Replaced 'router.url_path_for()' instances in client with use of our 'url_path_for()' function instead; this will keep server and client-side dependencies separate

Author: tieneupin

src/murfey/client/__init__.py

@@ -26,7 +26,7 @@
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.client.tui.app import MurfeyTUI
 from murfey.client.tui.status_bar import StatusBar
-from murfey.server.api.session_control import router as session_router
+from murfey.util.api import url_path_for
 from murfey.util.client import authorised_requests, read_config
 from murfey.util.models import Visit
 
@@ -38,7 +38,7 @@
 def _get_visit_list(api_base: ParseResult, instrument_name: str):
     proxy_path = api_base.path.rstrip("/")
     get_visits_url = api_base._replace(
-        path=f"{proxy_path}{session_router.url_path_for('get_current_visits', instrument_name=instrument_name)}"
+        path=f"{proxy_path}{url_path_for('session_control.router', 'get_current_visits', instrument_name=instrument_name)}"
     )
     server_reply = requests.get(get_visits_url.geturl())
     if server_reply.status_code != 200:

src/murfey/client/contexts/spa.py

@@ -15,10 +15,7 @@
     MurfeyID,
     MurfeyInstanceEnvironment,
 )
-from murfey.server.api.file_manip import router as file_manip_router
-from murfey.server.api.session_control import router as session_router
-from murfey.server.api.session_control import spa_router as session_spa_router
-from murfey.server.api.workflow import spa_router as workflow_spa_router
+from murfey.util.api import url_path_for
 from murfey.util.client import (
     authorised_requests,
     capture_get,
@@ -266,7 +263,7 @@ def gather_metadata(
         binning_factor = 1
         if environment:
             server_config_response = capture_get(
-                f"{str(environment.url.geturl())}{session_router.url_path_for('machine_info_by_instrument', instrument_name=environment.instrument_name)}"
+                f"{str(environment.url.geturl())}{url_path_for('session_control.router', 'machine_info_by_instrument', instrument_name=environment.instrument_name)}"
             )
             if server_config_response is None:
                 return None
@@ -430,7 +427,7 @@ def _position_analysis(
                         local_atlas_path,
                         grid_square=str(grid_square),
                     )[str(grid_square)]
-            gs_url = f"{str(environment.url.geturl())}{session_spa_router.url_path_for('register_grid_square', session_id=environment.murfey_session, gsid=grid_square)}"
+            gs_url = f"{str(environment.url.geturl())}{url_path_for('session_control.spa_router', 'register_grid_square', session_id=environment.murfey_session, gsid=grid_square)}"
             gs = grid_square_data(
                 grid_square_metadata_file,
                 grid_square,
@@ -471,7 +468,7 @@ def _position_analysis(
             )
         foil_hole = foil_hole_from_file(transferred_file)
         if foil_hole not in self._foil_holes[grid_square]:
-            fh_url = f"{str(environment.url.geturl())}{session_spa_router.url_path_for('register_foil_hole', session_id=environment.murfey_session, gs_name=grid_square)}"
+            fh_url = f"{str(environment.url.geturl())}{url_path_for('session_control.spa_router', 'register_foil_hole', session_id=environment.murfey_session, gs_name=grid_square)}"
             if environment.murfey_session is not None:
                 fh = foil_hole_data(
                     grid_square_metadata_file,
@@ -584,7 +581,7 @@ def post_transfer(
                         eer_fractionation_file = None
                         if file_transferred_to.suffix == ".eer":
                             response = capture_post(
-                                f"{str(environment.url.geturl())}{file_manip_router.url_path_for('write_eer_fractionation_file', visit_name=environment.visit, session_id=environment.murfey_session)}",
+                                f"{str(environment.url.geturl())}{url_path_for('file_manip.router', 'write_eer_fractionation_file', visit_name=environment.visit, session_id=environment.murfey_session)}",
                                 json={
                                     "eer_path": str(file_transferred_to),
                                     "fractionation": environment.data_collection_parameters[
@@ -613,7 +610,7 @@ def post_transfer(
                             )
                             foil_hole = None
 
-                        preproc_url = f"{str(environment.url.geturl())}{workflow_spa_router.url_path_for('request_spa_preprocessing', visit_name=environment.visit, session_id=environment.murfey_session)}"
+                        preproc_url = f"{str(environment.url.geturl())}{url_path_for('workflow.spa_router', 'request_spa_preprocessing', visit_name=environment.visit, session_id=environment.murfey_session)}"
                         preproc_data = {
                             "path": str(file_transferred_to),
                             "description": "",

src/murfey/client/contexts/spa_metadata.py

@@ -8,8 +8,7 @@
 from murfey.client.context import Context
 from murfey.client.contexts.spa import _file_transferred_to, _get_source
 from murfey.client.instance_environment import MurfeyInstanceEnvironment, SampleInfo
-from murfey.server.api.session_control import spa_router as session_spa_router
-from murfey.server.api.workflow import router as workflow_router
+from murfey.util.api import url_path_for
 from murfey.util.client import (
     authorised_requests,
     capture_post,
@@ -168,7 +167,7 @@ def post_transfer(
                 environment.samples[source] = SampleInfo(
                     atlas=Path(partial_path), sample=sample
                 )
-                url = f"{str(environment.url.geturl())}{workflow_router.url_path_for('register_dc_group', visit_name=environment.visit, session_id=environment.murfey_session)}"
+                url = f"{str(environment.url.geturl())}{url_path_for('workflow.router', 'register_dc_group', visit_name=environment.visit, session_id=environment.murfey_session)}"
                 dcg_search_dir = "/".join(
                     p for p in transferred_file.parent.parts if p != environment.visit
                 )
@@ -204,7 +203,7 @@ def post_transfer(
                 for gs, pos_data in gs_pix_positions.items():
                     if pos_data:
                         capture_post(
-                            f"{str(environment.url.geturl())}{session_spa_router.url_path_for('register_grid_square', session_id=environment.murfey_session, gsid=gs)}",
+                            f"{str(environment.url.geturl())}{url_path_for('session_control.spa_router', 'register_grid_square', session_id=environment.murfey_session, gsid=gs)}",
                             json={
                                 "tag": dcg_tag,
                                 "x_location": pos_data[0],
@@ -223,7 +222,7 @@ def post_transfer(
             and environment
         ):
             # Make sure we have a data collection group before trying to register grid square
-            url = f"{str(environment.url.geturl())}{workflow_router.url_path_for('register_dc_group', visit_name=environment.visit, session_id=environment.murfey_session)}"
+            url = f"{str(environment.url.geturl())}{url_path_for('workflow.router', 'register_dc_group', visit_name=environment.visit, session_id=environment.murfey_session)}"
             dcg_search_dir = "/".join(
                 p
                 for p in transferred_file.parent.parent.parts
@@ -272,7 +271,7 @@ def post_transfer(
             visitless_source = str(visitless_source_images_dirs[-1])
 
             if fh_positions:
-                gs_url = f"{str(environment.url.geturl())}{session_spa_router.url_path_for('register_grid_square', session_id=environment.murfey_session, gsid=gs_name)}"
+                gs_url = f"{str(environment.url.geturl())}{url_path_for('session_control.spa_router', 'register_grid_square', session_id=environment.murfey_session, gsid=gs_name)}"
                 gs_info = grid_square_data(
                     transferred_file,
                     int(gs_name),
@@ -297,7 +296,7 @@ def post_transfer(
 
             for fh, fh_data in fh_positions.items():
                 capture_post(
-                    f"{str(environment.url.geturl())}{session_spa_router.url_path_for('register_foil_hole', session_id=environment.murfey_session, gs_name=gs_name)}",
+                    f"{str(environment.url.geturl())}{url_path_for('session_control.spa_router', 'register_foil_hole', session_id=environment.murfey_session, gs_name=gs_name)}",
                     json={
                         "name": fh,
                         "x_location": fh_data.x_location,

src/murfey/client/contexts/tomo.py

@@ -17,10 +17,7 @@
     MurfeyID,
     MurfeyInstanceEnvironment,
 )
-from murfey.server.api.file_manip import router as file_manip_router
-from murfey.server.api.session_control import router as session_router
-from murfey.server.api.workflow import router as workflow_router
-from murfey.server.api.workflow import tomo_router as workflow_tomo_router
+from murfey.util.api import url_path_for
 from murfey.util.client import (
     authorised_requests,
     capture_post,
@@ -113,7 +110,7 @@ def register_tomography_data_collections(
             )
             return
         try:
-            dcg_url = f"{str(environment.url.geturl())}{workflow_router.url_path_for('register_dc_group', visit_name=environment.visit, session_id=environment.murfey_session)}"
+            dcg_url = f"{str(environment.url.geturl())}{url_path_for('workflow.router', 'register_dc_group', visit_name=environment.visit, session_id=environment.murfey_session)}"
             dcg_data = {
                 "experiment_type": "tomo",
                 "experiment_type_id": 36,
@@ -125,7 +122,7 @@ def register_tomography_data_collections(
 
             for tilt_series in self._tilt_series.keys():
                 if tilt_series not in self._tilt_series_with_pjids:
-                    dc_url = f"{str(environment.url.geturl())}{workflow_router.url_path_for('start_dc', visit_name=environment.visit, session_id=environment.murfey_session)}"
+                    dc_url = f"{str(environment.url.geturl())}{url_path_for('workflow.router', 'start_dc', visit_name=environment.visit, session_id=environment.murfey_session)}"
                     dc_data = {
                         "experiment_type": "tomography",
                         "file_extension": file_extension,
@@ -161,7 +158,7 @@ def register_tomography_data_collections(
                         )
                         capture_post(dc_url, json=dc_data)
 
-                        proc_url = f"{str(environment.url.geturl())}{workflow_router.url_path_for('register_proc', visit_name=environment.visit, session_id=environment.murfey_session)}"
+                        proc_url = f"{str(environment.url.geturl())}{url_path_for('workflow.router', 'register_proc', visit_name=environment.visit, session_id=environment.murfey_session)}"
                         for recipe in ("em-tomo-preprocess", "em-tomo-align"):
                             capture_post(
                                 proc_url,
@@ -266,7 +263,7 @@ def _add_tilt(
                 f"Tilt series {tilt_series} was previously thought complete but now {file_path} has been seen"
             )
             self._completed_tilt_series.remove(tilt_series)
-            rerun_url = f"{str(environment.url.geturl())}{workflow_tomo_router.url_path_for('register_tilt_series_for_rerun', visit_name=environment.visit)}"
+            rerun_url = f"{str(environment.url.geturl())}{url_path_for('workflow.tomo_router', 'register_tilt_series_for_rerun', visit_name=environment.visit)}"
             rerun_data = {
                 "session_id": environment.murfey_session,
                 "tag": tilt_series,
@@ -280,7 +277,7 @@ def _add_tilt(
         if not self._tilt_series.get(tilt_series):
             logger.info(f"New tilt series found: {tilt_series}")
             self._tilt_series[tilt_series] = [file_path]
-            ts_url = f"{str(environment.url.geturl())}{workflow_tomo_router.url_path_for('register_tilt_series', visit_name=environment.visit)}"
+            ts_url = f"{str(environment.url.geturl())}{url_path_for('workflow.tomo_router', 'register_tilt_series', visit_name=environment.visit)}"
             ts_data = {
                 "session_id": environment.murfey_session,
                 "tag": tilt_series,
@@ -309,7 +306,7 @@ def _add_tilt(
                     self._tilt_series[tilt_series].append(file_path)
 
         if environment:
-            tilt_url = f"{str(environment.url.geturl())}{workflow_tomo_router.url_path_for('register_tilt', visit_name=environment.visit, session_id=environment.murfey_session)}"
+            tilt_url = f"{str(environment.url.geturl())}{url_path_for('workflow.tomo_router', 'register_tilt', visit_name=environment.visit, session_id=environment.murfey_session)}"
             tilt_data = {
                 "movie_path": str(file_transferred_to),
                 "tilt_series_tag": tilt_series,
@@ -320,7 +317,7 @@ def _add_tilt(
             eer_fractionation_file = None
             if environment.data_collection_parameters.get("num_eer_frames"):
                 response = requests.post(
-                    f"{str(environment.url.geturl())}{file_manip_router.url_path_for('write_eer_fractionation_file', visit_name=environment.visit, session_id=environment.murfey_session)}",
+                    f"{str(environment.url.geturl())}{url_path_for('file_manip.router', 'write_eer_fractionation_file', visit_name=environment.visit, session_id=environment.murfey_session)}",
                     json={
                         "num_frames": environment.data_collection_parameters[
                             "num_eer_frames"
@@ -335,7 +332,7 @@ def _add_tilt(
                     },
                 )
                 eer_fractionation_file = response.json()["eer_fractionation_file"]
-            preproc_url = f"{str(environment.url.geturl())}{workflow_tomo_router.url_path_for('request_tomography_preprocessing', visit_name=environment.visit, session_id=environment.murfey_session)}"
+            preproc_url = f"{str(environment.url.geturl())}{url_path_for('workflow.tomo_router', 'request_tomography_preprocessing', visit_name=environment.visit, session_id=environment.murfey_session)}"
             preproc_data = {
                 "path": str(file_transferred_to),
                 "description": "",
@@ -495,7 +492,7 @@ def post_transfer(
 
                     # Always update the tilt series length in the database after an mdoc
                     if environment.murfey_session is not None:
-                        length_url = f"{str(environment.url.geturl())}{workflow_tomo_router.url_path_for('register_tile_series_length', session_id=environment.murfey_session)}"
+                        length_url = f"{str(environment.url.geturl())}{url_path_for('workflow.tomo_router', 'register_tile_series_length', session_id=environment.murfey_session)}"
                         capture_post(
                             length_url,
                             json={
@@ -512,7 +509,7 @@ def post_transfer(
                 f"The following tilt series are considered complete: {completed_tilts} "
                 f"after {transferred_file}"
             )
-            complete_url = f"{str(environment.url.geturl())}{workflow_tomo_router.url_path_for('register_completed_tilt_series', visit_name=environment.visit, session_id=environment.murfey_session)}"
+            complete_url = f"{str(environment.url.geturl())}{url_path_for('workflow.tomo_router', 'register_completed_tilt_series', visit_name=environment.visit, session_id=environment.murfey_session)}"
             capture_post(
                 complete_url,
                 json={
@@ -596,7 +593,7 @@ def gather_metadata(
             binning_factor = 1
             if environment:
                 server_config = requests.get(
-                    f"{str(environment.url.geturl())}{session_router.url_path_for('machine_info_by_instrument', instrument_name=environment.instrument_name)}"
+                    f"{str(environment.url.geturl())}{url_path_for('session_control.router', 'machine_info_by_instrument', instrument_name=environment.instrument_name)}"
                 ).json()
                 if (
                     server_config.get("superres")