Update to work with fairgraph 0.13.2, so that it will continue to function after the KG migration to openMINDS v4

Author: apdavison

validation_service_api/requirements.txt.lock

@@ -1,5 +1,4 @@
-#fairgraph==0.12.1
-fairgraph @ git+https://github.com/HumanBrainProject/fairgraph@stable
+fairgraph==0.13.2
 uvicorn==0.13.4
 fastapi==0.65.1
 itsdangerous==2.0.1

validation_service_api/validation_service/auth.py

@@ -138,7 +138,7 @@ async def get_person(self, kg_client):
         identity = await self.get_identity()
         family_name = identity["family_name"]
         given_name = identity["given_name"]
-        person = omcore.Person.list(kg_client, family_name=family_name, given_name=given_name, scope="any")
+        person = omcore.Person.list(kg_client, family_name=family_name, given_name=given_name, release_status="any")
         if person:
             if isinstance(person, list):
                 if len(person) > 1:

validation_service_api/validation_service/data_models.py

@@ -22,12 +22,12 @@ def _check_service_status():
         )
 
 
-def _get_model_by_id_or_alias(model_id, kg_client, scope, use_cache=False):
+def _get_model_by_id_or_alias(model_id, kg_client, release_status, use_cache=False):
     try:
         model_id = UUID(model_id)
-        model_project = Model.from_uuid(str(model_id), kg_client, scope=scope, use_cache=use_cache)
+        model_project = Model.from_uuid(str(model_id), kg_client, release_status=release_status, use_cache=use_cache)
     except ValueError:
-        model_project = Model.from_alias(model_id, kg_client, scope=scope)
+        model_project = Model.from_alias(model_id, kg_client, release_status=release_status)
     if not model_project:
         raise HTTPException(
             status_code=status.HTTP_404_NOT_FOUND,
@@ -37,26 +37,25 @@ def _get_model_by_id_or_alias(model_id, kg_client, scope, use_cache=False):
     return model_project
 
 
-def _get_model_instance_by_id(instance_id, kg_client, scope):
-    model_instance = ModelVersion.from_uuid(str(instance_id), kg_client, scope=scope)
+def _get_model_instance_by_id(instance_id, kg_client, release_status):
+    model_instance = ModelVersion.from_uuid(str(instance_id), kg_client, release_status=release_status)
     if model_instance is None:
         raise HTTPException(
             status_code=status.HTTP_404_NOT_FOUND,
             detail=f"Model instance with ID '{instance_id}' not found.",
         )
 
-    model_project = Model.list(kg_client, scope=scope, has_versions=model_instance, use_cache=False)
+    model_project = Model.list(kg_client, release_status=release_status, has_versions=model_instance)
     if not model_project:
         # we could get an empty response if the model_project has just been
         # updated and the KG is not consistent, so we wait and try again
         sleep(RETRY_INTERVAL)
-        model_project = Model.list(kg_client, scope=scope, has_versions=model_instance, use_cache=False)
+        model_project = Model.list(kg_client, release_status=release_status, has_versions=model_instance)
         if not model_project:
             # try the service client
             kg_service_client = get_kg_client_for_service_account()
-            model_project = Model.list(kg_service_client, scope="in progress", has_versions=model_instance, use_cache=False)
+            model_project = Model.list(kg_service_client, release_status="in progress", has_versions=model_instance)
             if not model_project:
-                raise Exception("foo")
                 # in case of a dangling model instance, where the parent model_project
                 # has been deleted but the instance wasn't
                 raise HTTPException(
@@ -67,13 +66,13 @@ def _get_model_instance_by_id(instance_id, kg_client, scope):
     return model_instance, model_project.uuid
 
 
-def _get_test_by_id_or_alias(test_id, kg_client, scope):
+def _get_test_by_id_or_alias(test_id, kg_client, release_status):
     try:
         test_id = UUID(test_id)
         get_test = ValidationTest.from_uuid
     except ValueError:
         get_test = ValidationTest.from_alias
-    test_definition = get_test(str(test_id), kg_client, scope=scope)
+    test_definition = get_test(str(test_id), kg_client, release_status=release_status)
     if not test_definition:  # None or empty list
         raise HTTPException(
             status_code=status.HTTP_404_NOT_FOUND,
@@ -88,8 +87,8 @@ def _get_test_by_id_or_alias(test_id, kg_client, scope):
     return test_definition
 
 
-def _get_test_instance_by_id(instance_id, kg_client, scope):
-    test_instance = ValidationTestVersion.from_uuid(str(instance_id), kg_client, scope=scope)
+def _get_test_instance_by_id(instance_id, kg_client, release_status):
+    test_instance = ValidationTestVersion.from_uuid(str(instance_id), kg_client, release_status=release_status)
     if test_instance is None:
         raise HTTPException(
             status_code=status.HTTP_404_NOT_FOUND,

validation_service_api/validation_service/db.py

@@ -157,7 +157,7 @@ def build_result_filters(
 def model_alias_exists(alias, client):
     if alias:
         # we deliberately use space=None to search across all spaces
-        model_with_same_alias = omcore.Model.from_alias(alias, client, space=None, scope="any")
+        model_with_same_alias = omcore.Model.from_alias(alias, client, space=None, release_status="any")
         if model_with_same_alias:
             # need this check because alias query doesn't do exact matching
             return model_with_same_alias.short_name == alias
@@ -167,7 +167,7 @@ def model_alias_exists(alias, client):
 def test_alias_exists(alias, client):
     if alias:
         # we deliberately use space=None to search across all spaces
-        test_with_same_alias = omcmp.ValidationTest.from_alias(alias, client, space=None, scope="any")
+        test_with_same_alias = omcmp.ValidationTest.from_alias(alias, client, space=None, release_status="any")
         if test_with_same_alias:
             # need this check because alias query doesn't do exact matching
             return test_with_same_alias.short_name == alias

validation_service_api/validation_service/queries.py

@@ -53,10 +53,11 @@ async def query_comments(
     try:
         kg_comments = omcore.Comment.list(
             kg_user_client,
-            scope="any",
+            release_status="any",
             follow_links={"commenter": {}},
             size=size,
             from_index=from_index,
+            api="query",
             **filters
         )
     except AuthenticationError as err:
@@ -97,7 +98,7 @@ async def get_comment(
 ):
     """Retrieve a specific comment identified by a UUID"""
     kg_user_client = get_kg_client_for_user_account(token)
-    obj = omcore.Comment.from_uuid(str(comment_id), kg_user_client, scope="any")
+    obj = omcore.Comment.from_uuid(str(comment_id), kg_user_client, release_status="any")
     if obj:
         return Comment.from_kg_object(obj, kg_user_client)
     else:
@@ -121,7 +122,7 @@ async def update_comment(
     """Retrieve a specific comment identified by a UUID"""
     kg_user_client = get_kg_client_for_user_account(token)
     original_comment = omcore.Comment.from_uuid(
-        str(comment_id), kg_user_client, scope="any"
+        str(comment_id), kg_user_client, release_status="any"
 
     )
 
@@ -146,7 +147,7 @@ async def update_comment(
         if comment_patch.status == PublicationStatus.draft:
             target_space = "myspace"
         else:
-            about = original_comment.about.resolve(kg_user_client, scope="any")
+            about = original_comment.about.resolve(kg_user_client, release_status="any")
             target_space = about.space
 
         if original_comment.space != target_space: