Merge together all similar tables

Author: stephen-riggs

src/murfey/util/db.py

@@ -11,12 +11,11 @@
 
 from murfey.util.processing_db import (
     CTF,
-    Atlas,
     MotionCorrection,
-    Movie as ProcessingMovie,
     ParticleClassificationGroup,
     ParticlePicker,
     RelativeIceThickness,
+    TiltImageAlignment,
     Tomogram,
 )
 
@@ -440,7 +439,14 @@ class DataCollectionGroup(SQLModel, table=True):  # type: ignore
             sa_relationship_kwargs={"cascade": "delete"},
         )
     )
-    Atlas: List["Atlas"] = Relationship(back_populates="DataCollectionGroup")
+    grid_squares: List["GridSquare"] = Relationship(
+        back_populates="data_collection_group",
+        sa_relationship_kwargs={"cascade": "delete"},
+    )
+    search_maps: List["SearchMap"] = Relationship(
+        back_populates="data_collection_group",
+        sa_relationship_kwargs={"cascade": "delete"},
+    )
 
 
 class NotificationParameter(SQLModel, table=True):  # type: ignore
@@ -480,7 +486,9 @@ class DataCollection(SQLModel, table=True):  # type: ignore
     processing_jobs: List["ProcessingJob"] = Relationship(
         back_populates="data_collection", sa_relationship_kwargs={"cascade": "delete"}
     )
-    Movie: List["ProcessingMovie"] = Relationship(back_populates="DataCollection")
+    movies: List["Movie"] = Relationship(
+        back_populates="data_collection", sa_relationship_kwargs={"cascade": "delete"}
+    )
     MotionCorrection: List["MotionCorrection"] = Relationship(
         back_populates="DataCollection"
     )
@@ -639,6 +647,7 @@ class MurfeyLedger(SQLModel, table=True):  # type: ignore
 class GridSquare(SQLModel, table=True):  # type: ignore
     id: Optional[int] = Field(primary_key=True, default=None)
     session_id: int = Field(foreign_key="session.id")
+    atlas_id: Optional[int] = Field(foreign_key="data_collection_group.id")
     name: int
     tag: str
     x_location: Optional[float]
@@ -650,6 +659,13 @@ class GridSquare(SQLModel, table=True):  # type: ignore
     thumbnail_size_x: Optional[int]
     thumbnail_size_y: Optional[int]
     pixel_size: Optional[float] = None
+    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
     image: str = ""
     session: Optional[Session] = Relationship(back_populates="grid_squares")
     clem_image_series: List["CLEMImageSeries"] = Relationship(
@@ -658,6 +674,9 @@ class GridSquare(SQLModel, table=True):  # type: ignore
     foil_holes: List["FoilHole"] = Relationship(
         back_populates="grid_square", sa_relationship_kwargs={"cascade": "delete"}
     )
+    data_collection_group: Optional["DataCollectionGroup"] = Relationship(
+        back_populates="grid_squares"
+    )
 
 
 class FoilHole(SQLModel, table=True):  # type: ignore
@@ -674,6 +693,11 @@ class FoilHole(SQLModel, table=True):  # type: ignore
     thumbnail_size_x: Optional[int]
     thumbnail_size_y: Optional[int]
     pixel_size: Optional[float] = None
+    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
     image: str = ""
     grid_square: Optional[GridSquare] = Relationship(back_populates="foil_holes")
     session: Optional[Session] = Relationship(back_populates="foil_holes")
@@ -688,13 +712,21 @@ class FoilHole(SQLModel, table=True):  # type: ignore
 class SearchMap(SQLModel, table=True):  # type: ignore
     id: Optional[int] = Field(primary_key=True, default=None)
     session_id: int = Field(foreign_key="session.id")
+    atlasId: Optional[int] = Field(foreign_key="data_collection_group.id")
     name: str
     tag: str
     x_location: Optional[float] = None
     y_location: Optional[float] = None
     x_stage_position: Optional[float] = None
     y_stage_position: Optional[float] = None
     pixel_size: Optional[float] = None
+    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
     image: str = ""
     binning: Optional[float] = None
     reference_matrix_m11: Optional[float] = None
@@ -715,17 +747,29 @@ class SearchMap(SQLModel, table=True):  # type: ignore
     tilt_series: List["TiltSeries"] = Relationship(
         back_populates="search_map", sa_relationship_kwargs={"cascade": "delete"}
     )
+    data_collection_group: Optional["DataCollectionGroup"] = Relationship(
+        back_populates="search_maps"
+    )
+    Tomogram: List["Tomogram"] = Relationship(back_populates="SearchMap")
 
 
 class Movie(SQLModel, table=True):  # type: ignore
     murfey_id: int = Field(primary_key=True, foreign_key="murfeyledger.id")
     foil_hole_id: int = Field(foreign_key="foilhole.id", nullable=True, default=None)
+    data_collection_id: Optional[int] = Field(foreign_key="datacollection.id")
     path: str
     image_number: int
     tag: str
     preprocessed: bool = False
+    createdTimeStamp: Optional[datetime] = None
+    movie_full_path: Optional[str] = None
     murfey_ledger: Optional[MurfeyLedger] = Relationship(back_populates="movies")
     foil_hole: Optional[FoilHole] = Relationship(back_populates="movies")
+    data_collection: Optional["DataCollection"] = Relationship(back_populates="movies")
+    MotionCorrection: List["MotionCorrection"] = Relationship(back_populates="Movie")
+    TiltImageAlignment: List["TiltImageAlignment"] = Relationship(
+        back_populates="Movie"
+    )
 
 
 class CtfParameters(SQLModel, table=True):  # type: ignore

src/murfey/util/processing_db.py

@@ -3,76 +3,7 @@
 
 from sqlmodel import Enum, Field, Relationship, SQLModel
 
-from murfey.util.db import AutoProcProgram, DataCollection, DataCollectionGroup
-
-
-class Atlas(SQLModel, table=True):  # type: ignore
-    atlasId: int = Field(primary_key=True, unique=True)
-    dataCollectionGroupId: int = Field(foreign_key="DataCollectionGroup.id")
-    atlasImage: str
-    pixelSize: float
-    cassetteSlot: Optional[int] = None
-    DataCollectionGroup: Optional["DataCollectionGroup"] = Relationship(
-        back_populates="Atlas"
-    )
-    GridSquare: List["GridSquare"] = Relationship(back_populates="Atlas")
-
-
-class GridSquare(SQLModel, table=True):  # type: ignore
-    gridSquareId: int = Field(primary_key=True, unique=True)
-    atlasId: int = Field(foreign_key="Atlas.atlasId")
-    gridSquareLabel: Optional[int] = None
-    gridSquareImage: Optional[str] = None
-    pixelLocationX: Optional[int] = None
-    pixelLocationY: Optional[int] = None
-    height: Optional[int] = None
-    width: Optional[int] = None
-    angle: Optional[float] = None
-    stageLocationX: Optional[float] = None
-    stageLocationY: Optional[float] = None
-    qualityIndicator: Optional[float] = None
-    pixelSize: Optional[float] = None
-    Atlas: Optional["Atlas"] = Relationship(back_populates="Atlas")
-    FoilHole: List["FoilHole"] = Relationship(back_populates="GridSquare")
-    Tomogram: List["Tomogram"] = Relationship(back_populates="GridSquare")
-
-
-class FoilHole(SQLModel, table=True):  # type: ignore
-    foilHoleId: int = Field(primary_key=True, unique=True)
-    gridSquareId: int = Field(foreign_key="GridSquare.gridSquareId")
-    foilHoleLabel: str
-    foilHoleImage: Optional[str] = None
-    pixelLocationX: Optional[int] = None
-    pixelLocationY: Optional[int] = None
-    diameter: Optional[int] = None
-    stageLocationX: Optional[float] = None
-    stageLocationY: Optional[float] = None
-    qualityIndicator: Optional[float] = None
-    pixelSize: Optional[float] = None
-    GridSquare: Optional["GridSquare"] = Relationship(back_populates="FoilHole")
-    Movie: List["Movie"] = Relationship(back_populates="FoilHole")
-
-
-class Movie(SQLModel, table=True):  # type: ignore
-    movieId: int = Field(primary_key=True, unique=True)
-    createdTimeStamp: datetime.datetime
-    dataCollectionId: Optional[int] = Field(foreign_key="DataCollection.id")
-    movieNumber: Optional[int] = None
-    movieFullPath: Optional[str] = None
-    positionX: Optional[float] = None
-    positionY: Optional[float] = None
-    nominalDefocus: Optional[float] = None
-    angle: Optional[float] = None
-    fluence: Optional[float] = None
-    numberOfFrames: Optional[int] = None
-    foilHoleId: Optional[int] = Field(foreign_key="FoilHole.foilHoleId")
-    templateLabel: Optional[int] = None
-    DataCollection: Optional["DataCollection"] = Relationship(back_populates="Movie")
-    FoilHole: Optional["FoilHole"] = Relationship(back_populates="Movie")
-    MotionCorrection: List["MotionCorrection"] = Relationship(back_populates="Movie")
-    TiltImageAlignment: List["TiltImageAlignment"] = Relationship(
-        back_populates="Movie"
-    )
+from murfey.util.db import AutoProcProgram, DataCollection, Movie, SearchMap
 
 
 class MotionCorrection(SQLModel, table=True):  # type: ignore
@@ -134,14 +65,14 @@ class Tomogram(SQLModel, table=True):  # type: ignore
     projXZ: Optional[str] = None
     recordTimeStamp: Optional[datetime.datetime] = None
     globalAlignmentQuality: Optional[float] = None
-    gridSquareId: Optional[int] = Field(foreign_key="GridSquare.gridSquareId")
+    gridSquareId: Optional[int] = Field(foreign_key="SearchMap.id")
     pixelLocationX: Optional[int] = None
     pixelLocationY: Optional[int] = None
     AutoProcProgram: Optional["AutoProcProgram"] = Relationship(
         back_populates="Tomogram"
     )
     DataCollection: Optional["DataCollection"] = Relationship(back_populates="Tomogram")
-    GridSquare: Optional["GridSquare"] = Relationship(back_populates="Tomogram")
+    SearchMap: Optional["SearchMap"] = Relationship(back_populates="Tomogram")
     ProcessedTomogram: List["ProcessedTomogram"] = Relationship(
         back_populates="Tomogram"
     )
@@ -309,6 +240,9 @@ class BFactorFit(SQLModel, table=True):  # type: ignore
 
 class CryoemInitialModel(SQLModel, table=True):  # type: ignore
     cryoemInitialModelId: int = Field(primary_key=True, unique=True)
+    particleClassificationId: int = Field(
+        foreign_key="ParticleClassification.particleClassificationId"
+    )
     resolution: Optional[float] = None
     numberOfParticles: Optional[int] = None
     ParticleClassification: List["ParticleClassification"] = Relationship(