Removed legacy function names for CLEM workflows, replacing them with 'run' instead

Author: tieneupin

pyproject.toml

@@ -98,10 +98,10 @@ GitHub = "https://github.com/DiamondLightSource/python-murfey"
 "murfey_machine" = "murfey.util.config:get_extended_machine_config"
 [project.entry-points."murfey.workflows"]
 "atlas_update" = "murfey.workflows.register_atlas_update:run"
-"clem.align_and_merge" = "murfey.workflows.clem.align_and_merge:submit_cluster_request"
-"clem.process_raw_lifs" = "murfey.workflows.clem.process_raw_lifs:zocalo_cluster_request"
-"clem.process_raw_tiffs" = "murfey.workflows.clem.process_raw_tiffs:zocalo_cluster_request"
-"clem.register_align_and_merge_result" = "murfey.workflows.clem.register_align_and_merge_results:register_align_and_merge_result"
+"clem.align_and_merge" = "murfey.workflows.clem.align_and_merge:run"
+"clem.process_raw_lifs" = "murfey.workflows.clem.process_raw_lifs:run"
+"clem.process_raw_tiffs" = "murfey.workflows.clem.process_raw_tiffs:run"
+"clem.register_align_and_merge_result" = "murfey.workflows.clem.register_align_and_merge_results:run"
 "clem.register_preprocessing_result" = "murfey.workflows.clem.register_preprocessing_results:run"
 "data_collection" = "murfey.workflows.register_data_collection:run"
 "data_collection_group" = "murfey.workflows.register_data_collection_group:run"

src/murfey/workflows/clem/align_and_merge.py

@@ -16,7 +16,7 @@
     pass  # Ignore if ISPyB credentials environment variable not set
 
 
-def submit_cluster_request(
+def run(
     # Session parameters
     session_id: int,
     instrument_name: str,

src/murfey/workflows/clem/process_raw_lifs.py

@@ -15,7 +15,7 @@
 logger = getLogger("murfey.workflows.clem.process_raw_lifs")
 
 
-def zocalo_cluster_request(
+def run(
     file: Path,
     root_folder: str,
     session_id: int,  # Provided by the client via the API endpoint

src/murfey/workflows/clem/process_raw_tiffs.py

@@ -15,7 +15,7 @@
     pass  # Ignore if ISPyB credentials environment variable not set
 
 
-def zocalo_cluster_request(
+def run(
     tiff_list: list[Path],
     root_folder: str,
     session_id: int,

src/murfey/workflows/clem/register_align_and_merge_results.py

@@ -40,9 +40,7 @@ def parse_stringified_list(cls, value):
         return value
 
 
-def register_align_and_merge_result(
-    message: dict, murfey_db: Session
-) -> dict[str, bool]:
+def run(message: dict, murfey_db: Session) -> dict[str, bool]:
     """
     session_id (recipe)
     register (wrapper)

src/murfey/workflows/clem/register_preprocessing_results.py

@@ -24,7 +24,7 @@
 from murfey.util.processing_params import (
     default_clem_processing_parameters as processing_params,
 )
-from murfey.workflows.clem.align_and_merge import submit_cluster_request
+from murfey.workflows.clem.align_and_merge import run as run_align_and_merge
 
 logger = logging.getLogger("murfey.workflows.clem.register_preprocessing_results")
 
@@ -589,7 +589,7 @@ def run(message: dict, murfey_db: Session) -> dict[str, bool]:
         # Request for image alignment and processing for the requested combinations
         for image_combo in image_combos_to_process:
             try:
-                submit_cluster_request(
+                run_align_and_merge(
                     session_id=session_id,
                     instrument_name=murfey_session.instrument_name,
                     series_name=result.series_name,

tests/workflows/clem/test_align_and_merge.py

@@ -6,7 +6,7 @@
 
 from murfey.server.ispyb import TransportManager
 from murfey.util.config import MachineConfig
-from murfey.workflows.clem.align_and_merge import submit_cluster_request
+from murfey.workflows.clem.align_and_merge import run
 
 # Folder and file settings
 session_id = 0
@@ -63,7 +63,7 @@ def metadata(processed_dir: Path):
 
 
 @patch("murfey.workflows.clem.align_and_merge.get_machine_config")
-def test_submit_cluster_request(
+def test_run(
     mock_get_machine_config,
     image_stacks: list[Path],
     metadata: Path,
@@ -86,7 +86,7 @@ def test_submit_cluster_request(
     }
 
     # Run the function
-    submit_cluster_request(
+    run(
         session_id=session_id,
         instrument_name=instrument_name,
         series_name=series_name_long,

tests/workflows/clem/test_process_raw_lifs.py

@@ -4,7 +4,7 @@
 import pytest
 
 from murfey.server.ispyb import TransportManager
-from murfey.workflows.clem.process_raw_lifs import zocalo_cluster_request
+from murfey.workflows.clem.process_raw_lifs import run
 
 # Set up variables
 visit_name = "cm12345-6"
@@ -29,7 +29,7 @@ def lif_file(raw_dir: Path):
     return file
 
 
-def test_zocalo_cluster_request(
+def test_run(
     lif_file: Path,
     raw_dir: Path,
 ):
@@ -38,7 +38,7 @@ def test_zocalo_cluster_request(
     mock_transport.feedback_queue = feedback_queue
 
     # Run the function with the listed parameters
-    zocalo_cluster_request(
+    run(
         file=lif_file,
         root_folder=root_folder,
         session_id=session_id,

tests/workflows/clem/test_process_raw_tiffs.py

@@ -4,7 +4,7 @@
 import pytest
 
 from murfey.server.ispyb import TransportManager
-from murfey.workflows.clem.process_raw_tiffs import zocalo_cluster_request
+from murfey.workflows.clem.process_raw_tiffs import run
 
 # Set up variables
 session_id = 0
@@ -49,7 +49,7 @@ def metadata(raw_dir: Path):
     return metadata
 
 
-def test_zocalo_cluster_request(
+def test_run(
     tiff_list: list[Path],
     metadata: Path,
     raw_dir: Path,
@@ -59,7 +59,7 @@ def test_zocalo_cluster_request(
     mock_transport.feedback_queue = feedback_queue
 
     # Run the function with the listed parameters
-    zocalo_cluster_request(
+    run(
         tiff_list=tiff_list,
         root_folder=root_folder,
         session_id=session_id,

tests/workflows/clem/test_register_preprocessing_results.py

@@ -254,7 +254,7 @@ def test_run(
 
     # Mock the align and merge workflow call
     mock_align_and_merge_call = mocker.patch(
-        "murfey.workflows.clem.register_preprocessing_results.submit_cluster_request"
+        "murfey.workflows.clem.register_preprocessing_results.run_align_and_merge"
     )
 
     preprocessing_messages = generate_preprocessing_messages(
@@ -340,7 +340,7 @@ def test_run_with_db(
 
     # Mock the align and merge workflow call
     mock_align_and_merge_call = mocker.patch(
-        "murfey.workflows.clem.register_preprocessing_results.submit_cluster_request"
+        "murfey.workflows.clem.register_preprocessing_results.run_align_and_merge"
     )
 
     # Patch the TransportManager object in the workflows called