Merge pull request #154 from ImagingDataCommons/idc-prod-sp

Sprint 15 Release

Author: s-paquette

cohorts/decorators.py

@@ -29,22 +29,30 @@
 def api_auth(function):
     def wrap(request, *args, **kwargs):
         try:
-            auth_header = request.META.get('HTTP_AUTHORIZATION',b'')
+            auth_header = request.META.get('HTTP_AUTHORIZATION',None)
+            if not auth_header:
+                logger.error("No Authorization header found for API call!")
+                return JsonResponse({'message': 'No API authorization header - please be sure to provide an API token for API calls.'}, status=403)
+
             # Force local dev to behave like deployed system
-            if settings.DEBUG:
-                auth_header = auth_header.encode('iso-8859-1')
+            # if settings.DEBUG:
+            #     if isinstance(auth_header,str):
+            #         auth_header = auth_header.encode('iso-8859-1')
             auth_header = auth_header.split()
 
-            # Check for our Auth Header Token key, whatever that is.
-            if not auth_header or auth_header[0].lower() != settings.API_AUTH_KEY.lower().encode():
-                return JsonResponse({'message':'API access token not provided, or the wrong key was used.'},status=403)
-
             # Make sure our Auth Header is the expected size
             if len(auth_header) == 1 or len(auth_header) > 2:
-                return JsonResponse({'message': 'API access token not provided, or the wrong key was used.'},status=403)
+                logger.error("Malformed Authorization header: {}".format(auth_header))
+                return JsonResponse({'message': 'Received malformed API authorization header.'},status=403)
+
+            # Check for our Auth Header Token key
+            if auth_header[0].lower() != settings.API_AUTH_KEY.lower():
+                logger.error("Invalid API Token key; received: {} - expected {}".format(
+                    auth_header[0].lower(), settings.API_AUTH_KEY.lower()))
+                return JsonResponse({'message':'API Auth token key not recognized.'},status=403)
 
             # Now actually validate with the token
-            token = auth_header[1].decode()
+            token = auth_header[1]
             Token.objects.select_related('user').get(key=token)
 
             # If a user was found, we've received a valid API call, and can proceed.

cohorts/models.py

@@ -100,20 +100,21 @@ def is_public(self):
 
     # Returns the data versions identified in the filter groups for this cohort
     # Returns a DataVersion QuerySet
-    def get_data_versions(self):
+    def get_data_versions(self, active=None):
 
-        data_versions = ImagingDataCommonsVersion.objects.filter(id__in=self.filter_group_set.all().values_list('data_version',flat=True))
+        data_versions = ImagingDataCommonsVersion.objects.filter(id__in=self.filter_group_set.all().values_list('data_version',flat=True)) \
+            if active is None else ImagingDataCommonsVersion.objects.filter(active=active, id__in=self.filter_group_set.all().values_list('data_version',flat=True))
 
         return data_versions.distinct()
 
     # Returns the list of data sources used by this cohort, as a function of the filters which define it
     # Return values can be
-    def get_data_sources(self, source_type=DataSource.SOLR):
+    def get_data_sources(self, source_type=DataSource.SOLR, active=None):
 
         cohort_filters = Filter.objects.select_related('attribute').filter(resulting_cohort=self)
         attributes = Attribute.objects.filter(id__in=cohort_filters.values_list('attribute', flat=True))
 
-        data_versions = self.get_data_versions()
+        data_versions = self.get_data_versions(active=active)
 
         sources = attributes.get_data_sources(data_versions, source_type)
 
@@ -136,6 +137,18 @@ def get_filters_by_data_source(self, source_type=None):
 
         return result
 
+
+    # Returns a dict of the filters defining this cohort organized by filter group
+    def get_filters_as_dict_simple(self):
+        result = []
+
+        filter_groups = self.filter_group_set.all()
+
+        for fg in filter_groups:
+            result.append(fg.filter_set.all().get_filter_set())
+        return result
+
+
     # Returns a dict of the filters defining this cohort organized by filter group
     def get_filters_as_dict(self):
         result = []
@@ -195,7 +208,7 @@ def get_filters_for_bq(self, prefix=None, suffix=None, counts=False, schema=None
         group_filter_dict = self.get_filters_as_dict()
 
         for group in group_filter_dict:
-            group_filters = {x: [y for y in x['values']] for x in group['filters']}
+            group_filters = {x['name']: [y for y in x['values']] for x in group['filters']}
             filter_sets.append(BigQuerySupport.build_bq_filter_and_params(
                 group_filters, field_prefix=prefix, param_suffix=suffix, with_count_toggle=counts,
                 type_schema=schema

cohorts/utils.py

@@ -148,7 +148,7 @@ def _save_cohort(user, filters=None, name=None, cohort_id=None, version=None, de
 
     return cohort_info
 
-def cohort_manifest(cohort, user, fields, limit):
+def cohort_manifest(cohort, user, fields, limit, offset):
     try:
         sources = cohort.get_data_sources()
         versions = cohort.get_data_versions()
@@ -158,7 +158,7 @@ def cohort_manifest(cohort, user, fields, limit):
         filters = {x['name']: x['values'] for x in group_filters[0]['filters']}
 
         cohort_records = get_collex_metadata(
-            filters, fields, limit, sources=sources, versions=versions, counts_only=False,
+            filters, fields, limit, offset, sources=sources, versions=versions, counts_only=False,
             collapse_on='SOPInstanceUID', records_only=True, sort="PatientID asc, StudyInstanceUID asc, SeriesInstanceUID asc, SOPInstanceUID asc")
 
         return cohort_records