Move most context API calls to use a lookup based on function name rather than hard-coding the URLs

Author: d-j-hatton

src/murfey/client/__init__.py

@@ -25,13 +25,25 @@
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.client.tui.app import MurfeyTUI
 from murfey.client.tui.status_bar import StatusBar
-from murfey.util.client import _get_visit_list, authorised_requests, read_config
+from murfey.util.client import authorised_requests, read_config
+from murfey.util.models import Visit
 
 log = logging.getLogger("murfey.client")
 
 requests.get, requests.post, requests.put, requests.delete = authorised_requests()
 
 
+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}/instruments/{instrument_name}/visits_raw"
+    )
+    server_reply = requests.get(get_visits_url.geturl())
+    if server_reply.status_code != 200:
+        raise ValueError(f"Server unreachable ({server_reply.status_code})")
+    return [Visit.parse_obj(v) for v in server_reply.json()]
+
+
 def write_config(config: configparser.ConfigParser):
     mcch = os.environ.get("MURFEY_CLIENT_CONFIG_HOME")
     murfey_client_config_home = Path(mcch) if mcch else Path.home()

src/murfey/client/contexts/spa.py

@@ -15,6 +15,8 @@
     MurfeyID,
     MurfeyInstanceEnvironment,
 )
+from murfey.server.api.file_manip import router as file_manip_router
+from murfey.server.api.workflow import spa_router as workflow_spa_router
 from murfey.util.client import (
     authorised_requests,
     capture_get,
@@ -580,7 +582,7 @@ def post_transfer(
                         eer_fractionation_file = None
                         if file_transferred_to.suffix == ".eer":
                             response = capture_post(
-                                f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/eer_fractionation_file",
+                                f"{str(environment.url.geturl())}{file_manip_router.url_path_for('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[
@@ -609,7 +611,7 @@ def post_transfer(
                             )
                             foil_hole = None
 
-                        preproc_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/spa_preprocess"
+                        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_data = {
                             "path": str(file_transferred_to),
                             "description": "",

src/murfey/client/contexts/spa_metadata.py

@@ -8,6 +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.workflow import router as workflow_router
 from murfey.util.client import (
     authorised_requests,
     capture_post,
@@ -166,7 +167,7 @@ def post_transfer(
                 environment.samples[source] = SampleInfo(
                     atlas=Path(partial_path), sample=sample
                 )
-                url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/register_data_collection_group"
+                url = f"{str(environment.url.geturl())}{workflow_router.url_path_for('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
                 )
@@ -221,7 +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())}/visits/{environment.visit}/{environment.murfey_session}/register_data_collection_group"
+            url = f"{str(environment.url.geturl())}{workflow_router.url_path_for('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

src/murfey/client/contexts/tomo.py

@@ -17,6 +17,9 @@
     MurfeyID,
     MurfeyInstanceEnvironment,
 )
+from murfey.server.api.file_manip import router as file_manip_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.client import (
     authorised_requests,
     capture_post,
@@ -109,7 +112,7 @@ def register_tomography_data_collections(
             )
             return
         try:
-            dcg_url = f"{str(environment.url.geturl())}/visits/{str(environment.visit)}/{environment.murfey_session}/register_data_collection_group"
+            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_data = {
                 "experiment_type": "tomo",
                 "experiment_type_id": 36,
@@ -121,7 +124,7 @@ 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())}/visits/{environment.visit}/{environment.murfey_session}/start_data_collection"
+                    dc_url = f"{str(environment.url.geturl())}{workflow_router.url_path_for('start_dc', visit_name=environment.visit, session_id=environment.murfey_session)}"
                     dc_data = {
                         "experiment_type": "tomography",
                         "file_extension": file_extension,
@@ -157,7 +160,7 @@ def register_tomography_data_collections(
                         )
                         capture_post(dc_url, json=dc_data)
 
-                        proc_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/register_processing_job"
+                        proc_url = f"{str(environment.url.geturl())}{workflow_router.url_path_for('register_proc', visit_name=environment.visit, session_id=environment.murfey_session)}"
                         for recipe in ("em-tomo-preprocess", "em-tomo-align"):
                             capture_post(
                                 proc_url,
@@ -262,7 +265,7 @@ 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())}/visits/{environment.visit}/rerun_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_data = {
                 "session_id": environment.murfey_session,
                 "tag": tilt_series,
@@ -276,7 +279,7 @@ 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())}/visits/{environment.visit}/tilt_series"
+            ts_url = f"{str(environment.url.geturl())}{workflow_tomo_router.url_path_for('register_tile_series', visit_name=environment.visit)}"
             ts_data = {
                 "session_id": environment.murfey_session,
                 "tag": tilt_series,
@@ -305,7 +308,7 @@ def _add_tilt(
                     self._tilt_series[tilt_series].append(file_path)
 
         if environment:
-            tilt_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/tilt"
+            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_data = {
                 "movie_path": str(file_transferred_to),
                 "tilt_series_tag": tilt_series,
@@ -316,7 +319,7 @@ def _add_tilt(
             eer_fractionation_file = None
             if environment.data_collection_parameters.get("num_eer_frames"):
                 response = requests.post(
-                    f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/eer_fractionation_file",
+                    f"{str(environment.url.geturl())}{file_manip_router.url_path_for('write_eer_fractionation_file', visit_name=environment.visit, session_id=environment.murfey_session)}",
                     json={
                         "num_frames": environment.data_collection_parameters[
                             "num_eer_frames"
@@ -331,7 +334,7 @@ def _add_tilt(
                     },
                 )
                 eer_fractionation_file = response.json()["eer_fractionation_file"]
-            preproc_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/tomography_preprocess"
+            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_data = {
                 "path": str(file_transferred_to),
                 "description": "",
@@ -491,7 +494,7 @@ 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())}/sessions/{environment.murfey_session}/tilt_series_length"
+                        length_url = f"{str(environment.url.geturl())}{workflow_tomo_router.url_path_for('register_tile_series_length', session_id=environment.murfey_session)}"
                         capture_post(
                             length_url,
                             json={
@@ -508,7 +511,7 @@ def post_transfer(
                 f"The following tilt series are considered complete: {completed_tilts} "
                 f"after {transferred_file}"
             )
-            complete_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/completed_tilt_series"
+            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)}"
             capture_post(
                 complete_url,
                 json={

src/murfey/server/api/session_info.py

@@ -28,6 +28,7 @@
     Tilt,
     TiltSeries,
 )
+from murfey.util.models import Visit
 
 logger = getLogger("murfey.server.api.session_info")
 
@@ -38,27 +39,6 @@
 )
 
 
-class Visit(BaseModel):
-    start: datetime
-    end: datetime
-    session_id: int
-    name: str
-    beamline: str
-    proposal_title: str
-
-    def __repr__(self) -> str:
-        return (
-            "Visit("
-            f"start='{self.start:%Y-%m-%d %H:%M}', "
-            f"end='{self.end:%Y-%m-%d %H:%M}', "
-            f"session_id='{self.session_id!r}',"
-            f"name={self.name!r}, "
-            f"beamline={self.beamline!r}, "
-            f"proposal_title={self.proposal_title!r}"
-            ")"
-        )
-
-
 @router.get("/instruments/{instrument_name}/visits_raw", response_model=List[Visit])
 def get_current_visits(instrument_name: str, db=murfey.server.ispyb.DB):
     return murfey.server.ispyb.get_all_ongoing_visits(instrument_name, db)

src/murfey/server/api/workflow.py

@@ -43,6 +43,7 @@
     Tilt,
     TiltSeries,
 )
+from murfey.util.models import ProcessingParametersSPA, ProcessingParametersTomo
 from murfey.util.processing_params import default_spa_parameters
 from murfey.util.tomo import midpoint
 
@@ -273,45 +274,6 @@ def register_proc(
 )
 
 
-class ProcessingParametersSPA(BaseModel):
-    tag: str
-    dose_per_frame: float
-    gain_ref: Optional[str]
-    experiment_type: str
-    voltage: float
-    image_size_x: int
-    image_size_y: int
-    pixel_size_on_image: str
-    motion_corr_binning: int
-    file_extension: str
-    acquisition_software: str
-    use_cryolo: bool
-    symmetry: str
-    mask_diameter: Optional[int]
-    boxsize: Optional[int]
-    downscale: bool
-    small_boxsize: Optional[int]
-    eer_fractionation_file: str = ""
-    particle_diameter: Optional[float]
-    magnification: Optional[int] = None
-    total_exposed_dose: Optional[float] = None
-    c2aperture: Optional[float] = None
-    exposure_time: Optional[float] = None
-    slit_width: Optional[float] = None
-    phase_plate: bool = False
-
-    class Base(BaseModel):
-        dose_per_frame: Optional[float]
-        gain_ref: Optional[str]
-        use_cryolo: bool
-        symmetry: str
-        mask_diameter: Optional[int]
-        boxsize: Optional[int]
-        downscale: bool
-        small_boxsize: Optional[int]
-        eer_fractionation: int
-
-
 @spa_router.post("/sessions/{session_id}/spa_processing_parameters")
 def register_spa_proc_params(
     session_id: MurfeySessionID, proc_params: ProcessingParametersSPA, db=murfey_db
@@ -541,29 +503,6 @@ async def request_spa_preprocessing(
 )
 
 
-class ProcessingParametersTomo(BaseModel):
-    dose_per_frame: Optional[float]
-    frame_count: int
-    tilt_axis: float
-    gain_ref: Optional[str]
-    experiment_type: str
-    voltage: float
-    image_size_x: int
-    image_size_y: int
-    pixel_size_on_image: str
-    motion_corr_binning: int
-    file_extension: str
-    tag: str
-    tilt_series_tag: str
-    eer_fractionation_file: Optional[str]
-    eer_fractionation: int
-
-    class Base(BaseModel):
-        dose_per_frame: Optional[float]
-        gain_ref: Optional[str]
-        eer_fractionation: int
-
-
 @tomo_router.post("/sessions/{session_id}/tomography_processing_parameters")
 def register_tomo_proc_params(
     session_id: MurfeySessionID, proc_params: ProcessingParametersTomo, db=murfey_db

src/murfey/util/client.py

@@ -17,12 +17,10 @@
 from functools import lru_cache, partial
 from pathlib import Path
 from typing import Awaitable, Callable, Optional, Union
-from urllib.parse import ParseResult, urlparse, urlunparse
+from urllib.parse import urlparse, urlunparse
 
 import requests
 
-from murfey.util.models import Visit
-
 logger = logging.getLogger("murfey.util.client")
 
 
@@ -74,17 +72,6 @@ def authorised_requests() -> tuple[Callable, Callable, Callable, Callable]:
 requests.get, requests.post, requests.put, requests.delete = authorised_requests()
 
 
-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}/instruments/{instrument_name}/visits_raw"
-    )
-    server_reply = requests.get(get_visits_url.geturl())
-    if server_reply.status_code != 200:
-        raise ValueError(f"Server unreachable ({server_reply.status_code})")
-    return [Visit.parse_obj(v) for v in server_reply.json()]
-
-
 def capture_post(url: str, json: Union[dict, list] = {}) -> Optional[requests.Response]:
     try:
         response = requests.post(url, json=json)