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Refactor AareDB backend and update schemas and paths.

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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
This commit is contained in:
GotthardG 2025-03-17 11:51:07 +01:00
parent db6164ac3f
commit 5a0047b6d5
8 changed files with 367 additions and 935 deletions
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10
backend/app/models.py
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@ -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)

116
backend/app/routers/sample.py
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@ -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)

46
backend/app/schemas.py
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@ -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

4
backend/main.py
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@ -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)

0
backend/tests/test_results.py Normal file
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6
frontend/fetch-openapi.js
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@ -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
}
})();

50
frontend/src/components/ResultGrid.tsx
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@ -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[] = [
{

1070
testfunctions.ipynb
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