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feat: SJIP-1059 add endpoint to check genes in trasncriptomics data #215

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merged 1 commit into from
Oct 29, 2024
Merged

feat: SJIP-1059 add endpoint to check genes in trasncriptomics data #215

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97 changes: 93 additions & 4 deletions src/app.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,13 @@ import {
} from './endpoints/sets/setsFeature';
import { Set, UpdateSetContentBody, UpdateSetTagBody } from './endpoints/sets/setsTypes';
import { getStatistics, getStudiesStatistics, Statistics } from './endpoints/statistics';
import { checkSampleIdsAndGene, fetchDiffGeneExp, fetchFacets, fetchSampleGeneExp } from './endpoints/transcriptomics';
import {
checkGenesExist,
checkSampleIdsAndGene,
fetchDiffGeneExp,
fetchFacets,
fetchSampleGeneExp,
} from './endpoints/transcriptomics';
import {
DiffGeneExpVolcano,
Facets as TranscriptomicsFacets,
Expand Down Expand Up @@ -745,8 +751,8 @@ describe('Express app (without Arranger)', () => {
.expect(403));

it('should return 200 if Authorization header contains valid token and no error occurs', async () => {
const sample_ids = ['bs-aa000aaa', 'bs-bbbb11b1'];
(checkSampleIdsAndGene as jest.Mock).mockImplementation(() => sample_ids);
const sampleIds = ['bs-aa000aaa', 'bs-bbbb11b1'];
(checkSampleIdsAndGene as jest.Mock).mockImplementation(() => sampleIds);

const token = getToken();

Expand All @@ -755,7 +761,7 @@ describe('Express app (without Arranger)', () => {
.set('Content-type', 'application/json')
.set({ Authorization: `Bearer ${token}` })
.send(requestBody)
.expect(200, sample_ids);
.expect(200, sampleIds);
expect((checkSampleIdsAndGene as jest.Mock).mock.calls.length).toEqual(1);
expect((checkSampleIdsAndGene as jest.Mock).mock.calls[0][0]).toEqual(requestBody.sample_ids);
expect((checkSampleIdsAndGene as jest.Mock).mock.calls[0][1]).toEqual(requestBody.ensembl_gene_id);
Expand All @@ -780,4 +786,87 @@ describe('Express app (without Arranger)', () => {
expect((checkSampleIdsAndGene as jest.Mock).mock.calls[0][1]).toEqual(requestBody.ensembl_gene_id);
});
});

describe('POST /transcriptomics/checkGenesExist', () => {
beforeEach(() => {
(checkGenesExist as jest.Mock).mockReset();
});

const requestBody = {
genes:
'CYB5R1,TBCA,TOMM5,NRXN2,ENSG00000163462.18,ENSG00000211592,ENSG000002137410,FUT7,AL139424,ENSG00000204882.4',
};

it('should return 403 if no Authorization header', () =>
request(app)
.post('/transcriptomics/checkGenesExist')
.set('Content-type', 'application/json')
.send(requestBody)
.expect(403));

it('should return 200 if Authorization header contains valid token and no error occurs', async () => {
const matchedGenes = [
{
gene_symbol: 'GPR20',
ensembl_gene_id: 'ENSG00000204882.4',
},
{
gene_symbol: 'TRIM46',
ensembl_gene_id: 'ENSG00000163462.18',
},
];
(checkGenesExist as jest.Mock).mockImplementation(() => matchedGenes);

const token = getToken();

await request(app)
.post('/transcriptomics/checkGenesExist')
.set('Content-type', 'application/json')
.set({ Authorization: `Bearer ${token}` })
.send(requestBody)
.expect(200, matchedGenes);
expect((checkGenesExist as jest.Mock).mock.calls.length).toEqual(1);
expect((checkGenesExist as jest.Mock).mock.calls[0][0]).toEqual([
'CYB5R1',
'TBCA',
'TOMM5',
'NRXN2',
'ENSG00000163462.18',
'ENSG00000211592',
'ENSG000002137410',
'FUT7',
'AL139424',
'ENSG00000204882.4',
]);
});

it('should return 500 if Authorization header contains valid token but an error occurs', async () => {
const expectedError = new Error('OOPS');
(checkGenesExist as jest.Mock).mockImplementation(() => {
throw expectedError;
});

const token = getToken();

await request(app)
.post('/transcriptomics/checkGenesExist')
.set('Content-type', 'application/json')
.set({ Authorization: `Bearer ${token}` })
.send(requestBody)
.expect(500, { error: 'Internal Server Error' });
expect((checkGenesExist as jest.Mock).mock.calls.length).toEqual(1);
expect((checkGenesExist as jest.Mock).mock.calls[0][0]).toEqual([
'CYB5R1',
'TBCA',
'TOMM5',
'NRXN2',
'ENSG00000163462.18',
'ENSG00000211592',
'ENSG000002137410',
'FUT7',
'AL139424',
'ENSG00000204882.4',
]);
});
});
});
16 changes: 15 additions & 1 deletion src/app.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,13 @@ import {
} from './endpoints/sets/setsFeature';
import { CreateSetBody, Set, SetSqon, UpdateSetContentBody, UpdateSetTagBody } from './endpoints/sets/setsTypes';
import { getStatistics, getStudiesStatistics } from './endpoints/statistics';
import { checkSampleIdsAndGene, fetchDiffGeneExp, fetchFacets, fetchSampleGeneExp } from './endpoints/transcriptomics';
import {
checkGenesExist,
checkSampleIdsAndGene,
fetchDiffGeneExp,
fetchFacets,
fetchSampleGeneExp,
} from './endpoints/transcriptomics';
import { cacheTTL, esHost, keycloakURL, userApiURL } from './env';
import { globalErrorHandler, globalErrorLogger } from './errors';
import {
Expand Down Expand Up @@ -187,6 +193,14 @@ export default (keycloak: Keycloak, getProject: (projectId: string) => ArrangerP
res.json(data);
});

app.postAsync('/transcriptomics/checkGenesExist', keycloak.protect(), async (req, res) => {
const genes: string = req.body.genes;

const data = await checkGenesExist(genes.split(','));

res.json(data);
});

app.postAsync('/authorized-studies', keycloak.protect(), computeAuthorizedStudiesForAllFences);

app.use(globalErrorLogger, globalErrorHandler);
Expand Down
78 changes: 76 additions & 2 deletions src/endpoints/transcriptomics/index.test.ts
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import EsInstance from '../../ElasticSearchClientInstance';
import { checkSampleIdsAndGene, fetchDiffGeneExp, fetchFacets, fetchSampleGeneExp } from '.';
import { DiffGeneExpVolcano, Facets, SampleGeneExpVolcano } from './types';
import { checkGenesExist, checkSampleIdsAndGene, fetchDiffGeneExp, fetchFacets, fetchSampleGeneExp } from '.';
import { DiffGeneExpVolcano, Facets, MatchedGene, SampleGeneExpVolcano } from './types';

jest.mock('../../ElasticSearchClientInstance');

Expand Down Expand Up @@ -493,4 +493,78 @@ describe('Transcriptomics', () => {
expect(result).toEqual(expectedResponse);
});
});

describe('checkGenesExist', () => {
beforeEach(() => {
(EsInstance.getInstance as jest.Mock).mockReset();
});

it('should return gene_symbol and ensembl_gene_id for the list of gene_symbol and or ensembl_gene_id received in param', async () => {
const mockEsResponseBody = {
took: 10,
timed_out: false,
_shards: {
total: 5,
successful: 5,
skipped: 0,
failed: 0,
},
hits: [],
aggregations: {
distinct_genes: {
after_key: {
gene_symbol: 'TRIM46',
ensembl_gene_id: 'ENSG00000163462.18',
},
buckets: [
{
key: {
gene_symbol: 'GPR20',
ensembl_gene_id: 'ENSG00000204882.4',
},
doc_count: 400,
},
{
key: {
gene_symbol: 'TRIM46',
ensembl_gene_id: 'ENSG00000163462.18',
},
doc_count: 400,
},
],
},
},
};

const expectedResponse: MatchedGene[] = [
{
gene_symbol: 'GPR20',
ensembl_gene_id: 'ENSG00000204882.4',
},
{
gene_symbol: 'TRIM46',
ensembl_gene_id: 'ENSG00000163462.18',
},
];

(EsInstance.getInstance as jest.Mock).mockImplementation(() => ({
search: async () => ({ body: mockEsResponseBody }),
}));

const result = await checkGenesExist([
'CYB5R1',
'TBCA',
'TOMM5',
'NRXN2',
'ENSG00000163462.18',
'ENSG00000211592',
'ENSG000002137410',
'FUT7',
'AL139424',
'ENSG00000204882.4',
]);

expect(result).toEqual(expectedResponse);
});
});
});
49 changes: 47 additions & 2 deletions src/endpoints/transcriptomics/index.ts
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Original file line number Diff line number Diff line change
@@ -1,5 +1,3 @@
import { max, min } from 'lodash';

import EsInstance from '../../ElasticSearchClientInstance';
import {
ES_CHROMOSOME_AGG_SIZE,
Expand All @@ -13,7 +11,9 @@ import {
DiffGeneExpVolcano,
Facets,
FetchDiffGeneExpResponse,
FetchDistinctGenesBySymbolOrEnsemblId,
FetchSampleGeneExpBySampleIdResponse,
MatchedGene,
SampleGeneExpPoint,
SampleGeneExpVolcano,
} from './types';
Expand Down Expand Up @@ -207,3 +207,48 @@ export const checkSampleIdsAndGene = async (sample_ids: string[], ensembl_gene_i

return sampleGeneExpBySample.by_sample.buckets.map(b => b.key);
};

export const checkGenesExist = async (genes: string[]): Promise<MatchedGene[]> => {
const client = EsInstance.getInstance();

const { body } = await client.search({
index: esSampleGeneExpIndex,
body: {
query: {
bool: {
should: [
{
terms: {
symbol: genes,
},
},
{
terms: {
ensembl_gene_id: genes,
},
},
],
},
},
size: 0,
aggs: {
distinct_genes: {
composite: {
sources: [
{ gene_symbol: { terms: { field: 'gene_symbol' } } },
{ ensembl_gene_id: { terms: { field: 'ensembl_gene_id' } } },
],
size: genes.length,
},
},
},
},
});

const distinctGenesBySymbolOrEnsemblId: FetchDistinctGenesBySymbolOrEnsemblId = body?.aggregations;

return distinctGenesBySymbolOrEnsemblId.distinct_genes.buckets.map(bucket => ({
gene_symbol: bucket.key.gene_symbol,
ensembl_gene_id: bucket.key.ensembl_gene_id,
}));
};
16 changes: 16 additions & 0 deletions src/endpoints/transcriptomics/types.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -107,3 +107,19 @@ export type FetchSampleGeneExpBySampleIdResponse = {
}[];
};
};

export type MatchedGene = {
gene_symbol: string;
ensembl_gene_id: string;
};

export type FetchDistinctGenesBySymbolOrEnsemblId = {
distinct_genes: {
buckets: {
key: {
gene_symbol: string;
ensembl_gene_id: string;
};
}[];
};
};
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