fix: attr error

mypy.ini

@@ -1,5 +1,4 @@
 [mypy]
-disable_error_code = attr-defined
 
 [mypy-foca.*]
 ignore_missing_imports = True

pro_wes/app.py

@@ -29,14 +29,14 @@ def _setup_first_start(app: App) -> None:
     """Set up application for first start."""
     with app.app.app_context():
         # create storage directory
-        work_dir = Path(current_app.config.foca.custom.post_runs.storage_path.resolve())
+        work_dir = Path(current_app.config.foca.custom.post_runs.storage_path.resolve())    # type: ignore
         work_dir.mkdir(parents=True, exist_ok=True)
         # set service info
         try:
             ServiceInfo().get_service_info()
         except NotFound:
             ServiceInfo().set_service_info(
-                data=current_app.config.foca.custom.service_info.dict()
+                data=current_app.config.foca.custom.service_info.dict() # type: ignore
             )
 
 

pro_wes/ga4gh/wes/models.py

@@ -158,7 +158,7 @@ def json_serialized_object_field_valid(  # pylint: disable=no-self-argument
                 value does not represent an object/dictionary.
         """
         if value == "" or value == "null" or value is None:
-            if field.name == "workflow_params":
+            if field == "workflow_params":
                 raise ValueError("field required")
             return "{}"
         try:

pro_wes/ga4gh/wes/service_info.py

@@ -30,7 +30,7 @@ class ServiceInfo:
     def __init__(self) -> None:
         """Class constructor."""
         self.config: Dict = current_app.config
-        self.foca_config: Config = self.config.foca
+        self.foca_config: Config = self.config.foca # type: ignore
         self.db_client_service_info: Collection = (
             self.foca_config.db.dbs["runStore"].collections["service_info"].client
         )

pro_wes/ga4gh/wes/workflow_runs.py

@@ -56,7 +56,7 @@ class WorkflowRuns:
     def __init__(self) -> None:
         """Class constructor."""
         self.config: Dict = current_app.config
-        self.foca_config: Config = current_app.config.foca
+        self.foca_config: Config = current_app.config.foca  # type: ignore
         self.db_client: Collection = (
             self.foca_config.db.dbs["runStore"].collections["runs"].client
         )

pro_wes/tasks/track_run_progress.py

@@ -57,7 +57,7 @@ def task__track_run_progress(  # pylint: disable=too-many-statements
         pro_wes.exceptions.EngineUnavailable: The remote service is unavailable
             or is not a valid WES service.
     """
-    foca_config: Config = current_app.config.foca
+    foca_config: Config = current_app.config.foca   # type: ignore
     controller_config: Dict = foca_config.custom.post_runs
 
     logger.info(f"[{self.request.id}] Start processing...")
@@ -95,7 +95,7 @@ def task__track_run_progress(  # pylint: disable=too-many-statements
     #    if not isinstance(response, RunLog):
     #        db_client.update_run_state(state=State.SYSTEM_ERROR.value)
     #        raise EngineProblem("Did not receive expected response.")
-    response.pop("request", None)
+    response.pop("request", None)   # type: ignore
     document: DbDocument = db_client.upsert_fields_in_root_object(
         root="run_log",
         **response.dict(),
@@ -105,7 +105,7 @@ def task__track_run_progress(  # pylint: disable=too-many-statements
     run_state: State = State.UNKNOWN
     attempt: int = 1
     while not run_state.is_finished:
-        sleep(controller_config.polling_wait)
+        sleep(controller_config.polling_wait)   # type: ignore
 
         # ensure WES endpoint is available
         assert document.wes_endpoint is not None, "No WES endpoint available."
@@ -117,14 +117,14 @@ def task__track_run_progress(  # pylint: disable=too-many-statements
                 timeout=foca_config.custom.defaults.timeout,
             )
         except EngineUnavailable as exc:
-            if attempt <= controller_config.polling_attempts:
+            if attempt <= controller_config.polling_attempts:   # type: ignore
                 attempt += 1
                 logger.warning(exc, exc_info=True)
                 continue
             db_client.update_run_state(state=State.SYSTEM_ERROR.value)
             raise
         if not isinstance(response, RunStatus):
-            if attempt <= controller_config.polling_attempts:
+            if attempt <= controller_config.polling_attempts:   # type: ignore
                 attempt += 1
                 logger.warning(f"Received error response: {response}")
                 continue
@@ -148,7 +148,7 @@ def task__track_run_progress(  # pylint: disable=too-many-statements
     #    if not isinstance(response, RunLog):
     #        db_client.update_run_state(state=State.SYSTEM_ERROR.value)
     #        raise EngineProblem("Did not receive expected response.")
-    response.pop("request", None)
+    response.pop("request", None)   # type: ignore
     document = db_client.upsert_fields_in_root_object(
         root="run_log",
         **dict(response),

tests/ga4gh/wes/endpoints/test_service_info.py

@@ -11,7 +11,7 @@
 
 from unittest.mock import MagicMock
 
-from pro_wes.ga4gh.wes.service_info import RegisterServiceInfo
+from pro_wes.ga4gh.wes.service_info import RegisterServiceInfo  # type: ignore
 from pro_wes.exceptions import (
     NotFound,
     ValidationError,