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  • icat/data-portal
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apps/cryoet/package.json
View file @ e5d5b566
......@@ -18,7 +18,7 @@
"dependencies": {
"@babel/eslint-parser": "^7.25.1",
"@edata-portal/core": "workspace:*",
"@edata-portal/icat-plus-api": "^1.8.12",
"@edata-portal/icat-plus-api": "^1.8.13",
"@fortawesome/fontawesome-svg-core": "^6.6.0",
"@fortawesome/free-solid-svg-icons": "^6.6.0",
"@fortawesome/react-fontawesome": "^0.2.2",
......
apps/dataset_viewer/package.json
View file @ e5d5b566
......@@ -18,7 +18,7 @@
"dependencies": {
"@babel/eslint-parser": "^7.25.1",
"@edata-portal/core": "workspace:*",
"@edata-portal/icat-plus-api": "^1.8.12",
"@edata-portal/icat-plus-api": "^1.8.13",
"@fortawesome/fontawesome-svg-core": "^6.6.0",
"@fortawesome/free-solid-svg-icons": "^6.6.0",
"@fortawesome/react-fontawesome": "^0.2.2",
......
apps/dataset_viewer/src/components/technique/saxs/saxsSampleChangerConfig.ts
View file @ e5d5b566
......@@ -4,6 +4,7 @@ import {
SnashoptConfigItem,
getDatasetName,
getDatasetParamValue,
getParameterByName,
isProcessed,
} from '@edata-portal/core';
import type { Dataset } from '@edata-portal/icat-plus-api';
......@@ -12,14 +13,28 @@ const isBuffer = (dataset: Dataset) => {
return getDatasetParamValue(dataset, 'SAXS_sample_type') === 'buffer';
};
const isIntegration = (dataset: Dataset): boolean => {
return getDatasetName(dataset).indexOf('integrate') !== -1;
};
const checkScanType = (
dataset: Dataset,
scanType: string,
keyword: string,
): boolean => {
// Retrieve the scanType parameter from the dataset
const parameter = getParameterByName('scanType', dataset.parameters);
const isSubtraction = (dataset: Dataset): boolean => {
return getDatasetName(dataset).indexOf('subtract') !== -1;
// Return true if scanType exists and matches the provided type
if (parameter?.value === scanType) {
return true;
}
// Check if the dataset name contains the specified keyword
return getDatasetName(dataset).includes(keyword);
};
const isIntegration = (dataset: Dataset): boolean =>
checkScanType(dataset, 'integration', 'integrate');
const isSubtraction = (dataset: Dataset): boolean =>
checkScanType(dataset, 'subtraction', 'subtract');
function sampleParameters() {
return [
{
......@@ -144,7 +159,7 @@ export function getSnapshotConfigByProcesssedDataset(
processedDataset: Dataset,
): SnashoptConfigItem[] {
/** if subtractiong */
if (processedDataset.name.indexOf('subtract') !== -1) {
if (isSubtraction(processedDataset)) {
return [
{
type: 'metadata',
......@@ -196,7 +211,7 @@ export function getSnapshotConfigByProcesssedDataset(
];
}
if (processedDataset.name.indexOf('integrate') !== -1) {
if (isIntegration(processedDataset)) {
return [
{
type: 'metadata',
......
apps/dataset_viewer/src/components/technique/tomo/TOMOSummaryView.tsx
View file @ e5d5b566
......@@ -4,26 +4,15 @@ import {
formatDateToDayAndTime,
Gallery,
getDatasetParamValue,
MetadataCard,
MetadataTable,
AttenuatorsWidget,
type MetadataTableParameter,
MetadataTableParameters,
} from '@edata-portal/core';
import { InstrumentSlitWidget } from '@edata-portal/core/src/components/metadata/InstrumentSlitWidget';
import type { Dataset } from '@edata-portal/icat-plus-api';
import { Card, Col, Container, Row } from 'react-bootstrap';
const addParam = (
params: MetadataTableParameter[],
dataset: Dataset,
key: string,
caption: string,
digits?: number,
) => {
const value = getDatasetParamValue(dataset, key) || undefined;
if (value) {
params.push({ caption, value, digits });
}
};
import { Col, Container, Row } from 'react-bootstrap';
const presetSummary = (dataset: Dataset): MetadataTableParameter[] => {
const params: MetadataTableParameter[] = [];
......@@ -34,10 +23,18 @@ const presetSummary = (dataset: Dataset): MetadataTableParameter[] => {
? formatDateToDayAndTime(getDatasetParamValue(dataset, 'endDate'))
: undefined;
if (startTime) {
params.push({ caption: 'Start', value: startTime });
params.push({
caption: 'Start',
value: startTime,
parameterName: 'startDate',
});
}
if (endTime) {
params.push({ caption: 'End', value: endTime });
params.push({
caption: 'End',
value: endTime,
parameterName: 'endDate',
});
}
return params;
};
......@@ -82,6 +79,7 @@ const beamParameters = (dataset: Dataset) => [
)
? `${convertUnitDatasetParameter(dataset, 'TOMOAcquisition_source_sample_distance', 'm', 1)} m`
: '',
parameterName: 'TOMOAcquisition_source_sample_distance',
},
{
caption: 'Ring current at start',
......@@ -93,26 +91,6 @@ const beamParameters = (dataset: Dataset) => [
},
];
const attenuatorsParameters = (dataset: Dataset): MetadataTableParameter[] => {
const params: MetadataTableParameter[] = [];
for (let i = 0; i < 15; i++) {
const index = (i + 1).toString().padStart(2, '0');
const type = getDatasetParamValue(
dataset,
`InstrumentAttenuator${index}_type`,
);
const thickness = getDatasetParamValue(
dataset,
`InstrumentAttenuator${index}_thickness`,
);
if (type && type.toLowerCase() !== 'empty') {
params.push({ caption: `Att${i + 1}`, value: `${type}, ${thickness}` });
}
}
return params;
};
const formatImagesDimensions = (dataset: Dataset) => {
const value = getDatasetParamValue(dataset, `InstrumentDetector01Rois_value`);
const dimensions = value?.split(',');
......@@ -135,6 +113,7 @@ const cameraParameters = (dataset: Dataset) => [
{
caption: 'Images dimensions (HxV)',
value: formatImagesDimensions(dataset),
parameterName: 'InstrumentDetector01Rois_value',
},
{
caption: 'Sample pixel size',
......@@ -155,6 +134,7 @@ const cameraParameters = (dataset: Dataset) => [
value: getDatasetParamValue(dataset, 'TOMOAcquisition_latency_time')
? `${convertUnitDatasetParameter(dataset, 'TOMOAcquisition_latency_time', 'ms', 1)} ms`
: '',
parameterName: 'TOMOAcquisition_latency_time',
},
{
caption: 'Acq mode',
......@@ -169,6 +149,7 @@ const cameraParameters = (dataset: Dataset) => [
value: getDatasetParamValue(dataset, 'TOMOAcquisition_magnification')
? `${convertToFixed(getDatasetParamValue(dataset, 'TOMOAcquisition_magnification'), 2)}x`
: '',
parameterName: 'TOMOAcquisition_magnification',
},
{
caption: 'Optic type',
......@@ -176,145 +157,7 @@ const cameraParameters = (dataset: Dataset) => [
},
];
const primarySlitsParameters = (dataset: Dataset): MetadataTableParameter[] => {
const params: MetadataTableParameter[] = [];
addParam(
params,
dataset,
'InstrumentSlitPrimary_horizontal_gap',
'Horizontal gap',
2,
);
addParam(
params,
dataset,
'InstrumentSlitPrimary_horizontal_offset',
'Horizontal offset',
2,
);
addParam(
params,
dataset,
'InstrumentSlitPrimary_vertical_gap',
'Vertical gap',
2,
);
addParam(
params,
dataset,
'InstrumentSlitPrimary_vertical_offset',
'Vertical offset',
2,
);
return params;
};
const secondarySlitsParameters = (
dataset: Dataset,
): MetadataTableParameter[] => {
const params: MetadataTableParameter[] = [];
addParam(
params,
dataset,
'InstrumentSlitSecondary_horizontal_gap',
'Horizontal gap',
2,
);
addParam(
params,
dataset,
'InstrumentSlitSecondary_horizontal_offset',
'Horizontal offset',
2,
);
addParam(
params,
dataset,
'InstrumentSlitSecondary_vertical_gap',
'Vertical gap',
2,
);
addParam(
params,
dataset,
'InstrumentSlitSecondary_vertical_offset',
'Vertical offset',
2,
);
return params;
};
const otherSlits = (
dataset: Dataset,
): { slitsTitles: string[]; otherSlitsData: MetadataTableParameter[][] } => {
const paramKeys = [
{ key: 'InstrumentSlits_horizontal_gap', caption: 'Horizontal gap' },
{ key: 'InstrumentSlits_horizontal_offset', caption: 'Horizontal offset' },
{ key: 'InstrumentSlits_vertical_gap', caption: 'Vertical gap' },
{ key: 'InstrumentSlits_vertical_offset', caption: 'Vertical offset' },
];
const values = paramKeys.map(({ key }) => getDatasetParamValue(dataset, key));
if (values.every((val) => val === null || val === undefined)) {
return { slitsTitles: ['Slits'], otherSlitsData: [] };
}
const splitArrays = values.map((val) =>
typeof val === 'string'
? val.split(/\s+/).filter(Boolean) // Split on spaces and remove empty entries
: val !== null && val !== undefined
? [String(val)]
: [],
);
// Ensure all split arrays have the same length
const slitsNumber = Math.max(...splitArrays.map((arr) => arr.length));
const allHaveSameLength = splitArrays.every(
(arr) => arr.length === slitsNumber,
);
if (allHaveSameLength) {
// Slit names if available, otherwise "Slits"
const slitNames = getDatasetParamValue(dataset, 'InstrumentSlits_name');
const slitTitles = slitNames
? slitNames
.split(/\s+/)
.slice(0, slitsNumber)
.map((name) => name.trim())
: Array(slitsNumber).fill('Slits');
// Data into separate rows per slit configuration
const slitData = Array.from({ length: slitsNumber }, (_, i) =>
paramKeys.map(({ caption }, j) => ({
caption,
value: splitArrays[j][i] || '',
digits: 2,
})),
);
return {
slitsTitles: slitTitles,
otherSlitsData: slitData,
};
}
return {
slitsTitles: ['Slits'],
otherSlitsData: [
paramKeys
.map(({ caption }, i) =>
values[i] !== null && values[i] !== undefined
? { caption, value: String(values[i]).trim(), digits: 2 }
: null,
)
.filter(Boolean) as MetadataTableParameter[],
],
};
};
export default function TOMOSummaryView({ dataset }: { dataset: Dataset }) {
const { slitsTitles, otherSlitsData } = otherSlits(dataset);
return (
<Container fluid>
<Row className="g-3">
......@@ -327,75 +170,28 @@ export default function TOMOSummaryView({ dataset }: { dataset: Dataset }) {
</Col>
)}
<Col xs="auto">
<TOMOMetadataCard
<MetadataCard
title="Acquisition parameters"
dataset={dataset}
parameters={acquisitionParameters()}
entity={dataset}
content={acquisitionParameters()}
/>
</Col>
<Col xs="auto">
<TOMOMetadataCard
<MetadataCard
title="Beam"
dataset={dataset}
parameters={beamParameters(dataset)}
entity={dataset}
content={beamParameters(dataset)}
/>
</Col>
{attenuatorsParameters(dataset).length > 0 && (
<Col xs="auto">
<TOMOMetadataCard
title="Attenuators"
dataset={dataset}
parameters={attenuatorsParameters(dataset)}
/>
</Col>
)}
<AttenuatorsWidget dataset={dataset} />
<Col xs="auto">
<TOMOMetadataCard
<MetadataCard
title="Camera and optics"
dataset={dataset}
parameters={cameraParameters(dataset)}
entity={dataset}
content={cameraParameters(dataset)}
/>
</Col>
{(primarySlitsParameters(dataset).length > 0 ||
secondarySlitsParameters(dataset).length > 0 ||
otherSlitsData.length > 0) && (
<Col xs="auto">
<Card>
<Card.Header className="text-center">Slits</Card.Header>
<Card.Body>
<Row>
{primarySlitsParameters(dataset).length > 0 && (
<Col xs="auto">
<TOMOMetadataCard
title="Primary Slits"
dataset={dataset}
parameters={primarySlitsParameters(dataset)}
/>
</Col>
)}
{secondarySlitsParameters(dataset).length > 0 && (
<Col xs="auto">
<TOMOMetadataCard
title="Secondary Slits"
dataset={dataset}
parameters={secondarySlitsParameters(dataset)}
/>
</Col>
)}
{otherSlitsData.map((params, index) => (
<Col xs="auto" key={index}>
<TOMOMetadataCard
title={slitsTitles[index] || 'Slits'}
dataset={dataset}
parameters={params}
/>
</Col>
))}
</Row>
</Card.Body>
</Card>
</Col>
)}
<InstrumentSlitWidget dataset={dataset} />
<Col xs="auto">
<Gallery dataset={dataset.outputDatasets?.[0]}></Gallery>
</Col>
......@@ -403,20 +199,3 @@ export default function TOMOSummaryView({ dataset }: { dataset: Dataset }) {
</Container>
);
}
function TOMOMetadataCard({
title,
dataset,
parameters,
}: {
title: string;
dataset: Dataset;
parameters: MetadataTableParameters;
}) {
return (
<Card>
<Card.Header className="text-center">{title}</Card.Header>
<MetadataTable entity={dataset} parameters={parameters}></MetadataTable>
</Card>
);
}
apps/logbook/package.json
View file @ e5d5b566
......@@ -18,7 +18,7 @@
"dependencies": {
"@babel/eslint-parser": "^7.25.1",
"@edata-portal/core": "workspace:*",
"@edata-portal/icat-plus-api": "^1.8.12",
"@edata-portal/icat-plus-api": "^1.8.13",
"@fortawesome/fontawesome-svg-core": "^6.6.0",
"@fortawesome/free-solid-svg-icons": "^6.6.0",
"@fortawesome/react-fontawesome": "^0.2.2",
......
apps/logistics/package.json
View file @ e5d5b566
......@@ -18,7 +18,7 @@
"dependencies": {
"@babel/eslint-parser": "^7.25.1",
"@edata-portal/core": "workspace:*",
"@edata-portal/icat-plus-api": "^1.8.12",
"@edata-portal/icat-plus-api": "^1.8.13",
"@fortawesome/fontawesome-svg-core": "^6.6.0",
"@fortawesome/free-solid-svg-icons": "^6.6.0",
"@fortawesome/react-fontawesome": "^0.2.2",
......
apps/logistics/src/components/spreadsheet/SpreadSheetImportExport.tsx
View file @ e5d5b566
......@@ -13,6 +13,8 @@ import {
} from 'react-bootstrap';
import * as XLSX from 'xlsx';
const HEADER_SEPARATOR = ' - ';
export function SpreadSheetImportExport({
onImport,
data,
......@@ -26,7 +28,12 @@ export function SpreadSheetImportExport({
}) {
return (
<Col xs={'auto'}>
<div className="bg-secondary rounded border p-3 mb-2">
<div
className="bg-gradient-secondary rounded border p-3 mb-2"
style={{
borderColor: 'var(--bs-secondary)',
}}
>
<Row className="g-1">
<Import onImport={onImport} columns={columns} />
<Export data={data} columns={columns} name={name} />
......@@ -41,16 +48,18 @@ function HandsOnTableHelpMessage() {
return (
<Col>
<Row>
<small>
<strong>Supported formats: CSV, XLS, XLSX</strong>
<br />
<i>
Columns should match the table below. You can download the template
file to fill in the data.
<div className="bg-secondary rounded" style={{ marginTop: '4px' }}>
<small>
<strong>Supported formats: CSV, XLS, XLSX</strong>
<br />
Import will overwrite the current table data.
</i>
</small>
<i>
Columns should match the table below. You can download the
template file to fill in the data.
<br />
Import will overwrite the current table data.
</i>
</small>
</div>
</Row>
</Col>
);
......@@ -75,7 +84,7 @@ function Import({
const firstRowIsHeader = firstRow.every((cell, i) => {
const column: InputColumnDescription = columns[i];
return (
String(cell).toLowerCase().trim() ===
String(cell).toLowerCase().split(HEADER_SEPARATOR)[0].trim() ===
(column.header || column.name || '').toLowerCase().trim()
);
});
......@@ -155,11 +164,33 @@ function Export({
const hasData = cleanData.length > 0;
const exportToXLSX = (exporting: any[][], name: string) => {
const headerCounts = columns.reduce(
(acc, column) => {
const key = column.header || column.name || '';
acc[key] = (acc[key] || 0) + 1;
return acc;
},
{} as Record<string, number>,
);
// return the columns and data to be exported
// if a column header is duplicated, we add the name
const getColumnsToExport = (exporting: any[][]) => {
const toExport = [
columns.map((c) => c.header || c.name || ''),
columns.map((c) => {
const header = c.header || c.name || '';
return headerCounts[header] > 1 &&
header.toLowerCase() !== c.name.toLowerCase()
? `${header}${HEADER_SEPARATOR}${c.name}`
: header;
}),
...exporting,
];
return toExport;
};
const exportToXLSX = (exporting: any[][], name: string) => {
const toExport = getColumnsToExport(exporting);
const sheet = XLSX.utils.aoa_to_sheet(toExport);
const workbook = XLSX.utils.book_new();
XLSX.utils.book_append_sheet(workbook, sheet, name.slice(0, 31));
......@@ -167,10 +198,7 @@ function Export({
};
const exportToCSV = (exporting: any[][], name: string) => {
const toExport = [
columns.map((c) => c.header || c.name || ''),
...exporting,
];
const toExport = getColumnsToExport(exporting);
const csv = Papa.unparse(toExport);
const blob = new Blob([csv], { type: 'text/csv;charset=utf-8;' });
const url = URL.createObjectURL(blob);
......
apps/maintenance/package.json
View file @ e5d5b566
......@@ -16,7 +16,7 @@
"fix:prettier": "prettier . --write"
},
"dependencies": {
"@edata-portal/icat-plus-api": "^1.8.12",
"@edata-portal/icat-plus-api": "^1.8.13",
"@fortawesome/fontawesome-svg-core": "^6.6.0",
"@fortawesome/free-solid-svg-icons": "^6.6.0",
"@fortawesome/react-fontawesome": "^0.2.2",
......
apps/mx/index.html
View file @ e5d5b566
<!doctype html>
<html lang="en"></html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<link rel="icon" type="image/svg+xml" href="/favicon.ico" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Data Portal</title>
</head>
<body>
<div id="root"></div>
<script type="module" src="/src/main.tsx"></script>
</body>
</html>
apps/mx/package.json
View file @ e5d5b566
......@@ -19,11 +19,14 @@
"@babel/eslint-parser": "^7.25.1",
"@edata-portal/core": "workspace:*",
"@edata-portal/h5": "workspace:*",
"@edata-portal/icat-plus-api": "^1.8.12",
"@edata-portal/icat-plus-api": "^1.8.13",
"@fortawesome/fontawesome-svg-core": "^6.6.0",
"@fortawesome/free-solid-svg-icons": "^6.6.0",
"@fortawesome/react-fontawesome": "^0.2.2",
"@tanstack/react-query": "^5.52.1",
"ajv": "^8.17.1",
"bootstrap": "^5.3.3",
"bootswatch": "^5.3.3",
"lodash": "^4.17.21",
"papaparse": "^5.4.1",
"react": "^18.3.1",
......
apps/mx/public/config/api.config.json 0 → 100644
View file @ e5d5b566
{
"icat_url": "https://icatplus.esrf.fr/",
"authentication": {
"anonymous": {
"plugin": "db",
"username": "reader",
"password": "reader"
},
"autoRefresh": true,
"autoRefreshThresholdMinutes": "60",
"authenticators": [
{
"name": "OpenID",
"enabled": true,
"title": "ESRF Single Sign On",
"plugin": "esrf",
"message": "Login with ESRF SSO",
"openidLogoutTransferToApp": true,
"refreshToken": true,
"minValidity": 600,
"configuration": {
"authority": "https://websso.esrf.fr/auth/realms/ESRF",
"clientId": "icat"
}
},
{
"name": "Database",
"title": "Database",
"enabled": true,
"message": "",
"plugin": "db"
}
]
}
}
apps/mx/public/config/ui.config.json 0 → 100644
View file @ e5d5b566
{
"applicationTitle": "Data Portal",
"facilityName": "ESRF",
"homePage": {
"policyMessage": "Public data is accessible to anyone. You need to be logged-in to visualize your data when it is under embargo. See <a href=\"https://www.esrf.fr/fr/home/UsersAndScience/UserGuide/esrf-data-policy.html\" target=\"_blank\" rel=\"noreferrer\">ESRF data policy</a> for more details."
},
"linkToPreviousVersion": {
"name": "Back to Data Portal V1",
"url": "https://data1.esrf.fr"
},
"knowledgeBasePage": "https://confluence.esrf.fr/display/DATAPOLWK/Knowledge+Base",
"loginForm": {
"accountCreationLink": "https://smis.esrf.fr/misapps/SMISWebClient/accountManager/searchExistingAccount.do?action=search",
"note": {
"enabled": true,
"title": "Important note",
"notes": [
{
"text": "In order to login to the Data Portal of the ESRF to send samples or browse embargoed data you need to be declared a member of a proposal on the ESRF User Portal. Once this is done your account will be activated <b>45 days</b> before the first experiment starts. If you need access earlier please contact the <a rel=\"noopener noreferrer\" target=\"_blank\" href=\"http://www.esrf.eu/UsersAndScience/UserGuide/Contacts\" >ESRF User Office</a>.<br/>Anonymous login to browse open data is always possible."
},
{
"text": "During 2019 and according to the General Data Protection Regulation, all portal users who did not consent to the <a href=\"http://www.esrf.fr/GDPR\" rel=\"noopener noreferrer\" target=\"_blank\" > User Portal Privacy Statement</a> have had their account deactivated. Please contact the <a rel=\"noopener noreferrer\" target=\"_blank\" href=\"http://www.esrf.eu/UsersAndScience/UserGuide/Contacts\" >User Office</a> if you wish to reactivate it."
}
]
}
},
"userPortal": {
"investigationParameterPkName": "Id",
"link": "https://smis.esrf.fr/misapps/SMISWebClient/protected/aform/manageAForm.do?action=view&expSessionVO.pk="
},
"doi": {
"link": "https://doi.esrf.fr/",
"minimalAbstractLength": 1000,
"minimalTitleLength": 40,
"facilityPrefix": "10.15151",
"facilitySuffix": "ESRF-DC",
"referenceDoi": "https://doi.esrf.fr/10.15151/ESRF-DC-2011729981"
},
"fileBrowser": {
"maxFileNb": 1000
},
"imageViewer": {
"fileExtensions": [".png", ".jpg", ".jpeg", ".tiff", ".gif"]
},
"h5Viewer": {
"url": "https://hibou.esrf.fr",
"fileExtensions": [".hdf5", ".h5", ".nexus", ".nx", ".nxs", ".cxi"]
},
"galleryViewer": {
"fileExtensions": ["jpeg", "jpg", "gif", "png", "svg"]
},
"textViewer": {
"maxFileSize": 5000000,
"fileExtensions": [
".txt",
".log",
".json",
".xml",
".csv",
".dat",
".inp",
".xds",
".descr",
".lp",
".hkl",
".site",
".asc",
".ini"
]
},
"feedback": {
"email": "dataportalrequests@esrf.fr",
"subject": "Feedback",
"body": "Hi,\n\n<< Please provide your feedback here. >>\n<< To report an issue, please include screenshots, reproduction steps, proposal number, beamline, etc. >>\n<< To suggest a new feature, please describe the needs this feature would fulfill. >>\n\nThanks"
},
"footer": {
"images": [
{
"src": "/images/esrf.jpg",
"alt": "ESRF",
"href": "https://www.esrf.fr/"
},
{
"src": "/images/CoreTrustSeal.png",
"alt": "CoreTrustSeal",
"href": "https://www.coretrustseal.org/"
}
]
},
"handsonTableLicenseKey": "non-commercial-and-evaluation",
"globus": {
"enabled": true,
"url": "https://app.globus.org/file-manager?",
"collections": [
{
"root": "/data/visitor/",
"origin": "/data",
"originId": "bfc3eff4-f5ca-4b4d-8532-e9a155f3613f"
},
{
"root": "/data/projects/hop",
"origin": "/data/projects/hop",
"originId": "340dc883-4b0d-476c-abb0-969e1ddd9dc0"
},
{
"root": "/data/projects/open-datasets",
"origin": "/data/projects/open-datasets/",
"originId": "8cbe8cdc-048a-48cf-b8a0-046a6af3ba44"
},
{
"root": "/data/projects/paleo",
"origin": "/data/projects/paleo/public",
"originId": "e8fb6c4b-9ab0-4a1c-a79d-d51cef0b8c3d"
}
],
"messageAlert": {
"enabled": true,
"message": "For users who want to download large volume of experimental data <strong>(&gt;2GB)</strong>, ESRF users can access the Globus service, please read the <a href=\"https://confluence.esrf.fr/display/SCKB/Globus\" target=\"_blank\">documentation</a> for proceeding."
}
},
"sample": {
"pageTemplateURL": "https://smis.esrf.fr/misapps/SMISWebClient/protected/samplesheet/view.do?pk=",
"editable": true,
"descriptionParameterName": "Sample_description",
"nonEditableParameterName": "Id",
"notesParameterName": "Sample_notes"
},
"logbook": {
"help": "https://confluence.esrf.fr/display/DATAPOLWK/Electronic+Logbook",
"defaultMonthPeriodForStaff": 1
},
"projects": [
{
"title": "The Human Organ Atlas",
"key": "The Human Organ Atlas",
"url": "https://human-organ-atlas.esrf.eu/datasets/{datasetId}",
"homepage": "https://human-organ-atlas.esrf.eu"
},
{
"title": "Paleontology database",
"key": "paleo",
"url": "http://paleo.esrf.fr/datasets/{datasetId}",
"homepage": "http://paleo.esrf.fr"
}
],
"features": {
"reprocessing": true,
"logbook": true,
"dmp": true,
"logistics": true
},
"tracking": {
"enabled": true,
"url": "https://matomo-srv-1.esrf.fr/",
"siteId": "14",
"tracker": "piwik.php",
"script": "piwik.js"
},
"mx": {
"pdb_map_mtz_viewer_url": "https://moorhen.esrf.fr"
},
"logistics": {
"transportOrganizationEnabled": false,
"facilityReimbursmentEnabled": true,
"facilityForwarderName": "FedEX",
"facilityForwarderAccount": "388310561",
"facilityForwarderNamePickup": ["FEDEX", "DHL express", "UPS"]
}
}
apps/mx/src/App.tsx 0 → 100644
View file @ e5d5b566
import {
AuthenticatedAPIProvider,
AuthenticatorProvider,
OpenIDProvider,
SideNavProvider,
UnauthenticatedAPIProvider,
} from '@edata-portal/core';
import { QueryClient, QueryClientProvider } from '@tanstack/react-query';
import { AppRouter } from 'standalone/routing/AppRouter';
import { ViewersProvider } from 'standalone/providers/ViewersProvider';
import { ConfigProvider } from 'standalone/providers/ConfigProvider';
import { Navigation } from 'standalone/routing/Navigation';
import 'standalone/scss/main.scss';
const queryClient = new QueryClient();
function App() {
return (
<>
<h1>MX Microfrontend Development</h1>
<QueryClientProvider client={queryClient}>
<ConfigProvider>
<AppContextProviders>
<ViewersProvider>
<SideNavProvider>
<AppRouter>
<Navigation />
</AppRouter>
</SideNavProvider>
</ViewersProvider>
</AppContextProviders>
</ConfigProvider>
</QueryClientProvider>
</>
);
}
function AppContextProviders({ children }: { children: React.ReactNode }) {
return (
<UnauthenticatedAPIProvider>
<AuthenticatorProvider>
<OpenIDProvider>
<AuthenticatedAPIProvider>{children}</AuthenticatedAPIProvider>
</OpenIDProvider>
</AuthenticatorProvider>
</UnauthenticatedAPIProvider>
);
}
export default App;
apps/mx/src/main.tsx 0 → 100644
View file @ e5d5b566
import React from 'react';
import ReactDOM from 'react-dom/client';
import App from 'App';
ReactDOM.createRoot(document.getElementById('root') as HTMLElement).render(
<React.StrictMode>
<App />
</React.StrictMode>,
);
apps/mx/src/standalone/InvestigationDatasets.tsx 0 → 100644
View file @ e5d5b566
import { usePath, useViewers } from '@edata-portal/core';
import {
useGetEndpoint,
INVESTIGATION_LIST_ENDPOINT,
} from '@edata-portal/icat-plus-api';
import { Alert } from 'react-bootstrap';
/**
* Fetches and displays the datasets related to a specific investigation.
*
* This component:
* - Retrieves the `investigationId` from the URL path.
* - Fetches the corresponding investigation using `useGetEndpoint`.
* - Renders an alert if no investigation is found.
* - Uses `viewInvestigation` from `useViewers()` to render the investigation details.
*
* @returns {JSX.Element} Investigation details or an error alert.
*/
export default function InvestigationDatasets(): JSX.Element {
const investigationId = usePath('investigationId');
const investigations = useGetEndpoint({
endpoint: INVESTIGATION_LIST_ENDPOINT,
params: { ids: investigationId },
});
const { viewInvestigation } = useViewers();
if (!investigations || investigations.length === 0) {
return <Alert variant="danger">Could not find investigation</Alert>;
}
return viewInvestigation(investigations[0]);
}
apps/mx/src/standalone/providers/ConfigProvider.tsx 0 → 100644
View file @ e5d5b566
import { ConfigContext } from '@edata-portal/core';
import { useSuspenseQueries } from '@tanstack/react-query';
import { useMemo } from 'react';
declare global {
interface Window {
remoteUrls: any;
}
}
export function ConfigProvider({ children }: { children: React.ReactNode }) {
const [api, ui, techniques] = useSuspenseQueries({
queries: [
{
queryKey: ['api.config'],
queryFn: async () => {
const response = await fetch('../config/api.config.json');
return await response.json();
},
},
{
queryKey: ['ui.config'],
queryFn: async () => {
const response = await fetch('../config/ui.config.json');
return await response.json();
},
},
{
queryKey: ['techniques.config'],
queryFn: async () => {
return [
{
name: 'Crystallography',
shortname: 'MX',
},
];
},
},
],
});
const value = useMemo(
() => ({
api: api.data,
ui: ui.data,
techniques: techniques.data,
}),
[api.data, techniques.data, ui.data],
);
return (
<ConfigContext.Provider value={value}>{children}</ConfigContext.Provider>
);
}
apps/mx/src/standalone/providers/ViewersProvider.tsx 0 → 100644
View file @ e5d5b566
import { ViewersContext } from '@edata-portal/core';
import { DatasetViewer } from 'standalone/viewers/DatasetViewer';
import { InvestigationViewer } from 'standalone/viewers/InvestigationViewer';
import { SampleViewer } from 'standalone/viewers/SampleViewer';
export function ViewersProvider({ children }: { children: React.ReactNode }) {
return (
<ViewersContext.Provider
value={{
viewSample: (sample, props) => (
<SampleViewer key={sample.id} sample={sample} props={props} />
),
viewDataset: (dataset, type, props) => (
<DatasetViewer
key={dataset.id}
dataset={dataset}
type={type}
props={props}
/>
),
viewInvestigation: (investigation, props) => (
<InvestigationViewer
key={investigation.id}
investigation={investigation}
props={props}
/>
),
}}
>
{children}
</ViewersContext.Provider>
);
}
apps/mx/src/standalone/routing/AppRouter.tsx 0 → 100644
View file @ e5d5b566
import InvestigationDatasets from 'standalone/InvestigationDatasets';
import { useMemo } from 'react';
import {
createBrowserRouter,
RouteObject,
RouterProvider,
} from 'react-router-dom';
export const routes: RouteObject[] = [
{
path: '/investigation/:investigationId',
element: <InvestigationDatasets></InvestigationDatasets>,
},
{
path: '*',
element: <div>Cheers</div>,
},
];
export function AppRouter({ children }: { children: JSX.Element }) {
const router = useMemo(() => {
return createBrowserRouter([
{
element: <>{children}</>,
children: routes,
id: 'home',
handle: { breadcrumb: 'Home' },
},
]);
}, [children]);
return <RouterProvider router={router} />;
}
apps/mx/src/standalone/routing/Navigation.tsx 0 → 100644
View file @ e5d5b566
import { Container } from 'react-bootstrap';
import { Outlet } from 'react-router-dom';
import { SideNavRenderer } from '@edata-portal/core';
export function Navigation() {
return (
<div
style={{
position: 'fixed',
top: 0,
left: 0,
right: 0,
bottom: 0,
display: 'flex',
flexDirection: 'column',
overflow: 'hidden',
}}
>
<Container
style={{
paddingTop: 20,
overflow: 'auto',
height: '100%',
position: 'relative',
display: 'flex',
flexDirection: 'column',
justifyContent: 'space-between',
}}
fluid
className="main"
>
<SideNavRenderer>
<Outlet />
</SideNavRenderer>
</Container>
</div>
);
}
apps/mx/src/standalone/scss/colors.scss 0 → 100644
View file @ e5d5b566
// custom theme colors
$primary: #2c3e50;
$secondary: #456c74;
$success: #18bc9c;
$info: #108cdf;
$warning: #f39c12;
$danger: #e74c3c;
$light: #ecf0f1;
$dark: #222222;
$dataset-raw: #b4ccd1;
$dataset-processed: #f9e69e;
$sample: #4d3d5f;
:root {
--primary: #{$primary};
--secondary: #{$secondary};
--success: #{$success};
--info: #{$info};
--warning: #{$warning};
--danger: #{$danger};
--light: #{$light};
--dark: #{$dark};
--dataset-raw: #{$dataset-raw};
--dataset-processed: #{$dataset-processed};
--sample: #{$sample};
}