Convert to Girder 5

Author: zachmullen

setup.py

@@ -63,13 +63,13 @@ def prerelease_local_scheme(version):
     ],
     extras_require={
         'girder': [
-            'girder>=3.0.4',
-            'girder-jobs>=3.0.3',
-            'girder-worker[girder]>=0.6.0',
+            'girder>=5.0.0a2',
+            'girder-jobs>=5.0.0a2',
+            'girder-worker[girder]>=5',
         ],
         'worker': [
             'docker>=2.6.0',
-            'girder-worker[worker]>=0.6.0',
+            'girder-worker[worker]>=5',
         ],
         'client': [
             'click',

slicer_cli_web/cli_list_entrypoint.py

@@ -1,14 +1,12 @@
 import argparse
 import json
+import logging
 import os
 import subprocess
 import sys
 import textwrap as _textwrap
 
-try:
-    from girder import logger
-except ImportError:
-    import logging as logger
+logger = logging.getLogger(__name__)
 
 
 class _MultilineHelpFormatter(argparse.HelpFormatter):

slicer_cli_web/girder_plugin.py

@@ -16,18 +16,22 @@
 
 import datetime
 import json
+import logging
 import os
+from pathlib import Path
 
-from girder import events, logger
+from girder import events
 from girder.constants import AccessType, TokenScope
-from girder.plugin import GirderPlugin, getPlugin
+from girder.plugin import GirderPlugin, getPlugin, registerPluginStaticContent
 from girder_jobs.constants import JobStatus
 from girder_jobs.models.job import Job
 
 from . import TOKEN_SCOPE_MANAGE_TASKS
 from .docker_resource import DockerResource
 from .models import DockerImageItem
 
+logger = logging.getLogger(__name__)
+
 
 def _onUpload(event):
     try:
@@ -48,13 +52,20 @@ def _onUpload(event):
 
 class SlicerCLIWebPlugin(GirderPlugin):
     DISPLAY_NAME = 'Slicer CLI Web'
-    CLIENT_SOURCE_PATH = 'web_client'
 
     def load(self, info):
         try:
             getPlugin('worker').load(info)
         except Exception:
-            logger.info('Girder working is unavailable')
+            logger.info('Girder worker is unavailable')
+
+        registerPluginStaticContent(
+            'slicer_cli_web',
+            css=['/style.css'],
+            js=['/girder-plugin-slicer-cli-web.umd.cjs'],
+            staticDir=Path(__file__).parent / 'web_client' / 'dist',
+            tree=info['serverRoot'],
+        )
 
         TokenScope.describeScope(
             TOKEN_SCOPE_MANAGE_TASKS, name='Manage Slicer CLI tasks',

slicer_cli_web/prepare_task.py

@@ -1,8 +1,8 @@
 import json
+import logging
 import os
 
 import jinja2
-from girder import logger
 from girder.api.rest import RestException
 from girder.constants import AccessType
 from girder.exceptions import FilePathException
@@ -17,6 +17,8 @@
 OPENAPI_DIRECT_TYPES = {'boolean', 'integer', 'float', 'double', 'string'}
 FOLDER_SUFFIX = '_folder'
 
+logger = logging.getLogger(__name__)
+
 
 def _to_file_volume(param, model):
     from girder_worker.docker.transforms.girder import (GirderFileIdToVolume,

slicer_cli_web/rest_slicer_cli.py

@@ -1,12 +1,12 @@
 import copy
 import itertools
 import json
+import logging
 import threading
 import time
 
 import cherrypy
 from bson.objectid import ObjectId
-from girder import logger
 from girder.api import access
 from girder.api.describe import Description, describeRoute
 from girder.api.rest import Resource, RestException, boundHandler, getApiUrl, getCurrentToken
@@ -30,6 +30,8 @@
 directory, geometry, transform, measurement, table).
 """
 
+logger = logging.getLogger(__name__)
+
 
 def stringifyParam(param):
     newparam = param.__class__()

slicer_cli_web/web_client/JobStatus.js

@@ -1,10 +1,14 @@
-import JobStatus from '@girder/jobs/JobStatus';
+const events = girder.events;
 
-const jobPluginIsCancelable = JobStatus.isCancelable;
-JobStatus.isCancelable = function (job) {
-    if (job.get('type').startsWith('slicer_cli_web_batch')) {
-        return ![JobStatus.CANCELED, JobStatus.WORKER_CANCELING || 824,
-            JobStatus.SUCCESS, JobStatus.ERROR].includes(job.get('status'));
-    }
-    return jobPluginIsCancelable(job);
-};
+// g:appload.before runs after all plugin static files have been loaded
+events.on('g:appload.before', () => {
+    const JobStatus = girder.plugins.jobs.JobStatus;
+    const jobPluginIsCancelable = JobStatus.isCancelable;
+    JobStatus.isCancelable = function (job) {
+        if (job.get('type').startsWith('slicer_cli_web_batch')) {
+            return ![JobStatus.CANCELED, JobStatus.WORKER_CANCELING || 824,
+                JobStatus.SUCCESS, JobStatus.ERROR].includes(job.get('status'));
+        }
+        return jobPluginIsCancelable(job);
+    };
+});

slicer_cli_web/web_client/collections/WidgetCollection.js

@@ -1,7 +1,7 @@
-import Backbone from 'backbone';
-
 import WidgetModel from '../models/WidgetModel';
 
+const Backbone = girder.Backbone;
+
 const WidgetCollection = Backbone.Collection.extend({
     model: WidgetModel,
 

slicer_cli_web/web_client/events.js

@@ -1,3 +1,3 @@
-import girderEvents from '@girder/core/events';
+const girderEvents = girder.events;
 
 export default girderEvents;

slicer_cli_web/web_client/main.js

@@ -1,5 +1,3 @@
-import { registerPluginNamespace } from '@girder/core/pluginUtils';
-
 // import modules for side effects
 import './routes';
 import './views/ItemView';
@@ -8,4 +6,6 @@ import './JobStatus';
 
 // expose symbols under girder.plugins
 import * as slicerCLIWeb from './index';
+
+const { registerPluginNamespace } = girder.pluginUtils;
 registerPluginNamespace('slicer_cli_web', slicerCLIWeb);

slicer_cli_web/web_client/models/WidgetModel.js

@@ -1,7 +1,8 @@
-import _ from 'underscore';
-import Backbone from 'backbone';
 import tinycolor from 'tinycolor2';
 
+const _ = girder._;
+const Backbone = girder.Backbone;
+
 /**
  * A backbone model controlling the behavior and rendering of widgets.
  */