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Split out separate function for DCG registration #901

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Merged
stephen-riggs merged 1 commit into from
Sep 24, 2026
Merged

Split out separate function for DCG registration #901

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152 changes: 83 additions & 69 deletions src/murfey/workflows/register_data_collection_group.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,13 +14,13 @@
logger = logging.getLogger("murfey.workflows.register_data_collection_group")


def run(message: dict, murfey_db: SQLModelSession) -> dict[str, bool]:
def register_dcg(
message: dict, murfey_db: SQLModelSession
) -> DataCollectionGroup | None:
# Fail immediately if no transport wrapper is found
if murfey.server._transport_object is None:
logger.error("Unable to find transport manager")
return {"success": False, "requeue": False}

logger.info(f"Registering the following data collection group: \n{message}")
return None

ispyb_session_id = get_session_id(
microscope=message["microscope"],
Expand All @@ -29,6 +29,76 @@ def run(message: dict, murfey_db: SQLModelSession) -> dict[str, bool]:
visit_number=message["visit_number"],
db=ISPyBSession(),
)
if ispyb_session_id is None:
murfey_dcg = DataCollectionGroup(
session_id=message["session_id"],
tag=message.get("tag"),
smartem_grid_uuid=message.get("smartem_grid_uuid"),
)
dcgid = murfey_dcg.id
else:
record = ISPyBDB.DataCollectionGroup(
sessionId=ispyb_session_id,
experimentTypeId=message["experiment_type_id"],
)

dcgid = murfey.server._transport_object.do_insert_data_collection_group(
record
).get("return_value", None)
if dcgid is None:
return None

atlas_record = ISPyBDB.Atlas(
dataCollectionGroupId=dcgid,
atlasImage=message.get("atlas", ""),
pixelSize=message.get("atlas_pixel_size", 0),
cassetteSlot=message.get("sample"),
)
# Optionally set the collection mode and color flags
if collection_mode := message.get("collection_mode"):
atlas_record.mode = collection_mode
if color_flags := message.get("color_flags", {}):
for col_name, value in color_flags.items():
setattr(atlas_record, col_name, value)
atlas_id = murfey.server._transport_object.do_insert_atlas(atlas_record).get(
"return_value", None
)

murfey_dcg = DataCollectionGroup(
id=dcgid,
atlas_id=atlas_id,
atlas=message.get("atlas", ""),
atlas_pixel_size=message.get("atlas_pixel_size"),
sample=message.get("sample"),
session_id=message["session_id"],
tag=message.get("tag"),
smartem_grid_uuid=message.get("smartem_grid_uuid"),
)
murfey_db.add(murfey_dcg)
if dcgid is not None and message.get("atlas_x_stage_position"):
atlas_site = ImagingSite(
dcg_id=dcgid,
session_id=message["session_id"],
site_name=message.get("tag"),
data_type="atlas",
pos_x=message.get("atlas_x_stage_position"),
pos_y=message.get("atlas_y_stage_position"),
image_pixels_x=message.get("atlas_width"),
image_pixels_y=message.get("atlas_height"),
image_pixel_size=message.get("atlas_pixel_size"),
)
murfey_db.add(atlas_site)
murfey_db.commit()
return murfey_dcg


def run(message: dict, murfey_db: SQLModelSession) -> dict[str, bool]:
# Fail immediately if no transport wrapper is found
if murfey.server._transport_object is None:
logger.error("Unable to find transport manager")
return {"success": False, "requeue": False}

logger.info(f"Registering the following data collection group: \n{message}")

if dcg_murfey := murfey_db.exec(
select(DataCollectionGroup)
Expand All @@ -37,73 +107,17 @@ def run(message: dict, murfey_db: SQLModelSession) -> dict[str, bool]:
).all():
dcgid = dcg_murfey[0].id
else:
if ispyb_session_id is None:
murfey_dcg = DataCollectionGroup(
session_id=message["session_id"],
tag=message.get("tag"),
smartem_grid_uuid=message.get("smartem_grid_uuid"),
)
dcgid = murfey_dcg.id
else:
record = ISPyBDB.DataCollectionGroup(
sessionId=ispyb_session_id,
experimentTypeId=message["experiment_type_id"],
murfey_dcg = register_dcg(message, murfey_db)
if murfey_dcg is None:
time.sleep(2)
logger.error(
"Failed to register the following data collection group: \n"
f"{message} \n"
"Requeuing message"
)
return {"success": False, "requeue": True}

dcgid = murfey.server._transport_object.do_insert_data_collection_group(
record
).get("return_value", None)

if dcgid is None:
time.sleep(2)
logger.error(
"Failed to register the following data collection group: \n"
f"{message} \n"
"Requeuing message"
)
return {"success": False, "requeue": True}

atlas_record = ISPyBDB.Atlas(
dataCollectionGroupId=dcgid,
atlasImage=message.get("atlas", ""),
pixelSize=message.get("atlas_pixel_size", 0),
cassetteSlot=message.get("sample"),
)
# Optionally set the collection mode and color flags
if collection_mode := message.get("collection_mode"):
atlas_record.mode = collection_mode
if color_flags := message.get("color_flags", {}):
for col_name, value in color_flags.items():
setattr(atlas_record, col_name, value)
atlas_id = murfey.server._transport_object.do_insert_atlas(
atlas_record
).get("return_value", None)

murfey_dcg = DataCollectionGroup(
id=dcgid,
atlas_id=atlas_id,
atlas=message.get("atlas", ""),
atlas_pixel_size=message.get("atlas_pixel_size"),
sample=message.get("sample"),
session_id=message["session_id"],
tag=message.get("tag"),
smartem_grid_uuid=message.get("smartem_grid_uuid"),
)
murfey_db.add(murfey_dcg)
if dcgid is not None and message.get("atlas_x_stage_position"):
atlas_site = ImagingSite(
dcg_id=dcgid,
session_id=message["session_id"],
site_name=message.get("tag"),
data_type="atlas",
pos_x=message.get("atlas_x_stage_position"),
pos_y=message.get("atlas_y_stage_position"),
image_pixels_x=message.get("atlas_width"),
image_pixels_y=message.get("atlas_height"),
image_pixel_size=message.get("atlas_pixel_size"),
)
murfey_db.add(atlas_site)
murfey_db.commit()
dcgid = murfey_dcg.id
murfey_db.close()

# Find out how many dcgs we have with this atlas
Expand Down
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