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Update ISPyB Inserts #693

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Merged
tieneupin merged 3 commits into from
Nov 18, 2025
Merged

Update ISPyB Inserts #693

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80cea4d
Insert CLEM data with correct experiment type ID
tieneupin Nov 14, 2025
920ace9
Removed the insertion of 'experiment_type_id' into DataCollectionGrou…
tieneupin Nov 14, 2025
fdac7ed
Add CLEM and FIB experiment type IDs to test ISPyB database
tieneupin Nov 14, 2025
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6 changes: 2 additions & 4 deletions src/murfey/client/contexts/spa_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down
3 changes: 1 addition & 2 deletions src/murfey/client/contexts/tomo.py
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Expand Up @@ -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,
Expand Down
6 changes: 2 additions & 4 deletions src/murfey/client/contexts/tomo_metadata.py
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Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down
3 changes: 1 addition & 2 deletions src/murfey/client/multigrid_control.py
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Expand Up @@ -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)
Expand Down
3 changes: 1 addition & 2 deletions src/murfey/client/tui/app.py
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Expand Up @@ -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)
Expand Down
2 changes: 0 additions & 2 deletions src/murfey/server/api/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,6 @@

class DCGroupParameters(BaseModel):
# DC = Data collection
experiment_type: str
experiment_type_id: int
tag: str
atlas: str = ""
Expand Down Expand Up @@ -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,
Expand Down
3 changes: 1 addition & 2 deletions src/murfey/workflows/clem/register_preprocessing_results.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
1 change: 0 additions & 1 deletion src/murfey/workflows/register_data_collection_group.py
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Expand Up @@ -47,7 +47,6 @@ def run(
else:
record = ISPyBDB.DataCollectionGroup(
sessionId=ispyb_session_id,
experimentType=message["experiment_type"],
experimentTypeId=message["experiment_type_id"],
)

Expand Down
2 changes: 2 additions & 0 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,8 @@ class ISPyBTableValues:
"Tomography": 36,
"Single Particle": 37,
"Atlas": 44,
"CLEM": 45,
"FIB": 46,
}


Expand Down
1 change: 0 additions & 1 deletion tests/workflows/test_register_data_collection_group.py
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Expand Up @@ -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,
Expand Down
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