Adjusted naming convention for LIF and TIFF processing functions and endpoints

Author: tieneupin

pyproject.toml

@@ -98,10 +98,10 @@ murfey = "murfey.client:run"
 [project.entry-points."murfey.config.extraction"]
 "murfey_machine" = "murfey.util.config:get_extended_machine_config"
 [project.entry-points."murfey.workflows.clem"]
-"lif_to_stack" = "murfey.workflows.clem.lif_to_stack:zocalo_cluster_request"
-"register_lif_preprocessing_result" = "murfey.workflows.clem.register_results:register_lif_preprocessing_result"
-"register_tiff_preprocessing_result" = "murfey.workflows.clem.register_results:register_tiff_preprocessing_result"
-"tiff_to_stack" = "murfey.workflows.clem.tiff_to_stack:zocalo_cluster_request"
+"process_raw_lifs" = "murfey.workflows.clem.process_raw_lifs:zocalo_cluster_request"
+"process_raw_tiffs" = "murfey.workflows.clem.process_raw_tiffs:zocalo_cluster_request"
+"register_lif_preprocessing_result" = "murfey.workflows.clem.register_preprocessing_results:register_lif_preprocessing_result"
+"register_tiff_preprocessing_result" = "murfey.workflows.clem.register_preprocessing_results:register_tiff_preprocessing_result"
 
 [tool.setuptools]
 package-dir = {"" = "src"}

src/murfey/client/contexts/clem.py

@@ -386,7 +386,7 @@ def process_lif_file(
 
         try:
             # Construct the URL to post the request to
-            url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/clem/preprocessing/lif_to_stack?lif_file={quote(str(lif_file), safe='')}"
+            url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/clem/preprocessing/process_raw_lifs?lif_file={quote(str(lif_file), safe='')}"
             # Validate
             if not url:
                 logger.error(
@@ -442,7 +442,7 @@ def process_tiff_series(
 
         try:
             # Construct URL for Murfey server to communicate with
-            url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/clem/preprocessing/tiff_to_stack"
+            url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/clem/preprocessing/process_raw_tiffs"
             if not url:
                 logger.error(
                     "URL could not be constructed from the environment and file path"

src/murfey/server/api/clem.py

@@ -632,16 +632,16 @@ def register_image_stack(
 
 
 @router.post(
-    "/sessions/{session_id}/clem/preprocessing/lif_to_stack"
+    "/sessions/{session_id}/clem/preprocessing/process_raw_lifs"
 )  # API posts to this URL
-def lif_to_stack(
+def process_raw_lifs(
     session_id: int,  # Used by the decorator
     lif_file: Path,
     db: Session = murfey_db,
 ):
     # Get command line entry point
     murfey_workflows = entry_points().select(
-        group="murfey.workflows.clem", name="lif_to_stack"
+        group="murfey.workflows.clem", name="process_raw_lifs"
     )
 
     # Use entry point if found
@@ -657,7 +657,7 @@ def lif_to_stack(
         # Pass arguments along to the correct workflow
         workflow: EntryPoint = list(murfey_workflows)[0]
         workflow.load()(
-            # Match the arguments found in murfey.workflows.lif_to_stack
+            # Match the arguments found in murfey.workflows.process_raw_lifs
             file=lif_file,
             root_folder="images",
             session_id=session_id,
@@ -671,15 +671,15 @@ def lif_to_stack(
         raise RuntimeError("The relevant Murfey workflow was not found")
 
 
-@router.post("/sessions/{session_id}/clem/preprocessing/tiff_to_stack")
-def tiff_to_stack(
+@router.post("/sessions/{session_id}/clem/preprocessing/process_raw_tiffs")
+def process_raw_tiffs(
     session_id: int,  # Used by the decorator
     tiff_info: TIFFSeriesInfo,
     db: Session = murfey_db,
 ):
     # Get command line entry point
     murfey_workflows = entry_points().select(
-        group="murfey.workflows.clem", name="tiff_to_stack"
+        group="murfey.workflows.clem", name="process_raw_tiffs"
     )
 
     # Use entry point if found
@@ -694,7 +694,7 @@ def tiff_to_stack(
         # Pass arguments to correct workflow
         workflow: EntryPoint = list(murfey_workflows)[0]
         workflow.load()(
-            # Match the arguments found in murfey.workflows.tiff_to_stack
+            # Match the arguments found in murfey.workflows.process_raw_tiffs
             tiff_list=tiff_info.tiff_files,
             root_folder="images",
             session_id=session_id,