Instances where a commit can happen without a close (#363)

I've found a couple of instances where the database can be committed to without then being closed:

- Tomography preprocessing flushes
- Particle picking registration if an ispyb picker id is not found

The second one of these would explain why we see spikes in database connections shortly after collections start. Once the picker id is found all the connections end up closed.

Closes #362

Author: stephen-riggs

src/murfey/server/__init__.py

@@ -809,15 +809,15 @@ def _register_picked_particles_use_boxsize(message: dict, _db=murfey_db):
         defocus_v=params_to_forward["ctf_values"]["DefocusV"],
         defocus_angle=params_to_forward["ctf_values"]["DefocusAngle"],
     )
-    murfey_db.add(ctf_params)
-    murfey_db.commit()
-    murfey_db.close()
+    _db.add(ctf_params)
+    _db.commit()
+    _db.close()
 
     # Set particle diameter as zero and send box sizes
-    relion_params = murfey_db.exec(
+    relion_params = _db.exec(
         select(db.SPARelionParameters).where(db.SPARelionParameters.pj_id == pj_id)
     ).one()
-    feedback_params = murfey_db.exec(
+    feedback_params = _db.exec(
         select(db.SPAFeedbackParameters).where(db.SPAFeedbackParameters.pj_id == pj_id)
     ).one()
 
@@ -874,6 +874,7 @@ def _register_picked_particles_use_boxsize(message: dict, _db=murfey_db):
     }
     if _transport_object:
         _transport_object.send("processing_recipe", zocalo_message, new_connection=True)
+    _db.close()
 
 
 def _release_2d_hold(message: dict, _db=murfey_db):
@@ -2127,6 +2128,7 @@ def _flush_tomography_preprocessing(message: dict):
             )
         murfey_db.delete(f)
         murfey_db.commit()
+        murfey_db.close()
 
 
 def _flush_grid_square_records(message: dict, _db=murfey_db, demo: bool = False):