Add further refinement uuids for the symmetrised run (#404)

Will need a recipe update to take effect

Author: stephen-riggs

src/murfey/server/__init__.py

@@ -460,9 +460,10 @@ def _murfey_class3ds(murfey_ids: List[int], particles_file: str, app_id: int, _d
     _db.close()
 
 
-def _murfey_refine(murfey_id: int, refine_dir: str, app_id: int, _db):
+def _murfey_refine(murfey_id: int, refine_dir: str, tag: str, app_id: int, _db):
     pj_id = _pj_id(app_id, _db, recipe="em-spa-refine")
     refine3d = db.Refine3D(
+        tag=tag,
         refine_dir=refine_dir,
         pj_id=pj_id,
         murfey_id=murfey_id,
@@ -501,7 +502,7 @@ def _3d_class_murfey_ids(particles_file: str, app_id: int, _db) -> Dict[str, int
     return {str(cl.class_number): cl.murfey_id for cl in classes}
 
 
-def _refine_murfey_id(refine_dir: str, app_id: int, _db) -> Dict[str, int]:
+def _refine_murfey_id(refine_dir: str, tag: str, app_id: int, _db) -> Dict[str, int]:
     pj_id = (
         _db.exec(select(db.AutoProcProgram).where(db.AutoProcProgram.id == app_id))
         .one()
@@ -511,6 +512,7 @@ def _refine_murfey_id(refine_dir: str, app_id: int, _db) -> Dict[str, int]:
         select(db.Refine3D)
         .where(db.Refine3D.refine_dir == refine_dir)
         .where(db.Refine3D.pj_id == pj_id)
+        .where(db.Refine3D.tag == tag)
     ).one()
     return refined_class.murfey_id
 
@@ -1028,7 +1030,14 @@ def _release_refine_hold(message: dict, _db=murfey_db):
         )
     ).one()
     refine_params = _db.exec(
-        select(db.RefineParameters).where(db.RefineParameters.pj_id == pj_id)
+        select(db.RefineParameters)
+        .where(db.RefineParameters.pj_id == pj_id)
+        .where(db.RefineParameters.tag == "first")
+    ).one()
+    symmetry_refine_params = _db.exec(
+        select(db.RefineParameters)
+        .where(db.RefineParameters.pj_id == pj_id)
+        .where(db.RefineParameters.tag == "symmetry")
     ).one()
     if refine_params.run:
         instrument_name = (
@@ -1052,9 +1061,19 @@ def _release_refine_hold(message: dict, _db=murfey_db):
                 "nr_iter": default_spa_parameters.nr_iter_3d,
                 "picker_id": feedback_params.picker_ispyb_id,
                 "refined_class_uuid": _refine_murfey_id(
-                    refine_params.refine_dir, _app_id(pj_id, _db), _db
+                    refine_dir=refine_params.refine_dir,
+                    tag=refine_params.tag,
+                    app_id=_app_id(pj_id, _db),
+                    _db=_db,
                 ),
                 "refined_grp_uuid": refine_params.murfey_id,
+                "symmetry_refined_class_uuid": _refine_murfey_id(
+                    refine_dir=symmetry_refine_params.refine_dir,
+                    tag=symmetry_refine_params.tag,
+                    app_id=_app_id(pj_id, _db),
+                    _db=_db,
+                ),
+                "symmetry_refined_grp_uuid": symmetry_refine_params.murfey_id,
                 "session_id": message["session_id"],
                 "autoproc_program_id": _app_id(
                     _pj_id(message["program_id"], _db, recipe="em-spa-refine"), _db
@@ -2186,7 +2205,9 @@ def _register_refinement(message: dict, _db=murfey_db, demo: bool = False):
     if feedback_params.hold_refine:
         # If waiting then save the message
         refine_params = _db.exec(
-            select(db.RefineParameters).where(db.RefineParameters.pj_id == pj_id)
+            select(db.RefineParameters)
+            .where(db.RefineParameters.pj_id == pj_id)
+            .where(db.RefineParameters.tag == "first")
         ).one()
         # refine_params.refine_dir is not set as it will be the same as before
         refine_params.run = True
@@ -2199,24 +2220,56 @@ def _register_refinement(message: dict, _db=murfey_db, demo: bool = False):
         # Send all other messages on to a container
         try:
             refine_params = _db.exec(
-                select(db.RefineParameters).where(db.RefineParameters.pj_id == pj_id)
+                select(db.RefineParameters)
+                .where(db.RefineParameters.pj_id == pj_id)
+                .where(db.RefineParameters.tag == "first")
+            ).one()
+            symmetry_refine_params = _db.exec(
+                select(db.RefineParameters)
+                .where(db.RefineParameters.pj_id == pj_id)
+                .where(db.RefineParameters.tag == "symmetry")
             ).one()
         except SQLAlchemyError:
             next_job = feedback_params.next_job
             refine_dir = f"{message['refine_dir']}{(feedback_params.next_job + 2):03}"
             refined_grp_uuid = _murfey_id(message["program_id"], _db)[0]
             refined_class_uuid = _murfey_id(message["program_id"], _db)[0]
+            symmetry_refined_grp_uuid = _murfey_id(message["program_id"], _db)[0]
+            symmetry_refined_class_uuid = _murfey_id(message["program_id"], _db)[0]
 
             refine_params = db.RefineParameters(
+                tag="first",
                 pj_id=pj_id,
                 murfey_id=refined_grp_uuid,
                 refine_dir=refine_dir,
                 class3d_dir=message["class3d_dir"],
                 class_number=message["best_class"],
             )
+            symmetry_refine_params = db.RefineParameters(
+                tag="symmetry",
+                pj_id=pj_id,
+                murfey_id=symmetry_refined_grp_uuid,
+                refine_dir=refine_dir,
+                class3d_dir=message["class3d_dir"],
+                class_number=message["best_class"],
+            )
             _db.add(refine_params)
+            _db.add(symmetry_refine_params)
             _db.commit()
-            _murfey_refine(refined_class_uuid, refine_dir, message["program_id"], _db)
+            _murfey_refine(
+                murfey_id=refined_class_uuid,
+                refine_dir=refine_dir,
+                tag="first",
+                app_id=message["program_id"],
+                _db=_db,
+            )
+            _murfey_refine(
+                murfey_id=symmetry_refined_class_uuid,
+                refine_dir=refine_dir,
+                tag="symmetry",
+                app_id=message["program_id"],
+                _db=_db,
+            )
 
             if relion_options["symmetry"] == "C1":
                 # Extra Refine, Mask, PostProcess beyond for determined symmetry
@@ -2239,9 +2292,19 @@ def _register_refinement(message: dict, _db=murfey_db, demo: bool = False):
                 "nr_iter": default_spa_parameters.nr_iter_3d,
                 "picker_id": other_options["picker_ispyb_id"],
                 "refined_class_uuid": _refine_murfey_id(
-                    refine_params.refine_dir, _app_id(pj_id, _db), _db
+                    refine_dir=refine_params.refine_dir,
+                    tag=refine_params.tag,
+                    app_id=_app_id(pj_id, _db),
+                    _db=_db,
                 ),
                 "refined_grp_uuid": refine_params.murfey_id,
+                "symmetry_refined_class_uuid": _refine_murfey_id(
+                    refine_dir=symmetry_refine_params.refine_dir,
+                    tag=symmetry_refine_params.tag,
+                    app_id=_app_id(pj_id, _db),
+                    _db=_db,
+                ),
+                "symmetry_refined_grp_uuid": symmetry_refine_params.murfey_id,
                 "session_id": message["session_id"],
                 "autoproc_program_id": _app_id(
                     _pj_id(message["program_id"], _db, recipe="em-spa-refine"), _db

src/murfey/util/db.py

@@ -707,6 +707,7 @@ class Class3D(SQLModel, table=True):  # type: ignore
 
 
 class RefineParameters(SQLModel, table=True):  # type: ignore
+    tag: str = Field(primary_key=True)
     refine_dir: str = Field(primary_key=True)
     pj_id: int = Field(primary_key=True, foreign_key="processingjob.id")
     murfey_id: int = Field(foreign_key="murfeyledger.id")
@@ -722,6 +723,7 @@ class RefineParameters(SQLModel, table=True):  # type: ignore
 
 
 class Refine3D(SQLModel, table=True):  # type: ignore
+    tag: str = Field(primary_key=True)
     refine_dir: str = Field(primary_key=True)
     pj_id: int = Field(primary_key=True, foreign_key="processingjob.id")
     murfey_id: int = Field(foreign_key="murfeyledger.id")