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✨ Add new public study routes #254

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Merged
evans-g-crsj merged 1 commit into from
Jun 18, 2025
Merged

✨ Add new public study routes #254

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7 changes: 7 additions & 0 deletions admin/arrangerProjectConf.json
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Collaborator Author

@evans-g-crsj evans-g-crsj Jun 18, 2025

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ne pas tenir compte

Original file line number Diff line number Diff line change
Expand Up @@ -183,6 +183,13 @@
"isArray": true
}
},
{
"field": "person.links",
"graphqlField": "participant",
"extendedFieldMappingInput": {
"isArray": true
}
},
{
"field": "contacts",
"graphqlField": "study",
Expand Down
29 changes: 29 additions & 0 deletions src/app.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ import { resolveSetIdMiddleware } from './middleware/resolveSetIdInSqon';
import { replaceIdsWithSetId, resolveSetsInAllSqonsWithMapper, resolveSetsInSqon } from './sqon/resolveSetInSqon';
import { Sqon } from './sqon/types';
import { resolveQueriesSetAliases } from './sqon/setSqon';
import { getPublicGraphs, getPublicStudy } from './endpoints/publicStudy/publicStudy';

export default (keycloak: Keycloak, getProject: (projectId: string) => ArrangerProject): Express => {
const app = express();
Expand Down Expand Up @@ -255,6 +256,34 @@ export default (keycloak: Keycloak, getProject: (projectId: string) => ArrangerP
}
});

app.get('/public-study/study/:code', async (req, res, next) => {
try {
const code = req.params.code;
if (!code || typeof code !== 'string') {
res.status(StatusCodes.UNPROCESSABLE_ENTITY).send('Bad Inputs');
return;
}
const study = await getPublicStudy(req.params.code);
res.send(study || {});
} catch (e) {
next(e);
}
});

app.get('/public-study/graphs/:code', async (req, res, next) => {
try {
const code = req.params.code;
if (!code || typeof code !== 'string') {
res.status(StatusCodes.UNPROCESSABLE_ENTITY).send('Bad Inputs');
return;
}
const study = await getPublicGraphs(req.params.code);
res.send(study || {});
} catch (e) {
next(e);
}
});

app.use(globalErrorLogger, globalErrorHandler);

return app;
Expand Down
178 changes: 178 additions & 0 deletions src/endpoints/publicStudy/publicStudy.ts
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Original file line number Diff line number Diff line change
@@ -0,0 +1,178 @@
import EsInstance from '../../ElasticSearchClientInstance';

type RData = {
[index: string]: any;
};

export const getPublicStudy = async (code: string): Promise<RData> => {
const client = EsInstance.getInstance();
const r = await client.search({
index: `study_centric`,
body: {
size: 1,
query: {
bool: {
must: [
{
term: {
study_code: {
value: code,
},
},
},
],
},
},
},
});
return r.body.hits?.hits?.map(x => x._source)?.[0];
};

export const getPublicGraphs = async (code: string): Promise<RData> => {
const client = EsInstance.getInstance();
const MAX_AGG_TERMS_SIZE = 10000;
const mr = await client.msearch({
body: [
{ index: `participant_centric` },
{
query: {
bool: {
must: [
{
term: {
'study.study_code': {
value: code,
},
},
},
],
},
},
track_total_hits: true,
size: 0,
aggs: {
sex: {
terms: {
field: 'sex',
size: MAX_AGG_TERMS_SIZE,
},
},
ethnicity: {
terms: {
field: 'ethnicity',
size: MAX_AGG_TERMS_SIZE,
},
},
race: {
terms: {
field: 'race',
size: MAX_AGG_TERMS_SIZE,
},
},
down_syndrome_status: {
terms: {
field: 'down_syndrome_status',
size: MAX_AGG_TERMS_SIZE,
},
},
files: {
nested: {
path: 'files',
},
aggs: {
data_category: {
terms: {
field: 'files.data_category',
size: MAX_AGG_TERMS_SIZE,
},
aggs: {
participants: {
reverse_nested: {},
},
},
},
data_type: {
terms: {
field: 'files.data_type',
size: MAX_AGG_TERMS_SIZE,
},
aggs: {
participants: {
reverse_nested: {},
},
},
},
},
},
},
},
{ index: `biospecimen_centric` },
{
query: {
bool: {
must: [
{
term: {
'study.study_code': {
value: code,
},
},
},
],
},
},
track_total_hits: true,
size: 0,
aggs: {
sample_type: {
terms: {
field: 'sample_type',
size: MAX_AGG_TERMS_SIZE,
},
},
status: {
terms: {
field: 'status',
size: MAX_AGG_TERMS_SIZE,
},
},
},
},
],
});

const rs = mr.body?.responses || [];
const participantsAggsData = rs[0];
const biospecimensAggsData = rs[1];

const flattenReversedCount = (
buckets: { key: string; doc_count: number; participants: { key: string; doc_count: number } }[],
) =>
buckets.map(b => ({
key: b.key,
doc_count: b.participants.doc_count,
}));

return {
participant_centric: {
total: participantsAggsData.hits.total.value,
data: {
race: participantsAggsData.aggregations.race.buckets,
ethnicity: participantsAggsData.aggregations.ethnicity.buckets,
down_syndrome_status: participantsAggsData.aggregations.down_syndrome_status.buckets,
sex: participantsAggsData.aggregations.sex.buckets,
files_data_category: flattenReversedCount(
participantsAggsData.aggregations.files.data_category.buckets,
),
files_data_type: flattenReversedCount(participantsAggsData.aggregations.files.data_type.buckets),
},
},
biospecimens_centric: {
total: biospecimensAggsData.hits.total.value,
data: {
sample_type: biospecimensAggsData.aggregations.sample_type.buckets,
status: biospecimensAggsData.aggregations.status.buckets,
},
},
};
};
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