wip

Author: vredchenko

docs/software-architecture.mermaid

@@ -1,4 +1,4 @@
-graph LR
+ graph TD
     subgraph k8s["Kubernetes Cluster (Scientific Compute)"]
         subgraph core["Core Services"]
             api["SmartEM Core Service & API"]
@@ -44,4 +44,4 @@ graph LR
     class infrastructure infra
     class ext ext
     %% Link styling
-    linkStyle 0,1,2,3,4,5,6,7,8 stroke:#666
+    linkStyle 0,1,2,3,4,5,6,7,8 stroke:#666

src/smartem_decisions/http_api.py

@@ -241,15 +241,11 @@ def delete_acquisition(acquisition_id: str, db: SqlAlchemySession = Depends(get_
     if not db_acquisition:
         raise HTTPException(status_code=404, detail="Acquisition not found")
 
-    # Publish the deletion event to RabbitMQ
+    
     success = publish_acquisition_deleted(acquisition_id)
     if not success:
         logger.error(f"Failed to publish acquisition deleted event for ID: {acquisition_id}")
 
-    # For immediate feedback, also delete from the database
-    db.delete(db_acquisition)
-    db.commit()
-
     return None
 
 
@@ -307,15 +303,11 @@ def delete_grid(grid_id: str, db: SqlAlchemySession = Depends(get_db)):
     if not db_grid:
         raise HTTPException(status_code=404, detail="Grid not found")
 
-    # Publish the deletion event to RabbitMQ
+    
     success = publish_grid_deleted(grid_id)
     if not success:
         logger.error(f"Failed to publish grid deleted event for ID: {grid_id}")
 
-    # For immediate feedback, also delete from the database
-    db.delete(db_grid)
-    db.commit()
-
     return None
 
 
@@ -405,15 +397,11 @@ def delete_atlas(atlas_id: str, db: SqlAlchemySession = Depends(get_db)):
     if not db_atlas:
         raise HTTPException(status_code=404, detail="Atlas not found")
 
-    # Publish the deletion event to RabbitMQ
+    
     success = publish_atlas_deleted(atlas_id)
     if not success:
         logger.error(f"Failed to publish atlas deleted event for ID: {atlas_id}")
 
-    # For immediate feedback, also delete from the database
-    db.delete(db_atlas)
-    db.commit()
-
     return None
 
 
@@ -534,15 +522,11 @@ def delete_atlas_tile(tile_id: str, db: SqlAlchemySession = Depends(get_db)):
     if not db_tile:
         raise HTTPException(status_code=404, detail="Atlas tile not found")
 
-    # Publish the deletion event to RabbitMQ
+    
     success = publish_atlas_tile_deleted(tile_id)
     if not success:
         logger.error(f"Failed to publish atlas tile deleted event for ID: {tile_id}")
 
-    # For immediate feedback, also delete from the database
-    db.delete(db_tile)
-    db.commit()
-
     return None
 
 
@@ -636,15 +620,11 @@ def delete_gridsquare(gridsquare_id: str, db: SqlAlchemySession = Depends(get_db
     if not db_gridsquare:
         raise HTTPException(status_code=404, detail="Grid Square not found")
 
-    # Publish the deletion event to RabbitMQ
+    
     success = publish_gridsquare_deleted(gridsquare_id)
     if not success:
         logger.error(f"Failed to publish grid square deleted event for ID: {gridsquare_id}")
 
-    # For immediate feedback, also delete from the database
-    db.delete(db_gridsquare)
-    db.commit()
-
     return None
 
 
@@ -735,15 +715,11 @@ def delete_foilhole(foilhole_id: str, db: SqlAlchemySession = Depends(get_db)):
     if not db_foilhole:
         raise HTTPException(status_code=404, detail="Foil Hole not found")
 
-    # Publish the deletion event to RabbitMQ
+    
     success = publish_foilhole_deleted(foilhole_id)
     if not success:
         logger.error(f"Failed to publish foil hole deleted event for ID: {foilhole_id}")
 
-    # For immediate feedback, also delete from the database
-    db.delete(db_foilhole)
-    db.commit()
-
     return None
 
 
@@ -837,15 +813,11 @@ def delete_micrograph(micrograph_id: str, db: SqlAlchemySession = Depends(get_db
     if not db_micrograph:
         raise HTTPException(status_code=404, detail="Micrograph not found")
 
-    # Publish the deletion event to RabbitMQ
+    
     success = publish_micrograph_deleted(micrograph_id)
     if not success:
         logger.error(f"Failed to publish micrograph deleted event for ID: {micrograph_id}")
 
-    # For immediate feedback, also delete from the database
-    db.delete(db_micrograph)
-    db.commit()
-
     return None
 
 
@@ -879,7 +851,7 @@ def create_foilhole_micrograph(
     response_data = {
         "id": micrograph.id,
         "foilhole_id": foilhole_id,
-        "status": MicrographStatus.NONE,  # Set default status
+        "status": MicrographStatus.NONE,  # Set default status TODO surely set whatever status was provided by client?
         **micrograph.model_dump(),
     }
 

src/smartem_decisions/model/database.py

@@ -29,7 +29,7 @@
 
 class Acquisition(SQLModel, table=True, table_name="acquisition"):
     __table_args__ = {"extend_existing": True}
-    id: str = Field(primary_key=True)
+    uuid: str = Field(primary_key=True)
     epu_id: str | None = Field(default=None)
     name: str
     status: AcquisitionStatus = Field(default=AcquisitionStatus.PLANNED, sa_column=Column(AcquisitionStatusType()))
@@ -45,9 +45,9 @@ class Acquisition(SQLModel, table=True, table_name="acquisition"):
 
 class Atlas(SQLModel, table=True, table_name="atlas"):
     __table_args__ = {"extend_existing": True}
-    id: str = Field(primary_key=True)
+    uuid: str = Field(primary_key=True)
     atlas_id: str = Field(default="")
-    grid_id: str | None = Field(default=None, foreign_key="grid.id")
+    grid_id: str | None = Field(default=None, foreign_key="grid.uuid")
     acquisition_date: datetime | None = Field(default=None)
     storage_folder: str | None = Field(default=None)
     description: str | None = Field(default=None)
@@ -60,8 +60,8 @@ class Atlas(SQLModel, table=True, table_name="atlas"):
 
 class Grid(SQLModel, table=True, table_name="grid"):
     __table_args__ = {"extend_existing": True}
-    id: str = Field(primary_key=True)
-    acquisition_id: str | None = Field(default=None, foreign_key="acquisition.id")
+    uuid: str = Field(primary_key=True)
+    acquisition_id: str | None = Field(default=None, foreign_key="acquisition.uuid")
     status: GridStatus = Field(default=GridStatus.NONE, sa_column=Column(GridStatusType()))
     name: str
     data_dir: str | None = Field(default=None)
@@ -83,8 +83,8 @@ class Grid(SQLModel, table=True, table_name="grid"):
 
 class AtlasTile(SQLModel, table=True, table_name="atlastile"):
     __table_args__ = {"extend_existing": True}
-    id: str = Field(primary_key=True)
-    atlas_id: str | None = Field(default=None, foreign_key="atlas.id")
+    uuid: str = Field(primary_key=True)
+    atlas_id: str | None = Field(default=None, foreign_key="atlas.uuid")
     tile_id: str = Field(default="")
     position_x: int | None = Field(default=None)
     position_y: int | None = Field(default=None)
@@ -97,8 +97,8 @@ class AtlasTile(SQLModel, table=True, table_name="atlastile"):
 
 class GridSquare(SQLModel, table=True, table_name="gridsquare"):
     __table_args__ = {"extend_existing": True}
-    id: str = Field(primary_key=True)
-    grid_id: str | None = Field(default=None, foreign_key="grid.id")
+    uuid: str = Field(primary_key=True)
+    grid_id: str | None = Field(default=None, foreign_key="grid.uuid")
     status: GridSquareStatus = Field(default=GridSquareStatus.NONE, sa_column=Column(GridSquareStatusType()))
     gridsquare_id: str = Field(default="")
     data_dir: str | None = Field(default=None)
@@ -132,8 +132,8 @@ class GridSquare(SQLModel, table=True, table_name="gridsquare"):
 
 class FoilHole(SQLModel, table=True, table_name="foilhole"):
     __table_args__ = {"extend_existing": True}
-    id: str = Field(primary_key=True)
-    gridsquare_id: str | None = Field(default=None, foreign_key="gridsquare.id")
+    uuid: str = Field(primary_key=True)
+    gridsquare_id: str | None = Field(default=None, foreign_key="gridsquare.uuid")
     status: FoilHoleStatus = Field(default=FoilHoleStatus.NONE, sa_column=Column(FoilHoleStatusType()))
     foilhole_id: str = Field(default="")
     center_x: float | None = Field(default=None)
@@ -157,8 +157,8 @@ class FoilHole(SQLModel, table=True, table_name="foilhole"):
 
 class Micrograph(SQLModel, table=True, table_name="micrograph"):
     __table_args__ = {"extend_existing": True}
-    id: str = Field(primary_key=True)
-    foilhole_id: str | None = Field(default=None, foreign_key="foilhole.id")
+    uuid: str = Field(primary_key=True)
+    foilhole_id: str | None = Field(default=None, foreign_key="foilhole.uuid")
     status: MicrographStatus = Field(default=MicrographStatus.NONE, sa_column=Column(MicrographStatusType()))
     micrograph_id: str = Field(default="")
     location_id: str | None = Field(default=None)
@@ -199,7 +199,7 @@ class QualityPredictionModel(SQLModel, table=True):
 class QualityPredictionModelParameter(SQLModel, table=True):
     __table_args__ = {"extend_existing": True}
     id: int | None = Field(default=None, primary_key=True)
-    grid_id: str = Field(foreign_key="grid.id")
+    grid_id: str = Field(foreign_key="grid.uuid")
     timestamp: datetime = Field(default_factory=datetime.now)
     prediction_model_name: str = Field(foreign_key="qualitypredictionmodel.name")
     key: str
@@ -211,8 +211,8 @@ class QualityPredictionModelParameter(SQLModel, table=True):
 class QualityPredictionModelWeight(SQLModel, table=True):
     __table_args__ = {"extend_existing": True}
     id: int | None = Field(default=None, primary_key=True)
-    grid_id: str = Field(foreign_key="grid.id")
-    micrograph_id: str | None = Field(default=None, foreign_key="micrograph.id")
+    grid_id: str = Field(foreign_key="grid.uuid")
+    micrograph_id: str | None = Field(default=None, foreign_key="micrograph.uuid")
     micrograph_quality: bool | None = Field(default=None)
     timestamp: datetime = Field(default_factory=datetime.now)
     origin: str | None = Field(default=None)
@@ -229,8 +229,8 @@ class QualityPrediction(SQLModel, table=True):
     timestamp: datetime = Field(default_factory=datetime.now)
     value: float
     prediction_model_name: str = Field(foreign_key="qualitypredictionmodel.name")
-    foilhole_id: str | None = Field(default=None, foreign_key="foilhole.id")
-    gridsquare_id: str | None = Field(default=None, foreign_key="gridsquare.id")
+    foilhole_id: str | None = Field(default=None, foreign_key="foilhole.uuid")
+    gridsquare_id: str | None = Field(default=None, foreign_key="gridsquare.uuid")
     foilhole: FoilHole | None = Relationship(back_populates="prediction")
     gridsquare: GridSquare | None = Relationship(back_populates="prediction")
     model: QualityPredictionModel | None = Relationship(back_populates="predictions")
@@ -270,39 +270,39 @@ def _create_db_and_tables(engine):
         try:
             # acquisition indexes
             sess.execute(
-                text("CREATE INDEX IF NOT EXISTS idx_acquisition_id_pattern ON acquisition (id text_pattern_ops);")
+                text("CREATE INDEX IF NOT EXISTS idx_acquisition_id_pattern ON acquisition (uuid text_pattern_ops);")
             )
-            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_acquisition_id_hash ON acquisition USING hash (id);"))
+            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_acquisition_id_hash ON acquisition USING hash (uuid);"))
             sess.execute(text("CREATE INDEX IF NOT EXISTS idx_acquisition_name ON acquisition (name);"))
 
             # atlas indexes
-            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_atlas_id_pattern ON atlas (id text_pattern_ops);"))
+            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_atlas_id_pattern ON atlas (uuid text_pattern_ops);"))
             sess.execute(text("CREATE INDEX IF NOT EXISTS idx_atlas_grid_id ON atlas (grid_id);"))
 
             # grid indexes
-            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_grid_id_pattern ON grid (id text_pattern_ops);"))
-            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_grid_id_hash ON grid USING hash (id);"))
+            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_grid_id_pattern ON grid (uuid text_pattern_ops);"))
+            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_grid_id_hash ON grid USING hash (uuid);"))
             sess.execute(text("CREATE INDEX IF NOT EXISTS idx_grid_acquisition_id ON grid (acquisition_id);"))
             sess.execute(text("CREATE INDEX IF NOT EXISTS idx_grid_name ON grid (name);"))
 
             # gridsquare indexes
             sess.execute(
-                text("CREATE INDEX IF NOT EXISTS idx_gridsquare_id_pattern ON gridsquare (id text_pattern_ops);")
+                text("CREATE INDEX IF NOT EXISTS idx_gridsquare_id_pattern ON gridsquare (uuid text_pattern_ops);")
             )
-            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_gridsquare_id_hash ON gridsquare USING hash (id);"))
+            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_gridsquare_id_hash ON gridsquare USING hash (uuid);"))
             sess.execute(text("CREATE INDEX IF NOT EXISTS idx_gridsquare_grid_id ON gridsquare (grid_id);"))
 
             # foilhole indexes
-            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_foilhole_id_pattern ON foilhole (id text_pattern_ops);"))
-            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_foilhole_id_hash ON foilhole USING hash (id);"))
+            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_foilhole_id_pattern ON foilhole (uuid text_pattern_ops);"))
+            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_foilhole_id_hash ON foilhole USING hash (uuid);"))
             sess.execute(text("CREATE INDEX IF NOT EXISTS idx_foilhole_gridsquare_id ON foilhole (gridsquare_id);"))
             sess.execute(text("CREATE INDEX IF NOT EXISTS idx_foilhole_quality ON foilhole (quality);"))
 
             # micrograph indexes
             sess.execute(
-                text("CREATE INDEX IF NOT EXISTS idx_micrograph_id_pattern ON micrograph (id text_pattern_ops);")
+                text("CREATE INDEX IF NOT EXISTS idx_micrograph_id_pattern ON micrograph (uuid text_pattern_ops);")
             )
-            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_micrograph_id_hash ON micrograph USING hash (id);"))
+            sess.execute(text("CREATE INDEX IF NOT EXISTS idx_micrograph_id_hash ON micrograph USING hash (uuid);"))
             sess.execute(text("CREATE INDEX IF NOT EXISTS idx_micrograph_foilhole_id ON micrograph (foilhole_id);"))
 
             sess.commit()
@@ -312,7 +312,7 @@ def _create_db_and_tables(engine):
 
         try:
             sess.execute(
-                text("CREATE INDEX IF NOT EXISTS idx_atlastile_id_pattern ON atlastile (id text_pattern_ops);")
+                text("CREATE INDEX IF NOT EXISTS idx_atlastile_id_pattern ON atlastile (uuid text_pattern_ops);")
             )
             sess.execute(text("CREATE INDEX IF NOT EXISTS idx_atlastile_atlas_id ON atlastile (atlas_id);"))
             sess.commit()