Refactor for no inheritance

Author: stephen-riggs

src/murfey/util/db.py

@@ -4,11 +4,22 @@
 """
 
 from datetime import datetime
-from typing import List, Optional
+from typing import TYPE_CHECKING, List, Optional
 
 import sqlalchemy
 from sqlmodel import Field, Relationship, SQLModel, create_engine
 
+if TYPE_CHECKING:
+    from murfey.util.processing_db import (
+        CTF,
+        MotionCorrection,
+        ParticleClassificationGroup,
+        ParticlePicker,
+        RelativeIceThickness,
+        TiltImageAlignment,
+        Tomogram,
+    )
+
 """
 GENERAL
 """
@@ -407,7 +418,7 @@ class Tilt(SQLModel, table=True):  # type: ignore
     tilt_series: Optional[TiltSeries] = Relationship(back_populates="tilts")
 
 
-class DataCollectionGroupModel(SQLModel, table=True):  # type: ignore
+class DataCollectionGroup(SQLModel, table=True):  # type: ignore
     id: int = Field(primary_key=True, unique=True)
     session_id: int = Field(foreign_key="session.id", primary_key=True)
     tag: str = Field(primary_key=True)
@@ -434,11 +445,14 @@ class DataCollectionGroupModel(SQLModel, table=True):  # type: ignore
             sa_relationship_kwargs={"cascade": "delete"},
         )
     )
-
-
-@mapper_registry.mapped
-class DataCollectionGroup(DataCollectionGroupModel, table=True):  # type: ignore
-    pass
+    grid_squares: Optional[List["GridSquare"]] = Relationship(
+        back_populates="data_collection_group",
+        sa_relationship_kwargs={"cascade": "delete"},
+    )
+    search_maps: Optional[List["SearchMap"]] = Relationship(
+        back_populates="data_collection_group",
+        sa_relationship_kwargs={"cascade": "delete"},
+    )
 
 
 class NotificationParameter(SQLModel, table=True):  # type: ignore
@@ -481,6 +495,12 @@ class DataCollection(SQLModel, table=True):  # type: ignore
     movies: List["Movie"] = Relationship(
         back_populates="data_collection", sa_relationship_kwargs={"cascade": "delete"}
     )
+    motion_correction: Optional[List["MotionCorrection"]] = Relationship(
+        back_populates="data_collection"
+    )
+    tomogram: Optional[List["Tomogram"]] = Relationship(
+        back_populates="data_collection"
+    )
 
 
 class ProcessingJob(SQLModel, table=True):  # type: ignore
@@ -582,6 +602,22 @@ class AutoProcProgram(SQLModel, table=True):  # type: ignore
     murfey_ids: List["MurfeyLedger"] = Relationship(
         back_populates="auto_proc_program", sa_relationship_kwargs={"cascade": "delete"}
     )
+    motion_correction: Optional[List["MotionCorrection"]] = Relationship(
+        back_populates="data_collection"
+    )
+    tomogram: Optional[List["Tomogram"]] = Relationship(
+        back_populates="auto_proc_program"
+    )
+    ctf: Optional[List["CTF"]] = Relationship(back_populates="auto_proc_program")
+    particle_picker: Optional[List["ParticlePicker"]] = Relationship(
+        back_populates="auto_proc_program"
+    )
+    relative_ice_thickness: Optional[List["RelativeIceThickness"]] = Relationship(
+        back_populates="auto_proc_program"
+    )
+    particle_classification_group: Optional[List["ParticleClassificationGroup"]] = (
+        Relationship(back_populates="auto_proc_program")
+    )
 
 
 class MurfeyLedger(SQLModel, table=True):  # type: ignore
@@ -640,6 +676,17 @@ class GridSquare(SQLModel, table=True):  # type: ignore
     foil_holes: List["FoilHole"] = Relationship(
         back_populates="grid_square", sa_relationship_kwargs={"cascade": "delete"}
     )
+    atlas_id: Optional[int] = Field(foreign_key="datacollectiongroup.id")
+    scaled_pixel_size: Optional[float] = None
+    pixel_location_x: Optional[int] = None
+    pixel_location_y: Optional[int] = None
+    height: Optional[int] = None
+    width: Optional[int] = None
+    angle: Optional[float] = None
+    quality_indicator: Optional[float] = None
+    data_collection_group: Optional["DataCollectionGroup"] = Relationship(
+        back_populates="grid_squares"
+    )
 
 
 class FoilHole(SQLModel, table=True):  # type: ignore
@@ -665,6 +712,11 @@ class FoilHole(SQLModel, table=True):  # type: ignore
     preprocess_stashes: List[PreprocessStash] = Relationship(
         back_populates="foil_hole", sa_relationship_kwargs={"cascade": "delete"}
     )
+    scaled_pixel_size: Optional[float] = None
+    pixel_location_x: Optional[int] = None
+    pixel_location_y: Optional[int] = None
+    diameter: Optional[int] = None
+    quality_indicator: Optional[float] = None
 
 
 class SearchMap(SQLModel, table=True):  # type: ignore
@@ -697,6 +749,18 @@ class SearchMap(SQLModel, table=True):  # type: ignore
     tilt_series: List["TiltSeries"] = Relationship(
         back_populates="search_map", sa_relationship_kwargs={"cascade": "delete"}
     )
+    atlas_id: Optional[int] = Field(foreign_key="datacollectiongroup.id")
+    scaled_pixel_size: Optional[float] = None
+    pixel_location_x: Optional[int] = None
+    pixel_location_y: Optional[int] = None
+    scaled_height: Optional[int] = None
+    scaled_width: Optional[int] = None
+    angle: Optional[float] = None
+    quality_indicator: Optional[float] = None
+    data_collection_group: Optional["DataCollectionGroup"] = Relationship(
+        back_populates="search_maps"
+    )
+    tomogram: Optional[List["Tomogram"]] = Relationship(back_populates="search_map")
 
 
 class Movie(SQLModel, table=True):  # type: ignore
@@ -710,6 +774,12 @@ class Movie(SQLModel, table=True):  # type: ignore
     murfey_ledger: Optional[MurfeyLedger] = Relationship(back_populates="movies")
     data_collection: Optional["DataCollection"] = Relationship(back_populates="movies")
     foil_hole: Optional[FoilHole] = Relationship(back_populates="movies")
+    motion_correction: Optional[List["MotionCorrection"]] = Relationship(
+        back_populates="movie"
+    )
+    tilt_image_alignment: Optional[List["TiltImageAlignment"]] = Relationship(
+        back_populates="movie"
+    )
 
 
 class CtfParameters(SQLModel, table=True):  # type: ignore