fix: Path as str

elixir-cloud-aai · Jan 22, 2024 · fc35bcf · fc35bcf
1 parent cab1605
commit fc35bcf
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/pro_wes/ga4gh/wes/workflow_runs.py b/pro_wes/ga4gh/wes/workflow_runs.py
@@ -414,7 +414,7 @@ def _create_run_environment(
                 charset=controller_config.id_charset,
                 length=controller_config.id_length,
             )
-            work_dir = Path(controller_config.storage_path).resolve() / run_id
+            work_dir: Path = Path(controller_config.storage_path).resolve() / run_id
 
             # try to create working directory
             try:
@@ -427,7 +427,7 @@ def _create_run_environment(
             # populate document
             document.run_log.run_id = run_id
             document.task_id = uuid()
-            document.work_dir = str(work_dir)  # type: ignore
+            document.work_dir = work_dir
             document.attachments = self._process_attachments(
                 work_dir=work_dir,
             )

diff --git a/pro_wes/tasks/track_run_progress.py b/pro_wes/tasks/track_run_progress.py
@@ -2,7 +2,7 @@
 
 import logging
 from time import sleep
-from typing import Dict, Optional
+from typing import Dict, Optional, Mapping
 
 from foca.database.register_mongodb import _create_mongo_client
 from foca.models.config import Config
@@ -98,7 +98,7 @@ def task__track_run_progress(  # pylint: disable=too-many-statements
     response.pop("request", None)
     document: DbDocument = db_client.upsert_fields_in_root_object(
         root="run_log",
-        **dict(response),
+        **response.dict(),
     )
 
     # track workflow run progress