Merge pull request #1504 from willdunklin/amend-dicomweb-assetstore

Make DICOMweb assetstore imports compatible with Girder generics

sources/dicom/large_image_source_dicom/assetstore/dicomweb_assetstore_adapter.py

@@ -1,3 +1,5 @@
+import json
+
 import cherrypy
 import requests
 from large_image_source_dicom.dicom_tags import dicom_key_to_tag
@@ -394,31 +396,10 @@ def _infer_file_size_singlepart_content_length(self, file):
         except ValueError:
             return
 
-    def importData(self, parent, parentType, params, progress, user, **kwargs):
-        """
-        Import DICOMweb WSI instances from a DICOMweb server.
-
-        :param parent: The parent object to import into.
-        :param parentType: The model type of the parent object.
-        :type parentType: str
-        :param params: Additional parameters required for the import process.
-            This dictionary may include the following keys:
-
-            :limit: (optional) limit the number of studies imported.
-            :search_filters: (optional) a dictionary of additional search
-                filters to use with dicomweb_client's `search_for_series()`
-                function.
-
-        :type params: dict
-        :param progress: Object on which to record progress if possible.
-        :type progress: :py:class:`girder.utility.progress.ProgressContext`
-        :param user: The Girder user performing the import.
-        :type user: dict or None
-        :return: a list of items that were created
-        """
+    def _importData(self, parent, parentType, params, progress, user):
         if parentType not in ('folder', 'user', 'collection'):
             msg = f'Invalid parent type: {parentType}'
-            raise RuntimeError(msg)
+            raise ValidationException(msg)
 
         limit = params.get('limit')
         search_filters = params.get('search_filters', {})
@@ -512,6 +493,65 @@ def importData(self, parent, parentType, params, progress, user, **kwargs):
 
         return items
 
+    def importData(self, parent, parentType, params, progress, user, **kwargs):
+        """
+        Import DICOMweb WSI instances from a DICOMweb server.
+
+        :param parent: The parent object to import into.
+        :param parentType: The model type of the parent object.
+        :type parentType: str
+        :param params: Additional parameters required for the import process.
+            This dictionary may include the following keys:
+
+            :limit: (optional) limit the number of studies imported.
+            :filters: (optional) a dictionary/JSON string of additional search
+                filters to use with dicomweb_client's `search_for_series()`
+                function.
+
+        :type params: dict
+        :param progress: Object on which to record progress if possible.
+        :type progress: :py:class:`girder.utility.progress.ProgressContext`
+        :param user: The Girder user performing the import.
+        :type user: dict or None
+        :return: a list of items that were created
+        """
+        # Validate the parameters
+        limit = params.get('limit') or None
+        if limit is not None:
+            error_msg = f'Invalid limit: {limit}'
+            try:
+                limit = int(limit)
+            except ValueError:
+                raise ValidationException(error_msg)
+
+            if limit < 1:
+                raise ValidationException(error_msg)
+
+        search_filters = params.get('filters', {})
+        if isinstance(search_filters, str):
+            try:
+                search_filters = json.loads(search_filters)
+            except json.JSONDecodeError as e:
+                msg = f'Invalid filters: "{params.get("filters")}". {e}'
+                raise ValidationException(msg)
+
+        items = self._importData(
+            parent,
+            parentType,
+            {
+                'limit': limit,
+                'search_filters': search_filters,
+            },
+            progress,
+            user,
+        )
+
+        if not items:
+            msg = 'No studies matching the search filters were found'
+            raise ValidationException(msg)
+
+        return items
+
     @property
     def auth_session(self):
         return _create_auth_session(self.assetstore_meta)

sources/dicom/large_image_source_dicom/assetstore/rest.py

@@ -1,15 +1,14 @@
-import json
-
 from girder.api import access
 from girder.api.describe import Description, autoDescribeRoute
 from girder.api.rest import Resource
 from girder.constants import TokenScope
 from girder.exceptions import RestException
 from girder.models.assetstore import Assetstore
-from girder.utility import assetstore_utilities
 from girder.utility.model_importer import ModelImporter
 from girder.utility.progress import ProgressContext
 
+from .dicomweb_assetstore_adapter import DICOMwebAssetstoreAdapter
+
 
 class DICOMwebAssetstoreResource(Resource):
     def __init__(self):
@@ -34,39 +33,14 @@ def _importData(self, assetstore, params, progress):
         parent = ModelImporter.model(destinationType).load(params['destinationId'], force=True,
                                                            exc=True)
 
-        limit = params.get('limit') or None
-        if limit is not None:
-            error_msg = 'Invalid limit'
-            try:
-                limit = int(limit)
-            except ValueError:
-                raise RestException(error_msg)
-
-            if limit < 1:
-                raise RestException(error_msg)
-
-        try:
-            search_filters = json.loads(params.get('filters') or '{}')
-        except json.JSONDecodeError as e:
-            msg = f'Invalid filters: {e}'
-            raise RestException(msg)
-
-        adapter = assetstore_utilities.getAssetstoreAdapter(assetstore)
-        items = adapter.importData(
+        return DICOMwebAssetstoreAdapter(assetstore).importData(
             parent,
             destinationType,
-            {
-                'limit': limit,
-                'search_filters': search_filters,
-            },
+            params,
             progress,
             user,
         )
 
-        if not items:
-            msg = 'No studies matching the search filters were found'
-            raise RestException(msg)
-
     @access.admin(scope=TokenScope.DATA_WRITE)
     @autoDescribeRoute(
         Description('Import references to DICOM objects from a DICOMweb server')

sources/dicom/large_image_source_dicom/web_client/main.js

@@ -1,7 +1,6 @@
-import './routes';
-
 // Extends and overrides API
 import './constants';
+import './views/DICOMwebImportView';
 import './views/AssetstoresView';
 import './views/EditAssetstoreWidget';
 import './views/NewAssetstoreWidget';

sources/dicom/large_image_source_dicom/web_client/templates/dicomwebAssetstoreImportButton.pug

@@ -1,6 +1,6 @@
 .g-assetstore-import-button-container
   a.g-dwas-import-button.btn.btn-sm.btn-success(
-      href=`#dicomweb_assetstore/${assetstore.get('_id')}/import`,
+      href=`#assetstore/${assetstore.get('_id')}/import`,
       title="Import references to DICOM objects from a DICOMweb server")
     i.icon-link-ext
     |  Import data

sources/dicom/large_image_source_dicom/web_client/views/DICOMwebImportView.js

@@ -5,6 +5,9 @@ import router from '@girder/core/router';
 import View from '@girder/core/views/View';
 import { restRequest } from '@girder/core/rest';
 
+import { assetstoreImportViewMap } from '@girder/core/views/body/AssetstoresView';
+import { AssetstoreType } from '@girder/core/constants';
+
 import DWASImportTemplate from '../templates/assetstoreImport.pug';
 
 const DICOMwebImportView = View.extend({
@@ -24,12 +27,12 @@ const DICOMwebImportView = View.extend({
             }
 
             this.$('.g-submit-dwas-import').addClass('disabled');
-            this.model.off().on('g:imported', function () {
+            this.assetstore.off().on('g:imported', function () {
                 router.navigate(destinationType + '/' + destinationId, { trigger: true });
             }, this).on('g:error', function (err) {
                 this.$('.g-submit-dwas-import').removeClass('disabled');
                 this.$('.g-validation-failed-message').html(err.responseJSON.message);
-            }, this).dicomwebImport({
+            }, this).import({
                 destinationId,
                 destinationType,
                 limit,
@@ -40,7 +43,7 @@ const DICOMwebImportView = View.extend({
         'click .g-open-browser': '_openBrowser'
     },
 
-    initialize: function () {
+    initialize: function (settings) {
         this._browserWidgetView = new BrowserWidget({
             parentView: this,
             titleText: 'Destination',
@@ -75,12 +78,13 @@ const DICOMwebImportView = View.extend({
                 }
             });
         });
+        this.assetstore = settings.assetstore;
         this.render();
     },
 
     render: function () {
         this.$el.html(DWASImportTemplate({
-            assetstore: this.model
+            assetstore: this.assetstore
         }));
 
         return this;
@@ -91,4 +95,6 @@ const DICOMwebImportView = View.extend({
     }
 });
 
+assetstoreImportViewMap[AssetstoreType.DICOMWEB] = DICOMwebImportView;
+
 export default DICOMwebImportView;

sources/dicom/setup.py

@@ -41,11 +41,14 @@ def prerelease_local_scheme(version):
     ],
 }
 
+girder_extras = [f'girder-large-image{limit_version}']
+
 if sys.version_info >= (3, 9):
     # For Python >= 3.9, include the DICOMweb plugin
     entry_points['girder.plugin'] = [
         'dicomweb = large_image_source_dicom.girder_plugin:DICOMwebPlugin',
     ]
+    girder_extras.append('girder>=3.2.3')
 
 setup(
     name='large-image-source-dicom',
@@ -71,7 +74,7 @@ def prerelease_local_scheme(version):
         'wsidicom>=0.9.0',
     ],
     extras_require={
-        'girder': f'girder-large-image{limit_version}',
+        'girder': girder_extras,
     },
     include_package_data=True,
     keywords='large_image, tile source',

sources/dicom/test_dicom/web_client_specs/dicomWebSpec.js

@@ -143,7 +143,7 @@ describe('DICOMWeb assetstore', function () {
         });
 
         waitsFor(function () {
-            return $('.g-validation-failed-message').html() === 'Invalid limit';
+            return $('.g-validation-failed-message').html() === 'Invalid limit: 1.3';
         }, 'Invalid limit check (float)');
 
         runs(function () {
@@ -156,7 +156,7 @@ describe('DICOMWeb assetstore', function () {
         });
 
         waitsFor(function () {
-            return $('.g-validation-failed-message').html() === 'Invalid limit';
+            return $('.g-validation-failed-message').html() === 'Invalid limit: -1';
         }, 'Invalid limit check (negative)');
 
         runs(function () {