Update ISPyB Inserts (#693)

* Insert CLEM data with correct experiment type ID
* Removed the insertion of 'experiment_type_id' into DataCollectionGroup tables due to deprecation of the field
* Add CLEM and FIB experiment type IDs to ISPyB test database

Author: tieneupin

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(

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,

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(

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)

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)

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,

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,

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"],
             )
 

tests/conftest.py

@@ -116,6 +116,8 @@ class ISPyBTableValues:
         "Tomography": 36,
         "Single Particle": 37,
         "Atlas": 44,
+        "CLEM": 45,
+        "FIB": 46,
     }
 
 

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,