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Safe inserts of search maps into database #754

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Merged
stephen-riggs merged 3 commits into from
Mar 5, 2026
Merged

Safe inserts of search maps into database #754

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72ed0fd
Safe inserts of search maps into database
stephen-riggs Mar 5, 2026
94326e8
all not one
stephen-riggs Mar 5, 2026
235b805
Sanitise input for log-injection
stephen-riggs Mar 5, 2026
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38 changes: 22 additions & 16 deletions src/murfey/workflows/spa/flush_spa_preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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 = (
Expand All @@ -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)
Expand Down Expand Up @@ -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 = (
Expand All @@ -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,
Expand Down
19 changes: 10 additions & 9 deletions src/murfey/workflows/tomo/tomo_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
)
Expand Down Expand Up @@ -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
Expand Down