Safe inserts of search maps into database (#754)

We currently run a .one() on search maps, grid squares and foil holes in the database.
If there is already one, but the ispyb insert fails we trigger the except clause and end up inserting a second one, which then keeps crashing and inserting more as the .one() fails.

The except on these inserts has been removed in this PR and instead an .all() is run on the values and the first one taken.
If the ispyb update fails this should then fall through to the outer try-except in the feedback.py

Author: stephen-riggs

src/murfey/workflows/spa/flush_spa_preprocess.py

@@ -53,13 +53,15 @@ def register_grid_square(
     if grid_square_params.width is not None:
         grid_square_params.width_scaled = int(grid_square_params.width / 7.8)
 
-    try:
-        grid_square = murfey_db.exec(
-            select(GridSquare)
-            .where(GridSquare.name == gsid)
-            .where(GridSquare.tag == grid_square_params.tag)
-            .where(GridSquare.session_id == session_id)
-        ).one()
+    grid_square_query = murfey_db.exec(
+        select(GridSquare)
+        .where(GridSquare.name == gsid)
+        .where(GridSquare.tag == grid_square_params.tag)
+        .where(GridSquare.session_id == session_id)
+    ).all()
+    if grid_square_query:
+        # Grid square already exists in the murfey database
+        grid_square = grid_square_query[0]
         grid_square.x_location = grid_square_params.x_location or grid_square.x_location
         grid_square.y_location = grid_square_params.y_location or grid_square.y_location
         grid_square.x_stage_position = (
@@ -84,7 +86,8 @@ def register_grid_square(
         grid_square.image = grid_square_params.image or grid_square.image
         if _transport_object:
             _transport_object.do_update_grid_square(grid_square.id, grid_square_params)
-    except Exception:
+    else:
+        # No existing grid square in the murfey database
         if _transport_object:
             dcg = murfey_db.exec(
                 select(DataCollectionGroup)
@@ -151,13 +154,15 @@ def register_foil_hole(
         jpeg_size = Image.open(secured_foil_hole_image_path).size
     else:
         jpeg_size = (0, 0)
-    try:
-        foil_hole = murfey_db.exec(
-            select(FoilHole)
-            .where(FoilHole.name == foil_hole_params.name)
-            .where(FoilHole.grid_square_id == gsid)
-            .where(FoilHole.session_id == session_id)
-        ).one()
+    foil_hole_query = murfey_db.exec(
+        select(FoilHole)
+        .where(FoilHole.name == foil_hole_params.name)
+        .where(FoilHole.grid_square_id == gsid)
+        .where(FoilHole.session_id == session_id)
+    ).all()
+    if foil_hole_query:
+        # Foil hole already exists in the murfey database
+        foil_hole = foil_hole_query[0]
         foil_hole.x_location = foil_hole_params.x_location or foil_hole.x_location
         foil_hole.y_location = foil_hole_params.y_location or foil_hole.y_location
         foil_hole.x_stage_position = (
@@ -183,7 +188,8 @@ def register_foil_hole(
             _transport_object.do_update_foil_hole(
                 foil_hole.id, gs.thumbnail_size_x / gs.readout_area_x, foil_hole_params
             )
-    except Exception:
+    else:
+        # No existing foil hole in the murfey database
         if _transport_object:
             fh_ispyb_response = _transport_object.do_insert_foil_hole(
                 gs.id,

src/murfey/workflows/tomo/tomo_metadata.py

@@ -31,14 +31,15 @@ def register_search_map_in_database(
         .where(DataCollectionGroup.session_id == session_id)
         .where(DataCollectionGroup.tag == search_map_params.tag)
     ).one()
-    try:
+    search_map_query = murfey_db.exec(
+        select(SearchMap)
+        .where(SearchMap.name == search_map_name)
+        .where(SearchMap.tag == search_map_params.tag)
+        .where(SearchMap.session_id == session_id)
+    ).all()
+    if search_map_query:
         # See if there is already a search map with this name and update if so
-        search_map = murfey_db.exec(
-            select(SearchMap)
-            .where(SearchMap.name == search_map_name)
-            .where(SearchMap.tag == search_map_params.tag)
-            .where(SearchMap.session_id == session_id)
-        ).one()
+        search_map = search_map_query[0]
         search_map.x_stage_position = (
             search_map_params.x_stage_position or search_map.x_stage_position
         )
@@ -100,8 +101,8 @@ def register_search_map_in_database(
         search_map.width = search_map_params.width or search_map.width
         if _transport_object:
             _transport_object.do_update_search_map(search_map.id, search_map_params)
-    except Exception as e:
-        logger.info(f"Registering new search map due to {e}", exc_info=True)
+    else:
+        logger.info(f"Registering new search map {sanitise(search_map_name)}")
         if _transport_object:
             sm_ispyb_response = _transport_object.do_insert_search_map(
                 dcg.atlas_id, search_map_params