Allow database override for reinjecting failed API calls

src/murfey/cli/repost_failed_calls.py

@@ -7,7 +7,7 @@
 from pathlib import Path
 from queue import Empty, Queue
 
-from sqlmodel import Session
+from sqlmodel import Session, create_engine
 from workflows.transport.pika_transport import PikaTransport
 
 import murfey.server.api.auth
@@ -25,7 +25,7 @@
 import murfey.server.api.session_info
 import murfey.server.api.websocket
 import murfey.server.api.workflow
-from murfey.server.murfey_db import get_murfey_db_session
+from murfey.server.murfey_db import url
 from murfey.util.config import security_from_file
 
 
@@ -162,7 +162,10 @@ def run():
     - feedback messages that can be sent back to rabbitmq
     """
     parser = argparse.ArgumentParser(
-        description="Purge and reinject failed murfey messages"
+        description=(
+            "Purge and reinject failed murfey messages. "
+            "Provide security configuration and set machine configuration."
+        )
     )
     parser.add_argument(
         "-c",
@@ -177,7 +180,6 @@ def run():
 
     # Read the security config file
     security_config = security_from_file(args.config)
-    murfey_db = get_murfey_db_session(security_config)
 
     # Purge the queue and repost/reinject any messages found
     dlq_dump_path = Path(args.dir)
@@ -187,7 +189,14 @@ def run():
         security_config.feedback_queue,
         security_config.rabbitmq_credentials,
     )
-    handle_failed_posts(exported_messages, murfey_db)
+
+    # Set up database and retry api calls
+    _url = url(security_config)
+    engine = create_engine(_url)
+    with Session(engine) as murfey_db:
+        handle_failed_posts(exported_messages, murfey_db)
+
+    # Reinject all remaining messages to rabbitmq
     handle_dlq_messages(exported_messages, security_config.rabbitmq_credentials)
 
     # Clean up any created directories

src/murfey/server/api/workflow.py

@@ -768,7 +768,7 @@ def register_completed_tilt_series(
     db.commit()
     for ts in tilt_series_db:
         if (
-            check_tilt_series_mc(ts.id)
+            check_tilt_series_mc(ts.id, db)
             and not ts.processing_requested
             and ts.tilt_series_length > 2
         ):
@@ -795,9 +795,9 @@ def register_completed_tilt_series(
             machine_config = get_machine_config(instrument_name=instrument_name)[
                 instrument_name
             ]
-            tilts = get_all_tilts(ts.id)
-            ids = get_job_ids(ts.id, collected_ids[3].id)
-            preproc_params = get_tomo_proc_params(ids.dcgid)
+            tilts = get_all_tilts(ts.id, db)
+            ids = get_job_ids(ts.id, collected_ids[3].id, db)
+            preproc_params = get_tomo_proc_params(ids.dcgid, db)
 
             first_tilt = db.exec(
                 select(Tilt).where(Tilt.tilt_series_id == ts.id)

src/murfey/server/demo_api.py

@@ -748,7 +748,7 @@ def register_dc_group(
 
     if dcg_params.atlas:
         _flush_grid_square_records(
-            {"session_id": session_id, "tag": dcg_params.tag}, demo=True
+            {"session_id": session_id, "tag": dcg_params.tag}, _db=db, demo=True
         )
     return dcg_params