updated main to accommmodate changes in search-adaptor to handle the …

src/hubmap_translator.py

@@ -712,6 +712,13 @@ def enqueue_reindex(self, entity_id, reindex_queue, priority):
             )
             collection_associations = []
             upload_associations = []
+            previous_revision_ids = []
+            next_revision_ids = []
+            neo4j_collection_ids = []
+            neo4j_upload_ids = []
+            neo4j_ancestor_ids = []
+            neo4j_descendant_ids = []
+
             if entity['entity_type'] in ['Collection', 'Epicollection']:
                 collection = self.get_collection_doc(entity_id=entity_id)
                 if 'datasets' in collection:
@@ -722,38 +729,29 @@ def enqueue_reindex(self, entity_id, reindex_queue, priority):
                 if 'associated_publication' in collection and collection['associated_publication']:
                     logger.info(f"Enqueueing associated_publication for {entity['entity_type']} {entity_id}")
                     collection_associations.append(collection['associated_publication'])
-
-                logger.info(f"Finished executing enqueue_reindex() for {entity['entity_type']} of uuid: {entity_id}")    
-                return job_id
 
-            if entity['entity_type'] == 'Upload':
+            elif entity['entity_type'] == 'Upload':
                 if 'datasets' in entity:
                     logger.info(f"Enqueueing {len(entity['datasets'])} datasets for Upload {entity_id}")
                     for dataset in entity['datasets']:
                         upload_associations.append(dataset['uuid'])
-                logger.info(f"Finished executing enqueue_reindex() for Upload of uuid: {entity_id}")
-                return job_id
-
-            logger.info(f"Calculating related entities for {entity_id}")
-
-            neo4j_ancestor_ids = self.call_entity_api(
-                entity_id=entity_id,
-                endpoint_base='ancestors',
-                endpoint_suffix=None,
-                url_property='uuid'
-            )
-
-            neo4j_descendant_ids = self.call_entity_api(
-                entity_id=entity_id,
-                endpoint_base='descendants',
-                endpoint_suffix=None,
-                url_property='uuid'
-            )
-
-            previous_revision_ids = []
-            next_revision_ids = []
-            neo4j_collection_ids = []
-            neo4j_upload_ids = []
+
+            else:
+                logger.info(f"Calculating related entities for {entity_id}")
+
+                neo4j_ancestor_ids = self.call_entity_api(
+                    entity_id=entity_id,
+                    endpoint_base='ancestors',
+                    endpoint_suffix=None,
+                    url_property='uuid'
+                )
+
+                neo4j_descendant_ids = self.call_entity_api(
+                    entity_id=entity_id,
+                    endpoint_base='descendants',
+                    endpoint_suffix=None,
+                    url_property='uuid'
+                )
 
             if entity['entity_type'] in ['Dataset', 'Publication']:
                 previous_revision_ids = self.call_entity_api(

src/main.py

@@ -33,10 +33,12 @@
 config['ONTOLOGY_API_BASE_URL'] = app.config['ONTOLOGY_API_BASE_URL'].strip('/')
 config['DEBUG_MODE'] = app.config['DEBUG_MODE']
 config['JOB_QUEUE_MODE'] = app.config['JOB_QUEUE_MODE']
-config['REDIS_HOST'] = app.config['REDIS_HOST']
-config['REDIS_PORT'] = app.config['REDIS_PORT']
-config['REDIS_DB'] = app.config['REDIS_DB']
-config['REDIS_PASSWORD'] = app.config['REDIS_PASSWORD']
+if config.get('JOB_QUEUE_MODE') == True:
+    config['REDIS_HOST'] = app.config.get('REDIS_HOST')
+    config['REDIS_PORT'] = app.config.get('REDIS_PORT')
+    config['REDIS_DB'] = app.config.get('REDIS_DB')
+    config['REDIS_PASSWORD'] = app.config.get('REDIS_PASSWORD')
+
 
 if not config['ONTOLOGY_API_BASE_URL']:
     raise Exception(f"Unable retrieve ontology information using"