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✨ New Upset route #229

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merged 1 commit into from
Jan 8, 2025
Merged

✨ New Upset route #229

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1 change: 1 addition & 0 deletions package-lock.json
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1 change: 1 addition & 0 deletions package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@
"dependencies": {
"@arranger/admin": "^2.19.4",
"@arranger/middleware": "^2.19.4",
"@arranger/mapping-utils": "^2.19.4",
"@arranger/server": "^2.19.4",
"@aws-sdk/client-s3": "^3.689.0",
"@aws-sdk/s3-request-presigner": "^3.689.0",
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10 changes: 10 additions & 0 deletions src/app.ts
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Expand Up @@ -18,6 +18,7 @@ import {
import { CreateSetBody, Set, SetSqon, UpdateSetContentBody, UpdateSetTagBody } from './endpoints/sets/setsTypes';
import { getStatistics, getStudiesStatistics } from './endpoints/statistics';
import transcriptomicsRouter from './endpoints/transcriptomics/route';
import { computeUpset } from './endpoints/upset';
import { esHost, keycloakURL, userApiURL } from './env';
import { globalErrorHandler, globalErrorLogger } from './errors';
import {
Expand Down Expand Up @@ -193,6 +194,15 @@ export default (keycloak: Keycloak, getProject: (projectId: string) => ArrangerP
computeAuthorizedStudiesForAllFences(req, res, next);
});

app.post('/upset', keycloak.protect(), async (req, res, next) => {
try {
const data = await computeUpset(req.body.sqon);
res.send(data);
} catch (e) {
next(e);
}
});

app.use(globalErrorLogger, globalErrorHandler);

return app;
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278 changes: 278 additions & 0 deletions src/endpoints/upset.test.ts
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Original file line number Diff line number Diff line change
@@ -0,0 +1,278 @@
import EsInstance from '../ElasticSearchClientInstance';
import { buildSteps, computeUpset, countIt, topN } from './upset';

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

const MOCK_ES_PARTICIPANT_MAPPINGS = {
statusCode: 200,
meta: {},
body: {
participant_centric_test: {
mappings: {
properties: {
diagnosis: {
type: 'nested',
properties: {
diagnosis_id: {
type: 'keyword',
},
},
},
down_syndrome_status: {
type: 'keyword',
},
family: {
properties: {
relations_to_proband: {
type: 'nested',
properties: {
participant_id: {
type: 'keyword',
},
},
},
},
},

fhir_id: {
type: 'keyword',
},
files: {
type: 'nested',
properties: {
biospecimens: {
type: 'nested',
properties: {
diagnoses: {
type: 'nested',
properties: {
diagnosis_mondo: {
type: 'keyword',
},
},
},
},
},
sequencing_experiment: {
type: 'nested',
properties: {
experiment_strategy: {
type: 'keyword',
},
},
},
},
},
mondo: {
type: 'nested',
properties: {
name: {
type: 'keyword',
},
},
},

non_observed_phenotype: {
type: 'nested',
properties: {
name: {
type: 'keyword',
},
},
},
observed_phenotype: {
type: 'nested',
properties: {
name: {
type: 'keyword',
},
},
},
outcomes: {
type: 'nested',
properties: {
fhir_id: {
type: 'keyword',
},
},
},
phenotype: {
type: 'nested',
properties: {
hpo_phenotype_not_observed: {
type: 'keyword',
},
},
},
study: {
properties: {
contacts: {
type: 'nested',
properties: {
name: {
type: 'keyword',
},
},
},
data_types: {
type: 'nested',
properties: {
data_type: {
type: 'keyword',
},
},
},
datasets: {
type: 'nested',
properties: {
dataset_name: {
type: 'keyword',
},
},
},

study_code: {
type: 'keyword',
},
study_id: {
type: 'keyword',
},
},
},
},
},
},
},
};

describe('Upset', () => {
describe(`${countIt.name} utils`, () => {
it('should count all elements of a list and sort them in descending order', async () => {
const data = ['a', 'b', 'b', 'a', 'c', 'a'];
const values = countIt(data);
expect(values).toEqual(
new Map([
['a', 3],
['b', 2],
['c', 1],
]),
);
});
});

describe(`${topN.name} utils`, () => {
it('should keep the first n keys of map that has counts as values', async () => {
const data = new Map([
['a', 4],
['b', 3],
['c', 6],
['d', 1],
['e', 10],
]);
const values = topN(data, 3);
expect(values).toEqual(['a', 'b', 'c']);
});
});

describe(`${buildSteps.name} utils`, () => {
it('should create from-size params for ES search ', async () => {
const max = 11;
const batchSize = 2;
const values = buildSteps(max, batchSize);
expect(values).toEqual([
{ from: 0, size: 2 },
{ from: 2, size: 2 },
{ from: 4, size: 2 },
{ from: 6, size: 2 },
{ from: 8, size: 2 },
{ from: 10, size: 2 },
]);
expect(values.length * batchSize).toBeGreaterThanOrEqual(max);
});
});

describe(`${computeUpset.name}`, () => {
beforeEach(() => {
(EsInstance.getInstance as jest.Mock).mockReset();
});

it('should compute top observed phenotypes with participants having them', async () => {
(EsInstance.getInstance as jest.Mock).mockImplementation(() => ({
search: async () => ({
body: {
took: 1699,
timed_out: false,
_shards: { total: 65, successful: 65, skipped: 0, failed: 0 },
hits: {
total: { value: 2, relation: 'eq' },
max_score: null,
hits: [
{
_index: 'participant_centric_test',
_type: '_doc',
_id: 'nQ1F4JMB0zu1NPYlkl2T',
_score: null,
_source: {
phenotype: [
{ hpo_phenotype_observed: 'Abnormality of the eye (HP:0000478)' },
{ hpo_phenotype_observed: 'Seizure (HP:0001250)' },
],
fhir_id: 'pt-223twf8ytr',
},
sort: ['pt-223twf8ytr'],
},
{
_index: 'participant_centric_test',
_type: '_doc',
_id: 'GglF4JMBRqsooo59goT2',
_score: null,
_source: {
phenotype: [
{
hpo_phenotype_observed: 'Ventricular septal defect (HP:0001629)',
},
{
hpo_phenotype_observed: 'Abnormality of the dentition (HP:0000164)',
},
{ hpo_phenotype_observed: 'Abnormality of the eye (HP:0000478)' },
],
fhir_id: 'pt-2282xh6dem',
},
sort: ['pt-2282xh6dem'],
},
],
},
},
statusCode: 200,
}),
indices: {
getMapping: async () => MOCK_ES_PARTICIPANT_MAPPINGS,
},
}));

const sqon = {
content: [
{
content: {
field: 'diagnosis.source_text',
index: 'participant',
value: ['Intellectual disability'],
},
op: 'in',
},
],
op: 'and',
};
const result = await computeUpset(sqon);
expect(result).toEqual({
data: [
{ name: 'Abnormality of the eye (HP:0000478)', elems: ['pt-223twf8ytr', 'pt-2282xh6dem'] },
{ name: 'Seizure (HP:0001250)', elems: ['pt-223twf8ytr'] },
{ name: 'Ventricular septal defect (HP:0001629)', elems: ['pt-2282xh6dem'] },
{ name: 'Abnormality of the dentition (HP:0000164)', elems: ['pt-2282xh6dem'] },
],
participantsCount: 2,
});
});
});
});
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