testing

scripts/loading/go/load_gpad.py

@@ -147,14 +147,16 @@ def load_go_annotations(gpad_file, noctua_gpad_file, gpi_file, annotation_type,
         log.info(str(datetime.now()))
         log.info("Uploading GPAD/GPI files to AWS...")
 
+        ENGINE_CREATED = 0
+
         update_database_load_file_to_s3(nex_session, gpad_file, source_to_id, 
-                                        edam_to_id, 'gpad')
+                                        edam_to_id, ENGINE_CREATED)
 
-        update_database_load_file_to_s3(nex_session, noctua_gpad_file, source_to_id, 
-                                        edam_to_id, 'gpad')
+        update_database_load_file_to_s3(nex_session, gpi_file, source_to_id,
+                                        edam_to_id, ENGINE_CREATED)
 
-        update_database_load_file_to_s3(nex_session, gpi_file, source_to_id, 
-                                        edam_to_id, 'gpi')
+        update_database_load_file_to_s3(nex_session, noctua_gpad_file, source_to_id, 
+                                        edam_to_id, ENGINE_CREATED)
 
     log.info(str(datetime.now()))
     log.info("Writing summary...")
@@ -586,12 +588,12 @@ def delete_extensions_evidences(nex_session, annotation_id):
     for x in to_delete_list:
         nex_session.delete(x)
 
-def update_database_load_file_to_s3(nex_session, go_file, source_to_id, edam_to_id, file_type):
+def update_database_load_file_to_s3(nex_session, go_file, source_to_id, edam_to_id, ENGINE_CREATED):
 
     import hashlib
 
     desc = "Gene Product Association Data (GPAD)"
-    if file_type == 'gpi':
+    if "gp_information" in go_file:
         desc = "Gene Product Information (GPI)"
 
     go_local_file = open(go_file, mode='rb')
@@ -601,7 +603,10 @@ def update_database_load_file_to_s3(nex_session, go_file, source_to_id, edam_to_
     go_row = nex_session.query(Filedbentity).filter_by(md5sum = go_md5sum).one_or_none()
 
     if go_row is not None:
+        log.info("The current version of " + go_file + " is already in the database.\n")
         return
+
+    log.info("Adding " + go_file + " to the database.\n")
 
     nex_session.query(Dbentity).filter_by(display_name=go_file, dbentity_status='Active').update({"dbentity_status": 'Archived'})
     nex_session.commit()
@@ -610,11 +615,12 @@ def update_database_load_file_to_s3(nex_session, go_file, source_to_id, edam_to_
     topic_id = edam_to_id.get('EDAM:0089')  ## topic:0089 Ontology and terminology
     format_id = edam_to_id.get('EDAM:3475') ## format:3475 TSV
 
-    if 'gp_association' in go_file:
+    if ENGINE_CREATED == 0:
         from sqlalchemy import create_engine
         from src.models import DBSession
         engine = create_engine(os.environ['NEX2_URI'], pool_recycle=3600)
         DBSession.configure(bind=engine)
+        ENGINE_CREATED = 1
 
     if go_row is None:
         upload_file(CREATED_BY, go_local_file,