Merge pull request #3 from genematx/raise-errors

Raise errors in the workflow

Author: genematx

data_validation.py

@@ -225,7 +225,7 @@ def data_validation_task(uid, beamline_acronym=BEAMLINE_OR_ENDSTATION):
 
     logger.info(f"Validating uid {uid}")
     start_time = time.monotonic()
-    validate(run_client, fix_errors=True, try_reading=True, raise_on_error=False)
+    validate(run_client, fix_errors=True, try_reading=True, raise_on_error=True)
     elapsed_time = time.monotonic() - start_time
     logger.info(f"Finished validating data; {elapsed_time = }")
 

metadata_exporter.py

@@ -30,22 +30,19 @@ def export_metadata_task(uid, beamline_acronym=BEAMLINE_OR_ENDSTATION):
         logger.info(f"Found data file at {fpath_orig}, proceeding with metadata export.")
     else:
         logger.error(f"Data file not found at {fpath_orig}, aborting metadata export.")
-        return
+        raise FileNotFoundError(f"Data file not found at {fpath_orig}")
 
     # Copy the file to the destination directory and update the fpath variable
     # For example:
     # /nsls2/data3/esm/proposals/commissioning/pass-319467/assets/mbs/2025/12/11/sample_name/TEST_0002.nxs
     # /nsls2/data3/esm/proposals/commissioning/pass-319467/export/2025_12_11/sample_name/TEST_0002.nxs
-    try:
-        prefix, suffix = str(fpath_orig).split('assets')
-        suffix = suffix.split('/', 2)[-1].replace('/', '_', 2)
-        fpath_dest = Path(prefix) / 'export' / suffix
-        Path(fpath_dest).parent.mkdir(parents=True, exist_ok=True)
-
-        shutil.copy(fpath_orig, fpath_dest)
-        logger.info(f"File '{fpath_orig}' copied successfully to '{fpath_dest}'")
-    except Exception as e:
-        logger.error(f"An error occurred while copying the file: {e}")
+    prefix, suffix = str(fpath_orig).split('assets')
+    suffix = suffix.split('/', 2)[-1].replace('/', '_', 2)
+    fpath_dest = Path(prefix) / 'export' / suffix
+    Path(fpath_dest).parent.mkdir(parents=True, exist_ok=True)
+
+    shutil.copy(fpath_orig, fpath_dest)
+    logger.info(f"File '{fpath_orig}' copied successfully to '{fpath_dest}'")
 
     # Read the metadata from Tiled
     primary = run_client["primary"].read(variables = ['mbs_escale_min', 'mbs_escale_max', 'mbs_num_steps', \

prefect.yaml

@@ -32,6 +32,7 @@ deployments:
         network: slirp4netns
         volumes:
           - /nsls2/data/esm/proposals:/nsls2/data/esm/proposals
+          - /nsls2/data3/esm/proposals:/nsls2/data3/esm/proposals
           - /nsls2/software/etc/tiled:/nsls2/software/etc/tiled
         container_create_kwargs:
           userns_mode: "keep-id:uid=402966,gid=402966"  # workflow-esm:workflow-esm