Merge pull request #25 from DigitalSlideArchive/add-dicomweb-support

Add initial DICOMweb assetstore support
DigitalSlideArchive · Nov 8, 2023 · ba13e01 · ba13e01
2 parents 102f727 + 3330e96
commit ba13e01
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Showing 4 changed files with 154 additions and 26 deletions.
diff --git a/import_tracker/__init__.py b/import_tracker/__init__.py
@@ -1,6 +1,6 @@
 import time
 
-from girder import plugin
+from girder import logger, plugin
 from girder.api.describe import autoDescribeRoute
 from girder.api.rest import boundHandler
 from girder.constants import AccessType
@@ -162,12 +162,100 @@ def shouldImportFileWrapper(self, path, params):
     AbstractAssetstoreAdapter.shouldImportFile = shouldImportFileWrapper
 
 
+def wrapDICOMImport(assetstoreResource):
+    baseImportData = assetstoreResource.importData
+    baseImportData.description.param(
+        'excludeExisting',
+        'If true, then a file with an import path that is already in the '
+        'system is not imported, even if it is not in the destination '
+        'hierarchy.', dataType='boolean', required=False, default=False)
+
+    @boundHandler(ctx=assetstoreResource)
+    @autoDescribeRoute(baseImportData.description)
+    def dwaImportDataWrapper(self, assetstore, destinationId, destinationType, filters,
+                             progress, excludeExisting):
+
+        user = self.getCurrentUser()
+        params = {
+            'destinationId': destinationId,
+            'destinationType': destinationType,
+            'filters': filters,
+            'progress': str(progress).lower(),
+        }
+        if excludeExisting:
+            params['excludeExisting'] = str(excludeExisting).lower()
+
+        importRecord = AssetstoreImport().createAssetstoreImport(assetstore, params)
+        job = Job().createJob(
+            title=f'Import from {assetstore["name"]}',
+            type='assetstore_import',
+            public=False,
+            user=user,
+            kwargs=params,
+        )
+        job = Job().updateJob(job, '%s - Starting import from %s\n' % (
+            time.strftime('%Y-%m-%d %H:%M:%S'),
+            assetstore['name']
+        ), status=JobStatus.RUNNING)
+
+        try:
+            with ProgressContext(progress, user=user, title='Importing data') as ctx:
+                try:
+                    jobRec = {
+                        'id': str(job['_id']),
+                        'count': 0,
+                        'skip': 0,
+                        'lastlog': time.time(),
+                        'logcount': 0,
+                    }
+                    self._importData(
+                        assetstore,
+                        params={
+                            **params,
+                            '_job': jobRec},
+                        progress=ctx)
+
+                    success = True
+                    Job().updateJob(job, '%s - Finished.  Checked %d, skipped %d\n' % (
+                        time.strftime('%Y-%m-%d %H:%M:%S'),
+                        jobRec['count'], jobRec['skip'],
+                    ), status=JobStatus.SUCCESS)
+
+                except ImportTrackerCancelError:
+                    Job().updateJob(job, '%s - Canceled' % (
+                        time.strftime('%Y-%m-%d %H:%M:%S'),
+                    ))
+                    success = 'canceled'
+
+        except Exception as exc:
+            Job().updateJob(job, '%s - Failed with %s\n' % (
+                time.strftime('%Y-%m-%d %H:%M:%S'),
+                exc,
+            ), status=JobStatus.ERROR)
+            success = False
+
+        importRecord = AssetstoreImport().markEnded(importRecord, success)
+        return importRecord
+
+    for key in {'accessLevel', 'description', 'requiredScopes'}:
+        setattr(dwaImportDataWrapper, key, getattr(baseImportData, key))
+
+    assetstoreResource.importData = dwaImportDataWrapper
+    assetstoreResource.removeRoute('POST', (':id', 'import'))
+    assetstoreResource.route('POST', (':id', 'import'), assetstoreResource.importData)
+
+
 class GirderPlugin(plugin.GirderPlugin):
     DISPLAY_NAME = 'import_tracker'
     CLIENT_SOURCE_PATH = 'web_client'
 
     def load(self, info):
         plugin.getPlugin('jobs').load(info)
+        try:
+            import large_image_source_dicom  # noqa
+            plugin.getPlugin('dicomweb').load(info)
+        except ImportError:
+            pass
         ModelImporter.registerModel(
             'assetstoreImport', AssetstoreImport, 'import_tracker'
         )
@@ -178,3 +266,8 @@ def load(self, info):
         wrapImportData(info['apiRoot'].assetstore)
 
         info['apiRoot'].folder.route('PUT', (':id', 'move'), moveFolder)
+
+        if hasattr(info['apiRoot'], 'dicomweb_assetstore'):
+            wrapDICOMImport(info['apiRoot'].dicomweb_assetstore)
+        else:
+            logger.info('dicomweb_assetstore not found')
diff --git a/import_tracker/web_client/main.js b/import_tracker/web_client/main.js
@@ -1,3 +1,5 @@
+import $ from 'jquery';
+
 import AssetstoreView from '@girder/core/views/body/AssetstoresView';
 import FilesystemImportView from '@girder/core/views/body/FilesystemImportView';
 import S3ImportView from '@girder/core/views/body/S3ImportView';
@@ -22,16 +24,23 @@ import './JobStatus';
 wrap(AssetstoreView, 'render', function (render) {
     // Call the underlying render function that we are wrapping
     render.call(this);
-
-    this.$el.find('.g-current-assetstores-container .g-body-title').after(
-        '<a class="g-view-imports btn btn-sm btn-primary" href="#assetstore/all_imports"><i class="icon-link-ext"></i>View all past Imports</a>'
-    );
-
-    // Inject new button into each assetstore
-    const assetstores = this.collection.toArray();
-    this.$('.g-assetstore-import-button-container').after(
-        (i) => importDataButton({ importsPageLink: `#assetstore/${assetstores[i].id}/imports` })
-    );
+    // defer adding buttons so optional plugins can render first.
+    window.setTimeout(() => {
+        this.$el.find('.g-current-assetstores-container .g-body-title').after(
+            '<a class="g-view-imports btn btn-sm btn-primary" href="#assetstore/all_imports"><i class="icon-link-ext"></i>View all past Imports</a>'
+        );
+
+        // Inject new button into each assetstore
+        const assetstores = this.collection;
+        this.$('.g-assetstore-import-button-container').after(
+            function () {
+                // we can't just use the index of the after call, since not
+                // all assetstores will have import buttons.
+                const assetstore = assetstores.get($(this).closest('.g-assetstore-buttons').find('[cid]').attr('cid'));
+                return importDataButton({ importsPageLink: `#assetstore/${assetstore.id}/imports` });
+            }
+        );
+    }, 0);
 });
 
 // Add duplicate_files option to Import Asset form

diff --git a/import_tracker/web_client/templates/importList.pug b/import_tracker/web_client/templates/importList.pug
@@ -21,7 +21,8 @@ table.g-imports-list-table
   -
     var anyRegex = false;
     var anyLeafed = false;
-    var anyNoProgress;
+    var anyImportPath = false;
+    var anyNoProgress = false;
     var otherParams = [];
     var showCount = false;
   for _import in imports
@@ -31,9 +32,11 @@ table.g-imports-list-table
       - anyLeafed = true
     if !_import.params.progress
       - anyNoProgress = true
-    - Object.keys(_import.params).forEach((key) => { if (['importPath', 'destinationId', 'destinationType', 'leafFoldersAsItems', 'progress', 'fileIncludeRegex', 'fileExcludeRegex'].indexOf(key) < 0 && otherParams.indexOf(key) < 0) { otherParams.push(key); } });
+    - Object.keys(_import.params).forEach((key) => { if (['importPath', 'destinationId', 'leafFoldersAsItems', 'progress', 'fileIncludeRegex', 'fileExcludeRegex'].indexOf(key) < 0 && otherParams.indexOf(key) < 0) { otherParams.push(key); } });
     if _import._count
-      - showCount = true;
+      - showCount = true
+    if _import.params.importPath
+      - anyImportPath = true
   thead
     tr
       th Actions
@@ -42,7 +45,8 @@ table.g-imports-list-table
       th Started
       th Ended
       th Assetstore Name
-      th Import Path
+      if anyImportPath
+        th Import Path
       //- th Destination Type
       th Destination Path
       if anyLeafed
@@ -59,11 +63,11 @@ table.g-imports-list-table
       tr
         td
           if assetstoreExists[i]
-            div(style='display: flex; justify-content: flex-end;')
+            div(style='display: flex; padding-left: 10px; padding-right: 10px;')
               button.re-import-btn.btn.btn-sm.btn-success(index=i, disabled=(_import._destinationPath =='does not exist'))
                 i.icon-cw
                 |  Re-Import
-              button.re-import-edit-btn.btn.btn-sm.btn-primary(index=i, style='margin-left: 5px;', data-toggle='tooltip', title='Edit Import Parameters')
+              button.re-import-edit-btn.btn.btn-sm.btn-primary(index=i, style='margin-left: 1em;', data-toggle='tooltip', title='Edit Import Parameters')
                 i.icon-pencil
         if showCount
           td(data-id=_import._count, data-toggle='tooltip', title=_import._count !== 1 ? `Imported ${_import._count} times` : 'Imported once')
@@ -74,11 +78,9 @@ table.g-imports-list-table
           span= _import.ended ? moment(_import.ended).format('YYYY-MM-DD HH:mm:ss.SSS') : ''
         td(data-id=_import._assetstoreName, data-toggle='tooltip', title=_import._assetstoreName)
           span= _import._assetstoreName
-        td(data-id=_import.params.importPath, data-toggle='tooltip', title=_import.params.importPath)
-          span= _import.params.importPath
-        //-
-          td
-            span= _import.params.destinationType
+        if anyImportPath
+          td(data-id=_import.params.importPath, data-toggle='tooltip', title=_import.params.importPath)
+            span= _import.params.importPath
         td(data-id=_import.params.destinationId, data-toggle='tooltip', title=_import._destinationPath + '\n' + _import.params.destinationId)
           span= _import._destinationPath
         if anyLeafed

diff --git a/import_tracker/web_client/views/importList.js b/import_tracker/web_client/views/importList.js
@@ -2,6 +2,7 @@ import $ from 'jquery';
 import moment from 'moment';
 
 import AssetstoreModel from '@girder/core/models/AssetstoreModel';
+import { AssetstoreType } from '@girder/core/constants';
 import View from '@girder/core/views/View';
 import router from '@girder/core/router';
 import { restRequest } from '@girder/core/rest';
@@ -22,11 +23,20 @@ var importList = View.extend({
             const assetstore = new AssetstoreModel({ _id: importEvent.assetstoreId });
             const destType = importEvent.params.destinationType;
             const destId = importEvent.params.destinationId;
+
             assetstore.off('g:imported').on('g:imported', function () {
                 router.navigate(destType + '/' + destId, { trigger: true });
             }, this).on('g:error', function (resp) {
                 this.$('.g-validation-failed-message').text(resp.responseJSON.message);
-            }, this).import(importEvent.params);
+            }, this);
+
+            assetstore.once('g:fetched', () => {
+                if (assetstore.get('type') === AssetstoreType.DICOMWEB) {
+                    assetstore.dicomwebImport(importEvent.params);
+                } else {
+                    assetstore.import(importEvent.params);
+                }
+            }).fetch();
         },
         'click .re-import-edit-btn': function (e) {
             const index = Number($(e.currentTarget).attr('index'));
@@ -35,10 +45,24 @@ var importList = View.extend({
                 return;
             }
 
+            // Navigate to re-import page
+            const navigate = (assetstoreId, importId) => {
+                const assetstore = new AssetstoreModel({ _id: assetstoreId });
+                assetstore.once('g:fetched', () => {
+                    if (assetstore.get('type') === AssetstoreType.DICOMWEB) {
+                        // Avoid adding previous import data for DICOMweb imports by navigating to blank import
+                        // TODO: Add DICOMweb-specific re-import view
+                        router.navigate(`dicomweb_assetstore/${assetstoreId}/import`, { trigger: true });
+                    } else {
+                        router.navigate(`assetstore/${assetstoreId}/re-import/${importId}`, { trigger: true });
+                    }
+                }).fetch();
+            };
+
             const assetstoreId = importEvent.assetstoreId;
-            const importId = importEvent._id;
+            const importId = importEvent._id; // Only individual imports have an _id
             if (importId) {
-                router.navigate(`assetstore/${assetstoreId}/re-import/${importId}`, { trigger: true });
+                navigate(assetstoreId, importId);
                 return;
             }
 
@@ -53,7 +77,7 @@ var importList = View.extend({
                     i.params.destinationType === importEvent.params.destinationType
                 )[0]._id;
 
-                router.navigate(`assetstore/${assetstoreId}/re-import/${importId}`, { trigger: true });
+                navigate(assetstoreId, importId);
             });
         }
     },