Merge pull request #456 from niaid/feature/notify-cleanup-on-crash

Notify and cleanup on workflow crash

em_workflows/brt/flow.py

@@ -528,6 +528,10 @@ def get_callback_result(callback_data: list) -> list:
         utils.notify_api_completion,
         utils.copy_workdirs_and_cleanup_hook,
     ],
+    on_crashed=[
+        utils.notify_api_completion,
+        utils.copy_workdirs_and_cleanup_hook,
+    ],
 )
 def brt_flow(
     # This block of params map are for adoc file specfication.

em_workflows/czi/flow.py

@@ -216,6 +216,10 @@ def update_file_metadata(file_path: FilePath, callback_with_zarr: Dict) -> Dict:
         utils.notify_api_completion,
         utils.copy_workdirs_and_cleanup_hook,
     ],
+    on_crashed=[
+        utils.notify_api_completion,
+        utils.copy_workdirs_and_cleanup_hook,
+    ],
 )
 async def czi_flow(
     file_share: str,

em_workflows/dm_conversion/flow.py

@@ -213,6 +213,10 @@ def scale_jpegs(file_path: FilePath, size: str) -> Optional[dict]:
         utils.notify_api_completion,
         utils.copy_workdirs_and_cleanup_hook,
     ],
+    on_crashed=[
+        utils.notify_api_completion,
+        utils.copy_workdirs_and_cleanup_hook,
+    ],
 )
 def dm_flow(
     file_share: str,

em_workflows/lrg_2d_rgb/flow.py

@@ -160,6 +160,10 @@ def gen_thumb(file_path: FilePath):
         utils.notify_api_completion,
         utils.copy_workdirs_and_cleanup_hook,
     ],
+    on_crashed=[
+        utils.notify_api_completion,
+        utils.copy_workdirs_and_cleanup_hook,
+    ],
 )
 # run_config=LocalRun(labels=[utils.get_environment()]),
 def lrg_2d_flow(

em_workflows/sem_tomo/flow.py

@@ -336,6 +336,10 @@ def gen_ng_metadata(fp_in: FilePath) -> Dict:
         utils.notify_api_completion,
         utils.copy_workdirs_and_cleanup_hook,
     ],
+    on_crashed=[
+        utils.notify_api_completion,
+        utils.copy_workdirs_and_cleanup_hook,
+    ],
 )
 def sem_tomo_flow(
     file_share: str,