dcgid__grid_squares_get"]; - }; - "/sessions/{session_id}/data_collection_groups/{dcgid}/grid_squares/{gsid}/num_movies": { - /** Get Number Of Movies From Grid Square */ - get: operations["get_number_of_movies_from_grid_square_sessions__session_id__data_collection_groups__dcgid__grid_squares__gsid__num_movies_get"]; - }; - "/sessions/{session_id}/data_collection_groups/{dcgid}/grid_squares/{gsid}/foil_holes": { - /** Get Foil Holes From Grid Square */ - get: operations["get_foil_holes_from_grid_square_sessions__session_id__data_collection_groups__dcgid__grid_squares__gsid__foil_holes_get"]; - }; - "/sessions/{session_id}/data_collection_groups/{dcgid}/grid_squares/{gsid}/foil_holes/{fhid}/num_movies": { - /** Get Number Of Movies From Foil Hole */ - get: operations["get_number_of_movies_from_foil_hole_sessions__session_id__data_collection_groups__dcgid__grid_squares__gsid__foil_holes__fhid__num_movies_get"]; - }; - "/sessions/{session_id}/grid_square/{gsid}": { - /** Register Grid Square */ - post: operations["register_grid_square_sessions__session_id__grid_square__gsid__post"]; - }; - "/sessions/{session_id}/foil_hole/{fh_name}": { - /** Get Foil Hole */ - get: operations["get_foil_hole_sessions__session_id__foil_hole__fh_name__get"]; - }; - "/sessions/{session_id}/grid_square/{gs_name}/foil_hole": { - /** Register Foil Hole */ - post: operations["register_foil_hole_sessions__session_id__grid_square__gs_name__foil_hole_post"]; - }; - "/visits/{visit_name}/tilt_series": { - /** Register Tilt Series */ - post: operations["register_tilt_series_visits__visit_name__tilt_series_post"]; - }; - "/visits/{visit_name}/{client_id}/completed_tilt_series": { - /** Register Completed Tilt Series */ - post: operations["register_completed_tilt_series_visits__visit_name___client_id__completed_tilt_series_post"]; - }; - "/clients/{client_id}/tilt_series/{tilt_series_tag}/tilts": { - /** Get Tilts */ - get: operations["get_tilts_clients__client_id__tilt_series__tilt_series_tag__tilts_get"]; - }; - "/visits/{visit_name}/{client_id}/tilt": { - /** Register Tilt */ - post: operations["register_tilt_visits__visit_name___client_id__tilt_post"]; - }; - "/instruments/{instrument_name}/visits_raw": { - /** Get Current Visits */ - get: operations["get_current_visits_instruments__instrument_name__visits_raw_get"]; - }; - "/visits/{visit_name}/context": { - /** Register Context */ - post: operations["register_context_visits__visit_name__context_post"]; - }; - "/visits/{visit_name}/files": { - /** Add File */ - post: operations["add_file_visits__visit_name__files_post"]; - }; - "/feedback": { - /** Send Murfey Message */ - post: operations["send_murfey_message_feedback_post"]; - }; - "/visits/{visit_name}/spa_processing": { - /** Request Spa Processing */ - post: operations["request_spa_processing_visits__visit_name__spa_processing_post"]; - }; - "/visits/{visit_name}/{session_id}/flush_spa_processing": { - /** Flush Spa Processing */ - post: operations["flush_spa_processing_visits__visit_name___session_id__flush_spa_processing_post"]; - }; - "/visits/{visit_name}/{session_id}/spa_preprocess": { - /** Request Spa Preprocessing */ - post: operations["request_spa_preprocessing_visits__visit_name___session_id__spa_preprocess_post"]; - }; - "/visits/{visit_name}/{client_id}/flush_tomography_processing": { - /** Flush Tomography Processing */ - post: operations["flush_tomography_processing_visits__visit_name___client_id__flush_tomography_processing_post"]; - }; - "/visits/{visit_name}/{client_id}/tomography_preprocess": { - /** Request Tomography Preprocessing */ - post: operations["request_tomography_preprocessing_visits__visit_name___client_id__tomography_preprocess_post"]; - }; - "/version": { - /** Get Version */ - get: operations["get_version_version_get"]; - }; - "/visits/{visit_name}/{session_id}/suggested_path": { - /** Suggest Path */ - post: operations["suggest_path_visits__visit_name___session_id__suggested_path_post"]; - }; - "/sessions/{session_id}/data_collection_groups": { - /** Get Dc Groups */ - get: operations["get_dc_groups_sessions__session_id__data_collection_groups_get"]; - }; - "/sessions/{session_id}/data_collection_groups/{dcgid}/data_collections": { - /** Get Data Collections */ - get: operations["get_data_collections_sessions__session_id__data_collection_groups__dcgid__data_collections_get"]; - }; - "/visits/{visit_name}/{session_id}/register_data_collection_group": { - /** Register Dc Group */ - post: operations["register_dc_group_visits__visit_name___session_id__register_data_collection_group_post"]; - }; - "/visits/{visit_name}/{session_id}/start_data_collection": { - /** Start Dc */ - post: operations["start_dc_visits__visit_name___session_id__start_data_collection_post"]; - }; - "/visits/{visit_name}/{session_id}/register_processing_job": { - /** Register Proc */ - post: operations["register_proc_visits__visit_name___session_id__register_processing_job_post"]; - }; - "/sessions/{session_id}/process_gain": { - /** Process Gain */ - post: operations["process_gain_sessions__session_id__process_gain_post"]; - }; - "/new_client_id/": { - /** New Client Id */ - get: operations["new_client_id_new_client_id__get"]; - }; - "/clients": { - /** Get Clients */ - get: operations["get_clients_clients_get"]; - }; - "/sessions": { - /** Get Sessions */ - get: operations["get_sessions_sessions_get"]; - }; - "/instruments/{instrument_name}/clients/{client_id}/session": { - /** Link Client To Session */ - post: operations["link_client_to_session_instruments__instrument_name__clients__client_id__session_post"]; - }; - "/clients/{client_id}/session": { - /** Remove Session */ - delete: operations["remove_session_clients__client_id__session_delete"]; - }; - "/sessions/{session_id}/rsyncers": { - /** Get Rsyncers For Session */ - get: operations["get_rsyncers_for_session_sessions__session_id__rsyncers_get"]; - }; - "/sessions/{session_id}": { - /** Remove Session By Id */ - delete: operations["remove_session_by_id_sessions__session_id__delete"]; - }; - "/visits/{visit_name}/{session_id}/eer_fractionation_file": { - /** Write Eer Fractionation File */ - post: operations["write_eer_fractionation_file_visits__visit_name___session_id__eer_fractionation_file_post"]; - }; - "/visits/{visit_name}/monitoring/{on}": { - /** Change Monitoring Status */ - post: operations["change_monitoring_status_visits__visit_name__monitoring__on__post"]; - }; - "/sessions/{session_id}/upstream_visits": { - /** Find Upstream Visits */ - get: operations["find_upstream_visits_sessions__session_id__upstream_visits_get"]; - }; - "/visits/{visit_name}/{session_id}/upstream_tiff_paths": { - /** Gather Upstream Tiffs */ - get: operations["gather_upstream_tiffs_visits__visit_name___session_id__upstream_tiff_paths_get"]; - }; - "/visits/{visit_name}/{session_id}/upstream_tiff/{tiff_path}": { - /** Get Tiff */ - get: operations["get_tiff_visits__visit_name___session_id__upstream_tiff__tiff_path__get"]; - }; - "/failed_client_post": { - /** Failed Client Post */ - post: operations["failed_client_post_failed_client_post_post"]; - }; - "/instruments/{instrument_name}/visits/{visit}/session/{name}": { - /** Create Session */ - post: operations["create_session_instruments__instrument_name__visits__visit__session__name__post"]; - }; - "/sessions/{session_id}/current_gain_ref": { - /** Update Current Gain Ref */ - put: operations["update_current_gain_ref_sessions__session_id__current_gain_ref_put"]; - }; - "/bootstrap/": { - /** - * Get Bootstrap Instructions - * @description Return a website containing instructions for installing the Murfey client on a - * machine with no internet access. - */ - get: operations["get_bootstrap_instructions_bootstrap__get"]; - }; - "/bootstrap/pip.whl": { - /** - * Get Pip Wheel - * @description Return a static version of pip. This does not need to be the newest or best, - * but has to be compatible with all supported Python versions. - * This is only used during bootstrapping by the client to identify and then - * download the actually newest appropriate version of pip. - */ - get: operations["get_pip_wheel_bootstrap_pip_whl_get"]; - }; - "/bootstrap/murfey.whl": { - /** - * Get Murfey Wheel - * @description Return a wheel file containing the latest release version of Murfey. We should - * not have to worry about the exact Python compatibility here, as long as - * murfey.bootstrap is compatible with all relevant versions of Python. - * This also ignores yanked releases, which again should be fine. - */ - get: operations["get_murfey_wheel_bootstrap_murfey_whl_get"]; - }; - "/cygwin/setup-x86_64.exe": { - /** - * Get Cygwin Setup - * @description Obtain and pass through a Cygwin installer from an official source. - * This is used during client bootstrapping and can download and install the - * Cygwin distribution that then remains on the client machines. - */ - get: operations["get_cygwin_setup_cygwin_setup_x86_64_exe_get"]; - }; - "/cygwin/{request_path}": { - /** - * Parse Cygwin Request - * @description Forward a Cygwin setup request to an official mirror. - */ - get: operations["parse_cygwin_request_cygwin__request_path__get"]; - }; - "/pypi/": { - /** - * Get Pypi Index - * @description Obtain list of all PyPI packages via the simple API (PEP 503). - */ - get: operations["get_pypi_index_pypi__get"]; - }; - "/pypi/{package}/": { - /** - * Get Pypi Package Downloads List - * @description Obtain list of all package downloads from PyPI via the simple API (PEP 503), and - * rewrite all download URLs to point to this server, under the current directory. - */ - get: operations["get_pypi_package_downloads_list_pypi__package___get"]; - }; - "/pypi/{package}/{filename}": { - /** - * Get Pypi File - * @description Obtain and pass through a specific download for a PyPI package. - */ - get: operations["get_pypi_file_pypi__package___filename__get"]; - }; - "/plugins/instruments/{instrument_name}/{package}": { - /** Get Plugin Wheel */ - get: operations["get_plugin_wheel_plugins_instruments__instrument_name___package__get"]; - }; - "/version/": { - /** Get Version */ - get: operations["get_version_version__get"]; - }; - "/sessions/{session_id}/clem/lif_files": { - /** Register Lif File */ - post: operations["register_lif_file_sessions__session_id__clem_lif_files_post"]; - }; - "/sessions/{session_id}/clem/tiff_files": { - /** Register Tiff File */ - post: operations["register_tiff_file_sessions__session_id__clem_tiff_files_post"]; - }; - "/sessions/{session_id}/clem/metadata_files": { - /** Register Clem Metadata */ - post: operations["register_clem_metadata_sessions__session_id__clem_metadata_files_post"]; - }; - "/sessions/{session_id}/clem/image_series": { - /** Register Image Series */ - post: operations["register_image_series_sessions__session_id__clem_image_series_post"]; - }; - "/sessions/{session_id}/clem/image_stacks": { - /** Register Image Stack */ - post: operations["register_image_stack_sessions__session_id__clem_image_stacks_post"]; - }; - "/sessions/{session_id}/lif_to_stack": { - /** Lif To Stack */ - post: operations["lif_to_stack_sessions__session_id__lif_to_stack_post"]; - }; - "/sessions/{session_id}/tiff_to_stack": { - /** Tiff To Stack */ - post: operations["tiff_to_stack_sessions__session_id__tiff_to_stack_post"]; - }; - "/sessions/{session_id}/cryolo_model": { - /** Get Cryolo Model Path */ - get: operations["get_cryolo_model_path_sessions__session_id__cryolo_model_get"]; - }; - "/token": { - /** Generate Token */ - post: operations["generate_token_token_post"]; - }; - "/sessions/{session_id}/token": { - /** Mint Session Token */ - get: operations["mint_session_token_sessions__session_id__token_get"]; - }; - "/validate_token": { - /** Simple Token Validation */ - get: operations["simple_token_validation_validate_token_get"]; - }; - "/display/microscope_image/": { - /** Get Mic Image */ - get: operations["get_mic_image_display_microscope_image__get"]; - }; - "/display/sessions/{session_id}/data_collection_groups/{dcgid}/grid_squares/{grid_square_name}/image": { - /** Get Grid Square Img */ - get: operations["get_grid_square_img_display_sessions__session_id__data_collection_groups__dcgid__grid_squares__grid_square_name__image_get"]; - }; - "/display/sessions/{session_id}/data_collection_groups/{dcgid}/grid_squares/{grid_square_name}/foil_holes/{foil_hole_name}/image": { - /** Get Foil Hole Img */ - get: operations["get_foil_hole_img_display_sessions__session_id__data_collection_groups__dcgid__grid_squares__grid_square_name__foil_holes__foil_hole_name__image_get"]; - }; - "/instruments/{instrument_name}/activate_instrument_server": { - /** Activate Instrument Server */ - post: operations["activate_instrument_server_instruments__instrument_name__activate_instrument_server_post"]; - }; - "/instruments/{instrument_name}/sessions/{session_id}/activate_instrument_server": { - /** Activate Instrument Server For Session */ - post: operations["activate_instrument_server_for_session_instruments__instrument_name__sessions__session_id__activate_instrument_server_post"]; - }; - "/sessions/{session_id}/multigrid_watcher": { - /** Start Multigrid Watcher */ - post: operations["start_multigrid_watcher_sessions__session_id__multigrid_watcher_post"]; - }; - "/sessions/{session_id}/provided_processing_parameters": { - /** Pass Proc Params To Instrument Server */ - post: operations["pass_proc_params_to_instrument_server_sessions__session_id__provided_processing_parameters_post"]; - }; - "/instruments/{instrument_name}/instrument_server": { - /** Check Instrument Server */ - get: operations["check_instrument_server_instruments__instrument_name__instrument_server_get"]; - }; - "/instruments/{instrument_name}/sessions/{session_id}/possible_gain_references": { - /** Get Possible Gain References */ - get: operations["get_possible_gain_references_instruments__instrument_name__sessions__session_id__possible_gain_references_get"]; - }; - "/sessions/{session_id}/upload_gain_reference": { - /** Request Gain Reference Upload */ - post: operations["request_gain_reference_upload_sessions__session_id__upload_gain_reference_post"]; - }; - "/visits/{visit_name}/{session_id}/upstream_tiff_data_request": { - /** Request Upstream Tiff Data Download */ - post: operations["request_upstream_tiff_data_download_visits__visit_name___session_id__upstream_tiff_data_request_post"]; - }; - "/sessions/{session_id}/stop_rsyncer": { - /** Stop Rsyncer */ - post: operations["stop_rsyncer_sessions__session_id__stop_rsyncer_post"]; - }; - "/sessions/{session_id}/finalise_rsyncer": { - /** Finalise Rsyncer */ - post: operations["finalise_rsyncer_sessions__session_id__finalise_rsyncer_post"]; - }; - "/sessions/{session_id}/remove_rsyncer": { - /** Remove Rsyncer */ - post: operations["remove_rsyncer_sessions__session_id__remove_rsyncer_post"]; - }; - "/sessions/{session_id}/restart_rsyncer": { - /** Restart Rsyncer */ - post: operations["restart_rsyncer_sessions__session_id__restart_rsyncer_post"]; - }; - "/instruments": { - /** Get Instrument Info */ - get: operations["get_instrument_info_instruments_get"]; - }; - "/instrument/{instrument_name}/image": { - /** Get Instrument Image */ - get: operations["get_instrument_image_instrument__instrument_name__image_get"]; - }; - "/ws/test/{client_id}": { - /** Close Ws Connection */ - delete: operations["close_ws_connection_ws_test__client_id__delete"]; - }; - "/ws/connect/{client_id}": { - /** Close Unrecorded Ws Connection */ - delete: operations["close_unrecorded_ws_connection_ws_connect__client_id__delete"]; - }; - "/visits/{visit_name}/smartem_atlas/": { - /** Request Smartem Atlas Analysis */ - post: operations["request_smartem_atlas_analysis_visits__visit_name__smartem_atlas__post"]; - }; -} - -export type webhooks = Record; - -export interface components { - schemas: { - /** Body_generate_token_token_post */ - Body_generate_token_token_post: { - /** Grant Type */ - grant_type?: string; - /** Username */ - username: string; - /** Password */ - password: string; - /** - * Scope - * @default - */ - scope?: string; - /** Client Id */ - client_id?: string; - /** Client Secret */ - client_secret?: string; - }; - /** Body_register_clem_metadata_sessions__session_id__clem_metadata_files_post */ - Body_register_clem_metadata_sessions__session_id__clem_metadata_files_post: { - /** - * Associated Tiffs - * @default [] - */ - associated_tiffs?: string[]; - /** - * Associated Stacks - * @default [] - */ - associated_stacks?: string[]; - }; - /** Body_register_image_series_sessions__session_id__clem_image_series_post */ - Body_register_image_series_sessions__session_id__clem_image_series_post: { - /** - * Parent Tiffs - * @default [] - */ - parent_tiffs?: string[]; - /** - * Child Stacks - * @default [] - */ - child_stacks?: string[]; - }; - /** Body_register_lif_file_sessions__session_id__clem_lif_files_post */ - Body_register_lif_file_sessions__session_id__clem_lif_files_post: { - /** - * Child Metadata - * @default [] - */ - child_metadata?: string[]; - /** - * Child Series - * @default [] - */ - child_series?: string[]; - /** - * Child Stacks - * @default [] - */ - child_stacks?: string[]; - }; - /** ClientEnvironment */ - ClientEnvironment: { - /** Client Id */ - client_id?: number; - /** - * Visit - * @default - */ - visit?: string; - /** Session Id */ - session_id?: number; - /** Connected */ - connected: boolean; - }; - /** ClientInfo */ - ClientInfo: { - /** Id */ - id: number; - }; - /** ContextInfo */ - ContextInfo: { - /** Experiment Type */ - experiment_type: string; - /** Acquisition Software */ - acquisition_software: string; - }; - /** CurrentGainRef */ - CurrentGainRef: { - /** Path */ - path: string; - }; - /** DCGroupParameters */ - DCGroupParameters: { - /** Experiment Type */ - experiment_type: string; - /** Experiment Type Id */ - experiment_type_id: number; - /** Tag */ - tag: string; - /** - * Atlas - * @default - */ - atlas?: string; - /** Sample */ - sample?: number; - }; - /** DCParameters */ - DCParameters: { - /** Voltage */ - voltage: number; - /** Pixel Size On Image */ - pixel_size_on_image: string; - /** Experiment Type */ - experiment_type: string; - /** Image Size X */ - image_size_x: number; - /** Image Size Y */ - image_size_y: number; - /** File Extension */ - file_extension: string; - /** Acquisition Software */ - acquisition_software: string; - /** Image Directory */ - image_directory: string; - /** Tag */ - tag: string; - /** Source */ - source: string; - /** Magnification */ - magnification: number; - /** Total Exposed Dose */ - total_exposed_dose?: number; - /** C2Aperture */ - c2aperture?: number; - /** Exposure Time */ - exposure_time?: number; - /** Slit Width */ - slit_width?: number; - /** - * Phase Plate - * @default false - */ - phase_plate?: boolean; - /** - * Data Collection Tag - * @default - */ - data_collection_tag?: string; - }; - /** DataCollection */ - DataCollection: { - /** Id */ - id: number; - /** Tag */ - tag: string; - /** Dcg Id */ - dcg_id: number; - }; - /** DataCollectionGroup */ - DataCollectionGroup: { - /** Id */ - id: number; - /** Session Id */ - session_id: number; - /** Tag */ - tag: string; - /** - * Atlas - * @default - */ - atlas?: string; - /** Sample */ - sample?: number; - }; - /** File */ - File: { - /** Name */ - name: string; - /** Description */ - description: string; - /** Size */ - size: number; - /** - * Timestamp - * Format: date-time - */ - timestamp: string; - /** Full Path */ - full_path: string; - }; - /** FoilHole */ - FoilHole: { - /** Id */ - id?: number; - /** Grid Square Id */ - grid_square_id: number; - /** Session Id */ - session_id: number; - /** Name */ - name: number; - /** X Location */ - x_location?: number; - /** Y Location */ - y_location?: number; - /** X Stage Position */ - x_stage_position?: number; - /** Y Stage Position */ - y_stage_position?: number; - /** Readout Area X */ - readout_area_x?: number; - /** Readout Area Y */ - readout_area_y?: number; - /** Thumbnail Size X */ - thumbnail_size_x?: number; - /** Thumbnail Size Y */ - thumbnail_size_y?: number; - /** Pixel Size */ - pixel_size?: number; - /** - * Image - * @default - */ - image?: string; - }; - /** FoilHoleParameters */ - FoilHoleParameters: { - /** Tag */ - tag: string; - /** Name */ - name: number; - /** X Location */ - x_location?: number; - /** Y Location */ - y_location?: number; - /** X Stage Position */ - x_stage_position?: number; - /** Y Stage Position */ - y_stage_position?: number; - /** Readout Area X */ - readout_area_x?: number; - /** Readout Area Y */ - readout_area_y?: number; - /** Thumbnail Size X */ - thumbnail_size_x?: number; - /** Thumbnail Size Y */ - thumbnail_size_y?: number; - /** Pixel Size */ - pixel_size?: number; - /** - * Image - * @default - */ - image?: string; - }; - /** FractionationParameters */ - FractionationParameters: { - /** Fractionation */ - fractionation: number; - /** Dose Per Frame */ - dose_per_frame: number; - /** - * Num Frames - * @default 0 - */ - num_frames?: number; - /** Eer Path */ - eer_path?: string; - /** - * Fractionation File Name - * @default eer_fractionation.txt - */ - fractionation_file_name?: string; - }; - /** GainReference */ - GainReference: { - /** - * Gain Ref - * Format: path - */ - gain_ref: string; - /** - * Rescale - * @default true - */ - rescale?: boolean; - /** - * Eer - * @default false - */ - eer?: boolean; - /** - * Tag - * @default - */ - tag?: string; - }; - /** GainReferenceRequest */ - GainReferenceRequest: { - /** - * Gain Path - * Format: path - */ - gain_path: string; - }; - /** GridSquare */ - GridSquare: { - /** Id */ - id?: number; - /** Session Id */ - session_id: number; - /** Name */ - name: number; - /** Tag */ - tag: string; - /** X Location */ - x_location?: number; - /** Y Location */ - y_location?: number; - /** X Stage Position */ - x_stage_position?: number; - /** Y Stage Position */ - y_stage_position?: number; - /** Readout Area X */ - readout_area_x?: number; - /** Readout Area Y */ - readout_area_y?: number; - /** Thumbnail Size X */ - thumbnail_size_x?: number; - /** Thumbnail Size Y */ - thumbnail_size_y?: number; - /** Pixel Size */ - pixel_size?: number; - /** - * Image - * @default - */ - image?: string; - }; - /** GridSquareParameters */ - GridSquareParameters: { - /** Tag */ - tag: string; - /** X Location */ - x_location?: number; - /** Y Location */ - y_location?: number; - /** X Stage Position */ - x_stage_position?: number; - /** Y Stage Position */ - y_stage_position?: number; - /** Readout Area X */ - readout_area_x?: number; - /** Readout Area Y */ - readout_area_y?: number; - /** Thumbnail Size X */ - thumbnail_size_x?: number; - /** Thumbnail Size Y */ - thumbnail_size_y?: number; - /** Pixel Size */ - pixel_size?: number; - /** - * Image - * @default - */ - image?: string; - }; - /** HTTPValidationError */ - HTTPValidationError: { - /** Detail */ - detail?: components["schemas"]["ValidationError"][]; - }; - /** InstrumentInfo */ - InstrumentInfo: { - /** Instrument Name */ - instrument_name: string; - /** Display Name */ - display_name: string; - /** Instrument Url */ - instrument_url: string; - }; - /** LifFileInfo */ - LifFileInfo: { - /** - * Name - * Format: path - */ - name: string; - /** Size */ - size: number; - /** Timestamp */ - timestamp: number; - /** - * Description - * @default - */ - description?: string; - }; - /** MachineConfig */ - MachineConfig: { - /** Acquisition Software */ - acquisition_software: string[]; - /** Calibrations */ - calibrations: { - [key: string]: { - [key: string]: Record | number; - }; - }; - /** Data Directories */ - data_directories: string[]; - /** - * Rsync Basepath - * Format: path - */ - rsync_basepath: string; - /** - * Default Model - * Format: path - */ - default_model: string; - /** - * Display Name - * @default - */ - display_name?: string; - /** - * Instrument Name - * @default - */ - instrument_name?: string; - /** - * Image Path - * Format: path - */ - image_path?: string; - /** - * Software Versions - * @default {} - */ - software_versions?: { - [key: string]: string; - }; - /** - * External Executables - * @default {} - */ - external_executables?: { - [key: string]: string; - }; - /** - * External Executables Eer - * @default {} - */ - external_executables_eer?: { - [key: string]: string; - }; - /** - * External Environment - * @default {} - */ - external_environment?: { - [key: string]: string; - }; - /** - * Rsync Module - * @default - */ - rsync_module?: string; - /** - * Create Directories - * @default { - * "atlas": "atlas" - * } - */ - create_directories?: { - [key: string]: string; - }; - /** - * Analyse Created Directories - * @default [] - */ - analyse_created_directories?: string[]; - /** - * Gain Reference Directory - * Format: path - */ - gain_reference_directory?: string; - /** - * Processed Directory Name - * @default processed - */ - processed_directory_name?: string; - /** - * Gain Directory Name - * @default processing - */ - gain_directory_name?: string; - /** - * Feedback Queue - * @default murfey_feedback - */ - feedback_queue?: string; - /** - * Node Creator Queue - * @default node_creator - */ - node_creator_queue?: string; - /** - * Superres - * @default false - */ - superres?: boolean; - /** - * Camera - * @default FALCON - */ - camera?: string; - /** - * Data Required Substrings - * @default {} - */ - data_required_substrings?: { - [key: string]: { - [key: string]: string[]; - }; - }; - /** - * Allow Removal - * @default false - */ - allow_removal?: boolean; - /** - * Modular Spa - * @default false - */ - modular_spa?: boolean; - /** - * Processing Enabled - * @default true - */ - processing_enabled?: boolean; - /** - * Machine Override - * @default - */ - machine_override?: string; - /** - * Processed Extra Directory - * @default - */ - processed_extra_directory?: string; - /** - * Plugin Packages - * @default {} - */ - plugin_packages?: { - [key: string]: string; - }; - /** - * Software Settings Output Directories - * @default {} - */ - software_settings_output_directories?: { - [key: string]: string[]; - }; - /** - * Process By Default - * @default true - */ - process_by_default?: boolean; - /** - * Recipes - * @default { - * "em-spa-bfactor": "em-spa-bfactor", - * "em-spa-class2d": "em-spa-class2d", - * "em-spa-class3d": "em-spa-class3d", - * "em-spa-preprocess": "em-spa-preprocess", - * "em-spa-refine": "em-spa-refine", - * "em-tomo-preprocess": "em-tomo-preprocess", - * "em-tomo-align": "em-tomo-align" - * } - */ - recipes?: { - [key: string]: string; - }; - /** - * Upstream Data Directories - * @default [] - */ - upstream_data_directories?: string[]; - /** - * Upstream Data Download Directory - * Format: path - */ - upstream_data_download_directory?: string; - /** - * Upstream Data Tiff Locations - * @default [ - * "processed" - * ] - */ - upstream_data_tiff_locations?: string[]; - /** - * Model Search Directory - * @default processing - */ - model_search_directory?: string; - /** - * Initial Model Search Directory - * @default processing/initial_model - */ - initial_model_search_directory?: string; - /** - * Failure Queue - * @default - */ - failure_queue?: string; - /** - * Instrument Server Url - * @default http://localhost:8001 - */ - instrument_server_url?: string; - /** - * Frontend Url - * @default http://localhost:3000 - */ - frontend_url?: string; - /** - * Murfey Url - * @default http://localhost:8000 - */ - murfey_url?: string; - }; - /** MagnificationLookup */ - MagnificationLookup: { - /** Magnification */ - magnification: number; - /** Pixel Size */ - pixel_size: number; - }; - /** MultigridWatcherSetup */ - MultigridWatcherSetup: { - /** - * Source - * Format: path - */ - source: string; - /** - * Skip Existing Processing - * @default false - */ - skip_existing_processing?: boolean; - }; - /** PostInfo */ - PostInfo: { - /** Url */ - url: string; - /** Data */ - data: Record; - }; - /** PreprocessingParametersTomo */ - PreprocessingParametersTomo: { - /** Dose Per Frame */ - dose_per_frame: number; - /** Gain Ref */ - gain_ref?: string; - /** Experiment Type */ - experiment_type: string; - /** Voltage */ - voltage: number; - /** Image Size X */ - image_size_x: number; - /** Image Size Y */ - image_size_y: number; - /** Pixel Size On Image */ - pixel_size_on_image: string; - /** Motion Corr Binning */ - motion_corr_binning: number; - /** Manual Tilt Offset */ - manual_tilt_offset: number; - /** File Extension */ - file_extension: string; - /** Tag */ - tag: string; - /** Tilt Series Tag */ - tilt_series_tag: string; - /** Eer Fractionation File */ - eer_fractionation_file?: string; - /** Eer Fractionation */ - eer_fractionation: number; - }; - /** ProcessFile */ - ProcessFile: { - /** Path */ - path: string; - /** Description */ - description: string; - /** Tag */ - tag: string; - /** Data Collection Id */ - data_collection_id?: number; - /** Image Number */ - image_number: number; - /** Pixel Size */ - pixel_size: number; - /** Dose Per Frame */ - dose_per_frame: number; - /** Processing Job */ - processing_job?: number; - /** Autoproc Program Id */ - autoproc_program_id?: number; - /** Mc Uuid */ - mc_uuid?: number; - /** - * Voltage - * @default 300 - */ - voltage?: number; - /** - * Mc Binning - * @default 1 - */ - mc_binning?: number; - /** Gain Ref */ - gain_ref?: string; - /** - * Extract Downscale - * @default 1 - */ - extract_downscale?: number; - /** Eer Fractionation File */ - eer_fractionation_file?: string; - /** Group Tag */ - group_tag?: string; - }; - /** ProcessingDetails */ - ProcessingDetails: { - data_collection_group: components["schemas"]["DataCollectionGroup"]; - /** Data Collections */ - data_collections: components["schemas"]["DataCollection"][]; - /** Processing Jobs */ - processing_jobs: components["schemas"]["ProcessingJob"][]; - relion_params: components["schemas"]["SPARelionParameters"]; - feedback_params: components["schemas"]["SPAFeedbackParameters"]; - }; - /** ProcessingJob */ - ProcessingJob: { - /** Id */ - id: number; - /** Recipe */ - recipe: string; - /** Dc Id */ - dc_id: number; - }; - /** ProcessingJobParameters */ - ProcessingJobParameters: { - /** Tag */ - tag: string; - /** Recipe */ - recipe: string; - /** - * Parameters - * @default {} - */ - parameters?: Record; - /** - * Experiment Type - * @default spa - */ - experiment_type?: string; - }; - /** ProcessingParametersSPA */ - ProcessingParametersSPA: { - /** Tag */ - tag: string; - /** Dose Per Frame */ - dose_per_frame: number; - /** Gain Ref */ - gain_ref?: string; - /** Experiment Type */ - experiment_type: string; - /** Voltage */ - voltage: number; - /** Image Size X */ - image_size_x: number; - /** Image Size Y */ - image_size_y: number; - /** Pixel Size On Image */ - pixel_size_on_image: string; - /** Motion Corr Binning */ - motion_corr_binning: number; - /** File Extension */ - file_extension: string; - /** Acquisition Software */ - acquisition_software: string; - /** Use Cryolo */ - use_cryolo: boolean; - /** Symmetry */ - symmetry: string; - /** Mask Diameter */ - mask_diameter?: number; - /** Boxsize */ - boxsize?: number; - /** Downscale */ - downscale: boolean; - /** Small Boxsize */ - small_boxsize?: number; - /** Eer Fractionation */ - eer_fractionation: number; - /** Particle Diameter */ - particle_diameter?: number; - /** Magnification */ - magnification?: number; - /** Total Exposed Dose */ - total_exposed_dose?: number; - /** C2Aperture */ - c2aperture?: number; - /** Exposure Time */ - exposure_time?: number; - /** Slit Width */ - slit_width?: number; - /** - * Phase Plate - * @default false - */ - phase_plate?: boolean; - }; - /** ProcessingParametersTomo */ - ProcessingParametersTomo: { - /** Manual Tilt Offset */ - manual_tilt_offset: number; - /** Tag */ - tag: string; - /** Tilt Series Tag */ - tilt_series_tag: string; - }; - /** ProvidedProcessingParameters */ - ProvidedProcessingParameters: { - /** Dose Per Frame */ - dose_per_frame: number; - /** - * Extract Downscale - * @default true - */ - extract_downscale?: boolean; - /** Particle Diameter */ - particle_diameter?: number; - /** - * Symmetry - * @default C1 - */ - symmetry?: string; - /** - * Eer Fractionation - * @default 20 - */ - eer_fractionation?: number; - }; - /** RegistrationMessage */ - RegistrationMessage: { - /** Registration */ - registration: string; - /** Params */ - params?: Record; - }; - /** RsyncInstance */ - RsyncInstance: { - /** Source */ - source: string; - /** - * Destination - * @default - */ - destination?: string; - /** Session Id */ - session_id: number; - /** - * Tag - * @default - */ - tag?: string; - /** - * Files Transferred - * @default 0 - */ - files_transferred?: number; - /** - * Files Counted - * @default 0 - */ - files_counted?: number; - /** - * Transferring - * @default false - */ - transferring?: boolean; - }; - /** RsyncerInfo */ - RsyncerInfo: { - /** Source */ - source: string; - /** Destination */ - destination: string; - /** Session Id */ - session_id: number; - /** - * Transferring - * @default true - */ - transferring?: boolean; - /** - * Increment Count - * @default 1 - */ - increment_count?: number; - /** - * Bytes - * @default 0 - */ - bytes?: number; - /** - * Increment Data Count - * @default 0 - */ - increment_data_count?: number; - /** - * Data Bytes - * @default 0 - */ - data_bytes?: number; - /** - * Tag - * @default - */ - tag?: string; - }; - /** SPAFeedbackParameters */ - SPAFeedbackParameters: { - /** Pj Id */ - pj_id: number; - /** - * Estimate Particle Diameter - * @default true - */ - estimate_particle_diameter?: boolean; - /** - * Hold Class2D - * @default false - */ - hold_class2d?: boolean; - /** - * Rerun Class2D - * @default false - */ - rerun_class2d?: boolean; - /** - * Hold Class3D - * @default false - */ - hold_class3d?: boolean; - /** - * Hold Refine - * @default false - */ - hold_refine?: boolean; - /** Class Selection Score */ - class_selection_score: number; - /** Star Combination Job */ - star_combination_job: number; - /** Initial Model */ - initial_model: string; - /** Next Job */ - next_job: number; - /** Picker Murfey Id */ - picker_murfey_id?: number; - /** Picker Ispyb Id */ - picker_ispyb_id?: number; - }; - /** SPAProcessFile */ - SPAProcessFile: { - /** Tag */ - tag: string; - /** Path */ - path: string; - /** Description */ - description: string; - /** Processing Job */ - processing_job?: number; - /** Data Collection Id */ - data_collection_id?: number; - /** Image Number */ - image_number: number; - /** Autoproc Program Id */ - autoproc_program_id?: number; - /** Foil Hole Id */ - foil_hole_id?: number; - /** Pixel Size */ - pixel_size?: number; - /** Dose Per Frame */ - dose_per_frame?: number; - /** - * Mc Binning - * @default 1 - */ - mc_binning?: number; - /** Gain Ref */ - gain_ref?: string; - /** - * Extract Downscale - * @default true - */ - extract_downscale?: boolean; - /** Eer Fractionation File */ - eer_fractionation_file?: string; - /** - * Source - * @default - */ - source?: string; - }; - /** SPAProcessingParameters */ - SPAProcessingParameters: { - /** Job Id */ - job_id: number; - }; - /** SPARelionParameters */ - SPARelionParameters: { - /** Pj Id */ - pj_id: number; - /** Angpix */ - angpix: number; - /** Dose Per Frame */ - dose_per_frame: number; - /** Gain Ref */ - gain_ref?: string; - /** Voltage */ - voltage: number; - /** Motion Corr Binning */ - motion_corr_binning: number; - /** Eer Grouping */ - eer_grouping: number; - /** Symmetry */ - symmetry: string; - /** Particle Diameter */ - particle_diameter?: number; - /** Downscale */ - downscale: boolean; - /** - * Do Icebreaker Jobs - * @default true - */ - do_icebreaker_jobs?: boolean; - /** - * Boxsize - * @default 256 - */ - boxsize?: number; - /** - * Small Boxsize - * @default 64 - */ - small_boxsize?: number; - /** - * Mask Diameter - * @default 190 - */ - mask_diameter?: number; - }; - /** Session */ - Session: { - /** Id */ - id: number; - /** Name */ - name: string; - /** - * Visit - * @default - */ - visit?: string; - /** - * Started - * @default false - */ - started?: boolean; - /** - * Current Gain Ref - * @default - */ - current_gain_ref?: string; - /** - * Instrument Name - * @default - */ - instrument_name?: string; - }; - /** SessionClients */ - SessionClients: { - session: components["schemas"]["Session"]; - /** Clients */ - clients: components["schemas"]["ClientEnvironment"][]; - }; - /** SessionInfo */ - SessionInfo: { - /** Session Id */ - session_id?: number; - /** - * Session Name - * @default - */ - session_name?: string; - /** - * Rescale - * @default true - */ - rescale?: boolean; - }; - /** SmartEMAtlasRequest */ - SmartEMAtlasRequest: { - /** - * Atlas Path - * Format: path - */ - atlas_path: string; - /** - * Output Dir - * Format: path - */ - output_dir: string; - /** - * Num Preds - * @default 15 - */ - num_preds?: number; - /** - * Cpus - * @default 4 - */ - cpus?: number; - }; - /** Source */ - Source: { - /** Rsync Source */ - rsync_source: string; - }; - /** SuggestedPathParameters */ - SuggestedPathParameters: { - /** - * Base Path - * Format: path - */ - base_path: string; - /** - * Touch - * @default false - */ - touch?: boolean; - /** - * Extra Directory - * @default - */ - extra_directory?: string; - }; - /** Tag */ - Tag: { - /** Tag */ - tag: string; - }; - /** TiffSeriesInfo */ - TiffSeriesInfo: { - /** Series Name */ - series_name: string; - /** Tiff Files */ - tiff_files: string[]; - /** Tiff Sizes */ - tiff_sizes: number[]; - /** Tiff Timestamps */ - tiff_timestamps: number[]; - /** - * Series Metadata - * Format: path - */ - series_metadata: string; - /** Metadata Size */ - metadata_size: number; - /** Metadata Timestamp */ - metadata_timestamp: number; - /** - * Description - * @default - */ - description?: string; - }; - /** TiltInfo */ - TiltInfo: { - /** Tilt Series Tag */ - tilt_series_tag: string; - /** Movie Path */ - movie_path: string; - /** Source */ - source: string; - }; - /** TiltSeriesGroupInfo */ - TiltSeriesGroupInfo: { - /** Tags */ - tags: string[]; - /** Source */ - source: string; - /** Tilt Series Lengths */ - tilt_series_lengths: number[]; - }; - /** TiltSeriesInfo */ - TiltSeriesInfo: { - /** Client Id */ - client_id: number; - /** Tag */ - tag: string; - /** Source */ - source: string; - }; - /** Token */ - Token: { - /** Access Token */ - access_token: string; - /** Token Type */ - token_type: string; - }; - /** ValidationError */ - ValidationError: { - /** Location */ - loc: (string | number)[]; - /** Message */ - msg: string; - /** Error Type */ - type: string; - }; - /** Visit */ - Visit: { - /** - * Start - * Format: date-time - */ - start: string; - /** - * End - * Format: date-time - */ - end: string; - /** Session Id */ - session_id: number; - /** Name */ - name: string; - /** Beamline */ - beamline: string; - /** Proposal Title */ - proposal_title: string; - }; - /** RsyncerSource */ - murfey__server__api__instrument__RsyncerSource: { - /** Source */ - source: string; - }; - /** RsyncerSource */ - murfey__util__models__RsyncerSource: { - /** Source */ - source: string; - }; - }; - responses: never; - parameters: never; - requestBodies: never; - headers: never; - pathItems: never; -} - -export type $defs = Record; - -export type external = Record; - -export interface operations { - /** Root */ - root__get: { - responses: { - /** @description Successful Response */ - 200: { - content: { - "text/html": string; - }; - }; - }; - }; - /** Machine Info */ - machine_info_machine_get: { - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["MachineConfig"]; - }; - }; - }; - }; - /** Machine Info By Name */ - machine_info_by_name_instruments__instrument_name__machine_get: { - parameters: { - path: { - instrument_name: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["MachineConfig"]; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Mic Image */ - get_mic_image_microscope_image__get: { - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - }; - }; - /** Get Mag Table */ - get_mag_table_mag_table__get: { - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["MagnificationLookup"][]; - }; - }; - }; - }; - /** Add To Mag Table */ - add_to_mag_table_mag_table__post: { - requestBody: { - content: { - "application/json": components["schemas"]["MagnificationLookup"][]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Remove Mag Table Row */ - remove_mag_table_row_mag_table__mag__delete: { - parameters: { - path: { - mag: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Instrument Display Name */ - get_instrument_display_name_instruments__instrument_name__instrument_name_get: { - parameters: { - path: { - instrument_name: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": string; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** All Visit Info */ - all_visit_info_instruments__instrument_name__visits__get: { - parameters: { - path: { - instrument_name: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Visit Info */ - visit_info_visits__visit_name__get: { - parameters: { - path: { - visit_name: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Client To Visit */ - register_client_to_visit_visits__visit_name__post: { - parameters: { - path: { - visit_name: string; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["ClientInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Count Number Of Movies */ - count_number_of_movies_num_movies_get: { - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": { - [key: string]: number; - }; - }; - }; - }; - }; - /** Register Rsyncer */ - register_rsyncer_sessions__session_id__rsyncer_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["RsyncerInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Delete Rsyncer */ - delete_rsyncer_sessions__session_id__rsyncer__source__delete: { - parameters: { - path: { - session_id: number; - source: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Stopped Rsyncer */ - register_stopped_rsyncer_sessions__session_id__rsyncer_stopped_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["murfey__util__models__RsyncerSource"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Restarted Rsyncer */ - register_restarted_rsyncer_sessions__session_id__rsyncer_started_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["murfey__util__models__RsyncerSource"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Rsyncers For Client */ - get_rsyncers_for_client_clients__client_id__rsyncers_get: { - parameters: { - path: { - client_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Session */ - get_session_session__session_id__get: { - parameters: { - path: { - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["SessionClients"]; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Increment Rsync File Count */ - increment_rsync_file_count_visits__visit_name__increment_rsync_file_count_post: { - parameters: { - path: { - visit_name: string; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["RsyncerInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Increment Rsync Transferred Files */ - increment_rsync_transferred_files_visits__visit_name__increment_rsync_transferred_files_post: { - parameters: { - path: { - visit_name: string; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["RsyncerInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Increment Rsync Transferred Files Prometheus */ - increment_rsync_transferred_files_prometheus_visits__visit_name__increment_rsync_transferred_files_prometheus_post: { - parameters: { - path: { - visit_name: string; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["RsyncerInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Spa Proc Param Details */ - get_spa_proc_param_details_sessions__session_id__spa_processing_parameters_get: { - parameters: { - path: { - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["ProcessingDetails"][]; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Spa Proc Params */ - register_spa_proc_params_sessions__session_id__spa_processing_parameters_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["ProcessingParametersSPA"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Tomo Preproc Params */ - register_tomo_preproc_params_sessions__session_id__tomography_preprocessing_parameters_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["PreprocessingParametersTomo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Tomo Proc Params */ - register_tomo_proc_params_clients__client_id__tomography_processing_parameters_post: { - parameters: { - path: { - client_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["ProcessingParametersTomo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Spa Proc Params */ - get_spa_proc_params_clients__client_id__spa_processing_parameters_get: { - parameters: { - path: { - client_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": Record[]; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Grid Squares */ - get_grid_squares_sessions__session_id__grid_squares_get: { - parameters: { - path: { - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Grid Squares From Dcg */ - get_grid_squares_from_dcg_sessions__session_id__data_collection_groups__dcgid__grid_squares_get: { - parameters: { - path: { - session_id: number; - dcgid: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["GridSquare"][]; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Number Of Movies From Grid Square */ - get_number_of_movies_from_grid_square_sessions__session_id__data_collection_groups__dcgid__grid_squares__gsid__num_movies_get: { - parameters: { - path: { - session_id: number; - dcgid: number; - gsid: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": number; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Foil Holes From Grid Square */ - get_foil_holes_from_grid_square_sessions__session_id__data_collection_groups__dcgid__grid_squares__gsid__foil_holes_get: { - parameters: { - path: { - session_id: number; - dcgid: number; - gsid: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["FoilHole"][]; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Number Of Movies From Foil Hole */ - get_number_of_movies_from_foil_hole_sessions__session_id__data_collection_groups__dcgid__grid_squares__gsid__foil_holes__fhid__num_movies_get: { - parameters: { - path: { - session_id: number; - dcgid: number; - gsid: number; - fhid: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": number; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Grid Square */ - register_grid_square_sessions__session_id__grid_square__gsid__post: { - parameters: { - path: { - session_id: number; - gsid: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["GridSquareParameters"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Foil Hole */ - get_foil_hole_sessions__session_id__foil_hole__fh_name__get: { - parameters: { - path: { - fh_name: number; - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": { - [key: string]: number; - }; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Foil Hole */ - register_foil_hole_sessions__session_id__grid_square__gs_name__foil_hole_post: { - parameters: { - path: { - gs_name: number; - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["FoilHoleParameters"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Tilt Series */ - register_tilt_series_visits__visit_name__tilt_series_post: { - parameters: { - path: { - visit_name: string; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["TiltSeriesInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Completed Tilt Series */ - register_completed_tilt_series_visits__visit_name___client_id__completed_tilt_series_post: { - parameters: { - path: { - visit_name: string; - client_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["TiltSeriesGroupInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Tilts */ - get_tilts_clients__client_id__tilt_series__tilt_series_tag__tilts_get: { - parameters: { - path: { - client_id: number; - tilt_series_tag: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Tilt */ - register_tilt_visits__visit_name___client_id__tilt_post: { - parameters: { - path: { - visit_name: string; - client_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["TiltInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Current Visits */ - get_current_visits_instruments__instrument_name__visits_raw_get: { - parameters: { - path: { - instrument_name: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["Visit"][]; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Context */ - register_context_visits__visit_name__context_post: { - requestBody: { - content: { - "application/json": components["schemas"]["ContextInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Add File */ - add_file_visits__visit_name__files_post: { - requestBody: { - content: { - "application/json": components["schemas"]["File"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Send Murfey Message */ - send_murfey_message_feedback_post: { - requestBody: { - content: { - "application/json": components["schemas"]["RegistrationMessage"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Request Spa Processing */ - request_spa_processing_visits__visit_name__spa_processing_post: { - parameters: { - path: { - visit_name: string; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["SPAProcessingParameters"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Flush Spa Processing */ - flush_spa_processing_visits__visit_name___session_id__flush_spa_processing_post: { - parameters: { - path: { - visit_name: string; - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["Tag"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Request Spa Preprocessing */ - request_spa_preprocessing_visits__visit_name___session_id__spa_preprocess_post: { - parameters: { - path: { - visit_name: string; - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["SPAProcessFile"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Flush Tomography Processing */ - flush_tomography_processing_visits__visit_name___client_id__flush_tomography_processing_post: { - parameters: { - path: { - visit_name: string; - client_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["Source"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Request Tomography Preprocessing */ - request_tomography_preprocessing_visits__visit_name___client_id__tomography_preprocess_post: { - parameters: { - path: { - visit_name: string; - client_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["ProcessFile"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Version */ - get_version_version_get: { - parameters: { - query?: { - client_version?: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Suggest Path */ - suggest_path_visits__visit_name___session_id__suggested_path_post: { - parameters: { - path: { - visit_name: string; - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["SuggestedPathParameters"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Dc Groups */ - get_dc_groups_sessions__session_id__data_collection_groups_get: { - parameters: { - path: { - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": { - [key: string]: components["schemas"]["DataCollectionGroup"]; - }; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Data Collections */ - get_data_collections_sessions__session_id__data_collection_groups__dcgid__data_collections_get: { - parameters: { - path: { - dcgid: number; - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["DataCollection"][]; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Dc Group */ - register_dc_group_visits__visit_name___session_id__register_data_collection_group_post: { - parameters: { - path: { - visit_name: string; - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["DCGroupParameters"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Start Dc */ - start_dc_visits__visit_name___session_id__start_data_collection_post: { - parameters: { - path: { - visit_name: string; - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["DCParameters"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["DCParameters"]; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Proc */ - register_proc_visits__visit_name___session_id__register_processing_job_post: { - parameters: { - path: { - visit_name: unknown; - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["ProcessingJobParameters"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Process Gain */ - process_gain_sessions__session_id__process_gain_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["GainReference"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** New Client Id */ - new_client_id_new_client_id__get: { - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - }; - }; - /** Get Clients */ - get_clients_clients_get: { - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - }; - }; - /** Get Sessions */ - get_sessions_sessions_get: { - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - }; - }; - /** Link Client To Session */ - link_client_to_session_instruments__instrument_name__clients__client_id__session_post: { - parameters: { - path: { - instrument_name: string; - client_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["SessionInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Remove Session */ - remove_session_clients__client_id__session_delete: { - parameters: { - path: { - client_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Rsyncers For Session */ - get_rsyncers_for_session_sessions__session_id__rsyncers_get: { - parameters: { - path: { - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["RsyncInstance"][]; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Remove Session By Id */ - remove_session_by_id_sessions__session_id__delete: { - parameters: { - path: { - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Write Eer Fractionation File */ - write_eer_fractionation_file_visits__visit_name___session_id__eer_fractionation_file_post: { - parameters: { - path: { - visit_name: string; - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["FractionationParameters"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": Record; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Change Monitoring Status */ - change_monitoring_status_visits__visit_name__monitoring__on__post: { - parameters: { - path: { - visit_name: string; - on: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Find Upstream Visits */ - find_upstream_visits_sessions__session_id__upstream_visits_get: { - parameters: { - path: { - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Gather Upstream Tiffs */ - gather_upstream_tiffs_visits__visit_name___session_id__upstream_tiff_paths_get: { - parameters: { - path: { - visit_name: string; - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Tiff */ - get_tiff_visits__visit_name___session_id__upstream_tiff__tiff_path__get: { - parameters: { - path: { - visit_name: string; - session_id: number; - tiff_path: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Failed Client Post */ - failed_client_post_failed_client_post_post: { - requestBody: { - content: { - "application/json": components["schemas"]["PostInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Create Session */ - create_session_instruments__instrument_name__visits__visit__session__name__post: { - parameters: { - path: { - instrument_name: string; - visit: string; - name: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": number; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Update Current Gain Ref */ - update_current_gain_ref_sessions__session_id__current_gain_ref_put: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["CurrentGainRef"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** - * Get Bootstrap Instructions - * @description Return a website containing instructions for installing the Murfey client on a - * machine with no internet access. - */ - get_bootstrap_instructions_bootstrap__get: { - responses: { - /** @description Successful Response */ - 200: { - content: { - "text/html": string; - }; - }; - }; - }; - /** - * Get Pip Wheel - * @description Return a static version of pip. This does not need to be the newest or best, - * but has to be compatible with all supported Python versions. - * This is only used during bootstrapping by the client to identify and then - * download the actually newest appropriate version of pip. - */ - get_pip_wheel_bootstrap_pip_whl_get: { - responses: { - /** @description Successful Response */ - 200: { - content: never; - }; - }; - }; - /** - * Get Murfey Wheel - * @description Return a wheel file containing the latest release version of Murfey. We should - * not have to worry about the exact Python compatibility here, as long as - * murfey.bootstrap is compatible with all relevant versions of Python. - * This also ignores yanked releases, which again should be fine. - */ - get_murfey_wheel_bootstrap_murfey_whl_get: { - responses: { - /** @description Successful Response */ - 200: { - content: never; - }; - }; - }; - /** - * Get Cygwin Setup - * @description Obtain and pass through a Cygwin installer from an official source. - * This is used during client bootstrapping and can download and install the - * Cygwin distribution that then remains on the client machines. - */ - get_cygwin_setup_cygwin_setup_x86_64_exe_get: { - responses: { - /** @description Successful Response */ - 200: { - content: never; - }; - }; - }; - /** - * Parse Cygwin Request - * @description Forward a Cygwin setup request to an official mirror. - */ - parse_cygwin_request_cygwin__request_path__get: { - parameters: { - path: { - request_path: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: never; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** - * Get Pypi Index - * @description Obtain list of all PyPI packages via the simple API (PEP 503). - */ - get_pypi_index_pypi__get: { - responses: { - /** @description Successful Response */ - 200: { - content: never; - }; - }; - }; - /** - * Get Pypi Package Downloads List - * @description Obtain list of all package downloads from PyPI via the simple API (PEP 503), and - * rewrite all download URLs to point to this server, under the current directory. - */ - get_pypi_package_downloads_list_pypi__package___get: { - parameters: { - path: { - package: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: never; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** - * Get Pypi File - * @description Obtain and pass through a specific download for a PyPI package. - */ - get_pypi_file_pypi__package___filename__get: { - parameters: { - path: { - package: string; - filename: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: never; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Plugin Wheel */ - get_plugin_wheel_plugins_instruments__instrument_name___package__get: { - parameters: { - path: { - instrument_name: string; - package: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: never; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Version */ - get_version_version__get: { - parameters: { - query?: { - client_version?: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Lif File */ - register_lif_file_sessions__session_id__clem_lif_files_post: { - parameters: { - query: { - lif_file: string; - master_metadata?: string; - }; - path: { - session_id: number; - }; - }; - requestBody?: { - content: { - "application/json": components["schemas"]["Body_register_lif_file_sessions__session_id__clem_lif_files_post"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Tiff File */ - register_tiff_file_sessions__session_id__clem_tiff_files_post: { - parameters: { - query: { - tiff_file: string; - associated_metadata?: string; - associated_series?: string; - associated_stack?: string; - }; - path: { - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Clem Metadata */ - register_clem_metadata_sessions__session_id__clem_metadata_files_post: { - parameters: { - query: { - metadata_file: string; - parent_lif?: string; - associated_series?: string; - }; - path: { - session_id: number; - }; - }; - requestBody?: { - content: { - "application/json": components["schemas"]["Body_register_clem_metadata_sessions__session_id__clem_metadata_files_post"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Image Series */ - register_image_series_sessions__session_id__clem_image_series_post: { - parameters: { - query: { - series_name: string; - parent_lif?: string; - associated_metadata?: string; - }; - path: { - session_id: number; - }; - }; - requestBody?: { - content: { - "application/json": components["schemas"]["Body_register_image_series_sessions__session_id__clem_image_series_post"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Register Image Stack */ - register_image_stack_sessions__session_id__clem_image_stacks_post: { - parameters: { - query: { - image_stack: string; - channel?: string; - parent_lif?: string; - associated_metadata?: string; - parent_series?: string; - }; - path: { - session_id: number; - }; - }; - requestBody?: { - content: { - "application/json": string[]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Lif To Stack */ - lif_to_stack_sessions__session_id__lif_to_stack_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["LifFileInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Tiff To Stack */ - tiff_to_stack_sessions__session_id__tiff_to_stack_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["TiffSeriesInfo"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Cryolo Model Path */ - get_cryolo_model_path_sessions__session_id__cryolo_model_get: { - parameters: { - path: { - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Generate Token */ - generate_token_token_post: { - requestBody: { - content: { - "application/x-www-form-urlencoded": components["schemas"]["Body_generate_token_token_post"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["Token"]; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Mint Session Token */ - mint_session_token_sessions__session_id__token_get: { - parameters: { - path: { - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Simple Token Validation */ - simple_token_validation_validate_token_get: { - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - }; - }; - /** Get Mic Image */ - get_mic_image_display_microscope_image__get: { - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - }; - }; - /** Get Grid Square Img */ - get_grid_square_img_display_sessions__session_id__data_collection_groups__dcgid__grid_squares__grid_square_name__image_get: { - parameters: { - path: { - session_id: number; - dcgid: number; - grid_square_name: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Foil Hole Img */ - get_foil_hole_img_display_sessions__session_id__data_collection_groups__dcgid__grid_squares__grid_square_name__foil_holes__foil_hole_name__image_get: { - parameters: { - path: { - session_id: number; - dcgid: number; - grid_square_name: number; - foil_hole_name: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Activate Instrument Server */ - activate_instrument_server_instruments__instrument_name__activate_instrument_server_post: { - parameters: { - path: { - instrument_name: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Activate Instrument Server For Session */ - activate_instrument_server_for_session_instruments__instrument_name__sessions__session_id__activate_instrument_server_post: { - parameters: { - path: { - instrument_name: string; - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Start Multigrid Watcher */ - start_multigrid_watcher_sessions__session_id__multigrid_watcher_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["MultigridWatcherSetup"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Pass Proc Params To Instrument Server */ - pass_proc_params_to_instrument_server_sessions__session_id__provided_processing_parameters_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["ProvidedProcessingParameters"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Check Instrument Server */ - check_instrument_server_instruments__instrument_name__instrument_server_get: { - parameters: { - path: { - instrument_name: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Possible Gain References */ - get_possible_gain_references_instruments__instrument_name__sessions__session_id__possible_gain_references_get: { - parameters: { - path: { - instrument_name: string; - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["File"][]; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Request Gain Reference Upload */ - request_gain_reference_upload_sessions__session_id__upload_gain_reference_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["GainReferenceRequest"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Request Upstream Tiff Data Download */ - request_upstream_tiff_data_download_visits__visit_name___session_id__upstream_tiff_data_request_post: { - parameters: { - path: { - visit_name: string; - session_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Stop Rsyncer */ - stop_rsyncer_sessions__session_id__stop_rsyncer_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["murfey__server__api__instrument__RsyncerSource"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Finalise Rsyncer */ - finalise_rsyncer_sessions__session_id__finalise_rsyncer_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["murfey__server__api__instrument__RsyncerSource"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Remove Rsyncer */ - remove_rsyncer_sessions__session_id__remove_rsyncer_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["murfey__server__api__instrument__RsyncerSource"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Restart Rsyncer */ - restart_rsyncer_sessions__session_id__restart_rsyncer_post: { - parameters: { - path: { - session_id: number; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["murfey__server__api__instrument__RsyncerSource"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Get Instrument Info */ - get_instrument_info_instruments_get: { - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": components["schemas"]["InstrumentInfo"][]; - }; - }; - }; - }; - /** Get Instrument Image */ - get_instrument_image_instrument__instrument_name__image_get: { - parameters: { - path: { - instrument_name: string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Close Ws Connection */ - close_ws_connection_ws_test__client_id__delete: { - parameters: { - path: { - client_id: number; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Close Unrecorded Ws Connection */ - close_unrecorded_ws_connection_ws_connect__client_id__delete: { - parameters: { - path: { - client_id: number | string; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; - /** Request Smartem Atlas Analysis */ - request_smartem_atlas_analysis_visits__visit_name__smartem_atlas__post: { - parameters: { - path: { - visit_name: string; - }; - }; - requestBody: { - content: { - "application/json": components["schemas"]["SmartEMAtlasRequest"]; - }; - }; - responses: { - /** @description Successful Response */ - 200: { - content: { - "application/json": unknown; - }; - }; - /** @description Validation Error */ - 422: { - content: { - "application/json": components["schemas"]["HTTPValidationError"]; - }; - }; - }; - }; -} diff --git a/murfey-frontend/src/setupTests.js b/murfey-frontend/src/setupTests.js deleted file mode 100644 index 1dd407a63..000000000 --- a/murfey-frontend/src/setupTests.js +++ /dev/null @@ -1,5 +0,0 @@ -// jest-dom adds custom jest matchers for asserting on DOM nodes. -// allows you to do things like: -// expect(element).toHaveTextContent(/react/i) -// learn more: https://github.com/testing-library/jest-dom -import "@testing-library/jest-dom"; diff --git a/murfey-frontend/src/styles/colours.tsx b/murfey-frontend/src/styles/colours.tsx deleted file mode 100644 index 1cc89cc1c..000000000 --- a/murfey-frontend/src/styles/colours.tsx +++ /dev/null @@ -1,16 +0,0 @@ -const colours = { - murfey: { - 50: { default: "#FBFBFB", _dark: "#525151" }, - 75: { derfault: "#F7F7F7", _dark: "#080808" }, - 100: { default: "#E7ECEF", _dark: "#383838" }, - 200: { default: "#CBD5E0", _dark: "#030303" }, - 300: { default: "#39435E", _dark: "#5f709e" }, - 400: { default: "#ACACF9", _dark: "#030405" }, - 500: { default: "#FC6321", _dark: "#050401" }, - 600: { default: "#5738BD", _dark: "#101a36" }, - 700: { default: "#2910A1", _dark: "#071d4a" }, - 800: { default: "#0E0055", _dark: "#023496" }, - }, -}; - -export { colours }; diff --git a/murfey-frontend/src/styles/components.ts b/murfey-frontend/src/styles/components.ts deleted file mode 100644 index daf1da12f..000000000 --- a/murfey-frontend/src/styles/components.ts +++ /dev/null @@ -1,325 +0,0 @@ -import { - defineStyleConfig, - defineStyle, - createMultiStyleConfigHelpers, - UseToastOptions, -} from "@chakra-ui/react"; -import { - cardAnatomy, - tabsAnatomy, - inputAnatomy, - numberInputAnatomy, - selectAnatomy, -} from "@chakra-ui/anatomy"; - -const baseToast: UseToastOptions = { - id: "main-toast", - status: "success", - duration: 6000, - isClosable: true, -}; - -const baseInput = { - field: { - bg: "white", - border: "solid 1px", - borderColor: "murfey.200", - borderRadius: 0, - }, -}; - -const Accordion = defineStyleConfig({ - baseStyle: { - container: { - border: "1px solid var(--chakra-colors-murfey-100)", - }, - }, -}); - -const Text = defineStyleConfig({ - variants: { - infoGroupText: { - wordBreak: "break-all", - display: "inline", - fontSize: "xs", - }, - }, -}); - -const Checkbox = defineStyleConfig({ - sizes: { - sm: { - control: { - height: "16px", - width: "16px", - }, - icon: { - height: "16px", - fontSize: "10px", - }, - label: { - fontSize: "14px", - height: "16px", - }, - }, - }, - baseStyle: { - control: { - borderColor: "murfey.600", - backgroundColor: "#FFF", - _checked: { - backgroundColor: "murfey.600", - borderColor: "murfey.600", - }, - }, - }, -}); - -const Table = defineStyleConfig({ - variants: { - diamondStriped: { - tbody: { - tr: { - _odd: { - bg: "murfey.100", - }, - _even: { - bg: "murfey.50", - }, - _hover: { - bg: "murfey.200", - }, - }, - }, - }, - }, -}); - -const CardHeader = defineStyleConfig({ - baseStyle: { - p: "10px !important", - h: "10%", - }, -}); - -const CardBody = defineStyleConfig({ - baseStyle: { - p: 2, - h: "90%", - }, -}); - -const { definePartsStyle, defineMultiStyleConfig } = - createMultiStyleConfigHelpers(cardAnatomy.keys); - -const baseCardStyle = definePartsStyle({ - container: { - p: 1, - borderWidth: "1px", - borderRadius: "lg", - borderColor: "murfey.200", - _hover: { - borderColor: "murfey.400", - cursor: "pointer", - }, - _selected: { - bg: "murfey.100", - fontWeight: "600", - borderBottomWidth: "3px", - }, - }, - header: { - p: 2, - cursor: "pointer", - _hover: { - color: "murfey.300", - }, - }, - body: { - px: 2, - height: "90%", - }, -}); - -const Card = defineMultiStyleConfig({ - baseStyle: baseCardStyle, - defaultProps: { variant: "outline" }, -}); - -const Button = defineStyleConfig({ - defaultProps: { - variant: "default", - }, - baseStyle: { - borderBottom: "2px solid rgba(0,0,0,0.2)", - }, - variants: { - default: { - color: "murfey.50", - bg: "murfey.600", - _hover: { - bgImage: "linear-gradient(rgb(0 0 0/30%) 0 0)", - _disabled: { - bg: "murfey.600", - }, - }, - }, - pgSelected: { - bg: "murfey.600", - color: "murfey.50", - cursor: "default", - }, - pgNotSelected: { - bg: "gray.200", - color: "charcoal", - fontSize: "sm", - _hover: { - bg: "murfey.200", - }, - }, - onBlue: { - color: "murfey.500", - borderColor: "murfey.500", - border: "1px solid", - fontSize: "sm", - _hover: { - color: "murfey.300", - bg: "murfey.500", - }, - }, - }, -}); - -const notFound = defineStyle({ - textAlign: "center", - color: "murfey.300", -}); - -const Heading = defineStyleConfig({ - variants: { - collection: { - fontSize: 20, - py: "4px", - }, - notFound, - notFoundSubtitle: { - ...notFound, - fontWeight: 200, - fontSize: 20, - paddingBottom: 10, - }, - }, -}); - -const { - definePartsStyle: defineInputStyle, - defineMultiStyleConfig: defineInputConfig, -} = createMultiStyleConfigHelpers(inputAnatomy.keys); - -const hiContrastInput = defineInputStyle({ - field: { - borderWidth: "1px", - borderColor: "murfey.800", - borderRadius: 0, - _invalid: { - borderColor: "red.500", - }, - }, -}); - -const baseInputStyle = defineInputStyle({ - ...baseInput, - addon: { - border: "solid 1px", - borderColor: "murfey.200", - background: "murfey.100", - }, -}); - -const Input = defineInputConfig({ - baseStyle: baseInputStyle, - variants: { "hi-contrast": hiContrastInput, default: baseInputStyle }, - defaultProps: { variant: "default" }, -}); - -const { defineMultiStyleConfig: defineNumberInputConfig } = - createMultiStyleConfigHelpers(numberInputAnatomy.keys); - -const NumberInput = defineNumberInputConfig({ - defaultProps: { variant: "default" }, - variants: { default: baseInput }, -}); - -const { defineMultiStyleConfig: defineSelectConfig } = - createMultiStyleConfigHelpers(selectAnatomy.keys); - -const Select = defineSelectConfig({ - defaultProps: { variant: "default" }, - variants: { default: baseInput, "hi-contrast": hiContrastInput }, -}); - -const { - definePartsStyle: defineTabsStyle, - defineMultiStyleConfig: defineTabsConfig, -} = createMultiStyleConfigHelpers(tabsAnatomy.keys); - -const baseTabsStyle = defineTabsStyle({ - tab: { - border: "1px solid", - borderColor: "murfey.200", - bg: "murfey.75", - borderBottom: "none", - _selected: { - bg: "murfey.50", - color: "murfey.700", - borderColor: "inherit", - borderBottom: "none", - borderTopColor: "murfey.700", - mb: "-2px", - }, - }, - tablist: { - borderBottom: "none", - }, - tabpanel: { - p: "2", - bg: "murfey.50", - border: "1px solid", - borderColor: "inherit", - }, -}); - -const Tabs = defineTabsConfig({ - baseStyle: baseTabsStyle, - defaultProps: { variant: "none" }, -}); - -const Code = defineStyleConfig({ - baseStyle: { - backgroundColor: "murfey.100", - color: "murfey.800", - }, -}); - -const Textarea = defineStyleConfig({ - variants: { "hi-contrast": hiContrastInput.field }, -}); - -export { - Accordion, - Button, - Table, - Text, - Heading, - Card, - CardHeader, - CardBody, - Tabs, - baseToast, - Checkbox, - Code, - Input, - Textarea, - NumberInput, - Select, -}; diff --git a/murfey-frontend/src/styles/main.css b/murfey-frontend/src/styles/main.css deleted file mode 100644 index ad6ec7d8b..000000000 --- a/murfey-frontend/src/styles/main.css +++ /dev/null @@ -1,29 +0,0 @@ -.rootContainer { - display: flex; - flex-direction: column; - height: 100%; - width: 100%; -} - -.footer { - flex-shrink: 0; -} - -.main { - margin: 0.3em 7.3vw !important; - flex: 1 0 auto; -} - -html, -body, -#root { - height: 100%; - background-color: var(--chakra-colors-murfey-50); -} - -.homeRoot > * { - padding: 4vh 10vw; - width: 100%; - justify-content: start; - align-items: start; -} diff --git a/murfey-frontend/src/styles/theme.tsx b/murfey-frontend/src/styles/theme.tsx deleted file mode 100644 index 500247036..000000000 --- a/murfey-frontend/src/styles/theme.tsx +++ /dev/null @@ -1,49 +0,0 @@ -import { ThemeConfig, extendTheme } from "@chakra-ui/react"; -import { colours } from "styles/colours"; -import { - Accordion, - Button, - Checkbox, - Heading, - Table, - Card, - Tabs, - Code, - Text, - Input, - Textarea, - NumberInput, - Select, -} from "./components"; - -const config: ThemeConfig = { - initialColorMode: "light", - useSystemColorMode: false, -}; - -export const theme = extendTheme({ - semanticTokens: { colors: colours }, - components: { - Accordion, - Checkbox, - Button, - Text, - Heading, - Table, - Card, - Tabs, - Code, - Input, - Textarea, - NumberInput, - Select, - }, - breakpoints: { - sm: "30em", - md: "48em", - lg: "62em", - xl: "80em", - "2xl": "150em", - }, - config, -}); diff --git a/murfey-frontend/src/utils/api/client.tsx b/murfey-frontend/src/utils/api/client.tsx deleted file mode 100644 index 7dd33767d..000000000 --- a/murfey-frontend/src/utils/api/client.tsx +++ /dev/null @@ -1,162 +0,0 @@ -import { createStandaloneToast } from "@chakra-ui/toast"; -import { baseToast } from "@diamondlightsource/ui-components"; -const { toast } = createStandaloneToast(); - -const controller = new AbortController(); - -const defaultSettings: Partial = { - credentials: - process.env.NODE_ENV === "development" ? "include" : "same-origin", -}; - -interface RequestConfig { - method: string; - headers: Record; - body?: string | FormData; - [k: string]: any; -} - -export interface Response { - status: number; - data: any; - headers: Record; - url: string; -} - -export const getPrefix = (prefix: string = "/api/") => { - if (prefix.substring(0, 1) === "/") { - return window.location.origin + prefix; - } - - return prefix; -}; - -export const client = async ( - endpoint: string, - customConfig: Record = {}, - body?: Record | FormData | null, - method: string | null = null, - errToast: boolean = true, - prefix: string = getPrefix( - sessionStorage.getItem("murfeyServerURL") ?? - process.env.REACT_APP_API_ENDPOINT, - ), -): Promise => { - const config: RequestConfig = { - method: method ? method : body != null ? "POST" : "GET", - ...customConfig, - headers: { - ...customConfig.headers, - }, - signal: controller.signal, - body: undefined, - ...defaultSettings, - }; - console.log(endpoint); - - if (body != null) { - if (!(body instanceof FormData)) { - config.body = JSON.stringify(body); - config.headers = { - ...config.headers, - Accept: "application/json", - "Content-Type": "application/json", - }; - } else { - config.body = body; - } - } - - try { - const token = sessionStorage.getItem("token"); - config.headers = { ...config.headers, Authorization: `Bearer ${token}` }; - const response = await fetch(prefix + endpoint, config); - const isJson = response.headers.get("content-type") === "application/json"; - - if (!isJson) console.log(endpoint); - - return { - status: response.status, - data: isJson ? await response.json() : await response.arrayBuffer(), - headers: response.headers, - url: response.url, - }; - } catch (err) { - if (!toast.isActive("main-toast") && errToast) { - toast({ - ...baseToast, - title: - "An error has occurred while fetching data, please try again later.", - status: "error", - }); - } - - throw err; - } -}; - -client.get = async ( - endpoint: string, - customConfig = {}, - errToast: boolean = true, -) => { - return await client( - endpoint, - (customConfig = { - ...customConfig, - }), - null, - "GET", - (errToast = errToast), - ); -}; - -client.hub_get = async ( - endpoint: string, - customConfig = {}, - errToast: boolean = true, -) => { - return await client( - endpoint, - (customConfig = { - ...customConfig, - }), - null, - "GET", - (errToast = errToast), - getPrefix(process.env.REACT_APP_HUB_ENDPOINT), - ); -}; - -client.delete = async (endpoint: string, customConfig = {}) => { - return await client( - endpoint, - (customConfig = { - ...customConfig, - }), - null, - "DELETE", - ); -}; - -client.post = async ( - endpoint: string, - body: Record | FormData, - customConfig = {}, -) => { - return await client(endpoint, { ...customConfig }, body); -}; - -client.put = async ( - endpoint: string, - body: Record | FormData, - customConfig = {}, -) => { - return await client(endpoint, { ...customConfig }, body, "PUT"); -}; - -export const prependApiUrl = (url: string) => - `${getPrefix( - sessionStorage.getItem("murfeyServerURL") ?? - process.env.REACT_APP_API_ENDPOINT, - )}${url}`; diff --git a/murfey-frontend/src/utils/generic.tsx b/murfey-frontend/src/utils/generic.tsx deleted file mode 100644 index dd06c16ea..000000000 --- a/murfey-frontend/src/utils/generic.tsx +++ /dev/null @@ -1,15 +0,0 @@ -const timeFormatter = new Intl.DateTimeFormat("en-GB", { - dateStyle: "short", - timeStyle: "short", -}); - -export const parseDate = (dateString: string | undefined) => { - const safeDate = dateString ?? ""; - const date = Date.parse(safeDate); - - if (isNaN(date)) { - return safeDate; - } - - return timeFormatter.format(date); -}; diff --git a/murfey-frontend/tsconfig.json b/murfey-frontend/tsconfig.json deleted file mode 100644 index faea932dd..000000000 --- a/murfey-frontend/tsconfig.json +++ /dev/null @@ -1,21 +0,0 @@ -{ - "compilerOptions": { - "target": "es2017", - "lib": ["dom", "dom.iterable", "esnext"], - "allowJs": true, - "skipLibCheck": true, - "esModuleInterop": true, - "allowSyntheticDefaultImports": true, - "strict": true, - "forceConsistentCasingInFileNames": true, - "noFallthroughCasesInSwitch": true, - "module": "esnext", - "moduleResolution": "node", - "resolveJsonModule": true, - "isolatedModules": true, - "noEmit": true, - "jsx": "react-jsx", - "baseUrl": "src" - }, - "include": ["src"] -} diff --git a/murfey-frontend/yarn.lock b/murfey-frontend/yarn.lock deleted file mode 100644 index 3d8fd8c14..000000000 --- a/murfey-frontend/yarn.lock +++ /dev/null @@ -1,11673 +0,0 @@ -# THIS IS AN AUTOGENERATED FILE. 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string-width "^4.2.0" - y18n "^5.0.5" - yargs-parser "^20.2.2" - -yocto-queue@^0.1.0: - version "0.1.0" - resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-0.1.0.tgz#0294eb3dee05028d31ee1a5fa2c556a6aaf10a1b" - integrity sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q== From b94d5e64189429a7ef78396168b6cbde1a9bbdf7 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Thu, 16 Jan 2025 12:28:59 +0000 Subject: [PATCH 14/30] Reverted file size check back to previous amount now that 'murfey-frontend' has been migrated --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ee9a38db6..00200fe5a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -8,7 +8,7 @@ repos: hooks: - id: check-added-large-files name: Checking for added large files - args: ["--maxkb=600"] + args: ["--maxkb=200"] fail_fast: True - id: check-case-conflict name: Checking for name case conflicts From aa472a4c5e307b82a11539cdf99c74285cb02cb7 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Fri, 17 Jan 2025 16:31:10 +0000 Subject: [PATCH 15/30] Optimised build instructions for 'murfey-server' to reduce image size --- Dockerfiles/murfey-server | 40 +++++++++++++++------------------------ 1 file changed, 15 insertions(+), 25 deletions(-) diff --git a/Dockerfiles/murfey-server b/Dockerfiles/murfey-server index b934108e5..de06fb3d6 100644 --- a/Dockerfiles/murfey-server +++ b/Dockerfiles/murfey-server @@ -2,7 +2,7 @@ # podman build --build-arg groupid= --build-arg userid= --build-arg groupname= --no-cache -f path/to/Dockerfiles/murfey-server -t murfey-server: path/to/python-murfey # Set up the Python base image to build with -FROM docker.io/library/python:3.12.8-slim-bullseye as build +FROM docker.io/library/python:3.12.8-slim-bullseye AS base # Define external build arguments ARG groupid @@ -11,6 +11,7 @@ ARG userid # Add system dependencies for the developer/build environment # Add the group and user ID to be used by Murfey +# Create virtual Python environment in which to install Murfey RUN apt-get update && \ apt-get upgrade -y && \ apt-get install -y --no-install-recommends \ @@ -21,33 +22,22 @@ RUN apt-get update && \ libpq-dev && \ busybox --install &&\ rm -rf /var/lib/apt/lists/* && \ - groupadd -r -g "${groupid}" "${groupname}" && useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" - -# Copy essential Murfey source files across from repo -COPY --chown="${userid}":"${groupid}" src/murfey/ /repos/python-murfey/src/murfey/ -COPY --chown="${userid}":"${groupid}" \ - pyproject.toml \ - setup.py \ - api-spec.yaml \ - AUTHORS.rst \ - catalog-info.yaml \ - LICENSE \ - MANIFEST.in \ - README.md \ - /repos/python-murfey/ - -# Set the repo as the current working directory -WORKDIR /repos/python-murfey + groupadd -r -g "${groupid}" "${groupname}" && \ + useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \ + python -m venv /venv && \ + chmod -R a+x /venv +ENV PATH=/venv/bin:$PATH -# Set up a virtual environment and install Murfey -RUN python -m venv /venv && \ - chmod -R a+x /venv && \ - /venv/bin/python -m pip install --upgrade \ +# Build Murfey in a different image +FROM base AS build +COPY --chown="${userid}":"${groupid}" ./ /python-murfey/ +RUN python -m pip install --upgrade \ pip \ build \ importlib-metadata \ psycopg2-binary && \ - /venv/bin/python -m pip install .[server] + python -m pip install /python-murfey[server] -# Prepend the virtual environment to PATH -ENV PATH=/venv/bin:$PATH +# Copy installed files across to final image +FROM base +COPY --from=build --chown="${userid}":"${groupid}" /venv/ /venv/ From 5f0b7747df46b577cbbd703fdd5b3a1018732c13 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Fri, 17 Jan 2025 17:51:38 +0000 Subject: [PATCH 16/30] Further optimised build instructions to reduce size and set necessary permissions --- Dockerfiles/murfey-server | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/Dockerfiles/murfey-server b/Dockerfiles/murfey-server index de06fb3d6..aba18a369 100644 --- a/Dockerfiles/murfey-server +++ b/Dockerfiles/murfey-server @@ -12,6 +12,7 @@ ARG userid # Add system dependencies for the developer/build environment # Add the group and user ID to be used by Murfey # Create virtual Python environment in which to install Murfey +# Change properties of said Python environment RUN apt-get update && \ apt-get upgrade -y && \ apt-get install -y --no-install-recommends \ @@ -20,15 +21,17 @@ RUN apt-get update && \ git \ net-tools \ libpq-dev && \ - busybox --install &&\ + busybox --install && \ rm -rf /var/lib/apt/lists/* && \ groupadd -r -g "${groupid}" "${groupname}" && \ useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \ python -m venv /venv && \ + chown -R "${userid}":"${groupid}" /venv && \ chmod -R a+x /venv ENV PATH=/venv/bin:$PATH # Build Murfey in a different image +# Change properties of the built Python environment FROM base AS build COPY --chown="${userid}":"${groupid}" ./ /python-murfey/ RUN python -m pip install --upgrade \ @@ -36,7 +39,8 @@ RUN python -m pip install --upgrade \ build \ importlib-metadata \ psycopg2-binary && \ - python -m pip install /python-murfey[server] + python -m pip install /python-murfey[server] && \ + chmod -R a+x /venv # Copy installed files across to final image FROM base From bfc624a0d7caf595990e53897541615dc4f62bbf Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Fri, 17 Jan 2025 17:57:04 +0000 Subject: [PATCH 17/30] Made similar changes to 'murfey-instrument-server' Dockerfile --- Dockerfiles/murfey-instrument-server | 45 ++++++++++++---------------- 1 file changed, 19 insertions(+), 26 deletions(-) diff --git a/Dockerfiles/murfey-instrument-server b/Dockerfiles/murfey-instrument-server index 2391692ac..2fc201061 100644 --- a/Dockerfiles/murfey-instrument-server +++ b/Dockerfiles/murfey-instrument-server @@ -2,7 +2,7 @@ # podman build --build-arg groupid= --build-arg userid= --build-arg groupname= --no-cache -f path/to/Dockerfiles/murfey-instrument-server -t murfey-instrument-server: path/to/python-murfey # Set up the Python base image to build with -FROM docker.io/library/python:3.12.8-slim-bullseye as build +FROM docker.io/library/python:3.12.8-slim-bullseye AS base # Define external build arguments ARG groupid @@ -11,6 +11,8 @@ ARG userid # Add system dependencies for the developer/build environment # Add the group and user ID to be used by Murfey +# Create virtual Python environment in which to install Murfey +# Change properties of said Python environment RUN apt-get update && \ apt-get upgrade -y && \ apt-get install -y --no-install-recommends \ @@ -19,34 +21,25 @@ RUN apt-get update && \ git \ net-tools \ libpq-dev && \ - busybox --install &&\ + busybox --install && \ rm -rf /var/lib/apt/lists/* && \ - groupadd -r -g "${groupid}" "${groupname}" && useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" - -# Copy essential Murfey source files across from repo -COPY --chown="${userid}":"${groupid}" src/murfey/ /repos/python-murfey/src/murfey/ -COPY --chown="${userid}":"${groupid}" \ - pyproject.toml \ - setup.py \ - api-spec.yaml \ - AUTHORS.rst \ - catalog-info.yaml \ - LICENSE \ - MANIFEST.in \ - README.md \ - /repos/python-murfey/ - -# Set the repo as the current working directory -WORKDIR /repos/python-murfey + groupadd -r -g "${groupid}" "${groupname}" && \ + useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \ + python -m venv /venv && \ + chown -R "${userid}":"${groupid}" /venv && \ + chmod -R a+x /venv +ENV PATH=/venv/bin:$PATH -# Set up a virtual environment and install Murfey -RUN python -m venv /venv && \ - chmod -R a+x /venv && \ - /venv/bin/python -m pip install --upgrade \ +# Build Murfey in a different image +FROM base AS build +COPY --chown="${userid}":"${groupid}" ./ /python-murfey/ +RUN python -m pip install --upgrade \ pip \ build \ importlib-metadata &&\ - /venv/bin/python -m pip install .[client,instrument-server] + python -m pip install /python-murfey[client,instrument-server] && \ + chmod -R a+x /venv -# Prepend the virtual environment to PATH -ENV PATH=/venv/bin:$PATH +# Copy installed files across to final image +FROM base +COPY --from=build --chown="${userid}":"${groupid}" /venv/ /venv/ From d0dacc35fb97914be82f4a61fae58d4cae49fcb6 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Fri, 17 Jan 2025 18:24:37 +0000 Subject: [PATCH 18/30] Optimised 'murfey-rsync' file as well --- Dockerfiles/murfey-rsync | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfiles/murfey-rsync b/Dockerfiles/murfey-rsync index 88c75a159..77ef74e27 100644 --- a/Dockerfiles/murfey-rsync +++ b/Dockerfiles/murfey-rsync @@ -9,6 +9,6 @@ ARG groupname ARG userid # Add any system dependencies for the developer/build environment here -RUN apk add --no-cache rsync - -RUN addgroup -S -g "${groupid}" "${groupname}" && adduser -S "${groupname}" -G "${groupname}" -u "${userid}" -s /bin/sh +RUN apk add --no-cache rsync && \ + addgroup -S -g "${groupid}" "${groupname}" && \ + adduser -S "${groupname}" -G "${groupname}" -u "${userid}" -s /bin/sh From 6c9b4de31dbeb27689eedc7d07e35676e41fddd1 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Mon, 20 Jan 2025 18:20:31 +0000 Subject: [PATCH 19/30] Fixed issue with user permissions not transferring correctly between images --- Dockerfiles/murfey-server | 62 ++++++++++++++++++++++----------------- 1 file changed, 35 insertions(+), 27 deletions(-) diff --git a/Dockerfiles/murfey-server b/Dockerfiles/murfey-server index aba18a369..0fb0c6260 100644 --- a/Dockerfiles/murfey-server +++ b/Dockerfiles/murfey-server @@ -1,47 +1,55 @@ # Template build command # podman build --build-arg groupid= --build-arg userid= --build-arg groupname= --no-cache -f path/to/Dockerfiles/murfey-server -t murfey-server: path/to/python-murfey -# Set up the Python base image to build with +# Set up the base image to build with FROM docker.io/library/python:3.12.8-slim-bullseye AS base -# Define external build arguments -ARG groupid -ARG groupname -ARG userid +# Install Vim in base image +RUN apt-get update && \ + apt-get upgrade -y && \ + apt-get install -y --no-install-recommends \ + vim \ + && \ + apt-get autoremove && \ + rm -rf /var/lib/apt/lists/* -# Add system dependencies for the developer/build environment -# Add the group and user ID to be used by Murfey -# Create virtual Python environment in which to install Murfey -# Change properties of said Python environment + +# Build Murfey in a separate image +FROM base as build +COPY ./ /python-murfey/ RUN apt-get update && \ apt-get upgrade -y && \ apt-get install -y --no-install-recommends \ build-essential \ busybox \ git \ + libpq-dev \ net-tools \ - libpq-dev && \ + && \ busybox --install && \ - rm -rf /var/lib/apt/lists/* && \ - groupadd -r -g "${groupid}" "${groupname}" && \ - useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \ python -m venv /venv && \ - chown -R "${userid}":"${groupid}" /venv && \ - chmod -R a+x /venv -ENV PATH=/venv/bin:$PATH - -# Build Murfey in a different image -# Change properties of the built Python environment -FROM base AS build -COPY --chown="${userid}":"${groupid}" ./ /python-murfey/ -RUN python -m pip install --upgrade \ + /venv/bin/python -m pip install --upgrade \ pip \ build \ importlib-metadata \ - psycopg2-binary && \ - python -m pip install /python-murfey[server] && \ - chmod -R a+x /venv + psycopg2-binary \ + && \ + /venv/bin/python -m pip install /python-murfey[server] + -# Copy installed files across to final image +# Transfer completed Murfey build to a clean image FROM base -COPY --from=build --chown="${userid}":"${groupid}" /venv/ /venv/ + +# Define external build arguments +ARG groupid +ARG groupname +ARG userid + +# Copy completed Murfey build across, install Vim, and set user and group permissions +COPY --from=build /venv/ /venv/ +RUN groupadd -r -g "${groupid}" "${groupname}" && \ + useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \ + chown -R "${userid}":"${groupid}" /venv && \ + chmod -R a+x /venv +ENV PATH=/venv/bin:$PATH +USER "${userid}":"${groupid}" From 35bfb2ad5ef23aac5d0738c12413812ea52a749e Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Mon, 20 Jan 2025 18:32:32 +0000 Subject: [PATCH 20/30] Applied same fix to 'murfey-instrument-server' and corrected section comments --- Dockerfiles/murfey-instrument-server | 55 ++++++++++++++++------------ Dockerfiles/murfey-server | 2 +- 2 files changed, 32 insertions(+), 25 deletions(-) diff --git a/Dockerfiles/murfey-instrument-server b/Dockerfiles/murfey-instrument-server index 2fc201061..cf922d24b 100644 --- a/Dockerfiles/murfey-instrument-server +++ b/Dockerfiles/murfey-instrument-server @@ -1,18 +1,22 @@ # Build command template # podman build --build-arg groupid= --build-arg userid= --build-arg groupname= --no-cache -f path/to/Dockerfiles/murfey-instrument-server -t murfey-instrument-server: path/to/python-murfey -# Set up the Python base image to build with +# Set up the base image to build with FROM docker.io/library/python:3.12.8-slim-bullseye AS base -# Define external build arguments -ARG groupid -ARG groupname -ARG userid +# Install Vim in base image +RUN apt-get update && \ + apt-get upgrade -y && \ + apt-get install -y --no-install-recommends \ + vim \ + && \ + apt-get autoremove && \ + rm -rf /var/lib/apt/lists/* -# Add system dependencies for the developer/build environment -# Add the group and user ID to be used by Murfey -# Create virtual Python environment in which to install Murfey -# Change properties of said Python environment + +# Build Murfey in a separate image +FROM base as build +COPY ./ /python-murfey/ RUN apt-get update && \ apt-get upgrade -y && \ apt-get install -y --no-install-recommends \ @@ -22,24 +26,27 @@ RUN apt-get update && \ net-tools \ libpq-dev && \ busybox --install && \ - rm -rf /var/lib/apt/lists/* && \ - groupadd -r -g "${groupid}" "${groupname}" && \ - useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \ python -m venv /venv && \ - chown -R "${userid}":"${groupid}" /venv && \ - chmod -R a+x /venv -ENV PATH=/venv/bin:$PATH - -# Build Murfey in a different image -FROM base AS build -COPY --chown="${userid}":"${groupid}" ./ /python-murfey/ -RUN python -m pip install --upgrade \ + /venv/bin/python -m pip install --upgrade \ pip \ build \ importlib-metadata &&\ - python -m pip install /python-murfey[client,instrument-server] && \ - chmod -R a+x /venv + /venv/bin/python -m pip install /python-murfey[client,instrument-server] + -# Copy installed files across to final image +# Transfer completed Murfey build to clean image FROM base -COPY --from=build --chown="${userid}":"${groupid}" /venv/ /venv/ + +# Define external build arguments +ARG groupid +ARG groupname +ARG userid + +# Copy completed Murfey build across and set user and group permissions +COPY --from=build /venv/ /venv/ +RUN groupadd -r -g "${groupid}" "${groupname}" && \ + useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \ + chown -R "${userid}":"${groupid}" /venv && \ + chmod -R a+x /venv +ENV PATH=/venv/bin:$PATH +USER "${userid}":"${groupid}" diff --git a/Dockerfiles/murfey-server b/Dockerfiles/murfey-server index 0fb0c6260..1ea74f0fa 100644 --- a/Dockerfiles/murfey-server +++ b/Dockerfiles/murfey-server @@ -45,7 +45,7 @@ ARG groupid ARG groupname ARG userid -# Copy completed Murfey build across, install Vim, and set user and group permissions +# Copy completed Murfey build across and set user and group permissions COPY --from=build /venv/ /venv/ RUN groupadd -r -g "${groupid}" "${groupname}" && \ useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \ From 155f4c42529731e50c2b99a5e8f9508a8bc3514a Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Thu, 23 Jan 2025 16:42:34 +0000 Subject: [PATCH 21/30] Added IMOD installation to 'murfey-server' image and added libpq-dev to final image --- Dockerfiles/murfey-server | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/Dockerfiles/murfey-server b/Dockerfiles/murfey-server index 1ea74f0fa..275504b87 100644 --- a/Dockerfiles/murfey-server +++ b/Dockerfiles/murfey-server @@ -4,17 +4,18 @@ # Set up the base image to build with FROM docker.io/library/python:3.12.8-slim-bullseye AS base -# Install Vim in base image +# Install Vim and PostgreSQL dependencies in base image RUN apt-get update && \ apt-get upgrade -y && \ apt-get install -y --no-install-recommends \ + libpq-dev \ vim \ && \ apt-get autoremove && \ rm -rf /var/lib/apt/lists/* -# Build Murfey in a separate image +# Build Murfey and IMOD in a separate image FROM base as build COPY ./ /python-murfey/ RUN apt-get update && \ @@ -22,8 +23,8 @@ RUN apt-get update && \ apt-get install -y --no-install-recommends \ build-essential \ busybox \ - git \ - libpq-dev \ + curl \ + # git \ net-tools \ && \ busybox --install && \ @@ -34,7 +35,11 @@ RUN apt-get update && \ importlib-metadata \ psycopg2-binary \ && \ - /venv/bin/python -m pip install /python-murfey[server] + /venv/bin/python -m pip install /python-murfey[server] && \ + curl https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_5.1.0_RHEL8-64_CUDA12.0.sh > imod_5.1.0_RHEL8-64_CUDA12.0.sh && \ + chmod +x imod_5.1.0_RHEL8-64_CUDA12.0.sh && \ + mkdir imod && \ + ./imod_5.1.0_RHEL8-64_CUDA12.0.sh -dir imod -skip -y # Transfer completed Murfey build to a clean image @@ -45,11 +50,13 @@ ARG groupid ARG groupname ARG userid -# Copy completed Murfey build across and set user and group permissions +# Copy completed Murfey and IMOD builds across and set user and group permissions COPY --from=build /venv/ /venv/ +COPY --from=build /imod/ /imod/ RUN groupadd -r -g "${groupid}" "${groupname}" && \ useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \ chown -R "${userid}":"${groupid}" /venv && \ chmod -R a+x /venv -ENV PATH=/venv/bin:$PATH +ENV PATH=/venv/bin:/imod-install/IMOD/bin:$PATH +ENV IMOD_DIR=/imod-install/IMOD USER "${userid}":"${groupid}" From 0517c26b2f04436f2417c8af251e2fa21736bf34 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Thu, 23 Jan 2025 16:46:08 +0000 Subject: [PATCH 22/30] Fixed comments --- Dockerfiles/murfey-server | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfiles/murfey-server b/Dockerfiles/murfey-server index 275504b87..ce3261743 100644 --- a/Dockerfiles/murfey-server +++ b/Dockerfiles/murfey-server @@ -15,7 +15,7 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* -# Build Murfey and IMOD in a separate image +# Build Murfey and IMOD in a branch image FROM base as build COPY ./ /python-murfey/ RUN apt-get update && \ @@ -42,10 +42,10 @@ RUN apt-get update && \ ./imod_5.1.0_RHEL8-64_CUDA12.0.sh -dir imod -skip -y -# Transfer completed Murfey build to a clean image +# Transfer completed builds to base image FROM base -# Define external build arguments +# Pass external build arguments to this stage ARG groupid ARG groupname ARG userid From 84d933ebd48fe0229efa06675cab9b981d610895 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Thu, 23 Jan 2025 17:50:24 +0000 Subject: [PATCH 23/30] Fixed incorrect environment paths --- Dockerfiles/murfey-server | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfiles/murfey-server b/Dockerfiles/murfey-server index ce3261743..57456ce4a 100644 --- a/Dockerfiles/murfey-server +++ b/Dockerfiles/murfey-server @@ -57,6 +57,6 @@ RUN groupadd -r -g "${groupid}" "${groupname}" && \ useradd -r -M "${groupname}" -u "${userid}" -g "${groupname}" && \ chown -R "${userid}":"${groupid}" /venv && \ chmod -R a+x /venv -ENV PATH=/venv/bin:/imod-install/IMOD/bin:$PATH -ENV IMOD_DIR=/imod-install/IMOD +ENV PATH=/venv/bin:/imod/IMOD/bin:$PATH +ENV IMOD_DIR=/imod/IMOD USER "${userid}":"${groupid}" From 00502e42ffa5a79566a815b0633ae448a3a01fce Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Fri, 24 Jan 2025 11:43:00 +0000 Subject: [PATCH 24/30] Removed confirmed unneeded build dependencies; updated comments --- Dockerfiles/murfey-instrument-server | 8 ++++---- Dockerfiles/murfey-server | 1 - 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/Dockerfiles/murfey-instrument-server b/Dockerfiles/murfey-instrument-server index cf922d24b..9bb4f5acd 100644 --- a/Dockerfiles/murfey-instrument-server +++ b/Dockerfiles/murfey-instrument-server @@ -14,7 +14,7 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* -# Build Murfey in a separate image +# Build Murfey in a branch image FROM base as build COPY ./ /python-murfey/ RUN apt-get update && \ @@ -22,9 +22,9 @@ RUN apt-get update && \ apt-get install -y --no-install-recommends \ build-essential \ busybox \ - git \ net-tools \ - libpq-dev && \ + libpq-dev \ + && \ busybox --install && \ python -m venv /venv && \ /venv/bin/python -m pip install --upgrade \ @@ -34,7 +34,7 @@ RUN apt-get update && \ /venv/bin/python -m pip install /python-murfey[client,instrument-server] -# Transfer completed Murfey build to clean image +# Transfer completed Murfey build to base image FROM base # Define external build arguments diff --git a/Dockerfiles/murfey-server b/Dockerfiles/murfey-server index 57456ce4a..bf2b30ce8 100644 --- a/Dockerfiles/murfey-server +++ b/Dockerfiles/murfey-server @@ -24,7 +24,6 @@ RUN apt-get update && \ build-essential \ busybox \ curl \ - # git \ net-tools \ && \ busybox --install && \ From 54cbb81320ebb00b4a9fb7c19f2ab9e522ed63b4 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Tue, 28 Jan 2025 18:17:29 +0000 Subject: [PATCH 25/30] Added 'rsync' to list of installed packages in instrument server container --- Dockerfiles/murfey-instrument-server | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfiles/murfey-instrument-server b/Dockerfiles/murfey-instrument-server index 9bb4f5acd..f4114e967 100644 --- a/Dockerfiles/murfey-instrument-server +++ b/Dockerfiles/murfey-instrument-server @@ -8,6 +8,7 @@ FROM docker.io/library/python:3.12.8-slim-bullseye AS base RUN apt-get update && \ apt-get upgrade -y && \ apt-get install -y --no-install-recommends \ + rsync \ vim \ && \ apt-get autoremove && \ From 6ee04406b75e0c0b633a085294679a1237809802 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Tue, 28 Jan 2025 18:18:11 +0000 Subject: [PATCH 26/30] Formatting --- Dockerfiles/murfey-instrument-server | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfiles/murfey-instrument-server b/Dockerfiles/murfey-instrument-server index f4114e967..dcd32d45f 100644 --- a/Dockerfiles/murfey-instrument-server +++ b/Dockerfiles/murfey-instrument-server @@ -31,7 +31,7 @@ RUN apt-get update && \ /venv/bin/python -m pip install --upgrade \ pip \ build \ - importlib-metadata &&\ + importlib-metadata && \ /venv/bin/python -m pip install /python-murfey[client,instrument-server] From c349e6e18bdbd38081ceef90922a5a9c00b32f36 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Mon, 10 Feb 2025 10:08:46 +0000 Subject: [PATCH 27/30] Skipped checking YAML files containing template expressions --- .pre-commit-config.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 00200fe5a..5e4d5e440 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -20,6 +20,7 @@ repos: name: Verifying JSON file syntax - id: check-yaml name: Verifying YAML file syntax + exclude: Helm/charts/.*?/templates/deployment\.yaml args: [--allow-multiple-documents] - id: check-toml name: Verifying TOML file syntax From 74b116beada6b975d514a84e4f569e67246e1eef Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Mon, 10 Feb 2025 10:16:34 +0000 Subject: [PATCH 28/30] Configured Prettier hook to ignore deployment.yaml files as well --- .pre-commit-config.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5e4d5e440..04d777267 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -104,4 +104,5 @@ repos: hooks: - id: prettier name: Formatting other file types according to Prettier + exclude: Helm/charts/.*?/templates/deployment\.yaml # types_or: [css, html, json, yaml] From dd0b15314ea3d0614d6a8c93577b99920e5f5b09 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Mon, 10 Feb 2025 10:17:06 +0000 Subject: [PATCH 29/30] Added Helm charts to deploy Murfey's components on a Kubernetes cluster --- Helm/Chart.yaml | 8 ++ .../murfey-instrument-server-clem/Chart.yaml | 4 + .../templates/deployment.yaml | 68 ++++++++++++++++ Helm/charts/murfey-rsync/Chart.yaml | 4 + .../murfey-rsync/templates/deployment.yaml | 62 +++++++++++++++ Helm/charts/murfey-server/Chart.yaml | 4 + .../murfey-server/templates/deployment.yaml | 78 +++++++++++++++++++ 7 files changed, 228 insertions(+) create mode 100644 Helm/Chart.yaml create mode 100644 Helm/charts/murfey-instrument-server-clem/Chart.yaml create mode 100644 Helm/charts/murfey-instrument-server-clem/templates/deployment.yaml create mode 100644 Helm/charts/murfey-rsync/Chart.yaml create mode 100644 Helm/charts/murfey-rsync/templates/deployment.yaml create mode 100644 Helm/charts/murfey-server/Chart.yaml create mode 100644 Helm/charts/murfey-server/templates/deployment.yaml diff --git a/Helm/Chart.yaml b/Helm/Chart.yaml new file mode 100644 index 000000000..f6ffd63ef --- /dev/null +++ b/Helm/Chart.yaml @@ -0,0 +1,8 @@ +apiVersion: v1 +name: murfey-services +description: Umbrella Helm chart for deploying the servers and daemons needed to enable Murfey to transfer and process data +version: 0.16.9 +dependencies: + - name: murfey-instrument-server-clem + - name: murfey-server + - name: murfey-rsync diff --git a/Helm/charts/murfey-instrument-server-clem/Chart.yaml b/Helm/charts/murfey-instrument-server-clem/Chart.yaml new file mode 100644 index 000000000..aa304a3e6 --- /dev/null +++ b/Helm/charts/murfey-instrument-server-clem/Chart.yaml @@ -0,0 +1,4 @@ +apiVersion: v1 +name: murfey-instrument-server-clem +description: Helm chart for deploying a Murfey instrument server, which executes orders to detect, modify, and transfer files on the instrument PC, and notifies the backend server about transferred files +version: 0.16.9 diff --git a/Helm/charts/murfey-instrument-server-clem/templates/deployment.yaml b/Helm/charts/murfey-instrument-server-clem/templates/deployment.yaml new file mode 100644 index 000000000..69fae72ef --- /dev/null +++ b/Helm/charts/murfey-instrument-server-clem/templates/deployment.yaml @@ -0,0 +1,68 @@ +apiVersion: v1 +kind: Service +metadata: + name: {{ .Values.appName }} + namespace: {{ .Values.global.namespace }} + labels: + app: {{ .Values.appName }} +spec: + type: LoadBalancer + externalTrafficPolicy: Cluster + ports: + {{- toYaml .Values.servicePorts | nindent 2 }} + selector: + app: {{ .Values.appName }} +--- +apiVersion: apps/v1 +kind: Deployment +metadata: + name: {{ .Values.appName }} + namespace: {{ .Values.global.namespace }} + labels: + app: {{ .Values.appName }} +spec: + replicas: {{ .Values.replicas }} + selector: + matchLabels: + app: {{ .Values.appName }} + template: + metadata: + labels: + app: {{ .Values.appName }} + spec: + securityContext: + runAsUser: {{ .Values.global.runAsUser }} + runAsGroup: {{ .Values.global.runAsGroup }} + volumes: + # Mount config files from secrets + - name: murfey-client-config + secret: + secretName: {{ .Values.global.murfeyClientConfigCLEMSecretName }} + items: + - key: {{ .Values.global.murfeyClientConfigCLEMFileName }} + path: .murfey + # Mount data directories + {{- toYaml .Values.extraVolumes | nindent 8 }} + containers: + - name: {{ .Values.appName }} + image: {{ .Values.image }} + imagePullPolicy: Always + securityContext: + privileged: false + volumeMounts: + # Mount Murfey client config + - name: murfey-client-config + mountPath: /murfey/config/.murfey + subPath: .murfey + readOnly: false + # Mount data directories + {{- toYaml .Values.extraVolumeMounts | nindent 12 }} + env: + - name: MURFEY_CLIENT_CONFIG_HOME + value: "/tmp" + ports: + - containerPort: {{ .Values.containerPort }} + command: + {{- toYaml .Values.command | nindent 12 }} + args: + {{- toYaml .Values.args | nindent 12 }} diff --git a/Helm/charts/murfey-rsync/Chart.yaml b/Helm/charts/murfey-rsync/Chart.yaml new file mode 100644 index 000000000..8babbb199 --- /dev/null +++ b/Helm/charts/murfey-rsync/Chart.yaml @@ -0,0 +1,4 @@ +apiVersion: v1 +name: murfey-rsync +description: Helm chart for deploying an rsync daemon, which is responsible for executing the transfer of files from the client storage directory to the server storage system +version: 0.16.9 diff --git a/Helm/charts/murfey-rsync/templates/deployment.yaml b/Helm/charts/murfey-rsync/templates/deployment.yaml new file mode 100644 index 000000000..3bbd29dfb --- /dev/null +++ b/Helm/charts/murfey-rsync/templates/deployment.yaml @@ -0,0 +1,62 @@ +apiVersion: v1 +kind: Service +metadata: + name: {{ .Values.appName }} +spec: + ports: + {{- toYaml .Values.servicePorts | nindent 2 }} + selector: + app: {{ .Values.appName }} + type: ClusterIP +--- +apiVersion: apps/v1 +kind: Deployment +metadata: + name: {{ .Values.appName }} + namespace: {{ .Values.global.namespace }} +spec: + replicas: 1 + selector: + matchLabels: + app: {{ .Values.appName }} + template: + metadata: + labels: + app: {{ .Values.appName }} + spec: + securityContext: + runAsUser: {{ .Values.global.runAsUser }} + runAsGroup: {{ .Values.global.runAsGroup }} + volumes: + - name: rsyncd-conf + secret: + secretName: {{ .Values.global.rsyncConfigSecretName }} + items: + - key: {{ .Values.global.rsyncConfigFileName }} + path: rsyncd.conf + # Mount data directories + {{- toYaml .Values.extraVolumes | nindent 8 }} + containers: + - name: {{ .Values.appName }} + image: {{ .Values.image }} + imagePullPolicy: Always + resources: + requests: + cpu: {{ .Values.cpuRequest }} + limits: + cpu: {{ .Values.cpuLimit }} + memory: {{ .Values.memoryLimit }} + volumeMounts: + # Mount rsync config files + - name: rsyncd-conf + mountPath: /murfey/rsync/rsyncd.conf + subPath: rsyncd.conf + readOnly: true + # Mount data directories + {{- toYaml .Values.extraVolumeMounts | nindent 12 }} + ports: + - containerPort: {{ .Values.containerPort }} + command: + {{- toYaml .Values.command | nindent 12 }} + args: + {{- toYaml .Values.args | nindent 12 }} diff --git a/Helm/charts/murfey-server/Chart.yaml b/Helm/charts/murfey-server/Chart.yaml new file mode 100644 index 000000000..c2b7ff143 --- /dev/null +++ b/Helm/charts/murfey-server/Chart.yaml @@ -0,0 +1,4 @@ +apiVersion: v1 +name: murfey-server +description: Helm chart for deploying a Murfey backend server, which is responsible for orchestrating the data transfer and processing workflow between the client PC and the storage system +version: 0.16.9 diff --git a/Helm/charts/murfey-server/templates/deployment.yaml b/Helm/charts/murfey-server/templates/deployment.yaml new file mode 100644 index 000000000..0901e3c24 --- /dev/null +++ b/Helm/charts/murfey-server/templates/deployment.yaml @@ -0,0 +1,78 @@ +apiVersion: v1 +kind: Service +metadata: + name: {{ .Values.appName }} + namespace: {{ .Values.global.namespace }} + labels: + app: {{ .Values.appName }} +spec: + type: LoadBalancer + externalTrafficPolicy: Cluster + ports: + {{- toYaml .Values.servicePorts | nindent 2 }} + selector: + app: {{ .Values.appName }} +--- +apiVersion: apps/v1 +kind: Deployment +metadata: + name: {{ .Values.appName }} + namespace: {{ .Values.global.namespace }} + labels: + app: {{ .Values.appName }} +spec: + replicas: {{ .Values.replicas }} + selector: + matchLabels: + app: {{ .Values.appName }} + template: + metadata: + labels: + app: {{ .Values.appName }} + spec: + securityContext: + runAsUser: {{ .Values.global.runAsUser }} + runAsGroup: {{ .Values.global.runAsGroup }} + volumes: + # Mount config files from secrets + - name: secrets + projected: + sources: + - secret: + name: {{ .Values.global.murfeyMachineConfigSecretName }} + - secret: + name: {{ .Values.global.murfeySecurityConfigSecretName }} + - secret: + name: {{ .Values.global.ispybSecretName }} + - secret: + name: {{ .Values.global.murfeyDBSecretName }} + - secret: + name: {{ .Values.global.rmqSecretName }} + # Mount data directories + {{- toYaml .Values.extraVolumes | nindent 8 }} + containers: + - name: {{ .Values.appName }} + image: {{ .Values.image }} + imagePullPolicy: Always + securityContext: + privileged: false + volumeMounts: + # Mount config files + - name: secrets + mountPath: /murfey/config + readOnly: true + # Mount data directories + {{- toYaml .Values.extraVolumeMounts | nindent 12 }} + env: + - name: MURFEY_MACHINE_CONFIGURATION + value: "/murfey/config/{{ .Values.global.murfeyMachineConfigFileName }}" + - name: MURFEY_SECURITY_CONFIGURATION + value: "/murfey/config/{{ .Values.global.murfeySecurityConfigFileName }}" + - name: ISPYB_CREDENTIALS + value: "/murfey/config/{{ .Values.global.ispybFileName }}" + ports: + - containerPort: {{ .Values.containerPort }} + command: + {{- toYaml .Values.command | nindent 12 }} + args: + {{- toYaml .Values.args | nindent 12 }} From 4bf988a69f668f6e120caa9f7c6b79ce38ccb8ef Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Mon, 10 Feb 2025 10:22:56 +0000 Subject: [PATCH 30/30] Enable automated version bumps of Helm chart versions as well --- .bumpversion.toml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/.bumpversion.toml b/.bumpversion.toml index f2a79f6c7..0090ed5b3 100644 --- a/.bumpversion.toml +++ b/.bumpversion.toml @@ -12,3 +12,23 @@ replace = '__version__ = "{new_version}"' filename = "pyproject.toml" search = 'version = "{current_version}"' replace = 'version = "{new_version}"' + +[[tool.bumpversion.files]] +filename = "Helm/Chart.yaml" +search = 'version: {current_version}' +replace = 'version: {new_version}' + +[[tool.bumpversion.files]] +filename = "Helm/charts/murfey-instrument-server-clem/Chart.yaml" +search = 'version: {current_version}' +replace = 'version: {new_version}' + +[[tool.bumpversion.files]] +filename = "Helm/charts/murfey-rsync/Chart.yaml" +search = 'version: {current_version}' +replace = 'version: {new_version}' + +[[tool.bumpversion.files]] +filename = "Helm/charts/murfey-server/Chart.yaml" +search = 'version: {current_version}' +replace = 'version: {new_version}'