Stop using deprecated property names in fairgraph

validation_service_api/validation_service/data_models.py

@@ -22,7 +22,7 @@
 import fairgraph
 import fairgraph.openminds.core as omcore
 import fairgraph.openminds.computation as omcmp
-import fairgraph.openminds.controlledterms as omterms
+import fairgraph.openminds.controlled_terms as omterms
 import fairgraph.openminds.publications as ompub
 
 from .examples import EXAMPLES
@@ -537,7 +537,7 @@ def from_kg_query(cls, item, client):
     def from_kg_object(cls, model_project, client):
         assert model_project.scope is not None
         instances = []
-        for inst_obj in as_list(model_project.versions):
+        for inst_obj in as_list(model_project.has_versions):
             try:
                 inst_obj = inst_obj.resolve(client, scope=model_project.scope)
                 assert isinstance(inst_obj, omcore.ModelVersion)
@@ -564,8 +564,8 @@ def from_kg_object(cls, model_project, client):
             data = dict(
                 id=model_project.uuid,
                 uri=model_project.id,
-                name=model_project.name,
-                alias=model_project.alias,
+                name=model_project.full_name,
+                alias=model_project.short_name,
                 author=[Person.from_kg_object(p, client)
                         for p in as_list(model_project.developers)],
                 owner=[Person.from_kg_object(p, client)
@@ -614,8 +614,8 @@ def to_kg_object(self, client):
                 study_targets.append(cell_type)
 
         model_project = omcore.Model(
-            name=self.name,
-            alias=self.alias,
+            full_name=self.name,
+            short_name=self.alias,
             description=self.description,
             abstraction_level=get_term("ModelAbstractionLevel", self.abstraction_level),
             model_scope=get_term("ModelScope", self.model_scope),
@@ -636,7 +636,7 @@ def to_kg_object(self, client):
                     instance.to_kg_object(model_project)
                     for instance in self.instances
                 ]
-            model_project.versions = model_versions
+            model_project.has_versions = model_versions
         return model_project
 
 
@@ -683,8 +683,8 @@ def from_kg_object(cls, model_project, client):
             obj = cls(
                 id=model_project.uuid,
                 uri=model_project.id,
-                name=model_project.name,
-                alias=model_project.alias,
+                name=model_project.full_name,
+                alias=model_project.short_name,
                 author=[Person.from_kg_object(p, client)
                         for p in as_list(model_project.developers)],
                 owner=[Person.from_kg_object(p, client)
@@ -895,7 +895,7 @@ def from_kg_query(cls, item, user_client, service_client):
 
     @classmethod
     def from_kg_object(cls, test_definition, client):
-        versions = [ver.resolve(client, scope="any") for ver in as_list(test_definition.versions)]
+        versions = [ver.resolve(client, scope="any") for ver in as_list(test_definition.has_versions)]
         instances = [
             ValidationTestInstance.from_kg_object(inst, test_definition.uuid, client) for inst in versions
         ]
@@ -943,8 +943,8 @@ def from_kg_object(cls, test_definition, client):
         obj = cls(
             id=test_definition.uuid,
             uri=test_definition.id,
-            name=test_definition.name,
-            alias=test_definition.alias,
+            name=test_definition.full_name,
+            alias=test_definition.short_name,
             implementation_status=implementation_status,
             private=is_private(test_definition.space),
             #custodians=test_definition.custodians,
@@ -986,8 +986,8 @@ def to_kg_object(self, client):
         if self.alias is None:
             self.alias = slugify(self.name)
         test_definition = omcmp.ValidationTest(
-            name=self.name,
-            alias=self.alias,
+            full_name=self.name,
+            short_name=self.alias,
             custodians=developers,
             description=self.description,
             developers=developers,
@@ -1007,7 +1007,7 @@ def to_kg_object(self, client):
                 instance.to_kg_object(test_definition=self)
                 for instance in self.instances
             ]
-            test_definition.versions = test_versions
+            test_definition.has_versions = test_versions
 
         return test_definition
 
@@ -1045,8 +1045,8 @@ def from_kg_object(cls, test_definition, client):
         obj = cls(
             id=test_definition.uuid,
             uri=test_definition.id,
-            name=test_definition.name,
-            alias=test_definition.alias,
+            name=test_definition.full_name,
+            alias=test_definition.short_name,
             implementation_status=None,  # to fix (test_definition.status or ImplementationStatus.proposal.value),
             private=is_private(test_definition),
             author=[Person.from_kg_object(p, client) for p in as_list(test_definition.developers)],
@@ -1311,12 +1311,12 @@ def from_kg_object(cls, validation_activity, client):
             data_type=data_type,
             timestamp=ensure_has_timezone(validation_activity.start_time),
             model_id=model.uuid,
-            model_name=model.name,
-            model_alias=model.alias,
+            model_name=model.full_name,
+            model_alias=model.short_name,
             model_version=model_instance.version_identifier,
             test_id=test.uuid,
-            test_name=test.name,
-            test_alias=test.alias
+            test_name=test.full_name,
+            test_alias=test.short_name
         )
 
 

validation_service_api/validation_service/db.py

@@ -46,13 +46,13 @@ def _get_model_instance_by_id(instance_id, kg_client, scope):
         )
 
     model_project = Model.list(kg_client, scope=scope, space=model_instance.space,
-                               versions=model_instance)
+                               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, space=model_instance.space,
-                                   versions=model_instance)
+                                   has_versions=model_instance)
         if not model_project:
             # in case of a dangling model instance, where the parent model_project
             # has been deleted but the instance wasn't

validation_service_api/validation_service/queries.py

@@ -160,7 +160,7 @@ def model_alias_exists(alias, client):
         model_with_same_alias = omcore.Model.from_alias(alias, client, space=None, scope="any")
         if model_with_same_alias:
             # need this check because alias query doesn't do exact matching
-            return model_with_same_alias.alias == alias
+            return model_with_same_alias.short_name == alias
     return False
 
 
@@ -170,7 +170,7 @@ def test_alias_exists(alias, client):
         test_with_same_alias = omcmp.ValidationTest.from_alias(alias, client, space=None, scope="any")
         if test_with_same_alias:
             # need this check because alias query doesn't do exact matching
-            return test_with_same_alias.alias == alias
+            return test_with_same_alias.short_name == alias
     return False
 
 

validation_service_api/validation_service/resources/models.py

@@ -458,7 +458,7 @@ async def delete_model(model_id: UUID, token: HTTPAuthorizationCredentials = Dep
             detail=f"Access to this model is restricted to members of Collab #{collab_id}",
         )
     model_project.delete(kg_client)
-    for model_instance in as_list(model_project.versions):
+    for model_instance in as_list(model_project.has_versions):
         # todo: we should possibly also delete repositories,
         # but need to check they're not shared with other instances
         model_instance.delete(kg_client)
@@ -478,7 +478,7 @@ async def get_model_instances(
         scope = "any"
     model_project = _get_model_by_id_or_alias(model_id, kg_client, scope)
     model_instances = []
-    for inst in as_list(model_project.versions):
+    for inst in as_list(model_project.has_versions):
         try:
             model_instance = ModelInstance.from_kg_object(inst, kg_client, model_project.uuid, scope)
         except ResolutionFailure:
@@ -520,7 +520,7 @@ async def get_latest_model_instance_given_model_id(
     model_project = _get_model_by_id_or_alias(model_id, kg_client, scope)
     model_instances = [
         ModelInstance.from_kg_object(inst, kg_client, model_project.uuid, scope)
-        for inst in as_list(model_project.versions)
+        for inst in as_list(model_project.has_versions)
     ]
     latest = sorted(model_instances, key=lambda inst: inst["timestamp"])[-1]
     return latest
@@ -538,7 +538,7 @@ async def get_model_instance_given_model_id(
         kg_client = get_kg_client_for_user_account(token)
         scope = "any"
     model_project = _get_model_by_id_or_alias(model_id, kg_client, scope)
-    for inst in as_list(model_project.versions):
+    for inst in as_list(model_project.has_versions):
         if UUID(inst.uuid) == model_instance_id:
             return ModelInstance.from_kg_object(inst, kg_client, model_project.uuid, scope)
     raise HTTPException(
@@ -587,7 +587,7 @@ async def create_model_instance(
         )
     # otherwise save to KG
     model_instance_kg.save(kg_user_client, space=model_project.space, recursive=True)
-    model_project.versions = as_list(model_project.versions) + [model_instance_kg]
+    model_project.has_versions = as_list(model_project.has_versions) + [model_instance_kg]
     model_project.save(kg_user_client, recursive=False)
     return ModelInstance.from_kg_object(model_instance_kg, kg_user_client, model_project.uuid, scope="any")
 
@@ -624,7 +624,7 @@ async def update_model_instance(
     kg_user_client = get_kg_client_for_user_account(token)
     model_instance_kg, retrieved_model_id = _get_model_instance_by_id(model_instance_id, kg_user_client, scope="any")
     model_project = _get_model_by_id_or_alias(model_id, kg_user_client, scope="any")
-    assert model_id == retrieved_model_id or model_id == model_project.alias
+    assert model_id == retrieved_model_id or model_id == model_project.short_name
     return await _update_model_instance(
         model_instance_kg, model_project, model_instance_patch, user
     )
@@ -702,7 +702,7 @@ async def delete_model_instance(
 
 
 async def _delete_model_instance(model_instance_id, model_project, kg_user_client):
-    model_instances = as_list(model_project.versions)
+    model_instances = as_list(model_project.has_versions)
     n_start = len(model_instances)
     for model_instance in model_instances[:]:
         # todo: we should possibly also delete child objects (repository, etc.),
@@ -713,5 +713,5 @@ async def _delete_model_instance(model_instance_id, model_project, kg_user_clien
             break
     if n_start > 0:
         assert len(model_instances) == n_start - 1
-    model_project.versions = model_instances
+    model_project.has_versions = model_instances
     model_project.save(kg_user_client, recursive=False)

validation_service_api/validation_service/resources/tests.py

@@ -320,7 +320,7 @@ async def delete_test(test_id: UUID, token: HTTPAuthorizationCredentials = Depen
     kg_client = get_kg_client_for_user_account(token)
     test_definition = omcmp.ValidationTest.from_uuid(str(test_id), kg_client, scope="in progress")
     test_definition.delete(kg_client)
-    for test_version in as_list(test_definition.versions):
+    for test_version in as_list(test_definition.has_versions):
         # todo: we should possibly also delete repositories,
         # but need to check they're not shared with other instances
         test_version.delete(kg_client)
@@ -340,7 +340,7 @@ def get_test_instances(
     test_definition = _get_test_by_id_or_alias(test_id, kg_client, scope)
     test_instances = [
         ValidationTestInstance.from_kg_object(inst, test_definition.uuid, kg_client)
-        for inst in as_list(test_definition.versions)
+        for inst in as_list(test_definition.has_versions)
     ]
     if version:
         test_instances = [inst for inst in test_instances if inst.version == version]
@@ -359,7 +359,7 @@ def get_test_instance_from_instance_id(
         kg_client = get_kg_client_for_user_account(token)
         scope = "any"
     inst = _get_test_instance_by_id(test_instance_id, kg_client, scope)
-    test_definition = omcmp.ValidationTest.list(kg_client, scope=scope, space=inst.space, versions=inst)[0]
+    test_definition = omcmp.ValidationTest.list(kg_client, scope=scope, space=inst.space, has_versions=inst)[0]
     return ValidationTestInstance.from_kg_object(inst, test_definition.uuid, kg_client)
 
 
@@ -377,7 +377,7 @@ def get_latest_test_instance_given_test_id(
     test_definition = _get_test_by_id_or_alias(test_id, kg_client, scope)
     test_instances = [
         ValidationTestInstance.from_kg_object(inst.resolve(kg_client, scope="in progress"), test_definition.uuid, kg_client)
-        for inst in as_list(test_definition.versions)
+        for inst in as_list(test_definition.has_versions)
     ]
     if len(test_instances) == 0:
         raise HTTPException(
@@ -401,7 +401,7 @@ def get_test_instance_given_test_id(
         kg_client = get_kg_client_for_user_account(token)
         scope = "any"
     test_definition = _get_test_by_id_or_alias(test_id, kg_client, scope)
-    for inst in as_list(test_definition.versions):
+    for inst in as_list(test_definition.has_versions):
         if UUID(inst.uuid) == test_instance_id:
             return ValidationTestInstance.from_kg_object(inst, test_definition.uuid, kg_client)
     raise HTTPException(
@@ -441,15 +441,15 @@ def create_test_instance(
     user = User(token, allow_anonymous=False)
     kg_client = get_kg_client_for_user_account(token)
     test_definition = _get_test_by_id_or_alias(test_id, kg_client, scope="any")
-    existing_versions = [obj.resolve(kg_client, scope="any") for obj in as_list(test_definition.versions)]
+    existing_versions = [obj.resolve(kg_client, scope="any") for obj in as_list(test_definition.has_versions)]
     if test_instance.version in (obj.version_identifier for obj in existing_versions):
         raise HTTPException(
             status_code=status.HTTP_409_CONFLICT,
             detail=f"Validation test {test_id} already has a version '{test_instance.version}"
         )
     test_instance_kg = test_instance.to_kg_object(ValidationTest.from_kg_object(test_definition, kg_client))
     test_instance_kg.save(kg_client, recursive=True, space=test_definition.space)
-    test_definition.versions = as_list(test_definition.versions) + [test_instance_kg]
+    test_definition.has_versions = as_list(test_definition.has_versions) + [test_instance_kg]
     test_definition.save(kg_client, recursive=False)
     return ValidationTestInstance.from_kg_object(test_instance_kg, test_definition.uuid, kg_client)
 
@@ -470,7 +470,7 @@ def update_test_instance_by_id(
     test_instance_kg = _get_test_instance_by_id(test_instance_id, kg_client, scope="any")
     test_definition_kg = omcmp.ValidationTest.list(
         kg_client, scope="any",
-        space=test_instance_kg.space, versions=test_instance_kg)[0]
+        space=test_instance_kg.space, has_versions=test_instance_kg)[0]
     test_definition = ValidationTest.from_kg_object(test_definition_kg, kg_client)
     return _update_test_instance(test_instance_kg, test_definition, test_instance_patch, kg_client)
 
@@ -523,8 +523,8 @@ async def delete_test_instance_by_id(
         )
     test_definition = omcmp.ValidationTest.list(
         kg_client, scope="in progress",
-        space=test_instance_kg.space, versions=test_instance_kg)[0]
-    test_definition.versions = [obj for obj in as_list(test_definition.versions) if obj.uuid != test_instance_id]
+        space=test_instance_kg.space, has_versions=test_instance_kg)[0]
+    test_definition.has_versions = [obj for obj in as_list(test_definition.has_versions) if obj.uuid != test_instance_id]
     test_definition.save(kg_client, recursive=False)
     test_instance_kg.delete(kg_client)
 
@@ -545,6 +545,6 @@ async def delete_test_instance(
             detail="Deleting test instances is restricted to admins",
         )
     test_definition = _get_test_by_id_or_alias(test_id, kg_client, scope="any")
-    test_definition.versions = [obj for obj in test_definition.versions if obj.uuid != test_instance_id]
+    test_definition.has_versions = [obj for obj in test_definition.has_versions if obj.uuid != test_instance_id]
     test_definition.save(kg_client, recursive=False)
     test_instance_kg.delete(kg_client)

validation_service_api/validation_service/tests/README.md

@@ -17,3 +17,7 @@ The token should be stored in an environment variable `VF_TEST_TOKEN`.
 From the "validation_service_api" subdirectory, run:
 
   $ pytest validation_service/tests
+
+To measure test coverage, run as follows:
+
+  $ pytest validation_service/tests --cov=validation_service --cov-report term --cov-report html

validation_service_api/validation_service/tests/fixtures.py

@@ -37,7 +37,7 @@ def private_model():
         developers=[omcore.Person(given_name="Frodo", family_name="Baggins"),
                     omcore.Person(given_name="Tom", family_name="Bombadil")],
         digital_identifier=None,
-        versions=None,
+        has_versions=None,
         homepage=None,
         how_to_cite=None,
         model_scope=omterms.ModelScope.by_name(