Remove the old SPA context

Author: stephen-riggs

src/murfey/client/analyser.py

@@ -16,7 +16,7 @@
 
 from murfey.client.context import Context
 from murfey.client.contexts.clem import CLEMContext
-from murfey.client.contexts.spa import SPAContext, SPAModularContext
+from murfey.client.contexts.spa import SPAModularContext
 from murfey.client.contexts.spa_metadata import SPAMetadataContext
 from murfey.client.contexts.tomo import TomographyContext
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
@@ -159,23 +159,7 @@ def _find_context(self, file_path: Path) -> bool:
             if split_file_name[0].startswith("FoilHole"):
                 if not self._context:
                     logger.info("Acquisition software: EPU")
-                    if self._environment:
-                        try:
-                            cfg = get_machine_config_client(
-                                str(self._environment.url.geturl()),
-                                instrument_name=self._environment.instrument_name,
-                                demo=self._environment.demo,
-                            )
-                        except Exception as e:
-                            logger.error(f"Exception encountered: {e}")
-                            cfg = {}
-                    else:
-                        cfg = {}
-                    self._context = (
-                        SPAModularContext("epu", self._basepath)
-                        if cfg.get("modular_spa")
-                        else SPAContext("epu", self._basepath)
-                    )
+                    self._context = SPAModularContext("epu", self._basepath)
                 self.parameters_model = ProcessingParametersSPA
                 return True
 
@@ -325,8 +309,7 @@ def _analyse(self):
                                         "form": dc_metadata,
                                         "dependencies": (
                                             spa_form_dependencies
-                                            if isinstance(self._context, SPAContext)
-                                            or isinstance(
+                                            if isinstance(
                                                 self._context, SPAModularContext
                                             )
                                             else {}
@@ -385,8 +368,7 @@ def _analyse(self):
                                         "form": dc_metadata,
                                         "dependencies": (
                                             spa_form_dependencies
-                                            if isinstance(self._context, SPAContext)
-                                            or isinstance(
+                                            if isinstance(
                                                 self._context, SPAModularContext
                                             )
                                             else {}

src/murfey/client/contexts/spa.py

@@ -285,7 +285,7 @@ def _get_xml_list_index(key: str, xml_list: list) -> int:
     raise ValueError(f"Key not found in XML list: {key}")
 
 
-class _SPAContext(Context):
+class SPAModularContext(Context):
     user_params = [
         ProcessingParameter(
             "dose_per_frame",
@@ -558,8 +558,6 @@ def gather_metadata(
         ) or True
         return metadata
 
-
-class SPAModularContext(_SPAContext):
     def _position_analysis(
         self,
         transferred_file: Path,
@@ -856,104 +854,3 @@ def _launch_spa_pipeline(
         url: str = "",
     ):
         return
-
-
-class SPAContext(_SPAContext):
-    def _register_data_collection(
-        self,
-        tag: str,
-        url: str,
-        data: dict,
-        environment: MurfeyInstanceEnvironment,
-    ):
-        logger.info(f"registering data collection with data {data}")
-        environment.id_tag_registry["data_collection"].append(tag)
-        image_directory = str(environment.default_destinations[Path(tag)])
-        json = {
-            "voltage": data["voltage"],
-            "pixel_size_on_image": data["pixel_size_on_image"],
-            "experiment_type": data["experiment_type"],
-            "image_size_x": data["image_size_x"],
-            "image_size_y": data["image_size_y"],
-            "file_extension": data["file_extension"],
-            "acquisition_software": data["acquisition_software"],
-            "image_directory": image_directory,
-            "tag": tag,
-            "source": tag,
-            "magnification": data["magnification"],
-            "total_exposed_dose": data.get("total_exposed_dose"),
-            "c2aperture": data.get("c2aperture"),
-            "exposure_time": data.get("exposure_time"),
-            "slit_width": data.get("slit_width"),
-            "phase_plate": data.get("phase_plate", False),
-        }
-        capture_post(url, json=json)
-
-    def post_transfer(
-        self,
-        transferred_file: Path,
-        environment: MurfeyInstanceEnvironment | None = None,
-        **kwargs,
-    ) -> bool:
-        return True
-
-    def _register_processing_job(
-        self,
-        tag: str,
-        environment: MurfeyInstanceEnvironment,
-        parameters: Dict[str, Any] | None = None,
-    ):
-        logger.info(f"registering processing job with parameters: {parameters}")
-        parameters = parameters or {}
-        environment.id_tag_registry["processing_job"].append(tag)
-        proc_url = f"{str(environment.url.geturl())}/visits/{environment.visit}/{environment.murfey_session}/register_processing_job"
-        machine_config = get_machine_config_client(
-            str(environment.url.geturl()),
-            instrument_name=environment.instrument_name,
-            demo=environment.demo,
-        )
-        image_directory = str(
-            Path(machine_config.get("rsync_basepath", "."))
-            / environment.default_destinations[Path(tag)]
-        )
-        if self._acquisition_software == "epu":
-            import_images = f"{Path(image_directory).resolve()}/GridSquare*/Data/*{parameters['file_extension']}"
-        else:
-            import_images = (
-                f"{Path(image_directory).resolve()}/*{parameters['file_extension']}"
-            )
-        msg: Dict[str, Any] = {
-            "tag": tag,
-            "source": tag,
-            "recipe": "ispyb-relion",
-            "parameters": {
-                "acquisition_software": parameters["acquisition_software"],
-                "voltage": parameters["voltage"],
-                "gain_ref": parameters["gain_ref"],
-                "dose_per_frame": parameters["dose_per_frame"],
-                "eer_grouping": parameters["eer_fractionation"],
-                "import_images": import_images,
-                "angpix": float(parameters["pixel_size_on_image"]) * 1e10,
-                "symmetry": parameters["symmetry"],
-                "boxsize": parameters["boxsize"],
-                "downscale": parameters["downscale"],
-                "small_boxsize": parameters["small_boxsize"],
-                "mask_diameter": parameters["mask_diameter"],
-                "use_cryolo": parameters["use_cryolo"],
-                "estimate_particle_diameter": parameters["estimate_particle_diameter"],
-            },
-        }
-        if parameters["particle_diameter"]:
-            msg["parameters"]["particle_diameter"] = parameters["particle_diameter"]
-        capture_post(proc_url, json=msg)
-
-    def _launch_spa_pipeline(
-        self,
-        tag: str,
-        jobid: int,
-        environment: MurfeyInstanceEnvironment,
-        url: str = "",
-    ):
-        environment.id_tag_registry["auto_proc_program"].append(tag)
-        data = {"job_id": jobid}
-        capture_post(url, json=data)

src/murfey/client/instance_environment.py

@@ -86,15 +86,6 @@ def dc_callback(cls, v, values):
                         l(k)
         return v
 
-    @validator("processing_job_ids")
-    def job_callback(cls, v, values):
-        with global_env_lock:
-            for l in values.get("listeners", {}).get("processing_job_ids", []):
-                for k in v.keys():
-                    if k not in values["id_tag_registry"]["auto_proc_program"]:
-                        l(k, v[k]["ispyb-relion"])
-        return v
-
     @validator("autoproc_program_ids")
     def app_callback(cls, v, values):
         # logger.info(f"autoproc program ids validator: {v}")

src/murfey/client/multigrid_control.py

@@ -13,7 +13,7 @@
 
 import murfey.client.websocket
 from murfey.client.analyser import Analyser
-from murfey.client.contexts.spa import SPAContext, SPAModularContext
+from murfey.client.contexts.spa import SPAModularContext
 from murfey.client.contexts.tomo import TomographyContext
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.client.rsync import RSyncer, RSyncerUpdate, TransferResult
@@ -443,7 +443,7 @@ def _start_dc(self, json, from_form: bool = False):
             )
             log.info("tomography processing flushed")
 
-        elif isinstance(context, SPAContext) or isinstance(context, SPAModularContext):
+        elif isinstance(context, SPAModularContext):
             url = f"{str(self._environment.url.geturl())}/visits/{str(self._environment.visit)}/{self.session_id}/register_data_collection_group"
             dcg_data = {
                 "experiment_type": "single particle",
@@ -515,31 +515,6 @@ def _start_dc(self, json, from_form: bool = False):
                     f"{self._environment.url.geturl()}/visits/{self._environment.visit}/{self.session_id}/flush_spa_processing",
                     json={"tag": str(source)},
                 )
-            if isinstance(context, SPAContext):
-                url = f"{str(self._environment.url.geturl())}/visits/{str(self._environment.visit)}/{self.session_id}/start_data_collection"
-                self._environment.listeners["data_collection_group_ids"] = {
-                    partial(
-                        context._register_data_collection,
-                        url=url,
-                        data=json,
-                        environment=self._environment,
-                    )
-                }
-                self._environment.listeners["data_collection_ids"] = {
-                    partial(
-                        context._register_processing_job,
-                        parameters=json,
-                        environment=self._environment,
-                    )
-                }
-                url = f"{str(self._environment.url.geturl())}/visits/{str(self._environment.visit)}/spa_processing"
-                self._environment.listeners["processing_job_ids"] = {
-                    partial(
-                        context._launch_spa_pipeline,
-                        url=url,
-                        environment=self._environment,
-                    )
-                }
 
     def _increment_file_count(
         self, observed_files: List[Path], source: str, destination: str

src/murfey/client/tui/app.py

@@ -15,7 +15,7 @@
 from textual.widgets import Button, Input
 
 from murfey.client.analyser import Analyser
-from murfey.client.contexts.spa import SPAContext, SPAModularContext
+from murfey.client.contexts.spa import SPAModularContext
 from murfey.client.contexts.tomo import TomographyContext
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.client.rsync import RSyncer, RSyncerUpdate, TransferResult
@@ -552,7 +552,7 @@ def _start_dc(self, json, from_form: bool = False):
                 json={"rsync_source": str(source)},
             )
             log.info("tomography processing flushed")
-        elif isinstance(context, SPAContext) or isinstance(context, SPAModularContext):
+        elif isinstance(context, SPAModularContext):
             url = f"{str(self._url.geturl())}/visits/{str(self._visit)}/{self._environment.murfey_session}/register_data_collection_group"
             dcg_data = {
                 "experiment_type": "single particle",
@@ -629,31 +629,6 @@ def _start_dc(self, json, from_form: bool = False):
                     f"{self.app._environment.url.geturl()}/visits/{self.app._environment.visit}/{self.app._environment.murfey_session}/flush_spa_processing",
                     json={"tag": str(source)},
                 )
-            if isinstance(context, SPAContext):
-                url = f"{str(self._url.geturl())}/visits/{str(self._visit)}/{self._environment.murfey_session}/start_data_collection"
-                self._environment.listeners["data_collection_group_ids"] = {
-                    partial(
-                        context._register_data_collection,
-                        url=url,
-                        data=json,
-                        environment=self._environment,
-                    )
-                }
-                self._environment.listeners["data_collection_ids"] = {
-                    partial(
-                        context._register_processing_job,
-                        parameters=json,
-                        environment=self._environment,
-                    )
-                }
-                url = f"{str(self._url.geturl())}/visits/{str(self._visit)}/spa_processing"
-                self._environment.listeners["processing_job_ids"] = {
-                    partial(
-                        context._launch_spa_pipeline,
-                        url=url,
-                        environment=self._environment,
-                    )
-                }
 
     def _set_request_destination(self, response: str):
         if response == "y":

src/murfey/client/tui/screens.py

@@ -47,7 +47,7 @@
 from werkzeug.utils import secure_filename
 
 from murfey.client.analyser import Analyser, spa_form_dependencies
-from murfey.client.contexts.spa import SPAContext, SPAModularContext
+from murfey.client.contexts.spa import SPAModularContext
 from murfey.client.contexts.tomo import TomographyContext
 from murfey.client.gain_ref import determine_gain_ref
 from murfey.client.instance_environment import (
@@ -257,18 +257,8 @@ def __init__(
         super().__init__(*args, **kwargs)
         self._selected_dir = basepath
         self._add_basepath = add_basepath
-        cfg = get_machine_config_client(
-            str(self.app._environment.url.geturl()),
-            instrument_name=self.app._environment.instrument_name,
-            demo=self.app._environment.demo,
-        )
-        self._context: (
-            Type[SPAModularContext] | Type[SPAContext] | Type[TomographyContext]
-        )
-        if cfg.get("modular_spa"):
-            self._context = SPAContext
-        else:
-            self._context = SPAModularContext
+        self._context: Type[SPAModularContext] | Type[TomographyContext]
+        self._context = SPAModularContext
 
     def compose(self):
         machine_data = requests.get(
@@ -975,7 +965,7 @@ class DestinationSelect(Screen):
     def __init__(
         self,
         transfer_routes: Dict[Path, str],
-        context: Type[SPAContext] | Type[SPAModularContext] | Type[TomographyContext],
+        context: Type[SPAModularContext] | Type[TomographyContext],
         *args,
         dependencies: Dict[str, FormDependency] | None = None,
         destination_overrides: Optional[Dict[Path, str]] = None,
@@ -994,9 +984,7 @@ def __init__(
     def compose(self):
         bulk = []
         with RadioSet():
-            yield RadioButton(
-                "SPA", value=self._context in (SPAContext, SPAModularContext)
-            )
+            yield RadioButton("SPA", value=self._context is SPAModularContext)
             yield RadioButton("Tomography", value=self._context is TomographyContext)
         if self.app._multigrid:
             machine_config = get_machine_config_client(
@@ -1142,15 +1130,7 @@ def on_switch_changed(self, event):
 
     def on_radio_set_changed(self, event: RadioSet.Changed) -> None:
         if event.index == 0:
-            cfg = get_machine_config_client(
-                str(self.app._environment.url.geturl()),
-                instrument_name=self.app._environment.instrument_name,
-                demo=self.app._environment.demo,
-            )
-            if cfg.get("modular_spa"):
-                self._context = SPAContext
-            else:
-                self._context = SPAModularContext
+            self._context = SPAModularContext
         else:
             self._context = TomographyContext
         self.app.pop_screen()

src/murfey/server/api/__init__.py

@@ -98,7 +98,6 @@
     Sample,
     SessionInfo,
     SPAProcessFile,
-    SPAProcessingParameters,
     SuggestedPathParameters,
     TiltInfo,
     TiltSeriesGroupInfo,
@@ -1058,16 +1057,6 @@ async def send_murfey_message(instrument_name: str, msg: RegistrationMessage):
         )
 
 
-@router.post("/visits/{visit_name}/spa_processing")
-async def request_spa_processing(visit_name: str, proc_params: SPAProcessingParameters):
-    zocalo_message = {
-        "parameters": {"ispyb_process": proc_params.job_id},
-        "recipes": ["ispyb-relion"],
-    }
-    if _transport_object:
-        _transport_object.send("processing_recipe", zocalo_message)
-
-
 @router.post("/visits/{visit_name}/{session_id}/spa_preprocess")
 async def request_spa_preprocessing(
     visit_name: str,