aligning column names with ISPyB

Author: d-j-hatton

src/murfey/util/db.py

@@ -415,7 +415,7 @@ class Tilt(SQLModel, table=True):  # type: ignore
 
 
 class DataCollectionGroup(SQLModel, table=True):  # type: ignore
-    id: int = Field(primary_key=True, unique=True)
+    dataCollectionGroupId: int = Field(primary_key=True, unique=True, alias="id")
     session_id: int = Field(foreign_key="session.id", primary_key=True)
     tag: str = Field(primary_key=True)
     atlas_id: Optional[int] = None
@@ -453,7 +453,7 @@ class DataCollectionGroup(SQLModel, table=True):  # type: ignore
 
 class NotificationParameter(SQLModel, table=True):  # type: ignore
     id: Optional[int] = Field(default=None, primary_key=True)
-    dcg_id: int = Field(foreign_key="datacollectiongroup.id")
+    dcg_id: int = Field(foreign_key="datacollectiongroup.dataCollectionGroupId")
     name: str
     min_value: float
     max_value: float
@@ -479,9 +479,11 @@ class NotificationValue(SQLModel, table=True):  # type: ignore
 
 
 class DataCollection(SQLModel, table=True):  # type: ignore
-    id: int = Field(primary_key=True, unique=True)
+    dataCollectionId: int = Field(primary_key=True, unique=True, alias="id")
     tag: str = Field(primary_key=True)
-    dcg_id: int = Field(foreign_key="datacollectiongroup.id")
+    dataCollectionGroupId: int = Field(
+        foreign_key="datacollectiongroup.dataCollectionGroupid", alias="dcg_id"
+    )
     data_collection_group: Optional[DataCollectionGroup] = Relationship(
         back_populates="data_collections"
     )
@@ -500,9 +502,11 @@ class DataCollection(SQLModel, table=True):  # type: ignore
 
 
 class ProcessingJob(SQLModel, table=True):  # type: ignore
-    id: int = Field(primary_key=True, unique=True)
+    processingJobId: int = Field(primary_key=True, unique=True, alias="id")
     recipe: str = Field(primary_key=True)
-    dc_id: int = Field(foreign_key="datacollection.id")
+    dataCollectionId: int = Field(
+        foreign_key="datacollection.dataCollectionId", alias="dc_id"
+    )
     data_collection: Optional[DataCollection] = Relationship(
         back_populates="processing_jobs"
     )
@@ -567,7 +571,7 @@ class PreprocessStash(SQLModel, table=True):  # type: ignore
 class SelectionStash(SQLModel, table=True):  # type: ignore
     id: Optional[int] = Field(default=None, primary_key=True)
     class_selection_score: float
-    pj_id: int = Field(foreign_key="processingjob.id")
+    pj_id: int = Field(foreign_key="processingjob.processingJobId")
     processing_job: Optional[ProcessingJob] = Relationship(
         back_populates="selection_stash"
     )
@@ -590,8 +594,10 @@ class TomographyProcessingParameters(SQLModel, table=True):  # type: ignore
 
 
 class AutoProcProgram(SQLModel, table=True):  # type: ignore
-    id: int = Field(primary_key=True, unique=True)
-    pj_id: int = Field(foreign_key="processingjob.id")
+    autoProcProgramId: int = Field(primary_key=True, unique=True, alias="id")
+    processingJobId: int = Field(
+        foreign_key="processingjob.processingJobId", alias="pj_id"
+    )
     processing_job: Optional[ProcessingJob] = Relationship(
         back_populates="auto_proc_programs"
     )
@@ -760,8 +766,12 @@ class SearchMap(SQLModel, table=True):  # type: ignore
 
 
 class Movie(SQLModel, table=True):  # type: ignore
-    murfey_id: int = Field(primary_key=True, foreign_key="murfeyledger.id")
-    data_collection_id: Optional[int] = Field(foreign_key="datacollection.id")
+    movieId: int = Field(
+        primary_key=True, foreign_key="murfeyledger.id", alias="murfey_id"
+    )
+    dataCollectionId: Optional[int] = Field(
+        foreign_key="datacollection.dataCollectionId", alias="data_collection_id"
+    )
     foil_hole_id: int = Field(foreign_key="foilhole.id", nullable=True, default=None)
     path: str
     image_number: int
@@ -780,7 +790,7 @@ class Movie(SQLModel, table=True):  # type: ignore
 
 class CtfParameters(SQLModel, table=True):  # type: ignore
     id: Optional[int] = Field(default=None, primary_key=True)
-    pj_id: int = Field(foreign_key="processingjob.id")
+    pj_id: int = Field(foreign_key="processingjob.processingJobId")
     micrographs_file: str
     coord_list_file: str
     extract_file: str
@@ -797,7 +807,7 @@ class CtfParameters(SQLModel, table=True):  # type: ignore
 
 class TomogramPicks(SQLModel, table=True):  # type: ignore
     tomogram: str = Field(primary_key=True)
-    pj_id: int = Field(foreign_key="processingjob.id")
+    pj_id: int = Field(foreign_key="processingjob.processingJobId")
     cbox_3d: str
     particle_count: int
     tomogram_pixel_size: float
@@ -808,15 +818,15 @@ class TomogramPicks(SQLModel, table=True):  # type: ignore
 
 class ParticleSizes(SQLModel, table=True):  # type: ignore
     id: Optional[int] = Field(default=None, primary_key=True)
-    pj_id: int = Field(foreign_key="processingjob.id")
+    pj_id: int = Field(foreign_key="processingjob.processingJobId")
     particle_size: float
     processing_job: Optional[ProcessingJob] = Relationship(
         back_populates="particle_sizes"
     )
 
 
 class SPARelionParameters(SQLModel, table=True):  # type: ignore
-    pj_id: int = Field(primary_key=True, foreign_key="processingjob.id")
+    pj_id: int = Field(primary_key=True, foreign_key="processingjob.processingJobId")
     angpix: float
     dose_per_frame: float
     gain_ref: Optional[str]
@@ -836,7 +846,7 @@ class SPARelionParameters(SQLModel, table=True):  # type: ignore
 
 
 class ClassificationFeedbackParameters(SQLModel, table=True):  # type: ignore
-    pj_id: int = Field(primary_key=True, foreign_key="processingjob.id")
+    pj_id: int = Field(primary_key=True, foreign_key="processingjob.processingJobId")
     estimate_particle_diameter: bool = True
     hold_class2d: bool = False
     rerun_class2d: bool = False
@@ -858,7 +868,7 @@ class ClassificationFeedbackParameters(SQLModel, table=True):  # type: ignore
 
 class Class2DParameters(SQLModel, table=True):  # type: ignore
     particles_file: str = Field(primary_key=True)
-    pj_id: int = Field(primary_key=True, foreign_key="processingjob.id")
+    pj_id: int = Field(primary_key=True, foreign_key="processingjob.processingJobId")
     murfey_id: int = Field(foreign_key="murfeyledger.id")
     class2d_dir: str
     batch_size: int
@@ -876,15 +886,15 @@ class Class2D(SQLModel, table=True):  # type: ignore
     particles_file: str = Field(
         primary_key=True,
     )
-    pj_id: int = Field(primary_key=True, foreign_key="processingjob.id")
+    pj_id: int = Field(primary_key=True, foreign_key="processingjob.processingJobId")
     murfey_id: int = Field(foreign_key="murfeyledger.id")
     processing_job: Optional[ProcessingJob] = Relationship(back_populates="class2ds")
     murfey_ledger: Optional[MurfeyLedger] = Relationship(back_populates="class2ds")
 
 
 class Class3DParameters(SQLModel, table=True):  # type: ignore
     particles_file: str = Field(primary_key=True)
-    pj_id: int = Field(primary_key=True, foreign_key="processingjob.id")
+    pj_id: int = Field(primary_key=True, foreign_key="processingjob.processingJobId")
     murfey_id: int = Field(foreign_key="murfeyledger.id")
     class3d_dir: str
     batch_size: int
@@ -904,7 +914,7 @@ class Class3DParameters(SQLModel, table=True):  # type: ignore
 class Class3D(SQLModel, table=True):  # type: ignore
     class_number: int = Field(primary_key=True)
     particles_file: str = Field(primary_key=True)
-    pj_id: int = Field(primary_key=True, foreign_key="processingjob.id")
+    pj_id: int = Field(primary_key=True, foreign_key="processingjob.processingJobId")
     murfey_id: int = Field(foreign_key="murfeyledger.id")
     # class3d_parameters: Optional[Class3DParameters] = Relationship(
     #    back_populates="class3ds"
@@ -916,7 +926,7 @@ 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")
+    pj_id: int = Field(primary_key=True, foreign_key="processingjob.processingJobId")
     murfey_id: int = Field(foreign_key="murfeyledger.id")
     class3d_dir: str
     class_number: int
@@ -932,15 +942,15 @@ 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")
+    pj_id: int = Field(primary_key=True, foreign_key="processingjob.processingJobId")
     murfey_id: int = Field(foreign_key="murfeyledger.id")
     processing_job: Optional[ProcessingJob] = Relationship(back_populates="refine3ds")
     murfey_ledger: Optional[MurfeyLedger] = Relationship(back_populates="refine3ds")
 
 
 class BFactorParameters(SQLModel, table=True):  # type: ignore
     project_dir: str = Field(primary_key=True)
-    pj_id: int = Field(primary_key=True, foreign_key="processingjob.id")
+    pj_id: int = Field(primary_key=True, foreign_key="processingjob.processingJobId")
     batch_size: int
     refined_grp_uuid: int
     refined_class_uuid: int
@@ -952,7 +962,7 @@ class BFactorParameters(SQLModel, table=True):  # type: ignore
 
 class BFactors(SQLModel, table=True):  # type: ignore
     bfactor_directory: str = Field(primary_key=True)
-    pj_id: int = Field(primary_key=True, foreign_key="processingjob.id")
+    pj_id: int = Field(primary_key=True, foreign_key="processingjob.processingJobId")
     number_of_particles: int
     resolution: float