Merge branch 'idc-test' of https://github.com/ImagingDataCommons/IDC-Common into idc-prod-sp

Author: s-paquette

cohorts/views/views_api_v1.py

@@ -53,8 +53,6 @@
 @require_http_methods(["POST"])
 def save_cohort_api(request):
     if debug: logger.debug('Called '+sys._getframe().f_code.co_name)
-
-    print(request.GET.get('email', ''))
     try:
         body = json.loads(request.body.decode('utf-8'))
         user = User.objects.get(email=request.GET.get('email', ''))
@@ -107,11 +105,6 @@ def cohort_manifest_api(request, cohort_id=0):
         }
         return JsonResponse(manifest_info)
 
-        # messages.error()
-        # messages.error(request, 'Cohort requested does not exist.')
-        # return redirect('/user_landing')
-
-    print(request.GET.get('email', ''))
     try:
         cohort = Cohort.objects.get(id=cohort_id)
     except ObjectDoesNotExist as e:
@@ -199,11 +192,6 @@ def cohort_query_api(request, cohort_id=0):
         }
         return JsonResponse(manifest_info)
 
-    # if cohort_id == 0:
-    #     messages.error(request, 'Cohort requested does not exist.')
-    #     return redirect('/user_landing')
-
-    # print(request.GET.get('email', ''))
     try:
         cohort = Cohort.objects.get(id=cohort_id)
     except ObjectDoesNotExist as e:
@@ -283,12 +271,7 @@ def cohort_preview_query_api(request):
 @require_http_methods(["GET"])
 def cohort_list_api(request):
     if debug: logger.debug('Called ' + sys._getframe().f_code.co_name)
-
-
-    print(request.GET.get('email', ''))
     try:
-        # response = cohorts_list(request)
-
         user = User.objects.get(email=request.GET.get('email', ''))
         cohortList = []
 
@@ -334,7 +317,6 @@ def cohort_list_api(request):
 def delete_cohort_api(request):
     if debug: logger.debug('Called {}'.format(sys._getframe().f_code.co_name))
     cohort_info = []
-    print(request.GET.get('email', ''))
     try:
         user = User.objects.get(email=request.GET.get('email', ''))
 

idc_collections/collex_metadata_utils.py

@@ -1100,6 +1100,11 @@ def create_query_set(solr_query, sources, source, all_ui_attrs, image_source, Da
                         query_set.append(solr_query['queries'][attr])
                     else:
                         attStr = solr_query['queries'][attr].replace('"', '\\"')
+                        # certain attributes values include quotes, ie Manufacturer = \"GE Healthcare\" which leads to 'subqueries'
+                        # in filter strings with nested quotes, ie,
+                        # _query_:"{!join to=StudyInstanceUID from=StudyInstanceUID}(+Manufacturer:(""GE Healthcare""))"))
+                        # in this case extra backslashes are needed around the inner quotes
+                        attStr = attStr.replace('\\\\"', '\\\\\\"')
                         attStr = '(_query_:"{!join to=' + default_join_field + ' from=' + default_join_field + '}' + attStr + '")'
                         query_set.append(attStr)
                 # If it's in another source for this program, we need to join on that source
@@ -1274,7 +1279,7 @@ def create_cart_query_string(query_list, partitions, join_with_child):
         "parentid": "PatientID",
         "id": "StudyInstanceUID",
         "fields": ["collection_id", "PatientID", "StudyInstanceUID", 'StudyDescription', 'Modality', 'StudyDate',
-                   'access', 'crdc_series_uuid', 'gcs_bucket', 'aws_bucket'],
+                   'access', 'crdc_series_uuid', 'gcs_bucket', 'aws_bucket', 'instance_size', 'source_DOI'],
         "facetfields": {
             "SeriesInstanceUID": "unique_series"
         },
@@ -1308,7 +1313,7 @@ def create_cart_query_string(query_list, partitions, join_with_child):
         "id": "SeriesInstanceUID",
         "fields": [
             "collection_id", "PatientID", "StudyInstanceUID", 'SeriesInstanceUID', 'SeriesNumber', 'SeriesDescription',
-            'aws_bucket', 'gcs_bucket', 'Modality', 'BodyPartExamined', 'access', 'crdc_series_uuid', 'SOPInstanceUID'
+            'aws_bucket', 'gcs_bucket', 'Modality', 'BodyPartExamined', 'access', 'crdc_series_uuid', 'instance_size', 'source_DOI'
         ],
         "facets": {
             "per_id": {
@@ -1700,8 +1705,12 @@ def get_table_data_with_cart_data(tabletype, sortarg, sortdir, current_filters,
         with_filter = False
     if (cart_query_str_all is not None) and (len(cart_query_str_all) > 0):
         with_cart = True
+
+    # ok this condition assumes every collection_id sent is valid. Correct for normal workflow from webapp
     if (tabletype == "collections"):
         sorted_ids = current_filters["collection_id"]
+        #also needed
+        num_found=len(sorted_ids)
     elif ("facetfields" in table_data) and (sortarg in table_data["facetfields"]):
         # when sorting by a 'facet' field (# of cases, # of studies etc.), we need to find the set of ids selected from
         # this field by the limit, offset params in a preliminary solr call, then add that set as a filter to limit the
@@ -2286,7 +2295,7 @@ def get_cart_data_serieslvl(filtergrp_list, partitions, field_list, limit, offse
             solr_query = build_solr_query(
                 copy.deepcopy(filtergrp),
                 with_tags_for_ex=False,
-                search_child_records_by=None
+                search_child_records_by=None, solr_default_op='AND'
             )
             query_set_for_filt = create_query_set(solr_query, aux_sources, image_source, all_ui_attrs, image_source,
                                                   DataSetType, default_join_field='StudyInstanceUID')

solr_helpers/__init__.py

@@ -25,6 +25,7 @@
     'obese': '[30 TO *]'
 }
 
+
 # Combined query and result formatter method
 # optionally will normalize facet counting so the response structure is the same for facets+docs and just facets
 def query_solr_and_format_result(query_settings, normalize_facets=True, normalize_groups=True, raw_format=False):
@@ -572,6 +573,11 @@ def build_solr_query(filters, comb_with='AND', with_tags_for_ex=False, subq_join
                     "{!join to=%s from=%s}%s" % (search_child_records_by[attr_name], search_child_records_by[attr_name],
                                                  query_str.replace("\"", "\\\"")))
 
+            # certain attributes values include quotes, ie Manufacturer = \"GE Healthcare\" which leads to 'subqueries'
+            # in filter strings with nested quotes, ie,
+            # _query_:"{!join to=StudyInstanceUID from=StudyInstanceUID}(+Manufacturer:(""GE Healthcare""))"))
+            # in this case extra backslashes are needed around the inner quotes
+            query_str = query_str.replace('\\\\"','\\\\\\"')
         full_query_str += query_str
 
         if with_tags_for_ex: