Merge pull request #614 from sennetconsortium/libpitt/594-prov

Libpitt/594 prov
sennetconsortium · Feb 12, 2025 · a41cdd9 · a41cdd9
2 parents b9478bc + abc655b
commit a41cdd9
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Showing 2 changed files with 15 additions and 13 deletions.
diff --git a/src/app.py b/src/app.py
@@ -807,23 +807,21 @@ def get_entity_provenance(id):
     if 'depth' in request.args:
         depth = int(request.args.get('depth'))
 
+    authorized = user_in_sennet_read_group(request)
+    data_access_level = 'public' if authorized is False else None
+
     # Convert neo4j json to dict
-    neo4j_result = app_neo4j_queries.get_provenance(neo4j_driver_instance, uuid, depth)
+    neo4j_result = app_neo4j_queries.get_provenance(neo4j_driver_instance, uuid, depth, data_access_level=data_access_level)
     raw_provenance_dict = dict(neo4j_result['json'])
 
     raw_descendants_dict = None
     if bool(request.args):
         # The parsed query string value is a string 'true'
         return_descendants = request.args.get('return_descendants')
 
-        # The value should be in a format expected by the apoc.path.subgraphAll.labelFilter config param
-        label_filter = request.args.get('filter', '')
-        allowable_filter_chars = "[a-zA-Z+/>\-|]"
-        label_filter = ''.join(re.findall(allowable_filter_chars, label_filter))
-
         if (return_descendants is not None) and (return_descendants.lower() == 'true'):
             neo4j_result_descendants = app_neo4j_queries.get_provenance(neo4j_driver_instance, uuid, depth, True,
-                                                                        label_filter)
+                                                                         data_access_level=data_access_level)
             raw_descendants_dict = dict(neo4j_result_descendants['json'])
 
     # Normalize the raw provenance nodes based on the yaml schema

diff --git a/src/app_neo4j_queries.py b/src/app_neo4j_queries.py
@@ -1465,7 +1465,7 @@ def add_entities_to_collection(neo4j_driver, collection_uuid, entitiy_uuids_list
 """
 
 
-def get_provenance(neo4j_driver, uuid, depth, return_descendants=None, query_filter=None):
+def get_provenance(neo4j_driver, uuid, depth, return_descendants=None, data_access_level=None):
     # max_level_str is the string used to put a limit on the number of levels to traverse
     max_level_str = ''
     if depth is not None and len(str(depth)) > 0:
@@ -1475,14 +1475,18 @@ def get_provenance(neo4j_driver, uuid, depth, return_descendants=None, query_fil
     if return_descendants:
         relationship_filter = '<USED|<WAS_GENERATED_BY'
 
-    label_filter = ''
-    if query_filter is not None and len(query_filter) > 0:
-        label_filter = f", labelFilter:'{query_filter}'"
+    predicate = ''
+    allow_nodes = ''
+    if data_access_level:
+        allow_nodes = ', allowlistNodes: allowlistNodes'
+        predicate = ("MATCH(allowedEntity:Entity)-[:WAS_GENERATED_BY]->(allowedActivity:Activity) "
+                     f"WHERE (allowedEntity.data_access_level = '{data_access_level}' OR allowedEntity.status = 'Published')  "
+                     "WITH n, collect(allowedEntity)+collect(allowedActivity) AS allowlistNodes ")
 
     # More info on apoc.path.subgraphAll() procedure: https://neo4j.com/labs/apoc/4.0/graph-querying/expand-subgraph/
     query = (f"MATCH (n:Entity) "
-             f"WHERE n.uuid = '{uuid}' "
-             f"CALL apoc.path.subgraphAll(n, {{ {max_level_str} relationshipFilter:'{relationship_filter}' {label_filter} }}) "
+             f"WHERE n.uuid = '{uuid}' {predicate} "
+             f"CALL apoc.path.subgraphAll(n, {{ {max_level_str} relationshipFilter:'{relationship_filter}' {allow_nodes} }}) "
              f"YIELD nodes, relationships "
              f"WITH [node in nodes | node {{ .*, label:labels(node)[0] }} ] as nodes, "
              f"[rel in relationships | rel {{ .*, fromNode: {{ label:labels(startNode(rel))[0], uuid:startNode(rel).uuid }}, toNode: {{ label:labels(endNode(rel))[0], uuid:endNode(rel).uuid }}, rel_data: {{ type: type(rel) }} }} ] as rels "