Renamed 'clem' backend server module to 'workflow_clem' to bring it in line with other workflow-related endpoint modules (#794)

Author: tieneupin

src/murfey/cli/repost_failed_calls.py

@@ -93,7 +93,6 @@ def handle_failed_posts(messages_path: list[Path], murfey_db: Session):
     # These imports need to happen after transport object is configured
     import murfey.server.api.auth
     import murfey.server.api.bootstrap
-    import murfey.server.api.clem
     import murfey.server.api.display
     import murfey.server.api.file_io_frontend
     import murfey.server.api.file_io_instrument
@@ -106,6 +105,7 @@ def handle_failed_posts(messages_path: list[Path], murfey_db: Session):
     import murfey.server.api.session_info
     import murfey.server.api.websocket
     import murfey.server.api.workflow
+    import murfey.server.api.workflow_clem
 
     for json_file in messages_path:
         with open(json_file, "r") as json_data:

src/murfey/client/contexts/clem.py

@@ -326,7 +326,7 @@ def process_lif_file(
         try:
             capture_post(
                 base_url=str(environment.url.geturl()),
-                router_name="clem.router",
+                router_name="workflow_clem.router",
                 function_name="process_raw_lifs",
                 token=self._token,
                 instrument_name=environment.instrument_name,
@@ -351,7 +351,7 @@ def process_tiff_series(
         try:
             capture_post(
                 base_url=str(environment.url.geturl()),
-                router_name="clem.router",
+                router_name="workflow_clem.router",
                 function_name="process_raw_tiffs",
                 token=self._token,
                 instrument_name=environment.instrument_name,

src/murfey/server/api/clem.py src/murfey/server/api/workflow_clem.pysrc/murfey/server/api/clem.py renamed to src/murfey/server/api/workflow_clem.py

@@ -12,7 +12,6 @@
 import murfey.server
 import murfey.server.api.auth
 import murfey.server.api.bootstrap
-import murfey.server.api.clem
 import murfey.server.api.display
 import murfey.server.api.file_io_frontend
 import murfey.server.api.file_io_instrument
@@ -26,6 +25,7 @@
 import murfey.server.api.session_info
 import murfey.server.api.websocket
 import murfey.server.api.workflow
+import murfey.server.api.workflow_clem
 import murfey.server.api.workflow_fib
 from murfey.server import template_files
 from murfey.util.config import get_security_config
@@ -97,7 +97,7 @@ class Settings(BaseSettings):
 app.include_router(murfey.server.api.workflow.correlative_router)
 app.include_router(murfey.server.api.workflow.spa_router)
 app.include_router(murfey.server.api.workflow.tomo_router)
-app.include_router(murfey.server.api.clem.router)
+app.include_router(murfey.server.api.workflow_clem.router)
 app.include_router(murfey.server.api.workflow_fib.router)
 
 app.include_router(murfey.server.api.prometheus.router)

src/murfey/server/main.py

@@ -382,28 +382,6 @@ murfey.server.api.bootstrap.version:
     path_params: []
     methods:
       - GET
-murfey.server.api.clem.router:
-  - path: /workflow/clem/sessions/{session_id}/process_raw_lifs
-    function: process_raw_lifs
-    path_params:
-      - name: session_id
-        type: int
-    methods:
-      - POST
-  - path: /workflow/clem/sessions/{session_id}/process_raw_tiffs
-    function: process_raw_tiffs
-    path_params:
-      - name: session_id
-        type: int
-    methods:
-      - POST
-  - path: /workflow/clem/sessions/{session_id}/align_and_merge_stacks
-    function: align_and_merge_stacks
-    path_params:
-      - name: session_id
-        type: int
-    methods:
-      - POST
 murfey.server.api.display.router:
   - path: /display/instruments/{instrument_name}/instrument_name
     function: get_instrument_display_name
@@ -1432,6 +1410,28 @@ murfey.server.api.workflow.tomo_router:
         type: int
     methods:
       - POST
+murfey.server.api.workflow_clem.router:
+  - path: /workflow/clem/sessions/{session_id}/process_raw_lifs
+    function: process_raw_lifs
+    path_params:
+      - name: session_id
+        type: int
+    methods:
+      - POST
+  - path: /workflow/clem/sessions/{session_id}/process_raw_tiffs
+    function: process_raw_tiffs
+    path_params:
+      - name: session_id
+        type: int
+    methods:
+      - POST
+  - path: /workflow/clem/sessions/{session_id}/align_and_merge_stacks
+    function: align_and_merge_stacks
+    path_params:
+      - name: session_id
+        type: int
+    methods:
+      - POST
 murfey.server.api.workflow_fib.router:
   - path: /workflow/fib/sessions/{session_id}/register_atlas
     function: register_fib_atlas