Refactor AareDB backend and update schemas and paths.

Revised backend schema definitions, removing unnecessary attributes and adding new configurations. Updated file path references to align with the aaredb structure. Cleaned up redundant notebook content and commented out unused database regeneration logic in the backend.

Added posting a result to the database

backend/app/models.py

@@ -278,10 +278,14 @@ class Results(Base):
     __tablename__ = "results"
 
     id = Column(Integer, primary_key=True, index=True, autoincrement=True)
-    #    pgroup = Column(String(255), nullable=False)
-    result = Column(JSON, nullable=True)
-    result_id = Column(Integer, ForeignKey("experiment_parameters.id"), nullable=False)
+    result = Column(JSON, nullable=False)  # store the full result object as JSON
     sample_id = Column(Integer, ForeignKey("samples.id"), nullable=False)
+    run_id = Column(Integer, ForeignKey("experiment_parameters.id"), nullable=False)
+
+    # optional relationships if you wish to query easily
+    # sample = relationship("SampleModel", backref="results")
+    # experiment_parameters = relationship("ExperimentParametersModel",
+    # backref="results")
 
 
 #    method = Column(String(255), nullable=False)

backend/app/routers/sample.py

@@ -14,8 +14,9 @@ from app.schemas import (
     SampleResult,
     ExperimentParametersCreate,
     ExperimentParametersRead,
-    # ResultResponse,
-    # ResultCreate,
+    ImageInfo,
+    ResultResponse,
+    ResultCreate,
 )
 from app.models import (
     Puck as PuckModel,
@@ -25,7 +26,7 @@ from app.models import (
     Dewar as DewarModel,
     ExperimentParameters as ExperimentParametersModel,
     # ExperimentParameters,
-    # Results,
+    Results as ResultsModel,
 )
 from app.dependencies import get_db
 import logging
@@ -246,8 +247,13 @@ async def get_sample_results(active_pgroup: str, db: Session = Depends(get_db)):
 
     results = []
     for sample in samples:
-        # Query images associated with the sample.
-        images = db.query(ImageModel).filter(ImageModel.sample_id == sample.id).all()
+        # Query images associated with the sample, including the related event_type
+        images = (
+            db.query(ImageModel)
+            .options(joinedload(ImageModel.sample_event))
+            .filter(ImageModel.sample_id == sample.id)
+            .all()
+        )
 
         # Query experiment parameters (which include beamline parameters) for the
         # sample.
@@ -259,27 +265,34 @@ async def get_sample_results(active_pgroup: str, db: Session = Depends(get_db)):
         print("Experiment Parameters for sample", sample.id, experiment_parameters)
 
         results.append(
-            {
-                "sample_id": sample.id,
-                "sample_name": sample.sample_name,
-                "puck_name": sample.puck.puck_name if sample.puck else None,
-                "dewar_name": sample.puck.dewar.dewar_name
+            SampleResult(
+                sample_id=sample.id,
+                sample_name=sample.sample_name,
+                puck_name=sample.puck.puck_name if sample.puck else None,
+                dewar_name=sample.puck.dewar.dewar_name
                 if (sample.puck and sample.puck.dewar)
                 else None,
-                "images": [
-                    {"id": img.id, "filepath": img.filepath, "comment": img.comment}
+                images=[
+                    ImageInfo(
+                        id=img.id,
+                        filepath=img.filepath,
+                        event_type=img.sample_event.event_type
+                        if img.sample_event
+                        else "Unknown",
+                        comment=img.comment,
+                    )
                     for img in images
                 ],
-                "experiment_runs": [
-                    {
-                        "id": ex.id,
-                        "run_number": ex.run_number,
-                        "beamline_parameters": ex.beamline_parameters,
-                        "sample_id": ex.sample_id,
-                    }
+                experiment_runs=[
+                    ExperimentParametersRead(
+                        id=ex.id,
+                        run_number=ex.run_number,
+                        beamline_parameters=ex.beamline_parameters,
+                        sample_id=ex.sample_id,
+                    )
                     for ex in experiment_parameters
                 ],
-            }
+            )
         )
 
     return results
@@ -318,32 +331,49 @@ def create_experiment_parameters_for_sample(
     db.commit()
     db.refresh(new_exp)
 
+    # Create a "Collecting" sample event associated with the new experiment parameters
+    new_event = SampleEventModel(
+        sample_id=sample_id,
+        event_type="Collecting",  # The event type
+        timestamp=datetime.now(),  # Use current timestamp
+    )
+    db.add(new_event)
+    db.commit()
+
     return new_exp
 
 
-# @router.post("/results", response_model=ResultResponse)
-# def create_result(result: ResultCreate, db: Session = Depends(get_db)):
-#    # Validate sample_id and result_id (optional but recommended)
-#    sample = db.query(SampleModel).filter_by(id=result.sample_id).first()
-#    if not sample:
-#        raise HTTPException(status_code=404, detail="Sample not found")
-#
-#    experiment = db.query(ExperimentParameters).filter_by(id=result.result_id).first()
-#    if not experiment:
-#        raise HTTPException(status_code=404, detail="Experiment parameters not found")
-#
-#    # Create a new Results entry
-#    result_obj = Results(
-#        sample_id=result.sample_id,
-#        result_id=result.result_id,
-#        result=result.result
-#    )
-#    db.add(result_obj)
-#    db.commit()
-#    db.refresh(result_obj)
-#
-#    return result_obj
-#
+@router.post("/processing-results", response_model=ResultResponse)
+def create_result(payload: ResultCreate, db: Session = Depends(get_db)):
+    # Check experiment existence
+    experiment = (
+        db.query(ExperimentParametersModel)
+        .filter(ExperimentParametersModel.id == payload.run_id)
+        .first()
+    )
+    if not experiment:
+        raise HTTPException(
+            status_code=404, detail="Experiment parameters (run) not found"
+        )
+
+    result_entry = ResultsModel(
+        sample_id=payload.sample_id,
+        run_id=payload.run_id,
+        result=payload.result.model_dump(),  # Serialize entire result to JSON
+    )
+
+    db.add(result_entry)
+    db.commit()
+    db.refresh(result_entry)
+
+    return ResultResponse(
+        id=result_entry.id,
+        sample_id=result_entry.sample_id,
+        run_id=result_entry.run_id,
+        result=payload.result,  # return original payload directly
+    )
+
+
 # @router.get("/results", response_model=list[ResultResponse])
 # def get_results(sample_id: int, result_id: int, db: Session = Depends(get_db)):
 #    query = db.query(Results)

backend/app/schemas.py

@@ -352,16 +352,6 @@ class SampleEventCreate(BaseModel):
     event_type: Literal[
         "Mounting", "Centering", "Failed", "Lost", "Collecting", "Unmounting"
     ]
-    # event_type: str
-    # Validate event_type against accepted event types
-    # @field_validator("event_type", mode="before")
-    # def validate_event_type(cls, value):
-    #    allowed = {"Mounting", "Centering", "Failed",
-    #    "Lost", "Collecting", "Unmounting"}
-    #    if value not in allowed:
-    #        raise ValueError(f"Invalid event_type: {value}.
-    #        Accepted values are: {allowed}")
-    #    return value
 
 
 class SampleEventResponse(SampleEventCreate):
@@ -374,10 +364,7 @@ class SampleEventResponse(SampleEventCreate):
 
 
 class Results(BaseModel):
-    id: int
-    pgroup: str
-    sample_id: int
-    method: str
+    pipeline: str
     resolution: float
     unit_cell: str
     spacegroup: str
@@ -393,10 +380,6 @@ class Results(BaseModel):
     unique_refl: int
     comments: Optional[constr(max_length=200)] = None
 
-    # Define attributes for Results here
-    class Config:
-        from_attributes = True
-
 
 class ContactCreate(BaseModel):
     pgroups: str
@@ -822,6 +805,21 @@ class ImageInfo(BaseModel):
     id: int
     filepath: str
     comment: Optional[str] = None
+    event_type: str
+    # run_number: Optional[int]
+
+    class Config:
+        from_attributes = True
+
+
+class characterizationParameters(BaseModel):
+    omegaStart_deg: float
+    oscillation_deg: float
+    omegaStep: float
+    chi: float
+    phi: float
+    numberOfImages: int
+    exposureTime_s: float
 
 
 class RotationParameters(BaseModel):
@@ -882,6 +880,7 @@ class BeamlineParameters(BaseModel):
     beamSizeWidth: Optional[float] = None
     beamSizeHeight: Optional[float] = None
     # dose_MGy: float
+    characterization: Optional[characterizationParameters] = None
     rotation: Optional[RotationParameters] = None
     gridScan: Optional[gridScanParamers] = None
     jet: Optional[jetParameters] = None
@@ -922,15 +921,18 @@ class SampleResult(BaseModel):
 
 class ResultCreate(BaseModel):
     sample_id: int
-    result_id: int
-    result: Optional[dict]
+    run_id: int
+    result: Results
+
+    class Config:
+        from_attributes = True
 
 
 class ResultResponse(BaseModel):
     id: int
     sample_id: int
-    result_id: int
-    result: Optional[dict]
+    run_id: int
+    result: Results
 
     class Config:
         from_attributes = True

backend/main.py

@@ -156,8 +156,8 @@ def on_startup():
             load_slots_data(db)
         else:  # dev or test environments
             print(f"{environment.capitalize()} environment: Regenerating database.")
-            Base.metadata.drop_all(bind=engine)
-            Base.metadata.create_all(bind=engine)
+            # Base.metadata.drop_all(bind=engine)
+            # Base.metadata.create_all(bind=engine)
             # from sqlalchemy.engine import reflection
             # from app.models import ExperimentParameters  # adjust the import as needed
             # inspector = reflection.Inspector.from_engine(engine)

frontend/fetch-openapi.js

@@ -171,12 +171,12 @@ async function fetchAndGenerate() {
 const backendDirectory = (() => {
     switch (nodeEnv) {
         case 'prod':
-            return path.resolve('/home/jungfrau/heidi-v2/backend/app'); // Production path
+            return path.resolve('/home/jungfrau/aaredb/backend/app'); // Production path
         case 'test':
-            return path.resolve('/home/jungfrau/heidi-v2/backend/app'); // Test path
+            return path.resolve('/home/jungfrau/aaredb/backend/app'); // Test path
         case 'dev':
         default:
-            return path.resolve('/Users/gotthardg/PycharmProjects/heidi-v2/backend/app'); // Development path
+            return path.resolve('/Users/gotthardg/PycharmProjects/aaredb/backend/app'); // Development path
     }
 })();
 

frontend/src/components/ResultGrid.tsx

@@ -11,6 +11,8 @@ interface ImageInfo {
     id: number;
     filepath: string;
     comment?: string;
+    event_type: string;
+    run_number?:number;
 }
 
 // This represents an experiment run as returned by your API.
@@ -87,7 +89,7 @@ interface TreeRow {
     sample_name?: string;
     puck_name?: string;
     dewar_name?: string;
-    images?: ImageInfo[];
+    images?: ImageInfo[];  // Images associated explicitly with this row (especially run items)
     run_number?: number;
     beamline_parameters?: ExperimentParameters['beamline_parameters'];
     experimentType?: string;
@@ -176,7 +178,13 @@ const ResultGrid: React.FC<ResultGridProps> = ({ activePgroup }) => {
     }, []);
 
     useEffect(() => {
-        // Fetch sample details and construct rows
+        if (!OpenAPI.BASE) {
+            console.error('OpenAPI.BASE is not set. Falling back to a default value.');
+            return;
+        }
+
+        setBasePath(`${OpenAPI.BASE}/`);
+
         SamplesService.getSampleResultsSamplesResultsGet(activePgroup)
             .then((response: SampleResult[]) => {
                 const treeRows: TreeRow[] = [];
@@ -190,28 +198,27 @@ const ResultGrid: React.FC<ResultGridProps> = ({ activePgroup }) => {
                         sample_name: sample.sample_name,
                         puck_name: sample.puck_name,
                         dewar_name: sample.dewar_name,
-                        images: sample.images,
+                        images: sample.images.filter(img => img.event_type === "Centering"),
                     };
                     treeRows.push(sampleRow);
 
-                    if (sample.experiment_runs) {
-                        sample.experiment_runs.forEach((run) => {
-                            const experimentType = getExperimentType(run);
-                            const numImages = getNumberOfImages(run);
-                            const runRow: TreeRow = {
-                                id: `run-${sample.sample_id}-${run.run_number}`,
-                                hierarchy: [sample.sample_id, run.run_number],
-                                type: 'run',
-                                sample_id: sample.sample_id,
-                                run_number: run.run_number,
-                                beamline_parameters: run.beamline_parameters,
-                                experimentType,
-                                numberOfImages: numImages,
-                                images: sample.images,
-                            };
-                            treeRows.push(runRow);
-                        });
-                    }
+                    sample.experiment_runs?.forEach(run => {
+                        const experimentType = getExperimentType(run);
+                        const numImages = getNumberOfImages(run);
+                        const runRow: TreeRow = {
+                            id: `run-${sample.sample_id}-${run.run_number}`,
+                            hierarchy: [sample.sample_id, run.run_number],
+                            type: 'run',
+                            sample_id: sample.sample_id,
+                            run_number: run.run_number,
+                            beamline_parameters: run.beamline_parameters,
+                            experimentType,
+                            numberOfImages: numImages,
+                            images: sample.images.filter(img =>
+                            img.event_type === "Collecting" ),
+                        };
+                        treeRows.push(runRow);
+                    });
                 });
 
                 setRows(treeRows);
@@ -221,6 +228,7 @@ const ResultGrid: React.FC<ResultGridProps> = ({ activePgroup }) => {
             });
     }, [activePgroup]);
 
+
     // Define the grid columns
     const columns: GridColDef[] = [
         {