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Update dependencies and migrate to Node 18 minimum support

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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.
This commit is contained in:
GotthardG 2025-03-04 10:42:24 +01:00
parent c3cf463f06
commit 2e1d87c31b
11 changed files with 1911 additions and 273 deletions
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8
backend/app/models.py
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@ -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"
#

62
backend/app/routers/sample.py
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@ -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

88
backend/app/schemas.py
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@ -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]] = []

9
backend/main.py
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@ -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

646
frontend/package-lock.json generated
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5
frontend/package.json
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@ -27,7 +27,8 @@
"@mui/icons-material": "^6.1.5",
"@mui/material": "^6.1.6",
"@mui/system": "^6.1.6",
"@mui/x-data-grid": "^7.23.3",
"@mui/x-data-grid-premium": "^7.27.2",
"@mui/x-tree-view": "^7.26.0",
"axios": "^1.7.7",
"chokidar": "^4.0.1",
"dayjs": "^1.11.13",
@ -59,7 +60,7 @@
"openapi-typescript": "^7.4.2",
"typescript": "^5.5.3",
"typescript-eslint": "^8.7.0",
"vite": "^5.4.8",
"vite": "^6.2.0",
"vite-plugin-svgr": "^4.2.0"
}
}

286
frontend/src/components/ResultGrid.tsx
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@ -1,30 +1,131 @@
// TypeScript (ResultGrid.tsx snippet)
import React, { useEffect, useState } from 'react';
import { DataGrid, GridColDef } from '@mui/x-data-grid';
import { DataGridPremium, GridColDef } from '@mui/x-data-grid-premium';
import IconButton from '@mui/material/IconButton';
import InfoIcon from '@mui/icons-material/Info';
import { OpenAPI, SamplesService } from '../../openapi';
import './SampleImage.css';
// Extend your image info interface if needed.
interface ImageInfo {
id: number;
filepath: string;
comment?: string;
}
// This represents an experiment run as returned by your API.
interface ExperimentParameters {
id: number;
run_number: number;
sample_id: number;
beamline_parameters: {
beamSizeHeight: number;
beamSizeWidth: number;
beamline: string;
beamlineFluxAtSample_ph_s: number;
cryojetTemperature_K?: number | null;
detector: {
beamCenterX_px: number;
beamCenterY_px: number;
detectorDistance_mm: number;
manufacturer: string;
model: string;
pixelSizeX_um: number;
pixelSizeY_um: number;
serialNumber: string;
type: string;
};
rotation?: {
chi: number;
exposureTime_s: number;
numberOfImages: number | null;
omegaStart_deg: number;
omegaStep: number;
phi: number;
} | null;
gridScan?: {
xStart: number;
xStep: number;
yStart: number;
yStep: number;
zStart: number;
zStep: number;
numberOfImages: number;
exposureTime_s: number;
} | null;
focusingOptic?: string;
humidifierHumidity?: number | null;
humidifierTemperature_K?: number | null;
jet?: any;
monochromator?: string;
ringCurrent_A?: number;
ringMode?: string;
synchrotron?: string;
transmission?: number;
undulator?: any;
undulatorgap_mm?: any;
wavelength?: number;
};
}
// Represents a sample returned by the API.
interface SampleResult {
sample_id: number;
sample_name: string;
puck_name?: string;
dewar_name?: string;
images: ImageInfo[];
experiment_runs?: ExperimentParameters[];
}
// A flat tree row type for the grid.
interface TreeRow {
id: string;
hierarchy: (string | number)[];
type: 'sample' | 'run';
sample_id: number;
sample_name?: string;
puck_name?: string;
dewar_name?: string;
images?: ImageInfo[];
run_number?: number;
beamline_parameters?: ExperimentParameters['beamline_parameters'];
experimentType?: string;
numberOfImages?: number;
}
interface ResultGridProps {
activePgroup: string;
}
// Helper function to safely get the number of images.
const getNumberOfImages = (run: ExperimentParameters): number => {
const params = run.beamline_parameters;
if (params.rotation && params.rotation.numberOfImages != null) {
return params.rotation.numberOfImages;
} else if (params.gridScan && params.gridScan.numberOfImages != null) {
return params.gridScan.numberOfImages;
}
return 0;
};
// Helper function to determine the experiment type.
const getExperimentType = (run: ExperimentParameters): string => {
const params = run.beamline_parameters;
if (params.rotation && params.rotation.numberOfImages != null && params.rotation.omegaStep != null) {
const numImages = params.rotation.numberOfImages;
const omegaStep = params.rotation.omegaStep;
if ([1, 2, 4].includes(numImages) && omegaStep === 90) {
return "Characterization";
}
return "Rotation";
} else if (params.gridScan) {
return "Grid Scan";
}
return "Rotation";
};
const ResultGrid: React.FC<ResultGridProps> = ({ activePgroup }) => {
const [rows, setRows] = useState<SampleResult[]>([]);
const [rows, setRows] = useState<TreeRow[]>([]);
const [basePath, setBasePath] = useState('');
useEffect(() => {
@ -44,99 +145,124 @@ const ResultGrid: React.FC<ResultGridProps> = ({ activePgroup }) => {
console.log('Environment Mode:', mode);
console.log('Resolved OpenAPI.BASE:', OpenAPI.BASE);
// Update the base path for images
setBasePath(`${OpenAPI.BASE}/`);
}, []);
useEffect(() => {
const fetchData = () => {
console.log("Fetching sample results for active_pgroup:", activePgroup);
SamplesService.getSampleResultsSamplesResultsGet(activePgroup)
.then((response: SampleResult[]) => {
console.log("Response received:", response);
setRows(response);
})
.catch((err: Error) => {
console.error("Error fetching sample results:", err);
console.log('Fetching sample results for active_pgroup:', activePgroup);
SamplesService.getSampleResultsSamplesResultsGet(activePgroup)
.then((response: SampleResult[]) => {
console.log('Response received:', response);
const treeRows: TreeRow[] = [];
response.forEach((sample) => {
// Add the sample row.
const sampleRow: TreeRow = {
id: `sample-${sample.sample_id}`,
hierarchy: [sample.sample_id],
type: 'sample',
sample_id: sample.sample_id,
sample_name: sample.sample_name,
puck_name: sample.puck_name,
dewar_name: sample.dewar_name,
images: sample.images,
};
treeRows.push(sampleRow);
// Add experiment run rows.
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);
});
}
});
};
// Fetch data initially.
fetchData();
// Set up an interval to refresh data every 15 seconds (adjust as needed)
const intervalId = setInterval(fetchData, 15000);
// Clean up when component unmounts or activePgroup changes.
return () => clearInterval(intervalId);
setRows(treeRows);
})
.catch((error) => {
console.error('Error fetching sample results:', error);
});
}, [activePgroup]);
// Define the grid columns, including the new processing results column.
const columns: GridColDef[] = [
{ field: 'sample_id', headerName: 'ID', width: 70 },
{ field: 'sample_name', headerName: 'Sample Name', width: 150 },
{ field: 'puck_name', headerName: 'Puck Name', width: 150 },
{ field: 'dewar_name', headerName: 'Dewar Name', width: 150 },
{
field: 'images',
headerName: 'Images',
width: 300,
field: 'sample_name',
headerName: 'Sample Name',
width: 200,
renderCell: (params) => (params.row.type === 'sample' ? params.value : null),
},
{
field: 'puck_name',
headerName: 'Puck Name',
width: 150,
renderCell: (params) => (params.row.type === 'sample' ? params.value : null),
},
{
field: 'dewar_name',
headerName: 'Dewar Name',
width: 150,
renderCell: (params) => (params.row.type === 'sample' ? params.value : null),
},
{
field: 'experimentType',
headerName: 'Experiment Type',
width: 150,
renderCell: (params) => (params.row.type === 'run' ? params.value : null),
},
{
field: 'numberOfImages',
headerName: 'Number of Images',
width: 150,
renderCell: (params) => (params.row.type === 'run' ? params.value : null),
},
{
field: 'processingResults',
headerName: 'Processing Results',
width: 180,
renderCell: (params) => {
const imageList: ImageInfo[] = params.value;
if (!imageList || imageList.length === 0) {
return null;
if (params.row.type === 'run') {
return (
<IconButton
aria-label="processing results placeholder"
onClick={() => {
// Placeholder for processing results details.
console.log('Clicked processing details for run', params.row.run_number);
}}
>
<InfoIcon />
</IconButton>
);
}
// Filter the images to include only the two bb_raster images
const filteredImages = imageList.filter(
(img) =>
img.filepath.includes("bb_raster_0") ||
img.filepath.includes("bb_raster_90")
);
if (filteredImages.length === 0) {
return null;
}
return (
<div style={{ display: 'flex', alignItems: 'center' }}>
{filteredImages.map((img) => {
const url = basePath + img.filepath;
return (
<img
key={img.id}
src={url}
alt={img.comment || 'sample'}
className="zoom-image"
style={{
width: 40,
height: 40,
marginRight: 5,
borderRadius: 4,
}}
/>
);
})}
</div>
);
return null;
},
},
];
return (
<DataGrid
rows={rows}
columns={columns}
pageSize={10}
getRowId={(row) => row.sample_id}
sx={{
'& .MuiDataGrid-cell': {
overflow: 'visible',
},
}}
/>
<div style={{ height: 600, width: '100%' }}>
<DataGridPremium
rows={rows}
columns={columns}
treeData
getTreeDataPath={(row: TreeRow) => row.hierarchy}
defaultGroupingExpansionDepth={-1}
getRowId={(row) => row.id}
/>
</div>
);
};

84
frontend/src/components/RunDetails.tsx Normal file
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@ -0,0 +1,84 @@
import {SimpleTreeView, TreeItem} from "@mui/x-tree-view";
import React from "react";
interface ExperimentParameters {
id: number;
run_number: number;
beamline_parameters: {
synchrotron: string;
beamline: string;
detector: {
manufacturer: string;
model: string;
type: string;
serial_number: string;
detector_distance_mm: number;
beam_center_x_px: number;
beam_center_y_px: number;
pixel_size_x_um: number;
pixel_size_y_um: number;
number_of_images: number;
exposure_time_s: number;
};
// Add additional fields if needed.
};
}
<SimpleTreeView
defaultCollapseIcon="▾"
defaultExpandIcon="▸"
sx={{ fontSize: '0.875rem' }}
>
<TreeItem nodeId="detector-group" label={<strong>Detector Details</strong>}>
<TreeItem nodeId="detector-group" label={<strong>Detector Details</strong>}>
<TreeItem
nodeId="detector-manufacturer"
label={`Manufacturer: ${detector?.manufacturer || 'N/A'}`}
/>
<TreeItem
nodeId="detector-model"
label={`Model: ${detector?.model || 'N/A'}`}
/>
<TreeItem
nodeId="detector-type"
label={`Type: ${detector?.type || 'N/A'}`}
/>
<TreeItem
nodeId="detector-serial"
label={`Serial Number: ${detector?.serial_number || 'N/A'}`}
/>
<TreeItem
nodeId="detector-distance"
label={`Distance (mm): ${detector?.detector_distance_mm ?? 'N/A'}`}
/>
<TreeItem
nodeId="beam-center"
label={
detector
? `Beam Center: x:${detector.beam_center_x_px}, y:${detector.beam_center_y_px}`
: 'Beam Center: N/A'
}
/>
<TreeItem
nodeId="pixel-size"
label={
detector
? `Pixel Size (µm): x:${detector.pixel_size_x_um}, y:${detector.pixel_size_y_um}`
: 'Pixel Size: N/A'
}
/>
<TreeItem
nodeId="img-count"
label={`Number of Images: ${detector?.number_of_images ?? 'N/A'}`}
/>
<TreeItem
nodeId="exposure-time"
label={`Exposure Time (s): ${detector?.exposure_time_s ?? 'N/A'}`}
/>
</TreeItem>
</TreeItem>
</SimpleTreeView>

2
frontend/src/components/SampleTracker.tsx
View File

@ -52,7 +52,7 @@ const SampleTracker: React.FC<SampleTrackerProps> = ({ activePgroup }) => {
fetchPucks();
const interval = setInterval(() => {
fetchPucks();
}, 1000);
}, 100000);
return () => clearInterval(interval);
}, [activePgroup]);

2
pyproject.toml
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@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
[project]
name = "aareDB"
version = "0.1.0a23"
version = "0.1.0a24"
description = "Backend for next gen sample management system"
authors = [{name = "Guillaume Gotthard", email = "guillaume.gotthard@psi.ch"}]
license = {text = "MIT"}

992
testfunctions.ipynb
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