Problems introduced by doppio branch

src/murfey/cli/repost_failed_calls.py

@@ -1,6 +1,7 @@
 import argparse
 import asyncio
 import json
+import os
 from datetime import datetime
 from functools import partial
 from inspect import getfullargspec, iscoroutinefunction
@@ -10,10 +11,6 @@
 from sqlmodel import Session, create_engine
 from workflows.transport.pika_transport import PikaTransport
 
-from murfey.server.murfey_db import url
-from murfey.server.run import _set_up_transport
-from murfey.util.config import security_from_file
-
 
 def dlq_purge(
     dlq_dump_path: Path, queue: str, rabbitmq_credentials: Path
@@ -191,10 +188,17 @@ def run():
     args = parser.parse_args()
 
     # Read the security config file
+    os.environ["MURFEY_SECURITY_CONFIGURATION"] = args.config
+
+    from murfey.util.config import security_from_file
+
     security_config = security_from_file(args.config)
 
     # Configure the transport
     PikaTransport().load_configuration_file(security_config.rabbitmq_credentials)
+
+    from murfey.server.run import _set_up_transport
+
     _set_up_transport("PikaTransport")
 
     # Now import transport object which was set up in the above step
@@ -212,6 +216,8 @@ def run():
     )
 
     # Set up database and retry api calls
+    from murfey.server.murfey_db import url
+
     _url = url(security_config)
     engine = create_engine(_url)
     with Session(engine) as murfey_db:

src/murfey/server/api/workflow.py

@@ -34,15 +34,15 @@
 
     from murfey.util.config import get_security_config
 
-    keycloak_client = KeycloakClient(
-        load_keycloak_config(
-            Path(
-                os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION")
-                or get_security_config().smartem_keycloak_config
-            )
-        )
-    )
-    SMARTEM_ACTIVE = True
+    if keycloak_config := (
+        os.getenv("SMARTEM_KEYCLOAK_CONFIGURATION")
+        or get_security_config().smartem_keycloak_config
+    ):
+        keycloak_client = KeycloakClient(load_keycloak_config(Path(keycloak_config)))
+        SMARTEM_ACTIVE = True
+    else:
+        keycloak_client = None
+        SMARTEM_ACTIVE = False
 except ImportError:
     keycloak_client = None
     SMARTEM_ACTIVE = False
@@ -695,8 +695,6 @@ async def request_spa_preprocessing(
                     "Failed to register micrograph with smartem", exc_info=True
                 )
 
-        db.close()
-
         recipe_name = machine_config.recipes.get(
             "em-spa-preprocess", "em-spa-preprocess"
         )
@@ -741,7 +739,7 @@ async def request_spa_preprocessing(
                 f"Pre-processing was requested for {sanitise(Path(proc_file.path).name)} "
                 "but no Zocalo transport object was found"
             )
-            return proc_file
+        db.close()
 
     else:
         for_stash = PreprocessStash(

src/murfey/util/processing_params.py

@@ -79,8 +79,9 @@ def motion_corrected_mrc(
     else:
         parts = [secure_filename(p) for p in input_movie.parts]
         visit_idx = parts.index(visit_name)
-        core = Path(*parts[: visit_idx + 1])
-        ppath = Path(*parts)
+        # Include leading slash which is removed in the secure parts above
+        core = Path("/") / Path(*parts[: visit_idx + 1])
+        ppath = Path("/") / Path(*parts)
         if machine_config.process_multiple_datasets:
             sub_dataset = ppath.relative_to(core).parts[0]
         else: