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Update dependencies and improve Python path handling

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Updated several frontend dependencies including MUI packages and added new ones like `@mui/x-charts`. Adjusted the Python path setup in the CI configuration to correctly point to the `aaredb` backend, ensuring accurate module resolution.
This commit is contained in:
GotthardG 2025-03-19 09:14:12 +01:00
parent 68f87f0d8d
commit 536cfcd34b
8 changed files with 487 additions and 63 deletions
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2
.gitlab-ci.yml
View File

@ -23,7 +23,7 @@ test:
script:
- source $VIRTUAL_ENV/bin/activate
- pip install -r requirements.txt
- export PYTHONPATH=$PYTHONPATH:/home/gitlab-runner/builds/t3_38ooWt/0/mx/heidi-v2/backend
- export PYTHONPATH=$PYTHONPATH:/home/gitlab-runner/builds/t3_38ooWt/0/mx/aaredb/backend
- cd /home/gitlab-runner/builds/t3_38ooWt/0/mx/heidi-v2 # Change to the project root
- pytest --cov=app --cov-report=xml # Run tests and generate coverage report

9
backend/app/schemas.py
View File

@ -363,6 +363,11 @@ class SampleEventResponse(SampleEventCreate):
from_attributes = True
class CurvePoint(BaseModel):
resolution: float
value: float
class Results(BaseModel):
pipeline: str
resolution: float
@ -371,8 +376,8 @@ class Results(BaseModel):
rmerge: float
rmeas: float
isig: float
cc: float
cchalf: float
cc: List[CurvePoint]
cchalf: List[CurvePoint]
completeness: float
multiplicity: float
nobs: int

4
config_prod.json
View File

@ -5,6 +5,6 @@
"SCHEMA_PATH": "./src/openapi.json",
"OUTPUT_DIRECTORY": "./openapi",
"PORT": 1492,
"SSL_KEY_PATH": "/home/jungfrau/heidi-v2/backend/ssl/mx-aare-test.psi.ch.key",
"SSL_CERT_PATH": "/home/jungfrau/heidi-v2/backend/ssl/mx-aare-test.psi.ch.pem"
"SSL_KEY_PATH": "/home/jungfrau/aaredb/backend/ssl/mx-aare-test.psi.ch.key",
"SSL_CERT_PATH": "/home/jungfrau/aaredb/backend/ssl/mx-aare-test.psi.ch.pem"
}

4
config_test.json
View File

@ -5,6 +5,6 @@
"SCHEMA_PATH": "./src/openapi.json",
"OUTPUT_DIRECTORY": "./openapi",
"PORT": 8081,
"SSL_KEY_PATH": "/home/jungfrau/heidi-v2/backend/ssl/mx-aare-test.psi.ch.key",
"SSL_CERT_PATH": "/home/jungfrau/heidi-v2/backend/ssl/mx-aare-test.psi.ch.pem"
"SSL_KEY_PATH": "/home/jungfrau/aaredb/backend/ssl/mx-aare-test.psi.ch.key",
"SSL_CERT_PATH": "/home/jungfrau/aaredb/backend/ssl/mx-aare-test.psi.ch.pem"
}

365
frontend/package-lock.json generated
View File

@ -22,8 +22,9 @@
"@mui/lab": "^6.0.0-beta.29",
"@mui/material": "^6.1.6",
"@mui/system": "^6.1.6",
"@mui/x-charts": "^7.28.0",
"@mui/x-data-grid-premium": "^7.27.2",
"@mui/x-tree-view": "^7.26.0",
"@mui/x-tree-view": "^7.28.0",
"axios": "^1.7.7",
"chokidar": "^4.0.1",
"dayjs": "^1.11.13",
@ -1790,6 +1791,84 @@
}
}
},
"node_modules/@mui/x-charts": {
"version": "7.28.0",
"resolved": "https://registry.npmjs.org/@mui/x-charts/-/x-charts-7.28.0.tgz",
"integrity": "sha512-TNfq/rQfGKnjTaEITkY6l09NpMxwMwRTgLiDw+JQsS/7gwBBJUmMhEOj67BaFeYTsroFLUYeggiAj+RTSryd4A==",
"license": "MIT",
"dependencies": {
"@babel/runtime": "^7.25.7",
"@mui/utils": "^5.16.6 || ^6.0.0 || ^7.0.0 || ^7.0.0-beta",
"@mui/x-charts-vendor": "7.20.0",
"@mui/x-internals": "7.28.0",
"@react-spring/rafz": "^9.7.5",
"@react-spring/web": "^9.7.5",
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},
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}
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},
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},
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"resolved": "https://registry.npmjs.org/@mui/x-data-grid/-/x-data-grid-7.27.2.tgz",
@ -2088,14 +2167,14 @@
}
},
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"@mui/x-internals": "7.26.0",
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"@mui/x-internals": "7.28.0",
"@types/react-transition-group": "^4.4.11",
"clsx": "^2.1.1",
"prop-types": "^15.8.1",
@ -2111,8 +2190,8 @@
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@ -2126,13 +2205,13 @@
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},
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@ -2203,6 +2282,78 @@
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@ -2900,6 +3051,57 @@
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"version": "4.1.0",
"resolved": "https://registry.npmjs.org/d3-time-format/-/d3-time-format-4.1.0.tgz",
"integrity": "sha512-dJxPBlzC7NugB2PDLwo9Q8JiTR3M3e4/XANkreKSUxF8vvXKqm1Yfq4Q5dl8budlunRVlUUaDUgFt7eA8D6NLg==",
"license": "ISC",
"dependencies": {
"d3-time": "1 - 3"
},
"engines": {
"node": ">=12"
}
},
"node_modules/date-arithmetic": {
"version": "4.1.0",
"resolved": "https://registry.npmjs.org/date-arithmetic/-/date-arithmetic-4.1.0.tgz",
@ -3970,6 +4287,15 @@
"dev": true,
"license": "MIT"
},
"node_modules/delaunator": {
"version": "5.0.1",
"resolved": "https://registry.npmjs.org/delaunator/-/delaunator-5.0.1.tgz",
"integrity": "sha512-8nvh+XBe96aCESrGOqMp/84b13H9cdKbG5P2ejQCh4d4sK9RL4371qou9drQjMhvnPmhWl5hnmqbEE0fXr9Xnw==",
"license": "ISC",
"dependencies": {
"robust-predicates": "^3.0.2"
}
},
"node_modules/delayed-stream": {
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/delayed-stream/-/delayed-stream-1.0.0.tgz",
@ -4910,6 +5236,15 @@
"integrity": "sha512-k/vGaX4/Yla3WzyMCvTQOXYeIHvqOKtnqBduzTHpzpQZzAskKMhZ2K+EnBiSM9zGSoIFeMpXKxa4dYeZIQqewQ==",
"license": "ISC"
},
"node_modules/internmap": {
"version": "2.0.3",
"resolved": "https://registry.npmjs.org/internmap/-/internmap-2.0.3.tgz",
"integrity": "sha512-5Hh7Y1wQbvY5ooGgPbDaL5iYLAPzMTUrjMulskHLH6wnv/A+1q5rgEaiuqEjB+oxGXIVZs1FF+R/KPN3ZSQYYg==",
"license": "ISC",
"engines": {
"node": ">=12"
}
},
"node_modules/invariant": {
"version": "2.2.4",
"resolved": "https://registry.npmjs.org/invariant/-/invariant-2.2.4.tgz",
@ -6371,6 +6706,12 @@
"url": "https://github.com/sponsors/isaacs"
}
},
"node_modules/robust-predicates": {
"version": "3.0.2",
"resolved": "https://registry.npmjs.org/robust-predicates/-/robust-predicates-3.0.2.tgz",
"integrity": "sha512-IXgzBWvWQwE6PrDI05OvmXUIruQTcoMDzRsOd5CDvHCVLcLHMTSYvOK5Cm46kWqlV3yAbuSpBZdJ5oP5OUoStg==",
"license": "Unlicense"
},
"node_modules/rollup": {
"version": "4.30.1",
"resolved": "https://registry.npmjs.org/rollup/-/rollup-4.30.1.tgz",

3
frontend/package.json
View File

@ -29,8 +29,9 @@
"@mui/lab": "^6.0.0-beta.29",
"@mui/material": "^6.1.6",
"@mui/system": "^6.1.6",
"@mui/x-charts": "^7.28.0",
"@mui/x-data-grid-premium": "^7.27.2",
"@mui/x-tree-view": "^7.26.0",
"@mui/x-tree-view": "^7.28.0",
"axios": "^1.7.7",
"chokidar": "^4.0.1",
"dayjs": "^1.11.13",

105
frontend/src/components/RunDetails.tsx
View File

@ -4,7 +4,10 @@ import {
} from '@mui/material';
import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
import './SampleImage.css';
import { DataGridPremium, GridColDef } from "@mui/x-data-grid-premium";
import { DataGridPremium, GridColDef, GridValueGetterParams } from "@mui/x-data-grid-premium";
import { LineChart } from '@mui/x-charts/LineChart';
import { SamplesService } from "../../openapi";
interface RunDetailsProps {
@ -15,6 +18,10 @@ interface RunDetailsProps {
onHeightChange?: (height: number) => void;
}
interface CCPoint {
resolution: number;
value: number;
}
interface ExperimentParameters {
run_number: number;
@ -26,6 +33,7 @@ interface ExperimentParameters {
interface ProcessingResults {
id: number;
pipeline: string;
resolution: number;
unit_cell: string;
@ -33,8 +41,8 @@ interface ProcessingResults {
rmerge: number;
rmeas: number;
isig: number;
cc: number;
cchalf: number;
cc: CCPoint[];
cchalf: CCPoint[];
completeness: number;
multiplicity: number;
nobs: number;
@ -43,6 +51,7 @@ interface ProcessingResults {
comments?: string | null;
}
const RunDetails: React.FC<RunDetailsProps> = ({ run, onHeightChange, basePath, runId, sample_id }) => {
const containerRef = useRef<HTMLDivElement | null>(null);
const [currentHeight, setCurrentHeight] = useState<number>(0);
@ -71,8 +80,8 @@ const RunDetails: React.FC<RunDetailsProps> = ({ run, onHeightChange, basePath,
rmerge: res.result?.rmerge ?? 0,
rmeas: res.result?.rmeas ?? 0,
isig: res.result?.isig ?? 0,
cc: res.result?.cc ?? 0,
cchalf: res.result?.cchalf ?? 0,
cc: res.result?.cc || [],
cchalf: res.result?.cchalf || [],
completeness: res.result?.completeness ?? 0,
multiplicity: res.result?.multiplicity ?? 0,
nobs: res.result?.nobs ?? 0,
@ -88,22 +97,38 @@ const RunDetails: React.FC<RunDetailsProps> = ({ run, onHeightChange, basePath,
};
const resultColumns: GridColDef[] = [
{field: 'pipeline', headerName: 'Pipeline', flex: 1},
{field: 'resolution', headerName: 'Resolution (Å)', flex: 1},
{field: 'unit_cell', headerName: 'Unit Cell (Å)', flex: 1.5},
{field: 'spacegroup', headerName: 'Spacegroup', flex: 1},
{field: 'rmerge', headerName: 'Rmerge', flex: 1},
{field: 'rmeas', headerName: 'Rmeas', flex: 1},
{field: 'isig', headerName: 'I/sig(I)', flex: 1},
{field: 'cc', headerName: 'CC', flex: 1},
{field: 'cchalf', headerName: 'CC(1/2)', flex: 1},
{field: 'completeness', headerName: 'Completeness (%)', flex: 1},
{field: 'multiplicity', headerName: 'Multiplicity', flex: 1},
{field: 'nobs', headerName: 'N obs.', flex: 1},
{field: 'total_refl', headerName: 'Total Reflections', flex: 1},
{field: 'unique_refl', headerName: 'Unique Reflections', flex: 1},
{field: 'comments', headerName: 'Comments', flex: 2},
const resultColumns: GridColDef<ProcessingResults>[] = [
{ field: 'pipeline', headerName: 'Pipeline', flex: 1 },
{ field: 'resolution', headerName: 'Resolution (Å)', flex: 1 },
{ field: 'unit_cell', headerName: 'Unit Cell (Å)', flex: 1.5 },
{ field: 'spacegroup', headerName: 'Spacegroup', flex: 1 },
{ field: 'rmerge', headerName: 'Rmerge', flex: 1 },
{ field: 'rmeas', headerName: 'Rmeas', flex: 1 },
{ field: 'isig', headerName: 'I/sig(I)', flex: 1 },
{
field: 'cc',
headerName: 'CC',
flex: 1,
valueGetter: (params: GridValueGetterParams<ProcessingResults, string>) =>
Array.isArray(params.row?.cc)
? params.row.cc.map((point: CCPoint) => `${point.value.toFixed(2)}@${point.resolution.toFixed(2)}`).join(', ')
: '',
},
{
field: 'cchalf',
headerName: 'CC(1/2)',
flex: 1,
valueGetter: (params: GridValueGetterParams<ProcessingResults, string>) =>
Array.isArray(params.row?.cchalf)
? params.row.cchalf.map((point: CCPoint) => `${point.value.toFixed(2)}@${point.resolution.toFixed(2)}`).join(', ')
: '',
},
{ field: 'completeness', headerName: 'Completeness (%)', flex: 1 },
{ field: 'multiplicity', headerName: 'Multiplicity', flex: 1 },
{ field: 'nobs', headerName: 'N obs.', flex: 1 },
{ field: 'total_refl', headerName: 'Total Reflections', flex: 1 },
{ field: 'unique_refl', headerName: 'Unique Reflections', flex: 1 },
{ field: 'comments', headerName: 'Comments', flex: 2 },
];
const updateHeight = () => {
@ -260,12 +285,12 @@ const RunDetails: React.FC<RunDetailsProps> = ({ run, onHeightChange, basePath,
<AccordionDetails style={{width: '100%', overflowX: 'auto'}}>
{processingResult ? (
<div style={{width: '100%'}}>
<DataGridPremium
rows={processingResult.map((res, idx) => ({id: idx, ...res}))}
<DataGridPremium<ProcessingResults>
rows={processingResult.map((res, idx) => ({ id: idx, ...res }))}
columns={resultColumns}
autoHeight
hideFooter
columnVisibilityModel={{id: false}}
columnVisibilityModel={{ id: false }}
disableColumnResize={false}
/>
</div>
@ -276,6 +301,38 @@ const RunDetails: React.FC<RunDetailsProps> = ({ run, onHeightChange, basePath,
</Accordion>
</div>
{processingResult && processingResult.length > 0 && (
<div style={{width: 400, marginTop: '16px' }}>
<Typography variant="h6" gutterBottom>CC and CC(1/2) vs Resolution</Typography>
<LineChart
xAxis={[
{
data: processingResult[0].cc
.map((point) => point.resolution) // Grab the resolution values
.reverse(), // Reverse the data for resolution
label: 'Resolution (Å)',
reverse: true, // This ensures the visual flip on the chart, low-res to right and high-res to left
},
]}
series={[
{
data: processingResult[0].cc
.map((point) => point.value)
.reverse(), // Reverse the CC values to match the reversed resolution
label: 'CC',
},
{
data: processingResult[0].cchalf
.map((point) => point.value)
.reverse(), // Reverse the CC(1/2) values to match the reversed resolution
label: 'CC(1/2)',
},
]}
height={300}
/>
</div>
)}
{/* Modal for Zoomed Image */}
<Modal open={modalOpen} onClose={closeModal}>
<Box

58
testfunctions.ipynb
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