Update dependencies and migrate to Node 18 minimum support

Upgraded multiple package versions, including `@esbuild` and dependencies like `@mui/x-data-grid-premium`. Adjusted `node` engine requirement to `>=18` for compatibility. This ensures modernization and alignment with current toolchain standards.

backend/app/models.py

@@ -260,6 +260,14 @@ class Image(Base):
     sample_id = Column(Integer, ForeignKey("samples.id"), nullable=False)
 
 
+class ExperimentParameters(Base):
+    __tablename__ = "experiment_parameters"
+    id = Column(Integer, primary_key=True, index=True, autoincrement=True)
+    run_number = Column(Integer, nullable=False)
+    beamline_parameters = Column(JSON, nullable=True)
+    sample_id = Column(Integer, ForeignKey("samples.id"), nullable=False)
+
+
 # class Results(Base):
 #    __tablename__ = "results"
 #

backend/app/routers/sample.py

@@ -12,6 +12,8 @@ from app.schemas import (
     Image,
     ImageCreate,
     SampleResult,
+    ExperimentParametersCreate,
+    ExperimentParametersRead,
 )
 from app.models import (
     Puck as PuckModel,
@@ -19,6 +21,7 @@ from app.models import (
     SampleEvent as SampleEventModel,
     Image as ImageModel,
     Dewar as DewarModel,
+    ExperimentParameters as ExperimentParametersModel,
 )
 from app.dependencies import get_db
 import logging
@@ -192,7 +195,7 @@ async def upload_sample_image(
 
 @router.get("/results", response_model=List[SampleResult])
 async def get_sample_results(active_pgroup: str, db: Session = Depends(get_db)):
-    # Query samples for the active pgroup using joins
+    # Query samples for the active pgroup using joins.
     samples = (
         db.query(SampleModel)
         .join(SampleModel.puck)
@@ -207,8 +210,18 @@ async def get_sample_results(active_pgroup: str, db: Session = Depends(get_db)):
 
     results = []
     for sample in samples:
-        # Query images associated with each sample
+        # Query images associated with the sample.
         images = db.query(ImageModel).filter(ImageModel.sample_id == sample.id).all()
+
+        # Query experiment parameters (which include beamline parameters) for the
+        # sample.
+        experiment_parameters = (
+            db.query(ExperimentParametersModel)
+            .filter(ExperimentParametersModel.sample_id == sample.id)
+            .all()
+        )
+        print("Experiment Parameters for sample", sample.id, experiment_parameters)
+
         results.append(
             {
                 "sample_id": sample.id,
@@ -221,7 +234,52 @@ async def get_sample_results(active_pgroup: str, db: Session = Depends(get_db)):
                     {"id": img.id, "filepath": img.filepath, "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,
+                    }
+                    for ex in experiment_parameters
+                ],
             }
         )
 
     return results
+
+
+@router.post(
+    "/samples/{sample_id}/experiment_parameters",
+    response_model=ExperimentParametersRead,
+)
+def create_experiment_parameters_for_sample(
+    sample_id: int,
+    exp_params: ExperimentParametersCreate,
+    db: Session = Depends(get_db),
+):
+    # Calculate the new run_number for the given sample.
+    # This assumes that the run_number is computed as one plus the maximum
+    # current value.
+    last_exp = (
+        db.query(ExperimentParametersModel)
+        .filter(ExperimentParametersModel.sample_id == sample_id)
+        .order_by(ExperimentParametersModel.run_number.desc())
+        .first()
+    )
+    new_run_number = last_exp.run_number + 1 if last_exp else 1
+
+    # Create a new ExperimentParameters record. The beamline_parameters are
+    # stored as JSON.
+    new_exp = ExperimentParametersModel(
+        run_number=new_run_number,
+        beamline_parameters=exp_params.beamline_parameters.dict()
+        if exp_params.beamline_parameters
+        else None,
+        sample_id=sample_id,
+    )
+    db.add(new_exp)
+    db.commit()
+    db.refresh(new_exp)
+
+    return new_exp

backend/app/schemas.py

@@ -812,9 +812,97 @@ class ImageInfo(BaseModel):
     comment: Optional[str] = None
 
 
+class RotationParameters(BaseModel):
+    omegaStart_deg: float
+    omegaStep: float
+    chi: float
+    phi: float
+    numberOfImages: int
+    exposureTime_s: float
+
+
+class gridScanParamers(BaseModel):
+    xStart: float
+    xStep: float
+    yStart: float
+    yStep: float
+    zStart: float
+    zStep: float
+    numberOfImages: int
+    exposureTime_s: float
+
+
+class jetParameters(BaseModel):
+    hplc_pump_ml_min: float
+    pressure_bar: float
+    jetDiameter_um: int
+    jetSpeed_mm_s: float
+    exposureTime_s: float
+
+
+class detector(BaseModel):
+    manufacturer: str
+    model: str
+    type: str
+    serialNumber: str
+    detectorDistance_mm: float
+    beamCenterX_px: float
+    beamCenterY_px: float
+    pixelSizeX_um: float
+    pixelSizeY_um: float
+
+
+class BeamlineParameters(BaseModel):
+    synchrotron: str
+    beamline: str
+    detector: detector
+    wavelength: float
+    # energy: float
+    ringCurrent_A: float
+    ringMode: str
+    undulator: Optional[str] = None
+    undulatorgap_mm: Optional[float] = None
+    monochromator: str
+    # bandwidth_percent: float
+    transmission: float
+    focusingOptic: str
+    beamlineFluxAtSample_ph_s: Optional[float] = None
+    beamSizeWidth: Optional[float] = None
+    beamSizeHeight: Optional[float] = None
+    # dose_MGy: float
+    rotation: Optional[RotationParameters] = None
+    gridScan: Optional[gridScanParamers] = None
+    jet: Optional[jetParameters] = None
+    cryojetTemperature_K: Optional[float] = None
+    humidifierTemperature_K: Optional[float] = None
+    humidifierHumidity: Optional[float] = None
+    # experimentalHutchTemerature_K: Optional[float] = None
+    # experimentalHutchHumidity_percent: Optional[float] = None
+    # beamstopDistance_mm: Optional[float] = None
+    # beamstopDiameter_mm: Optional[float] = None
+
+
+class ExperimentParametersBase(BaseModel):
+    run_number: int
+    beamline_parameters: Optional[BeamlineParameters] = None
+    sample_id: int
+
+
+class ExperimentParametersCreate(ExperimentParametersBase):
+    run_number: Optional[int] = None
+
+
+class ExperimentParametersRead(ExperimentParametersBase):
+    id: int
+
+    class Config:
+        from_attributes = True
+
+
 class SampleResult(BaseModel):
     sample_id: int
     sample_name: str
     puck_name: Optional[str]
     dewar_name: Optional[str]
     images: List[ImageInfo]
+    experiment_runs: Optional[List[ExperimentParametersRead]] = []

backend/main.py

@@ -139,6 +139,15 @@ def on_startup():
             print(f"{environment.capitalize()} environment: Regenerating database.")
             # 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)
+            # tables_exist = inspector.get_table_names()
+            #
+            # if ExperimentParameters.__tablename__ not in tables_exist:
+            #    print("Creating missing table: ExperimentParameters")
+            #    ExperimentParameters.__table__.create(bind=engine)
+            #
             if environment == "dev":
                 from app.database import load_sample_data