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Displaying Processing Results in the frontend

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GotthardG 2025-03-17 16:45:50 +01:00
parent 5a0047b6d5
commit 68f87f0d8d
5 changed files with 271 additions and 172 deletions
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41
backend/app/routers/sample.py
View File

@ -17,6 +17,7 @@ from app.schemas import (
ImageInfo, ImageInfo,
ResultResponse, ResultResponse,
ResultCreate, ResultCreate,
Results as ProcessingResults,
) )
from app.models import ( from app.models import (
Puck as PuckModel, Puck as PuckModel,
@ -374,17 +375,29 @@ def create_result(payload: ResultCreate, db: Session = Depends(get_db)):
) )
# @router.get("/results", response_model=list[ResultResponse]) @router.get(
# def get_results(sample_id: int, result_id: int, db: Session = Depends(get_db)): "/processing-results/{sample_id}/{run_id}", response_model=List[ResultResponse]
# query = db.query(Results) )
# async def get_results_for_run_and_sample(
# if sample_id: sample_id: int, run_id: int, db: Session = Depends(get_db)
# query = query.filter(Results.sample_id == sample_id) ):
# if result_id: results = (
# query = query.filter(Results.result_id == result_id) db.query(ResultsModel)
# .filter(ResultsModel.sample_id == sample_id, ResultsModel.run_id == run_id)
# results = query.all() .all()
# if not results: )
# raise HTTPException(status_code=404, detail="No results found")
# if not results:
# return results raise HTTPException(status_code=404, detail="Results not found.")
formatted_results = [
ResultResponse(
id=result.id,
sample_id=result.sample_id,
run_id=result.run_id,
result=ProcessingResults(**result.result),
)
for result in results
]
return formatted_results

2
backend/pyproject.toml
View File

@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
[project] [project]
name = "aareDB" name = "aareDB"
version = "0.1.0a25" version = "0.1.0a26"
description = "Backend for next gen sample management system" description = "Backend for next gen sample management system"
authors = [{name = "Guillaume Gotthard", email = "guillaume.gotthard@psi.ch"}] authors = [{name = "Guillaume Gotthard", email = "guillaume.gotthard@psi.ch"}]
license = {text = "MIT"} license = {text = "MIT"}

6
frontend/src/components/ResultGrid.tsx
View File

@ -85,6 +85,7 @@ interface TreeRow {
id: string; id: string;
hierarchy: (string | number)[]; hierarchy: (string | number)[];
type: 'sample' | 'run'; type: 'sample' | 'run';
experimentId?: number;
sample_id: number; sample_id: number;
sample_name?: string; sample_name?: string;
puck_name?: string; puck_name?: string;
@ -209,6 +210,7 @@ const ResultGrid: React.FC<ResultGridProps> = ({ activePgroup }) => {
id: `run-${sample.sample_id}-${run.run_number}`, id: `run-${sample.sample_id}-${run.run_number}`,
hierarchy: [sample.sample_id, run.run_number], hierarchy: [sample.sample_id, run.run_number],
type: 'run', type: 'run',
experimentId: run.id,
sample_id: sample.sample_id, sample_id: sample.sample_id,
run_number: run.run_number, run_number: run.run_number,
beamline_parameters: run.beamline_parameters, beamline_parameters: run.beamline_parameters,
@ -307,8 +309,10 @@ const ResultGrid: React.FC<ResultGridProps> = ({ activePgroup }) => {
return ( return (
<RunDetails <RunDetails
run={params.row} run={params.row}
runId={params.row.experimentId}
sample_id={params.row.sample_id}
basePath={basePath} basePath={basePath}
onHeightChange={(height: number) => handleDetailPanelHeightChange(params.row.id, height)} // Pass callback for dynamic height onHeightChange={height => handleDetailPanelHeightChange(params.row.id, height)}
/> />
); );
} }

370
frontend/src/components/RunDetails.tsx
View File

@ -1,196 +1,279 @@
import React, { useEffect, useRef, useState } from 'react'; import React, { useEffect, useRef, useState } from 'react';
import { import {
Accordion, Accordion, AccordionSummary, AccordionDetails, Typography, Grid, Modal, Box
AccordionSummary,
AccordionDetails,
Typography,
Grid,
Modal,
Box
} from '@mui/material'; } from '@mui/material';
import ExpandMoreIcon from '@mui/icons-material/ExpandMore'; import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
import './SampleImage.css'; import './SampleImage.css';
import { DataGridPremium, GridColDef } from "@mui/x-data-grid-premium";
import { SamplesService } from "../../openapi";
interface RunDetailsProps { interface RunDetailsProps {
run: ExperimentParameters; run: TreeRow;
runId: number;
sample_id: number;
basePath: string; basePath: string;
onHeightChange?: (height: number) => void; // Callback to notify the parent about height changes onHeightChange?: (height: number) => void;
} }
const RunDetails: React.FC<RunDetailsProps> = ({ run, onHeightChange, basePath }) => {
const containerRef = useRef<HTMLDivElement | null>(null); // Ref to track component height interface ExperimentParameters {
run_number: number;
id: number;
sample_id: number;
beamline_parameters: BeamlineParameters;
images: Image[];
}
interface ProcessingResults {
pipeline: string;
resolution: number;
unit_cell: string;
spacegroup: string;
rmerge: number;
rmeas: number;
isig: number;
cc: number;
cchalf: number;
completeness: number;
multiplicity: number;
nobs: number;
total_refl: number;
unique_refl: number;
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); const [currentHeight, setCurrentHeight] = useState<number>(0);
const [modalOpen, setModalOpen] = useState<boolean>(false); // For modal state const [modalOpen, setModalOpen] = useState<boolean>(false);
const [selectedImage, setSelectedImage] = useState<string | null>(null); // Tracks the selected image for the modal const [selectedImage, setSelectedImage] = useState<string | null>(null);
const [expandedResults, setExpandedResults] = useState(false);
const [processingResult, setProcessingResult] = useState<ProcessingResults[] | null>(null);
const { beamline_parameters, images } = run; const {beamline_parameters, images} = run;
const { synchrotron, beamline, detector } = beamline_parameters; const {synchrotron, beamline, detector} = beamline_parameters;
useEffect(() => {
fetchResults(sample_id, runId); // fetching based on experimentId
}, [runId]);
const fetchResults = async (sample_id: number, runId: number) => {
try {
const results = await SamplesService.getResultsForRunAndSampleSamplesProcessingResultsSampleIdRunIdGet(sample_id, runId);
// Explicitly handle nested results
const mappedResults: ProcessingResults[] = results.map((res): ProcessingResults => ({
pipeline: res.result?.pipeline || 'N/A',
resolution: res.result.resolution ?? 0,
unit_cell: res.result?.unit_cell || 'N/A',
spacegroup: res.result?.spacegroup || 'N/A',
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,
completeness: res.result?.completeness ?? 0,
multiplicity: res.result?.multiplicity ?? 0,
nobs: res.result?.nobs ?? 0,
total_refl: res.result?.total_refl ?? 0,
unique_refl: res.result?.unique_refl ?? 0,
comments: res.result?.comments || null,
}));
setProcessingResult(mappedResults);
} catch (error) {
console.error('Error fetching results:', error);
}
};
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},
];
// Calculate and notify the parent about height changes
const updateHeight = () => { const updateHeight = () => {
if (containerRef.current) { if (containerRef.current) {
const newHeight = containerRef.current.offsetHeight; const newHeight = containerRef.current.offsetHeight;
if (newHeight !== currentHeight) { if (newHeight !== currentHeight && onHeightChange) {
setCurrentHeight(newHeight); setCurrentHeight(newHeight);
if (onHeightChange) { onHeightChange(newHeight);
onHeightChange(newHeight);
}
} }
} }
}; };
useEffect(() => { useEffect(() => {
updateHeight(); // Update height on initial render
}, []);
useEffect(() => {
// Update height whenever the component content changes
const observer = new ResizeObserver(updateHeight); const observer = new ResizeObserver(updateHeight);
if (containerRef.current) { if (containerRef.current) observer.observe(containerRef.current);
observer.observe(containerRef.current); return () => observer.disconnect();
} }, [containerRef.current, processingResult]);
return () => {
observer.disconnect();
};
}, [containerRef]);
const handleImageClick = (imagePath: string) => { const handleImageClick = (imagePath: string) => {
setSelectedImage(imagePath); setSelectedImage(imagePath);
setModalOpen(true); // Open the modal when the image is clicked setModalOpen(true);
}; };
const closeModal = () => { const closeModal = () => {
setSelectedImage(null); // Clear the current image setSelectedImage(null);
setModalOpen(false); setModalOpen(false);
}; };
return ( return (
<div <div
className="details-panel" // Add the class here className="details-panel"
ref={containerRef} // Attach the ref to the main container ref={containerRef}
style={{ style={{
display: 'flex', display: 'flex',
flexDirection: 'column', // Stack children vertically
gap: '16px', gap: '16px',
padding: '16px', padding: '16px',
border: '1px solid #ccc', border: '1px solid #ccc',
borderRadius: '4px', borderRadius: '4px',
alignItems: 'flex-start',
}} }}
> >
{/* Main Details Section */} {/* Wrap details and images together */}
<div style={{ flexGrow: 1 }}> <div style={{display: 'flex', gap: '16px', alignItems: 'flex-start'}}>
<Typography variant="h6" gutterBottom> {/* Main Details Section */}
Run {run.run_number} Details <div style={{flexGrow: 1}}>
</Typography> <Typography variant="h6" gutterBottom>
<Typography variant="subtitle1" gutterBottom> Run {run.run_number} Details
Beamline: {beamline} | Synchrotron: {synchrotron} </Typography>
</Typography> <Typography variant="subtitle1" gutterBottom>
Beamline: {beamline} | Synchrotron: {synchrotron}
</Typography>
{/* Detector Details Accordion */} {/* Detector Details Accordion */}
<Accordion> <Accordion>
<AccordionSummary <AccordionSummary
expandIcon={<ExpandMoreIcon />} expandIcon={<ExpandMoreIcon/>}
aria-controls="detector-content" aria-controls="detector-content"
id="detector-header" id="detector-header"
> >
<Typography> <Typography><strong>Detector Details</strong></Typography>
<strong>Detector Details</strong> </AccordionSummary>
</Typography> <AccordionDetails>
</AccordionSummary> <Typography>Manufacturer: {detector?.manufacturer || 'N/A'}</Typography>
<AccordionDetails> <Typography>Model: {detector?.model || 'N/A'}</Typography>
<Typography>Manufacturer: {detector?.manufacturer || 'N/A'}</Typography> <Typography>Type: {detector?.type || 'N/A'}</Typography>
<Typography>Model: {detector?.model || 'N/A'}</Typography> <Typography>
<Typography>Type: {detector?.type || 'N/A'}</Typography> Beam Center (px): x: {detector?.beamCenterX_px || 'N/A'},
<Typography> y: {detector?.beamCenterY_px || 'N/A'}
Beam Center (px): x: {detector?.beamCenterX_px || 'N/A'}, y: {detector?.beamCenterY_px || 'N/A'} </Typography>
</Typography> </AccordionDetails>
</AccordionDetails> </Accordion>
</Accordion>
{/* Beamline Details Accordion */} {/* Beamline Details Accordion */}
<Accordion> <Accordion>
<AccordionSummary <AccordionSummary expandIcon={<ExpandMoreIcon/>}>
expandIcon={<ExpandMoreIcon />} <Typography><strong>Beamline Details</strong></Typography>
aria-controls="beamline-content" </AccordionSummary>
id="beamline-header" <AccordionDetails>
> <Typography>Synchrotron: {beamline_parameters?.synchrotron || 'N/A'}</Typography>
<Typography> <Typography>Ring mode: {beamline_parameters?.ringMode || 'N/A'}</Typography>
<strong>Beamline Details</strong> <Typography>Ring current: {beamline_parameters?.ringCurrent_A || 'N/A'}</Typography>
</Typography> <Typography>Beamline: {beamline_parameters?.beamline || 'N/A'}</Typography>
</AccordionSummary> <Typography>Undulator: {beamline_parameters?.undulator || 'N/A'}</Typography>
<AccordionDetails> <Typography>Undulator gap: {beamline_parameters?.undulatorgap_mm || 'N/A'}</Typography>
<Typography>Synchrotron: {beamline_parameters?.synchrotron || 'N/A'}</Typography> <Typography>Focusing optic: {beamline_parameters?.focusingOptic || 'N/A'}</Typography>
<Typography>Ring mode: {beamline_parameters?.ringMode || 'N/A'}</Typography> <Typography>Monochromator: {beamline_parameters?.monochromator || 'N/A'}</Typography>
<Typography>Ring current: {beamline_parameters?.ringCurrent_A || 'N/A'}</Typography> </AccordionDetails>
<Typography>Beamline: {beamline_parameters?.beamline || 'N/A'}</Typography> </Accordion>
<Typography>Undulator: {beamline_parameters?.undulator || 'N/A'}</Typography>
<Typography>Undulator gap: {beamline_parameters?.undulatorgap_mm || 'N/A'}</Typography>
<Typography>Focusing optic: {beamline_parameters?.focusingOptic || 'N/A'}</Typography>
<Typography>Monochromator: {beamline_parameters?.monochromator || 'N/A'}</Typography>
</AccordionDetails>
</Accordion>
{/* Beam Characteristics Accordion */} {/* Beam Characteristics Accordion */}
<Accordion> <Accordion>
<AccordionSummary <AccordionSummary expandIcon={<ExpandMoreIcon/>}>
expandIcon={<ExpandMoreIcon />} <Typography><strong>Beam Characteristics</strong></Typography>
aria-controls="beam-content" </AccordionSummary>
id="beam-header" <AccordionDetails>
> <Typography>Wavelength: {beamline_parameters?.wavelength || 'N/A'}</Typography>
<Typography> <Typography>Energy: {beamline_parameters?.energy || 'N/A'}</Typography>
<strong>Beam Characteristics</strong> <Typography>Transmission: {beamline_parameters?.transmission || 'N/A'}</Typography>
<Typography>
Beam focus (µm): vertical: {beamline_parameters?.beamSizeHeight || 'N/A'},
horizontal:{' '}
{beamline_parameters?.beamSizeWidth || 'N/A'}
</Typography>
<Typography>Flux at sample
(ph/s): {beamline_parameters?.beamlineFluxAtSample_ph_s || 'N/A'}</Typography>
</AccordionDetails>
</Accordion>
</div>
{/* Image Section */}
<div style={{width: '900px'}}>
<Typography variant="h6" gutterBottom>
Associated Images
</Typography>
{images && images.length > 0 ? (
<Grid container spacing={1}>
{images.map((img) => (
<Grid item xs={4} key={img.id}>
<div
className="image-container"
onClick={() => handleImageClick(`${basePath || ''}${img.filepath}`)}
style={{cursor: 'pointer'}}
>
<img
src={`${basePath || ''}${img.filepath}`}
alt={img.comment || 'Image'}
className="zoom-image"
style={{
width: '100%',
maxWidth: '100%',
borderRadius: '4px',
}}
/>
</div>
</Grid>
))}
</Grid>
) : (
<Typography variant="body2" color="textSecondary">
No images available.
</Typography> </Typography>
</AccordionSummary> )}
<AccordionDetails> </div>
<Typography>Wavelength: {beamline_parameters?.wavelength || 'N/A'}</Typography>
<Typography>Energy: {beamline_parameters?.energy || 'N/A'}</Typography>
<Typography>Transmission: {beamline_parameters?.transmission || 'N/A'}</Typography>
<Typography>
Beam focus (µm): vertical: {beamline_parameters?.beamSizeHeight || 'N/A'}, horizontal:{' '}
{beamline_parameters?.beamSizeWidth || 'N/A'}
</Typography>
<Typography>Flux at sample (ph/s): {beamline_parameters?.beamlineFluxAtSample_ph_s || 'N/A'}</Typography>
</AccordionDetails>
</Accordion>
</div> </div>
{/* Image Section */} {/* Processing Results Accordion - Full Width Below */}
<div style={{ width: '900px' }}> <div style={{width: '100%'}}>
<Typography variant="h6" gutterBottom> <Accordion expanded={expandedResults} onChange={(e, expanded) => setExpandedResults(expanded)}>
Associated Images <AccordionSummary expandIcon={<ExpandMoreIcon/>}>
</Typography> <Typography><strong>Processing Results</strong></Typography>
{images && images.length > 0 ? ( </AccordionSummary>
<Grid container spacing={1}> <AccordionDetails style={{width: '100%', overflowX: 'auto'}}>
{images.map((img) => ( {processingResult ? (
<Grid item xs={4} key={img.id}> <div style={{width: '100%'}}>
<div <DataGridPremium
className="image-container" rows={processingResult.map((res, idx) => ({id: idx, ...res}))}
onClick={() => handleImageClick(`${basePath || ''}${img.filepath}`)} // Open modal with image columns={resultColumns}
style={{ autoHeight
cursor: 'pointer', hideFooter
}} columnVisibilityModel={{id: false}}
> disableColumnResize={false}
<img />
src={`${basePath || ''}${img.filepath}`} // Ensure basePath </div>
alt={img.comment || 'Image'} ) : (
className="zoom-image" <Typography variant="body2" color="textSecondary">Loading results...</Typography>
style={{ )}
width: '100%', // Ensure the image takes the full width of its container </AccordionDetails>
maxWidth: '100%', // Prevent any overflow </Accordion>
borderRadius: '4px',
}}
/>
</div>
</Grid>
))}
</Grid>
) : (
<Typography variant="body2" color="textSecondary">
No images available.
</Typography>
)}
</div> </div>
{/* Modal for Zoomed Image */} {/* Modal for Zoomed Image */}
@ -224,5 +307,4 @@ const RunDetails: React.FC<RunDetailsProps> = ({ run, onHeightChange, basePath }
</div> </div>
); );
}; };
export default RunDetails; export default RunDetails;

24
testfunctions.ipynb
View File

@ -3,8 +3,8 @@
{ {
"metadata": { "metadata": {
"ExecuteTime": { "ExecuteTime": {
"end_time": "2025-03-17T10:32:07.119518Z", "end_time": "2025-03-17T15:41:26.497650Z",
"start_time": "2025-03-17T10:32:06.622836Z" "start_time": "2025-03-17T15:41:25.771778Z"
} }
}, },
"cell_type": "code", "cell_type": "code",
@ -385,8 +385,8 @@
{ {
"metadata": { "metadata": {
"ExecuteTime": { "ExecuteTime": {
"end_time": "2025-03-17T10:32:10.718097Z", "end_time": "2025-03-17T15:41:47.722623Z",
"start_time": "2025-03-17T10:32:10.716192Z" "start_time": "2025-03-17T15:41:47.720727Z"
} }
}, },
"cell_type": "code", "cell_type": "code",
@ -736,8 +736,8 @@
{ {
"metadata": { "metadata": {
"ExecuteTime": { "ExecuteTime": {
"end_time": "2025-03-17T10:46:08.211213Z", "end_time": "2025-03-17T15:42:07.300875Z",
"start_time": "2025-03-17T10:46:08.193139Z" "start_time": "2025-03-17T15:42:07.279495Z"
} }
}, },
"cell_type": "code", "cell_type": "code",
@ -750,12 +750,12 @@
"from aareDBclient.rest import ApiException\n", "from aareDBclient.rest import ApiException\n",
"\n", "\n",
"# Your actual sample and experiment IDs\n", "# Your actual sample and experiment IDs\n",
"sample_id = 123 # Replace with valid IDs\n", "sample_id = sample_id # Replace with valid IDs\n",
"run_id = 1 # Replace with valid run_id\n", "run_id = 1 # Replace with valid run_id\n",
"\n", "\n",
"# Create random Results payload\n", "# Create random Results payload\n",
"results_data = Results(\n", "results_data = Results(\n",
" pipeline=\"autoproc\",\n", " pipeline=\"fastproc\",\n",
" resolution=round(random.uniform(1.0, 4.0), 2),\n", " resolution=round(random.uniform(1.0, 4.0), 2),\n",
" unit_cell=f\"{random.uniform(20, 120):.2f}, {random.uniform(20, 120):.2f}, \"\n", " unit_cell=f\"{random.uniform(20, 120):.2f}, {random.uniform(20, 120):.2f}, \"\n",
" f\"{random.uniform(20, 120):.2f}, {random.uniform(60, 120):.2f}, \"\n", " f\"{random.uniform(20, 120):.2f}, {random.uniform(60, 120):.2f}, \"\n",
@ -804,9 +804,9 @@
"output_type": "stream", "output_type": "stream",
"text": [ "text": [
"DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): 127.0.0.1:8000\n", "DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): 127.0.0.1:8000\n",
"/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/connectionpool.py:1097: InsecureRequestWarning: Unverified HTTPS request is being made to host '127.0.0.1'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings\n", "/Users/gotthardg/PycharmProjects/aaredb/.venv/lib/python3.12/site-packages/urllib3/connectionpool.py:1097: InsecureRequestWarning: Unverified HTTPS request is being made to host '127.0.0.1'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings\n",
" warnings.warn(\n", " warnings.warn(\n",
"DEBUG:urllib3.connectionpool:https://127.0.0.1:8000 \"POST /samples/processing-results HTTP/1.1\" 200 369\n" "DEBUG:urllib3.connectionpool:https://127.0.0.1:8000 \"POST /samples/processing-results HTTP/1.1\" 200 367\n"
] ]
}, },
{ {
@ -814,11 +814,11 @@
"output_type": "stream", "output_type": "stream",
"text": [ "text": [
"API call successful:\n", "API call successful:\n",
"ResultResponse(id=2, sample_id=123, run_id=1, result=Results(pipeline='autoproc', resolution=1.94, unit_cell='23.86, 89.07, 37.39, 63.99, 88.77, 81.42', spacegroup='P41212', rmerge=0.072, rmeas=0.07, isig=29.58, cc=0.758, cchalf=0.915, completeness=93.12, multiplicity=6.1, nobs=279922, total_refl=83994, unique_refl=47041, comments='Random auto-generated test entry'))\n" "ResultResponse(id=4, sample_id=247, run_id=1, result=Results(pipeline='fastproc', resolution=3.93, unit_cell='56.27, 40.58, 26.64, 93.74, 90.52, 99.53', spacegroup='C2', rmerge=0.097, rmeas=0.13, isig=21.29, cc=0.989, cchalf=0.802, completeness=98.46, multiplicity=6.35, nobs=273232, total_refl=217336, unique_refl=11189, comments='Random auto-generated test entry'))\n"
] ]
} }
], ],
"execution_count": 9 "execution_count": 3
}, },
{ {
"metadata": { "metadata": {