Merge pull request #684 from hubmapconsortium/Derek-Furst/update-neo4j

Derek furst/update neo4j

Author: yuanzhou

src/requirements.txt

@@ -1,11 +1,7 @@
-Flask==2.1.3
-neo4j==4.4
+Flask==3.0.3
+neo4j==5.20.0
 prov==2.0.0
-
-# Flask 2.1.3 installs the latest Werkzeug==3.0.0 (released on 9/30/2023) and causing import issues 
-# Use a pinned version 2.3.7 (the latest release before 3.0.0) to mitigate temporaryly
-# Will upgrade Flask to newer version later on across all APIs. 10/3/2023 - Zhou
-Werkzeug==2.3.7
+Werkzeug==3.0.3
 
 # For interacting with memcached
 pymemcache==4.0.0
@@ -14,7 +10,7 @@ pymemcache==4.0.0
 nested-lookup==0.2.22
 
 # The commons package requires requests>=2.22.0 and PyYAML>=5.3.1
-requests==2.25.1
+requests==2.32.0
 PyYAML==5.4.1
 
 # Use the published package from PyPI as default

src/schema/schema_neo4j_queries.py

@@ -500,7 +500,7 @@ def get_dataset_organ_and_donor_info(neo4j_driver, uuid):
     with neo4j_driver.session() as session:
         # To improve the query performance, we implement the two-step queries to drastically reduce the DB hits
         sample_query = (f"MATCH (e:Dataset)<-[:ACTIVITY_INPUT|ACTIVITY_OUTPUT*]-(s:Sample) "
-                        f"WHERE e.uuid='{uuid}' AND s.sample_category='organ' AND EXISTS(s.organ) "
+                        f"WHERE e.uuid='{uuid}' AND s.sample_category='organ' AND s.organ IS NOT NULL "
                         f"RETURN DISTINCT s.organ AS organ_name, s.uuid AS sample_uuid")
 
         logger.info("======get_dataset_organ_and_donor_info() sample_query======")
@@ -513,7 +513,7 @@ def get_dataset_organ_and_donor_info(neo4j_driver, uuid):
             sample_uuid = sample_record['sample_uuid']
 
             donor_query = (f"MATCH (s:Sample)<-[:ACTIVITY_OUTPUT]-(a:Activity)<-[:ACTIVITY_INPUT]-(d:Donor) "
-                           f"WHERE s.uuid='{sample_uuid}' AND s.sample_category='organ' AND EXISTS(s.organ) "
+                           f"WHERE s.uuid='{sample_uuid}' AND s.sample_category='organ' AND s.organ IS NOT NULL "
                            f"RETURN DISTINCT d.metadata AS donor_metadata")
 
             logger.info("======get_dataset_organ_and_donor_info() donor_query======")