Rationalise the api

Author: stephen-riggs

src/murfey/server/api/file_io_instrument.py

@@ -34,7 +34,7 @@ class SuggestedPathParameters(BaseModel):
     extra_directory: str = ""
 
 
-@router.post("/visits/{visit_name}/{session_id}/suggested_path")
+@router.post("/visits/{visit_name}/sessions/{session_id}/suggested_path")
 def suggest_path(
     visit_name: str, session_id: int, params: SuggestedPathParameters, db=murfey_db
 ):
@@ -125,7 +125,7 @@ class FractionationParameters(BaseModel):
     fractionation_file_name: str = "eer_fractionation.txt"
 
 
-@router.post("/visits/{visit_name}/{session_id}/eer_fractionation_file")
+@router.post("/visits/{visit_name}/sessions/{session_id}/eer_fractionation_file")
 async def write_eer_fractionation_file(
     visit_name: str,
     session_id: int,

src/murfey/server/api/instrument.py

@@ -353,7 +353,7 @@ async def request_gain_reference_upload(
     return data
 
 
-@router.post("/visits/{visit_name}/{session_id}/upstream_tiff_data_request")
+@router.post("/visits/{visit_name}/sessions/{session_id}/upstream_tiff_data_request")
 async def request_upstream_tiff_data_download(
     visit_name: str, session_id: MurfeySessionID, db=murfey_db
 ):

src/murfey/server/api/session_control.py

@@ -424,7 +424,9 @@ async def find_upstream_visits(session_id: MurfeySessionID, db=murfey_db):
     return upstream_visits
 
 
-@correlative_router.get("/visits/{visit_name}/{session_id}/upstream_tiff_paths")
+@correlative_router.get(
+    "/visits/{visit_name}/sessions/{session_id}/upstream_tiff_paths"
+)
 async def gather_upstream_tiffs(visit_name: str, session_id: int, db=murfey_db):
     """
     Looks for TIFF files associated with the current session in the permitted storage
@@ -446,7 +448,7 @@ async def gather_upstream_tiffs(visit_name: str, session_id: int, db=murfey_db):
 
 
 @correlative_router.get(
-    "/visits/{visit_name}/{session_id}/upstream_tiff/{tiff_path:path}"
+    "/visits/{visit_name}/sessions/{session_id}/upstream_tiff/{tiff_path:path}"
 )
 async def get_tiff(visit_name: str, session_id: int, tiff_path: str, db=murfey_db):
     instrument_name = (

src/murfey/server/api/session_info.py

@@ -135,7 +135,7 @@ class SessionClients(BaseModel):
     clients: List[ClientEnvironment]
 
 
-@router.get("/session/{session_id}")
+@router.get("/sessions/{session_id}")
 async def get_session(session_id: MurfeySessionID, db=murfey_db) -> SessionClients:
     session = db.exec(select(Session).where(Session.id == session_id)).one()
     clients = db.exec(
@@ -419,7 +419,9 @@ async def find_upstream_visits(session_id: MurfeySessionID, db=murfey_db):
     return upstream_visits
 
 
-@correlative_router.get("/visits/{visit_name}/{session_id}/upstream_tiff_paths")
+@correlative_router.get(
+    "/visits/{visit_name}/sessions/{session_id}/upstream_tiff_paths"
+)
 async def gather_upstream_tiffs(visit_name: str, session_id: int, db=murfey_db):
     """
     Looks for TIFF files associated with the current session in the permitted storage
@@ -441,7 +443,7 @@ async def gather_upstream_tiffs(visit_name: str, session_id: int, db=murfey_db):
 
 
 @correlative_router.get(
-    "/visits/{visit_name}/{session_id}/upstream_tiff/{tiff_path:path}"
+    "/visits/{visit_name}/sessions/{session_id}/upstream_tiff/{tiff_path:path}"
 )
 async def get_tiff(visit_name: str, session_id: int, tiff_path: str, db=murfey_db):
     instrument_name = (

src/murfey/server/api/workflow.py

@@ -90,7 +90,9 @@ class DCGroupParameters(BaseModel):
     atlas_pixel_size: float = 0
 
 
-@router.post("/visits/{visit_name}/{session_id}/register_data_collection_group")
+@router.post(
+    "/visits/{visit_name}/sessions/{session_id}/register_data_collection_group"
+)
 def register_dc_group(
     visit_name, session_id: MurfeySessionID, dcg_params: DCGroupParameters, db=murfey_db
 ):
@@ -197,7 +199,7 @@ class DCParameters(BaseModel):
     data_collection_tag: str = ""
 
 
-@router.post("/visits/{visit_name}/{session_id}/start_data_collection")
+@router.post("/visits/{visit_name}/sessions/{session_id}/start_data_collection")
 def start_dc(
     visit_name, session_id: MurfeySessionID, dc_params: DCParameters, db=murfey_db
 ):
@@ -263,7 +265,7 @@ class ProcessingJobParameters(BaseModel):
     experiment_type: str = "spa"
 
 
-@router.post("/visits/{visit_name}/{session_id}/register_processing_job")
+@router.post("/visits/{visit_name}/sessions/{session_id}/register_processing_job")
 def register_proc(
     visit_name: str,
     session_id: MurfeySessionID,
@@ -346,7 +348,7 @@ class Tag(BaseModel):
     tag: str
 
 
-@spa_router.post("/visits/{visit_name}/{session_id}/flush_spa_processing")
+@spa_router.post("/visits/{visit_name}/sessions/{session_id}/flush_spa_processing")
 def flush_spa_processing(
     visit_name: str, session_id: MurfeySessionID, tag: Tag, db=murfey_db
 ):
@@ -378,7 +380,7 @@ class SPAProcessFile(BaseModel):
     source: str = ""
 
 
-@spa_router.post("/visits/{visit_name}/{session_id}/spa_preprocess")
+@spa_router.post("/visits/{visit_name}/sessions/{session_id}/spa_preprocess")
 async def request_spa_preprocessing(
     visit_name: str,
     session_id: MurfeySessionID,
@@ -553,7 +555,9 @@ class Source(BaseModel):
     rsync_source: str
 
 
-@tomo_router.post("/visits/{visit_name}/{session_id}/flush_tomography_processing")
+@tomo_router.post(
+    "/visits/{visit_name}/sessions/{session_id}/flush_tomography_processing"
+)
 def flush_tomography_processing(
     visit_name: str, session_id: MurfeySessionID, rsync_source: Source, db=murfey_db
 ):
@@ -638,7 +642,7 @@ class TomoProcessFile(BaseModel):
     group_tag: Optional[str] = None
 
 
-@tomo_router.post("/visits/{visit_name}/{session_id}/tomography_preprocess")
+@tomo_router.post("/visits/{visit_name}/sessions/{session_id}/tomography_preprocess")
 async def request_tomography_preprocessing(
     visit_name: str,
     session_id: MurfeySessionID,
@@ -741,7 +745,7 @@ async def request_tomography_preprocessing(
     return proc_file
 
 
-@tomo_router.post("/visits/{visit_name}/{session_id}/completed_tilt_series")
+@tomo_router.post("/visits/{visit_name}/sesisons{session_id}/completed_tilt_series")
 def register_completed_tilt_series(
     visit_name: str,
     session_id: MurfeySessionID,
@@ -872,7 +876,7 @@ class TiltInfo(BaseModel):
     source: str
 
 
-@tomo_router.post("/visits/{visit_name}/{session_id}/tilt")
+@tomo_router.post("/visits/{visit_name}/sessions{session_id}/tilt")
 async def register_tilt(
     visit_name: str, session_id: MurfeySessionID, tilt_info: TiltInfo, db=murfey_db
 ):
@@ -1006,7 +1010,9 @@ class MillingParameters(BaseModel):
     raw_directory: str
 
 
-@correlative_router.post("/visits/{year}/{visit_name}/{session_id}/make_milling_gif")
+@correlative_router.post(
+    "/year/{year}/visits/{visit_name}/sessions/{session_id}/make_milling_gif"
+)
 async def make_gif(
     year: int,
     visit_name: str,

src/murfey/util/route_manifest.yaml

@@ -436,7 +436,7 @@ murfey.server.api.file_io_frontend.router:
     methods:
       - POST
 murfey.server.api.file_io_instrument.router:
-  - path: /file_io/instrument/visits/{visit_name}/{session_id}/suggested_path
+  - path: /file_io/instrument/visits/{visit_name}/sessions/{session_id}/suggested_path
     function: suggest_path
     path_params:
       - name: visit_name
@@ -457,7 +457,7 @@ murfey.server.api.file_io_instrument.router:
     path_params: []
     methods:
       - POST
-  - path: /file_io/instrument/visits/{visit_name}/{session_id}/eer_fractionation_file
+  - path: /file_io/instrument/visits/{visit_name}/sessions/{session_id}/eer_fractionation_file
     function: write_eer_fractionation_file
     path_params:
       - name: visit_name
@@ -542,7 +542,7 @@ murfey.server.api.instrument.router:
     path_params: []
     methods:
       - POST
-  - path: /instrument_server/visits/{visit_name}/{session_id}/upstream_tiff_data_request
+  - path: /instrument_server/visits/{visit_name}/sessions/{session_id}/upstream_tiff_data_request
     function: request_upstream_tiff_data_download
     path_params:
       - name: visit_name
@@ -671,7 +671,7 @@ murfey.server.api.session_control.correlative_router:
     path_params: []
     methods:
       - GET
-  - path: /session_control/correlative/visits/{visit_name}/{session_id}/upstream_tiff_paths
+  - path: /session_control/correlative/visits/{visit_name}/sessions/{session_id}/upstream_tiff_paths
     function: gather_upstream_tiffs
     path_params:
       - name: visit_name
@@ -680,7 +680,7 @@ murfey.server.api.session_control.correlative_router:
         type: int
     methods:
       - GET
-  - path: /session_control/correlative/visits/{visit_name}/{session_id}/upstream_tiff/{tiff_path:path}
+  - path: /session_control/correlative/visits/{visit_name}/sessions/{session_id}/upstream_tiff/{tiff_path:path}
     function: get_tiff
     path_params:
       - name: visit_name
@@ -861,7 +861,7 @@ murfey.server.api.session_info.correlative_router:
     path_params: []
     methods:
       - GET
-  - path: /session_info/correlative/visits/{visit_name}/{session_id}/upstream_tiff_paths
+  - path: /session_info/correlative/visits/{visit_name}/sessions/{session_id}/upstream_tiff_paths
     function: gather_upstream_tiffs
     path_params:
       - name: visit_name
@@ -870,7 +870,7 @@ murfey.server.api.session_info.correlative_router:
         type: int
     methods:
       - GET
-  - path: /session_info/correlative/visits/{visit_name}/{session_id}/upstream_tiff/{tiff_path:path}
+  - path: /session_info/correlative/visits/{visit_name}/sessions/{session_id}/upstream_tiff/{tiff_path:path}
     function: get_tiff
     path_params:
       - name: visit_name
@@ -918,7 +918,7 @@ murfey.server.api.session_info.router:
     path_params: []
     methods:
       - GET
-  - path: /session_info/session/{session_id}
+  - path: /session_info/sessions/{session_id}
     function: get_session
     path_params: []
     methods:
@@ -1105,7 +1105,7 @@ murfey.server.api.workflow.correlative_router:
         type: str
     methods:
       - POST
-  - path: /workflow/correlative/visits/{year}/{visit_name}/{session_id}/make_milling_gif
+  - path: /workflow/correlative/year/{year}/visits/{visit_name}/sessions/{session_id}/make_milling_gif
     function: make_gif
     path_params:
       - name: year
@@ -1117,21 +1117,21 @@ murfey.server.api.workflow.correlative_router:
     methods:
       - POST
 murfey.server.api.workflow.router:
-  - path: /workflow/visits/{visit_name}/{session_id}/register_data_collection_group
+  - path: /workflow/visits/{visit_name}/sessions/{session_id}/register_data_collection_group
     function: register_dc_group
     path_params:
       - name: visit_name
         type: typing.Any
     methods:
       - POST
-  - path: /workflow/visits/{visit_name}/{session_id}/start_data_collection
+  - path: /workflow/visits/{visit_name}/sessions/{session_id}/start_data_collection
     function: start_dc
     path_params:
       - name: visit_name
         type: typing.Any
     methods:
       - POST
-  - path: /workflow/visits/{visit_name}/{session_id}/register_processing_job
+  - path: /workflow/visits/{visit_name}/sessions/{session_id}/register_processing_job
     function: register_proc
     path_params:
       - name: visit_name
@@ -1144,14 +1144,14 @@ murfey.server.api.workflow.spa_router:
     path_params: []
     methods:
       - POST
-  - path: /workflow/spa/visits/{visit_name}/{session_id}/flush_spa_processing
+  - path: /workflow/spa/visits/{visit_name}/sessions/{session_id}/flush_spa_processing
     function: flush_spa_processing
     path_params:
       - name: visit_name
         type: str
     methods:
       - POST
-  - path: /workflow/spa/visits/{visit_name}/{session_id}/spa_preprocess
+  - path: /workflow/spa/visits/{visit_name}/sessions/{session_id}/spa_preprocess
     function: request_spa_preprocessing
     path_params:
       - name: visit_name
@@ -1164,7 +1164,7 @@ murfey.server.api.workflow.tomo_router:
     path_params: []
     methods:
       - POST
-  - path: /workflow/tomo/visits/{visit_name}/{session_id}/flush_tomography_processing
+  - path: /workflow/tomo/visits/{visit_name}/sessions/{session_id}/flush_tomography_processing
     function: flush_tomography_processing
     path_params:
       - name: visit_name
@@ -1185,14 +1185,14 @@ murfey.server.api.workflow.tomo_router:
         type: int
     methods:
       - POST
-  - path: /workflow/tomo/visits/{visit_name}/{session_id}/tomography_preprocess
+  - path: /workflow/tomo/visits/{visit_name}/sessions/{session_id}/tomography_preprocess
     function: request_tomography_preprocessing
     path_params:
       - name: visit_name
         type: str
     methods:
       - POST
-  - path: /workflow/tomo/visits/{visit_name}/{session_id}/completed_tilt_series
+  - path: /workflow/tomo/visits/{visit_name}/sessions/{session_id}/completed_tilt_series
     function: register_completed_tilt_series
     path_params:
       - name: visit_name
@@ -1206,7 +1206,7 @@ murfey.server.api.workflow.tomo_router:
         type: str
     methods:
       - POST
-  - path: /workflow/tomo/visits/{visit_name}/{session_id}/tilt
+  - path: /workflow/tomo/visits/{visit_name}/sessions/{session_id}/tilt
     function: register_tilt
     path_params:
       - name: visit_name