From 80cea4d36354bbe6a659442bf88b8945a71762ec Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Fri, 14 Nov 2025 18:09:42 +0000 Subject: [PATCH 1/3] Insert CLEM data with correct experiment type ID --- src/murfey/workflows/clem/register_preprocessing_results.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/murfey/workflows/clem/register_preprocessing_results.py b/src/murfey/workflows/clem/register_preprocessing_results.py index e79da1d0..ccbc99b7 100644 --- a/src/murfey/workflows/clem/register_preprocessing_results.py +++ b/src/murfey/workflows/clem/register_preprocessing_results.py @@ -225,8 +225,7 @@ def _register_dcg_and_atlas( "visit_number": visit_number, "session_id": session_id, "tag": dcg_name, - "experiment_type": "experiment", - "experiment_type_id": None, + "experiment_type_id": 45, "atlas": atlas_name, "atlas_pixel_size": atlas_pixel_size, "sample": None, From 920ace9d99406bfeaf81cb21047b381a2b3e0153 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Fri, 14 Nov 2025 18:11:05 +0000 Subject: [PATCH 2/3] Removed the insertion of 'experiment_type_id' into DataCollectionGroup tables due to deprecation of the field --- src/murfey/client/contexts/spa_metadata.py | 6 ++---- src/murfey/client/contexts/tomo.py | 3 +-- src/murfey/client/contexts/tomo_metadata.py | 6 ++---- src/murfey/client/multigrid_control.py | 3 +-- src/murfey/client/tui/app.py | 3 +-- src/murfey/server/api/workflow.py | 2 -- src/murfey/workflows/register_data_collection_group.py | 1 - tests/workflows/test_register_data_collection_group.py | 1 - 8 files changed, 7 insertions(+), 18 deletions(-) diff --git a/src/murfey/client/contexts/spa_metadata.py b/src/murfey/client/contexts/spa_metadata.py index 18fdb500..f8c2e54f 100644 --- a/src/murfey/client/contexts/spa_metadata.py +++ b/src/murfey/client/contexts/spa_metadata.py @@ -177,8 +177,7 @@ def post_transfer( return dcg_tag = str(dcg_images_dirs[-1]) dcg_data = { - "experiment_type": "single particle", - "experiment_type_id": 37, + "experiment_type_id": 37, # Single particle "tag": dcg_tag, "atlas": str( _atlas_destination( @@ -248,8 +247,7 @@ def post_transfer( return dcg_tag = str(dcg_images_dirs[-1]) dcg_data = { - "experiment_type": "single particle", - "experiment_type_id": 37, + "experiment_type_id": 37, # Single particle "tag": dcg_tag, } capture_post( diff --git a/src/murfey/client/contexts/tomo.py b/src/murfey/client/contexts/tomo.py index 3439759a..6c4eff7e 100644 --- a/src/murfey/client/contexts/tomo.py +++ b/src/murfey/client/contexts/tomo.py @@ -102,8 +102,7 @@ def register_tomography_data_collections( return try: dcg_data = { - "experiment_type": "tomo", - "experiment_type_id": 36, + "experiment_type_id": 36, # Tomo "tag": str(self._basepath), "atlas": "", "sample": None, diff --git a/src/murfey/client/contexts/tomo_metadata.py b/src/murfey/client/contexts/tomo_metadata.py index dfd18049..45d22a22 100644 --- a/src/murfey/client/contexts/tomo_metadata.py +++ b/src/murfey/client/contexts/tomo_metadata.py @@ -22,8 +22,7 @@ def ensure_dcg_exists( return None dcg_tag = str(source).replace(f"/{environment.visit}", "") dcg_data = { - "experiment_type": "tomo", - "experiment_type_id": 36, + "experiment_type_id": 36, # Tomo "tag": dcg_tag, } capture_post( @@ -107,8 +106,7 @@ def post_transfer( p for p in transferred_file.parent.parts if p != environment.visit ).replace("//", "/") dcg_data = { - "experiment_type": "tomo", - "experiment_type_id": 36, + "experiment_type_id": 36, # Tomo "tag": dcg_tag, "atlas": str( _atlas_destination( diff --git a/src/murfey/client/multigrid_control.py b/src/murfey/client/multigrid_control.py index 7c5de07c..78b61614 100644 --- a/src/murfey/client/multigrid_control.py +++ b/src/murfey/client/multigrid_control.py @@ -611,8 +611,7 @@ def _start_dc(self, metadata_json, from_form: bool = False): elif isinstance(context, SPAModularContext): dcg_data = { - "experiment_type": "single particle", - "experiment_type_id": 37, + "experiment_type_id": 37, # Single particle "tag": str(source), "atlas": ( str(self._environment.samples[source].atlas) diff --git a/src/murfey/client/tui/app.py b/src/murfey/client/tui/app.py index 2c1bda45..334a4518 100644 --- a/src/murfey/client/tui/app.py +++ b/src/murfey/client/tui/app.py @@ -562,8 +562,7 @@ def _start_dc(self, metadata_json, from_form: bool = False): log.info("Tomography processing flushed") elif isinstance(context, SPAModularContext): dcg_data = { - "experiment_type": "single particle", - "experiment_type_id": 37, + "experiment_type_id": 37, # Single particle "tag": str(source), "atlas": ( str(self._environment.samples[source].atlas) diff --git a/src/murfey/server/api/workflow.py b/src/murfey/server/api/workflow.py index ddd60e09..fcc793de 100644 --- a/src/murfey/server/api/workflow.py +++ b/src/murfey/server/api/workflow.py @@ -83,7 +83,6 @@ class DCGroupParameters(BaseModel): # DC = Data collection - experiment_type: str experiment_type_id: int tag: str atlas: str = "" @@ -159,7 +158,6 @@ def register_dc_group( else: dcg_parameters = { "start_time": str(datetime.now()), - "experiment_type": dcg_params.experiment_type, "experiment_type_id": dcg_params.experiment_type_id, "tag": dcg_params.tag, "session_id": session_id, diff --git a/src/murfey/workflows/register_data_collection_group.py b/src/murfey/workflows/register_data_collection_group.py index 18631808..54126fdd 100644 --- a/src/murfey/workflows/register_data_collection_group.py +++ b/src/murfey/workflows/register_data_collection_group.py @@ -47,7 +47,6 @@ def run( else: record = ISPyBDB.DataCollectionGroup( sessionId=ispyb_session_id, - experimentType=message["experiment_type"], experimentTypeId=message["experiment_type_id"], ) diff --git a/tests/workflows/test_register_data_collection_group.py b/tests/workflows/test_register_data_collection_group.py index efe46a6e..7447dc22 100644 --- a/tests/workflows/test_register_data_collection_group.py +++ b/tests/workflows/test_register_data_collection_group.py @@ -66,7 +66,6 @@ def test_run( "visit_number": ExampleVisit.visit_number, "session_id": ExampleVisit.murfey_session_id, "tag": "some_text", - "experiment_type": "single particle", "experiment_type_id": 0, "atlas": "some_file", "atlas_pixel_size": 1e-9, From fdac7ed59b8dc476f3ecc229e4923912da6eb8c9 Mon Sep 17 00:00:00 2001 From: Eu Pin Tien Date: Fri, 14 Nov 2025 18:46:36 +0000 Subject: [PATCH 3/3] Add CLEM and FIB experiment type IDs to test ISPyB database --- tests/conftest.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/conftest.py b/tests/conftest.py index 4429e607..99b08b4c 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -116,6 +116,8 @@ class ISPyBTableValues: "Tomography": 36, "Single Particle": 37, "Atlas": 44, + "CLEM": 45, + "FIB": 46, }