Renamed table

Author: stephen-riggs

src/murfey/cli/inject_spa_processing.py

@@ -13,12 +13,12 @@
 from murfey.util.config import get_machine_config, get_microscope, get_security_config
 from murfey.util.db import (
     AutoProcProgram,
+    ClassificationFeedbackParameters,
     ClientEnvironment,
     DataCollection,
     DataCollectionGroup,
     Movie,
     ProcessingJob,
-    SPAFeedbackParameters,
     SPARelionParameters,
 )
 from murfey.util.processing_params import default_spa_parameters
@@ -137,9 +137,9 @@ def run():
             .where(ProcessingJob.recipe == "em-spa-preprocess")
         ).one()
         params = murfey_db.exec(
-            select(SPARelionParameters, SPAFeedbackParameters)
+            select(SPARelionParameters, ClassificationFeedbackParameters)
             .where(SPARelionParameters.pj_id == collected_ids[2].id)
-            .where(SPAFeedbackParameters.pj_id == SPARelionParameters.pj_id)
+            .where(ClassificationFeedbackParameters.pj_id == SPARelionParameters.pj_id)
         ).one()
         proc_params: dict | None = dict(params[0])
         feedback_params = params[1]

src/murfey/cli/spa_ispyb_messages.py

@@ -364,7 +364,7 @@ def run():
         small_boxsize=metadata["small_boxsize"],
         mask_diameter=metadata["mask_diameter"],
     )
-    feedback_params = db.SPAFeedbackParameters(
+    feedback_params = db.ClassificationFeedbackParameters(
         pj_id=collected_ids[2].id,
         estimate_particle_diameter=not bool(metadata["particle_diameter"]),
         hold_class2d=False,

src/murfey/server/api/session_info.py

@@ -34,6 +34,7 @@
 from murfey.util import sanitise
 from murfey.util.config import MachineConfig, get_machine_config
 from murfey.util.db import (
+    ClassificationFeedbackParameters,
     ClientEnvironment,
     DataCollection,
     DataCollectionGroup,
@@ -43,7 +44,6 @@
     ProcessingJob,
     RsyncInstance,
     Session,
-    SPAFeedbackParameters,
     SPARelionParameters,
     Tilt,
     TiltSeries,
@@ -272,7 +272,7 @@ class ProcessingDetails(BaseModel):
     data_collections: List[DataCollection]
     processing_jobs: List[ProcessingJob]
     relion_params: SPARelionParameters
-    feedback_params: SPAFeedbackParameters
+    feedback_params: ClassificationFeedbackParameters
 
 
 @spa_router.get("/sessions/{session_id}/spa_processing_parameters")
@@ -285,13 +285,13 @@ def get_spa_proc_param_details(
             DataCollection,
             ProcessingJob,
             SPARelionParameters,
-            SPAFeedbackParameters,
+            ClassificationFeedbackParameters,
         )
         .where(DataCollectionGroup.session_id == session_id)
         .where(DataCollectionGroup.id == DataCollection.dcg_id)
         .where(DataCollection.id == ProcessingJob.dc_id)
         .where(SPARelionParameters.pj_id == ProcessingJob.id)
-        .where(SPAFeedbackParameters.pj_id == ProcessingJob.id)
+        .where(ClassificationFeedbackParameters.pj_id == ProcessingJob.id)
     ).all()
     if not params:
         return None

src/murfey/server/api/workflow.py

@@ -43,6 +43,7 @@
 from murfey.util.config import get_machine_config
 from murfey.util.db import (
     AutoProcProgram,
+    ClassificationFeedbackParameters,
     DataCollection,
     DataCollectionGroup,
     FoilHole,
@@ -53,7 +54,6 @@
     SearchMap,
     Session,
     SessionProcessingParameters,
-    SPAFeedbackParameters,
     SPARelionParameters,
     Tilt,
     TiltSeries,
@@ -408,9 +408,9 @@ async def request_spa_preprocessing(
             .where(ProcessingJob.recipe == "em-spa-preprocess")
         ).one()
         params = db.exec(
-            select(SPARelionParameters, SPAFeedbackParameters)
+            select(SPARelionParameters, ClassificationFeedbackParameters)
             .where(SPARelionParameters.pj_id == collected_ids[2].id)
-            .where(SPAFeedbackParameters.pj_id == SPARelionParameters.pj_id)
+            .where(ClassificationFeedbackParameters.pj_id == SPARelionParameters.pj_id)
         ).one()
         proc_params: Optional[dict] = dict(params[0])
         feedback_params = params[1]

src/murfey/server/demo_api.py

@@ -47,6 +47,7 @@
 )
 from murfey.util.db import (
     AutoProcProgram,
+    ClassificationFeedbackParameters,
     ClientEnvironment,
     DataCollection,
     DataCollectionGroup,
@@ -58,7 +59,6 @@
     ProcessingJob,
     RsyncInstance,
     Session,
-    SPAFeedbackParameters,
     SPARelionParameters,
     Tilt,
     TiltSeries,
@@ -242,7 +242,7 @@ class ProcessingDetails(BaseModel):
     data_collections: List[DataCollection]
     processing_jobs: List[ProcessingJob]
     relion_params: SPARelionParameters
-    feedback_params: SPAFeedbackParameters
+    feedback_params: ClassificationFeedbackParameters
 
 
 @router.get("/sessions/{session_id}/spa_processing_parameters")
@@ -255,13 +255,13 @@ def get_spa_proc_param_details(
             DataCollection,
             ProcessingJob,
             SPARelionParameters,
-            SPAFeedbackParameters,
+            ClassificationFeedbackParameters,
         )
         .where(DataCollectionGroup.session_id == session_id)
         .where(DataCollectionGroup.id == DataCollection.dcg_id)
         .where(DataCollection.id == ProcessingJob.dc_id)
         .where(SPARelionParameters.pj_id == ProcessingJob.id)
-        .where(SPAFeedbackParameters.pj_id == ProcessingJob.id)
+        .where(ClassificationFeedbackParameters.pj_id == ProcessingJob.id)
     ).all()
     if not params:
         return None
@@ -558,9 +558,9 @@ def flush_spa_processing(
         .where(ProcessingJob.recipe == "em-spa-preprocess")
     ).one()
     params = db.exec(
-        select(SPARelionParameters, SPAFeedbackParameters)
+        select(SPARelionParameters, ClassificationFeedbackParameters)
         .where(SPARelionParameters.pj_id == collected_ids[2].id)
-        .where(SPAFeedbackParameters.pj_id == SPARelionParameters.pj_id)
+        .where(ClassificationFeedbackParameters.pj_id == SPARelionParameters.pj_id)
     ).one()
     proc_params = dict(params[0])
     feedback_params = params[1]

src/murfey/server/feedback.py

@@ -313,13 +313,15 @@ def _pj_id(app_id: int, _db, recipe: str = "") -> int:
 
 def _get_spa_params(
     app_id: int, _db
-) -> Tuple[db.SPARelionParameters, db.SPAFeedbackParameters]:
+) -> Tuple[db.SPARelionParameters, db.ClassificationFeedbackParameters]:
     pj_id = _pj_id(app_id, _db, recipe="em-spa-preprocess")
     relion_params = _db.exec(
         select(db.SPARelionParameters).where(db.SPARelionParameters.pj_id == pj_id)
     ).one()
     feedback_params = _db.exec(
-        select(db.SPAFeedbackParameters).where(db.SPAFeedbackParameters.pj_id == pj_id)
+        select(db.ClassificationFeedbackParameters).where(
+            db.ClassificationFeedbackParameters.pj_id == pj_id
+        )
     ).one()
     _db.expunge(relion_params)
     _db.expunge(feedback_params)
@@ -412,8 +414,8 @@ def _release_3d_hold(message: dict, _db):
         )
     ).one()
     feedback_params = _db.exec(
-        select(db.SPAFeedbackParameters).where(
-            db.SPAFeedbackParameters.pj_id == pj_id_params
+        select(db.ClassificationFeedbackParameters).where(
+            db.ClassificationFeedbackParameters.pj_id == pj_id_params
         )
     ).one()
     class3d_params = _db.exec(
@@ -490,8 +492,8 @@ def _release_refine_hold(message: dict, _db):
         )
     ).one()
     feedback_params = _db.exec(
-        select(db.SPAFeedbackParameters).where(
-            db.SPAFeedbackParameters.pj_id == pj_id_params
+        select(db.ClassificationFeedbackParameters).where(
+            db.ClassificationFeedbackParameters.pj_id == pj_id_params
         )
     ).one()
     refine_params = _db.exec(
@@ -582,8 +584,8 @@ def _register_incomplete_2d_batch(message: dict, _db, demo: bool = False):
         )
     ).one()
     feedback_params = _db.exec(
-        select(db.SPAFeedbackParameters).where(
-            db.SPAFeedbackParameters.pj_id == pj_id_params
+        select(db.ClassificationFeedbackParameters).where(
+            db.ClassificationFeedbackParameters.pj_id == pj_id_params
         )
     ).one()
     if feedback_params.hold_class2d:
@@ -706,8 +708,8 @@ def _register_complete_2d_batch(message: dict, _db, demo: bool = False):
         )
     ).one()
     feedback_params = _db.exec(
-        select(db.SPAFeedbackParameters).where(
-            db.SPAFeedbackParameters.pj_id == pj_id_params
+        select(db.ClassificationFeedbackParameters).where(
+            db.ClassificationFeedbackParameters.pj_id == pj_id_params
         )
     ).one()
     _db.expunge(relion_params)
@@ -913,7 +915,7 @@ def _flush_class2d(
     app_id: int,
     _db,
     relion_params: db.SPARelionParameters | None = None,
-    feedback_params: db.SPAFeedbackParameters | None = None,
+    feedback_params: db.ClassificationFeedbackParameters | None = None,
 ):
     instrument_name = (
         _db.exec(select(db.Session).where(db.Session.id == session_id))
@@ -934,8 +936,8 @@ def _flush_class2d(
         _db.expunge(relion_params)
     if not feedback_params:
         feedback_params = _db.exec(
-            select(db.SPAFeedbackParameters).where(
-                db.SPAFeedbackParameters.pj_id == pj_id_params
+            select(db.ClassificationFeedbackParameters).where(
+                db.ClassificationFeedbackParameters.pj_id == pj_id_params
             )
         ).one()
         _db.expunge(feedback_params)
@@ -1012,8 +1014,8 @@ def _register_class_selection(message: dict, _db, demo: bool = False):
     ).all()
     # Add the class selection score to the database
     feedback_params = _db.exec(
-        select(db.SPAFeedbackParameters).where(
-            db.SPAFeedbackParameters.pj_id == pj_id_params
+        select(db.ClassificationFeedbackParameters).where(
+            db.ClassificationFeedbackParameters.pj_id == pj_id_params
         )
     ).one()
     _db.expunge(feedback_params)
@@ -1202,8 +1204,8 @@ def _register_3d_batch(message: dict, _db, demo: bool = False):
     ).one()
     relion_options = dict(relion_params)
     feedback_params = _db.exec(
-        select(db.SPAFeedbackParameters).where(
-            db.SPAFeedbackParameters.pj_id == pj_id_params
+        select(db.ClassificationFeedbackParameters).where(
+            db.ClassificationFeedbackParameters.pj_id == pj_id_params
         )
     ).one()
     other_options = dict(feedback_params)
@@ -1380,8 +1382,8 @@ def _register_initial_model(message: dict, _db, demo: bool = False):
     pj_id_params = _pj_id(message["program_id"], _db, recipe="em-spa-preprocess")
     # Add the initial model file to the database
     feedback_params = _db.exec(
-        select(db.SPAFeedbackParameters).where(
-            db.SPAFeedbackParameters.pj_id == pj_id_params
+        select(db.ClassificationFeedbackParameters).where(
+            db.ClassificationFeedbackParameters.pj_id == pj_id_params
         )
     ).one()
     feedback_params.initial_model = message.get("initial_model")
@@ -1547,8 +1549,8 @@ def _register_refinement(message: dict, _db, demo: bool = False):
     ).one()
     relion_options = dict(relion_params)
     feedback_params = _db.exec(
-        select(db.SPAFeedbackParameters).where(
-            db.SPAFeedbackParameters.pj_id == pj_id_params
+        select(db.ClassificationFeedbackParameters).where(
+            db.ClassificationFeedbackParameters.pj_id == pj_id_params
         )
     ).one()
     other_options = dict(feedback_params)
@@ -1695,8 +1697,8 @@ def _register_bfactors(message: dict, _db, demo: bool = False):
     ).one()
     relion_options = dict(relion_params)
     feedback_params = _db.exec(
-        select(db.SPAFeedbackParameters).where(
-            db.SPAFeedbackParameters.pj_id == pj_id_params
+        select(db.ClassificationFeedbackParameters).where(
+            db.ClassificationFeedbackParameters.pj_id == pj_id_params
         )
     ).one()
 
@@ -2258,7 +2260,7 @@ def feedback_callback(header: dict, message: dict, _db=murfey_db) -> None:
                     eer_fractionation_file=message["eer_fractionation_file"],
                     symmetry=message["symmetry"],
                 )
-                feedback_params = db.SPAFeedbackParameters(
+                feedback_params = db.ClassificationFeedbackParameters(
                     pj_id=collected_ids[2].id,
                     estimate_particle_diameter=True,
                     hold_class2d=False,

src/murfey/workflows/spa/flush_spa_preprocess.py

@@ -13,6 +13,7 @@
 from murfey.util.config import get_machine_config, get_microscope
 from murfey.util.db import (
     AutoProcProgram,
+    ClassificationFeedbackParameters,
     DataCollection,
     DataCollectionGroup,
     FoilHole,
@@ -22,7 +23,7 @@
     ProcessingJob,
 )
 from murfey.util.db import Session as MurfeySession
-from murfey.util.db import SPAFeedbackParameters, SPARelionParameters
+from murfey.util.db import SPARelionParameters
 from murfey.util.models import FoilHoleParameters, GridSquareParameters
 from murfey.util.processing_params import cryolo_model_path, default_spa_parameters
 from murfey.util.spa_metadata import (
@@ -337,9 +338,9 @@ def flush_spa_preprocess(message: dict, murfey_db: Session, demo: bool = False)
         .where(ProcessingJob.recipe == recipe_name)
     ).one()
     params = murfey_db.exec(
-        select(SPARelionParameters, SPAFeedbackParameters)
+        select(SPARelionParameters, ClassificationFeedbackParameters)
         .where(SPARelionParameters.pj_id == collected_ids[2].id)
-        .where(SPAFeedbackParameters.pj_id == SPARelionParameters.pj_id)
+        .where(ClassificationFeedbackParameters.pj_id == SPARelionParameters.pj_id)
     ).one()
     proc_params = params[0]
     feedback_params = params[1]

src/murfey/workflows/spa/picking.py

@@ -17,6 +17,7 @@
 from murfey.util.config import get_machine_config
 from murfey.util.db import (
     AutoProcProgram,
+    ClassificationFeedbackParameters,
     CtfParameters,
     DataCollection,
     Movie,
@@ -27,7 +28,7 @@
     SelectionStash,
 )
 from murfey.util.db import Session as MurfeySession
-from murfey.util.db import SPAFeedbackParameters, SPARelionParameters
+from murfey.util.db import SPARelionParameters
 from murfey.util.processing_params import default_spa_parameters
 
 logger = getLogger("murfey.workflows.spa.picking")
@@ -77,7 +78,9 @@ def _register_picked_particles_use_diameter(
         ).one()
         relion_options = dict(relion_params)
         feedback_params = _db.exec(
-            select(SPAFeedbackParameters).where(SPAFeedbackParameters.pj_id == pj_id)
+            select(ClassificationFeedbackParameters).where(
+                ClassificationFeedbackParameters.pj_id == pj_id
+            )
         ).one()
 
         particle_diameter = relion_params.particle_diameter
@@ -262,7 +265,9 @@ def _register_picked_particles_use_boxsize(message: dict, _db: Session):
         select(SPARelionParameters).where(SPARelionParameters.pj_id == pj_id)
     ).one()
     feedback_params = _db.exec(
-        select(SPAFeedbackParameters).where(SPAFeedbackParameters.pj_id == pj_id)
+        select(ClassificationFeedbackParameters).where(
+            ClassificationFeedbackParameters.pj_id == pj_id
+        )
     ).one()
 
     if feedback_params.picker_ispyb_id is None and _transport_object:
@@ -447,8 +452,9 @@ def particles_picked(message: dict, murfey_db: Session) -> bool:
     murfey_db.add(movie)
     murfey_db.commit()
     feedback_params = murfey_db.exec(
-        select(SPAFeedbackParameters).where(
-            SPAFeedbackParameters.pj_id == _pj_id(message["program_id"], murfey_db)
+        select(ClassificationFeedbackParameters).where(
+            ClassificationFeedbackParameters.pj_id
+            == _pj_id(message["program_id"], murfey_db)
         )
     ).one()
     if feedback_params.estimate_particle_diameter: