Remove references to the TomographyProcessingParameters table

Author: stephen-riggs

src/murfey/client/multigrid_control.py

@@ -411,12 +411,6 @@ def _start_dc(self, json, from_form: bool = False):
         source = Path(json["source"])
         context = self.analysers[source]._context
         if isinstance(context, TomographyContext):
-            if from_form:
-                capture_post(
-                    f"{self._environment.url.geturl()}/clients/{self._environment.client_id}/tomography_processing_parameters",
-                    json=json,
-                )
-
             source = Path(json["source"])
             context.register_tomography_data_collections(
                 file_extension=json["file_extension"],

src/murfey/server/__init__.py

@@ -190,15 +190,6 @@ def get_job_ids(tilt_series_id: int, appid: int) -> JobIDs:
     )
 
 
-def get_tomo_proc_params(pj_id: int, *args) -> db.TomographyProcessingParameters:
-    results = murfey_db.exec(
-        select(db.TomographyProcessingParameters).where(
-            db.TomographyProcessingParameters.pj_id == pj_id
-        )
-    ).one()
-    return results
-
-
 def get_tomo_preproc_params(dcg_id: int, *args) -> db.TomographyPreprocessingParameters:
     results = murfey_db.exec(
         select(db.TomographyPreprocessingParameters).where(

src/murfey/server/api/__init__.py

@@ -70,7 +70,6 @@
     SPARelionParameters,
     Tilt,
     TiltSeries,
-    TomographyProcessingParameters,
 )
 from murfey.util.models import (
     BLSampleImageParameters,
@@ -92,7 +91,6 @@
     PreprocessingParametersTomo,
     ProcessingJobParameters,
     ProcessingParametersSPA,
-    ProcessingParametersTomo,
     RegistrationMessage,
     RsyncerInfo,
     RsyncerSource,
@@ -640,41 +638,6 @@ def register_tomo_preproc_params(
         _transport_object.send(_transport_object.feedback_queue, zocalo_message)
 
 
-@router.post("/sessions/{session_id}/tomography_processing_parameters")
-def register_tomo_proc_params(
-    session_id: MurfeySessionID, proc_params: ProcessingParametersTomo, db=murfey_db
-):
-    log.info(
-        f"Registering tomography processing parameters {sanitise(proc_params.tag)}, {sanitise(proc_params.tilt_series_tag)}"
-    )
-    collected_ids = db.exec(
-        select(
-            DataCollectionGroup,
-            DataCollection,
-            ProcessingJob,
-            AutoProcProgram,
-        )
-        .where(DataCollectionGroup.session_id == session_id)
-        .where(DataCollectionGroup.tag == proc_params.tag)
-        .where(DataCollection.tag == proc_params.tilt_series_tag)
-        .where(DataCollection.dcg_id == DataCollectionGroup.id)
-        .where(ProcessingJob.dc_id == DataCollection.id)
-        .where(AutoProcProgram.pj_id == ProcessingJob.id)
-        .where(ProcessingJob.recipe == "em-tomo-preprocess")
-    ).one()
-    if not db.exec(
-        select(func.count(TomographyProcessingParameters.pj_id)).where(
-            TomographyProcessingParameters.pj_id == collected_ids[2].id
-        )
-    ).one():
-        tomogram_params = TomographyProcessingParameters(
-            pj_id=collected_ids[2].id, manual_tilt_offset=proc_params.manual_tilt_offset
-        )
-        db.add(tomogram_params)
-    db.commit()
-    db.close()
-
-
 class Tag(BaseModel):
     tag: str
 

src/murfey/server/demo_api.py

@@ -58,7 +58,6 @@
     Tilt,
     TiltSeries,
     TomographyPreprocessingParameters,
-    TomographyProcessingParameters,
 )
 from murfey.util.models import (
     ClientInfo,
@@ -75,7 +74,6 @@
     PreprocessingParametersTomo,
     ProcessingJobParameters,
     ProcessingParametersSPA,
-    ProcessingParametersTomo,
     RegistrationMessage,
     RsyncerInfo,
     RsyncerSource,
@@ -513,57 +511,8 @@ def register_tomo_preproc_params(
             gain_ref=proc_params.gain_ref,
             motion_corr_binning=proc_params.motion_corr_binning,
             voltage=proc_params.voltage,
-            # manual_tilt_offset=proc_params.manual_tilt_offset,
         )
         db.add(params)
-    if not db.exec(
-        select(func.count(TomographyProcessingParameters.pj_id)).where(
-            TomographyProcessingParameters.pj_id == collected_ids[2].id
-        )
-    ).one():
-        tomogram_params = TomographyProcessingParameters(
-            pj_id=collected_ids[2].id, manual_tilt_offset=proc_params.manual_tilt_offset
-        )
-        db.add(tomogram_params)
-    db.commit()
-    db.close()
-
-
-@router.post("/clients/{client_id}/tomography_processing_parameters")
-def register_tomo_proc_params(
-    client_id: int, proc_params: ProcessingParametersTomo, db=murfey_db
-):
-    client = db.exec(
-        select(ClientEnvironment).where(ClientEnvironment.client_id == client_id)
-    ).one()
-    session_id = client.session_id
-    log.info(
-        f"Registering tomography processing parameters {sanitise(proc_params.tag)}, {sanitise(proc_params.tilt_series_tag)}, {session_id}"
-    )
-    collected_ids = db.exec(
-        select(
-            DataCollectionGroup,
-            DataCollection,
-            ProcessingJob,
-            AutoProcProgram,
-        )
-        .where(DataCollectionGroup.session_id == session_id)
-        .where(DataCollectionGroup.tag == proc_params.tag)
-        .where(DataCollection.tag == proc_params.tilt_series_tag)
-        .where(DataCollection.dcg_id == DataCollectionGroup.id)
-        .where(ProcessingJob.dc_id == DataCollection.id)
-        .where(AutoProcProgram.pj_id == ProcessingJob.id)
-        .where(ProcessingJob.recipe == "em-tomo-preprocess")
-    ).one()
-    if not db.exec(
-        select(func.count(TomographyProcessingParameters.pj_id)).where(
-            TomographyProcessingParameters.pj_id == collected_ids[2].id
-        )
-    ).one():
-        tomogram_params = TomographyProcessingParameters(
-            pj_id=collected_ids[2].id, manual_tilt_offset=proc_params.manual_tilt_offset
-        )
-        db.add(tomogram_params)
     db.commit()
     db.close()
 

src/murfey/util/db.py

@@ -448,12 +448,6 @@ class ProcessingJob(SQLModel, table=True):  # type: ignore
     spa_feedback_parameters: List["SPAFeedbackParameters"] = Relationship(
         back_populates="processing_job", sa_relationship_kwargs={"cascade": "delete"}
     )
-    tomography_processing_parameters: List["TomographyProcessingParameters"] = (
-        Relationship(
-            back_populates="processing_job",
-            sa_relationship_kwargs={"cascade": "delete"},
-        )
-    )
     ctf_parameters: List["CtfParameters"] = Relationship(
         back_populates="processing_job", sa_relationship_kwargs={"cascade": "delete"}
     )
@@ -514,14 +508,6 @@ class TomographyPreprocessingParameters(SQLModel, table=True):  # type: ignore
     )
 
 
-class TomographyProcessingParameters(SQLModel, table=True):  # type: ignore
-    pj_id: int = Field(primary_key=True, foreign_key="processingjob.id")
-    manual_tilt_offset: int
-    processing_job: Optional[ProcessingJob] = Relationship(
-        back_populates="tomography_processing_parameters"
-    )
-
-
 class AutoProcProgram(SQLModel, table=True):  # type: ignore
     id: int = Field(primary_key=True, unique=True)
     pj_id: int = Field(foreign_key="processingjob.id")

src/murfey/util/models.py

@@ -372,9 +372,3 @@ class Base(BaseModel):
         gain_ref: Optional[str]
         manual_tilt_offset: float
         eer_fractionation: int
-
-
-class ProcessingParametersTomo(BaseModel):
-    manual_tilt_offset: int
-    tag: str
-    tilt_series_tag: str