Merge pull request #1327 from psavery/dicomweb-filters

Add DICOMweb filters and "limit" parameter

sources/dicom/large_image_source_dicom/assetstore/dicomweb_assetstore_adapter.py

@@ -118,12 +118,13 @@ def importData(self, parent, parentType, params, progress, user, **kwargs):
         :param params: Additional parameters required for the import process.
             This dictionary may include the following keys:
 
-            :auth: (optional) if the DICOMweb server requires authentication,
-                this should be an authentication handler derived from
-                requests.auth.AuthBase.
+            :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.
+            :auth: (optional) if the DICOMweb server requires authentication,
+                this should be an authentication handler derived from
+                requests.auth.AuthBase.
 
         :type params: dict
         :param progress: Object on which to record progress if possible.
@@ -138,6 +139,7 @@ def importData(self, parent, parentType, params, progress, user, **kwargs):
 
         from wsidicom.uid import WSI_SOP_CLASS_UID
 
+        limit = params.get('limit')
         search_filters = params.get('search_filters', {})
 
         meta = self.assetstore[DICOMWEB_META_KEY]
@@ -148,7 +150,9 @@ def importData(self, parent, parentType, params, progress, user, **kwargs):
         series_uid_key = dicom_key_to_tag('SeriesInstanceUID')
 
         # We are only searching for WSI datasets. Ignore all others.
-        # FIXME: is this actually working?
+        # FIXME: is this actually working? For the SLIM server at
+        # https://imagingdatacommons.github.io/slim/, none of the series
+        # report a SOPClassUID, but we still get all results anyways.
         search_filters = {
             'SOPClassUID': WSI_SOP_CLASS_UID,
             **search_filters,
@@ -162,8 +166,7 @@ def importData(self, parent, parentType, params, progress, user, **kwargs):
 
         # FIXME: might need to search in chunks for larger web servers
         series_results = client.search_for_series(
-            fields=fields, search_filters=search_filters)
-
+            fields=fields, limit=limit, search_filters=search_filters)
         items = []
         for i, result in enumerate(series_results):
             if progress:

sources/dicom/large_image_source_dicom/assetstore/rest.py

@@ -1,3 +1,5 @@
+import json
+
 from girder.api import access
 from girder.api.describe import Description, describeRoute
 from girder.api.rest import Resource, loadmodel
@@ -32,24 +34,46 @@ def _importData(self, assetstore, params):
         parent = ModelImporter.model(parentType).load(params['parentId'], 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)
+
         progress = self.boolParam('progress', params, default=False)
 
         adapter = assetstore_utilities.getAssetstoreAdapter(assetstore)
 
         with ProgressContext(
             progress, user=user, title='Importing DICOM references',
         ) as ctx:
-            adapter.importData(
+            items = adapter.importData(
                 parent,
                 parentType,
                 {
-                    'search_filters': params.get('filters', {}),
+                    'limit': limit,
+                    'search_filters': search_filters,
                     'auth': None,
                 },
                 ctx,
                 user,
             )
 
+            if not items:
+                msg = 'No DICOM objects matching the search filters were found'
+                raise RestException(msg)
+
     @access.admin
     @loadmodel(model='assetstore')
     @describeRoute(
@@ -61,6 +85,8 @@ def _importData(self, assetstore, params):
         .param('parentType', 'The type of the parent object to import into.',
                enum=('folder', 'user', 'collection'),
                required=False)
+        .param('limit', 'The maximum number of results to import.',
+               required=False, dataType='int')
         .param('filters', 'Any search parameters to filter DICOM objects.',
                required=False)
         .param('progress', 'Whether to record progress on this operation ('

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

@@ -21,6 +21,12 @@ form.g-dwas-import-form
       .input-group-btn
         button.g-open-browser.btn.btn-default(type="button")
           i.icon-folder-open
+    label(for="g-dwas-import-limit") Limit (Studies)
+    input#g-dwas-import-limit.form-control(
+        type="number", step="1", min="1", value="")
+    label(for="g-dwas-import-filters") Filters
+    textarea#g-dwas-import-filters.form-control(rows="10",
+        placeholder="Valid JSON. e.g.:\n\n{\n    \"PatientID\": \"ABC123\"\n}")
   .g-validation-failed-message
   button.g-submit-assetstore-import.btn.btn-success(type="submit")
     i.icon-link-ext

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

@@ -12,19 +12,28 @@ const AssetstoreImportView = View.extend({
         'submit .g-dwas-import-form': function (e) {
             e.preventDefault();
             this.$('.g-validation-failed-message').empty();
-            this.$('.g-submit-dwas-import').addClass('disabled');
 
             const parentType = this.$('#g-dwas-import-dest-type').val();
             const parentId = this.$('#g-dwas-import-dest-id').val().trim().split(/\s/)[0];
+            const filters = this.$('#g-dwas-import-filters').val().trim();
+            const limit = this.$('#g-dwas-import-limit').val().trim();
+
+            if (!parentId) {
+                this.$('.g-validation-failed-message').html('Invalid Destination ID');
+                return;
+            }
 
+            this.$('.g-submit-dwas-import').addClass('disabled');
             this.model.off().on('g:imported', function () {
                 router.navigate(parentType + '/' + parentId, { trigger: true });
             }, this).on('g:error', function (err) {
                 this.$('.g-submit-dwas-import').removeClass('disabled');
-                this.$('.g-validation-failed-message').html(err.responseText);
+                this.$('.g-validation-failed-message').html(err.responseJSON.message);
             }, this).dicomwebImport({
                 parentId,
                 parentType,
+                limit,
+                filters,
                 progress: true
             });
         },

sources/dicom/test_dicom/web_client_specs/dicomWebSpec.js

@@ -92,9 +92,75 @@ describe('DICOMWeb assetstore', function () {
         }, 'Import page to load');
 
         runs(function () {
-            // Set the needed options and begin the import
+            // In the import page, trigger a few errors to check validation.
+            // Test error when no ID is set.
+            $('.g-submit-assetstore-import').trigger('click');
+        });
+
+        waitsFor(function () {
+            return $('.g-validation-failed-message').html() === 'Invalid Destination ID';
+        }, 'Invalid ID check');
+
+        runs(function () {
+            // Set dest type and dest id
             $('#g-dwas-import-dest-type').val(parentType);
             $('#g-dwas-import-dest-id').val(parentId);
+
+            // Test error for an invalid limit
+            $('#g-dwas-import-limit').val('1.3');
+            $('.g-submit-assetstore-import').trigger('click');
+        });
+
+        waitsFor(function () {
+            return $('.g-validation-failed-message').html() === 'Invalid limit';
+        }, 'Invalid limit check (float)');
+
+        runs(function () {
+            // Make sure this is cleared (we will be checking the same message).
+            $('.g-validation-failed-message').html('');
+
+            // Test error for negative limit
+            $('#g-dwas-import-limit').val('-1');
+            $('.g-submit-assetstore-import').trigger('click');
+        });
+
+        waitsFor(function () {
+            return $('.g-validation-failed-message').html() === 'Invalid limit';
+        }, 'Invalid limit check (negative)');
+
+        runs(function () {
+            // Fix the limit
+            $('#g-dwas-import-limit').val('1');
+
+            // Test error for invalid JSON in the filters parameter
+            const filters = '{';
+            $('#g-dwas-import-filters').val(filters);
+            $('.g-submit-assetstore-import').trigger('click');
+        });
+
+        waitsFor(function () {
+            return $('.g-validation-failed-message').html().startsWith('Invalid filters');
+        }, 'Invalid filters check');
+
+        runs(function () {
+            // Perform a search where no results are returned
+            const filters = '{"SeriesInstanceUID": "DOES_NOT_EXIST"}';
+            $('#g-dwas-import-filters').val(filters);
+            $('.g-submit-assetstore-import').trigger('click');
+        });
+
+        waitsFor(function () {
+            const msg = 'No DICOM objects matching the search filters were found';
+            return $('.g-validation-failed-message').html() === msg;
+        }, 'No results check');
+
+        runs(function () {
+            // Fix the filters
+            // We will only import this specific SeriesInstanceUID
+            const filters = '{"SeriesInstanceUID": "' + verifyItemName + '"}';
+            $('#g-dwas-import-filters').val(filters);
+
+            // This one should work fine
             $('.g-submit-assetstore-import').trigger('click');
         });