Merge branch 'master' into 'production'

resolve import issues

See merge request !30

config/default.env

@@ -12,7 +12,10 @@ NACSOS_DB__PASSWORD="root"
 NACSOS_DB__DATABASE="nacsos_core"
 
 NACSOS_PIPES__API_URL="http://localhost:8000/api"
-NACSOS_PIPES__TOKEN=""
+NACSOS_PIPES__TOKEN="bfed6708-f4b6-48d9-8c81-925cd4e7f3a5"
+NACSOS_PIPES__USERNAME="system"
+NACSOS_PIPES__USER_ID="4138daf5-69b7-405b-b364-ccafaef25a01"
+#NACSOS_PIPES__PW="kbt2t1h1t7jb1g086755bg2x8wvbmu45kqvf7g7v5vqdbmv6g0wr14akl98406g"
 
 #NACSOS_USERS__DEFAULT_USER="user1"
 NACSOS_USERS__DEFAULT_USER
\ No newline at end of file

requirements.txt

-fastapi==0.92.0
+fastapi==0.93.0
 hypercorn==0.14.3
 toml==0.10.2
 email-validator==1.3.1

requirements_dev.txt

 flake8==6.0.0
 tox==4.4.6
-pytest==7.2.1
+pytest==7.2.2
 pytest-cov==4.0.0
-mypy==1.0.1
+mypy==1.1.1
 types-toml==0.10.8.5
 types-PyYAML==6.0.12.8
\ No newline at end of file

server/api/routes/annotations.py

@@ -140,9 +140,13 @@ async def get_scheme_definitions_for_project(project_id: str,
 async def _construct_annotation_item(assignment: AssignmentModel, project_id: str) -> AnnotationItem:
     if assignment.assignment_id is None:
         raise MissingInformationError('No `assignment_id` set for `assignment`.')
+
     scope = await read_assignment_scope(assignment_scope_id=assignment.assignment_scope_id, db_engine=db_engine)
-    scheme = await read_annotation_scheme(annotation_scheme_id=assignment.annotation_scheme_id, db_engine=db_engine)
+    if scope is None:
+        raise AnnotationSchemeNotFoundError(f'No annotation scope found in DB for id '
+                                            f'{assignment.assignment_scope_id}')
 
+    scheme = await read_annotation_scheme(annotation_scheme_id=assignment.annotation_scheme_id, db_engine=db_engine)
     if scheme is None:
         raise AnnotationSchemeNotFoundError(f'No annotation scheme found in DB for id '
                                             f'{assignment.annotation_scheme_id}')
@@ -153,7 +157,11 @@ async def _construct_annotation_item(assignment: AssignmentModel, project_id: st
     project = await read_project_by_id(project_id=project_id, engine=db_engine)
     if project is None:
         raise ProjectNotFoundError(f'No project found in DB for id {project_id}')
+
     item = await read_any_item_by_item_id(item_id=assignment.item_id, item_type=project.type, engine=db_engine)
+    if item is None:
+        raise MissingInformationError(f'No item found in DB for id {assignment.item_id}')
+
     return AnnotationItem(scheme=merged_scheme, assignment=assignment, scope=scope, item=item)
 
 

server/api/routes/imports.py

@@ -60,6 +60,8 @@ async def trigger_import(import_id: str,
                          permissions: UserPermissions = Depends(UserPermissionChecker('imports_edit'))):
     import_details = await read_import(import_id=import_id, engine=db_engine)
 
+    print(import_details.__dict__)
+
     if import_details is not None and str(import_details.project_id) == str(permissions.permissions.project_id):
         if import_details.type == ImportType.jsonl:
             return await submit_jsonl_import_task(import_id=import_id,

server/api/routes/project/permissions.py

@@ -45,7 +45,10 @@ async def get_all_user_permissions(permission=Depends(UserPermissionChecker('own
                 .options(selectinload(ProjectPermissions.user)))
         result = (await session.execute(stmt)).scalars().all()
 
-        return [UserPermission(**{**row.__dict__, 'user': row.user.__dict__}) for row in result]
+        return [UserPermission.parse_obj({
+            'user': row.user.__dict__,
+            **row.__dict__
+        }) for row in result]
 
 
 @router.put('/permission', response_model=str)

server/util/config.py

@@ -132,6 +132,6 @@ class Settings(BaseSettings):
 
 
 conf_file = os.environ.get('NACSOS_CONFIG', 'config/default.env')
-settings = Settings(_env_file=conf_file, _env_file_encoding='utf-8')
+settings = Settings(_env_file=conf_file, _env_file_encoding='utf-8')  # type: ignore[call-arg]  # FIXME
 
 __all__ = ['settings']