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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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