@molgenis/vip-report-template 2.7.3 → 3.0.0

package/tests/unit/globals/utils.spec.ts

@@ -1,453 +0,0 @@
-import { getConsequences, getInheritanceModesGeneSelector, getPhenotypesSelector, getVariant } from '@/globals/utils';
-import { Vcf } from '@molgenis/vip-report-api';
-import { mock } from 'ts-mockito';
-import { Consequence } from '@/types/Consequence';
-
-const expectedMetadata = {
-  effect: { id: 'Consequence', type: 'STRING', number: { type: 'OTHER' }, description: 'Consequence' },
-  symbol: { id: 'SYMBOL', type: 'STRING', number: { type: 'NUMBER', count: 1 }, description: 'SYMBOL' },
-  incompletePenetrance: {
-    id: 'IncompletePenetrance',
-    type: 'FLAG',
-    number: { type: 'NUMBER', count: 1 },
-    description: 'IncompletePenetrance'
-  },
-  inheritance: {
-    id: 'InheritanceModesGene',
-    type: 'STRING',
-    number: { type: 'OTHER' },
-    description: 'InheritanceModesGene'
-  },
-  hgvsC: { id: 'hgvsC', type: 'STRING', number: { type: 'NUMBER', count: 1 }, description: 'hgvsC' },
-  hgvsP: { id: 'hgvsP', type: 'STRING', number: { type: 'NUMBER', count: 1 }, description: 'hgvsP' },
-  pubMed: {
-    id: 'PUBMED',
-    type: 'INTEGER',
-    number: { type: 'OTHER' },
-    description: 'Pubmed ID(s) of publications that cite existing variant'
-  },
-  clinVar: {
-    id: 'CLIN_SIG',
-    type: 'STRING',
-    number: { type: 'OTHER' },
-    description: 'ClinVar clinical significance of the dbSNP variant'
-  },
-  gnomAD: {
-    id: 'gnomAD_AF',
-    type: 'FLOAT',
-    number: { type: 'NUMBER', count: 1 },
-    description: 'Frequency of existing variant in gnomAD exomes combined population'
-  },
-  mvl: {
-    id: 'VKGL_UMCG',
-    type: 'STRING',
-    number: { type: 'NUMBER', count: 1 },
-    description: 'UMCG Managed variant list Classification'
-  },
-  vkgl: {
-    id: 'VKGL_CL',
-    type: 'STRING',
-    number: { type: 'NUMBER', count: 1 },
-    description: 'VKGL public consensus'
-  }
-};
-
-function createCsqInfoMetadata(): Vcf.InfoMetadata {
-  const effectInfoMetadata = mock<Vcf.InfoMetadata>();
-  effectInfoMetadata.id = 'Consequence';
-  const symbolInfoMetadata = mock<Vcf.InfoMetadata>();
-  symbolInfoMetadata.id = 'SYMBOL';
-  const hgvsCInfoMetadata = mock<Vcf.InfoMetadata>();
-  hgvsCInfoMetadata.id = 'HGVSc';
-  const hgvsPInfoMetadata = mock<Vcf.InfoMetadata>();
-  hgvsPInfoMetadata.id = 'HGVSp';
-
-  const infoMetadata = mock<Vcf.InfoMetadata>();
-  infoMetadata.id = 'CSQ';
-  infoMetadata.nested = {
-    separator: '|',
-    items: [effectInfoMetadata, hgvsCInfoMetadata, hgvsPInfoMetadata, symbolInfoMetadata]
-  };
-
-  return infoMetadata;
-}
-
-function createCsqInfoMetadataExtended(): Vcf.InfoMetadata {
-  const pubMedMetadata = mock<Vcf.InfoMetadata>();
-  pubMedMetadata.id = 'PUBMED';
-  const clinSigMetadata = mock<Vcf.InfoMetadata>();
-  clinSigMetadata.id = 'CLIN_SIG';
-  const vkglMetadata = mock<Vcf.InfoMetadata>();
-  vkglMetadata.id = 'VKGL_CL';
-  const mvlMetadata = mock<Vcf.InfoMetadata>();
-  mvlMetadata.id = 'VKGL_UMCG';
-  const gnomADMetadata = mock<Vcf.InfoMetadata>();
-  gnomADMetadata.id = 'gnomAD_AF';
-  const hpoMetadata = mock<Vcf.InfoMetadata>();
-  hpoMetadata.id = 'HPO';
-  const inheritanceModesGeneMetadata = mock<Vcf.InfoMetadata>();
-  inheritanceModesGeneMetadata.id = 'InheritanceModesGene';
-  const pickMetadata = mock<Vcf.InfoMetadata>();
-  pickMetadata.id = 'PICK';
-  const alleleNumMetadata = mock<Vcf.InfoMetadata>();
-  alleleNumMetadata.id = 'ALLELE_NUM';
-
-  const csqInfoMetadata = createCsqInfoMetadata();
-  if (csqInfoMetadata.nested !== undefined) {
-    csqInfoMetadata.nested.items.push(pubMedMetadata);
-    csqInfoMetadata.nested.items.push(clinSigMetadata);
-    csqInfoMetadata.nested.items.push(mvlMetadata);
-    csqInfoMetadata.nested.items.push(vkglMetadata);
-    csqInfoMetadata.nested.items.push(gnomADMetadata);
-    csqInfoMetadata.nested.items.push(hpoMetadata);
-    csqInfoMetadata.nested.items.push(inheritanceModesGeneMetadata);
-    csqInfoMetadata.nested.items.push(pickMetadata);
-    csqInfoMetadata.nested.items.push(alleleNumMetadata);
-  }
-  return csqInfoMetadata;
-}
-
-function createAnnInfoMetadata(): Vcf.InfoMetadata {
-  const effectInfoMetadata = mock<Vcf.InfoMetadata>();
-  effectInfoMetadata.id = 'Annotation';
-  const hgvsCInfoMetadata = mock<Vcf.InfoMetadata>();
-  hgvsCInfoMetadata.id = 'HGVS.c';
-  const hgvsPInfoMetadata = mock<Vcf.InfoMetadata>();
-  hgvsPInfoMetadata.id = 'HGVS.p';
-  const symbolInfoMetadata = mock<Vcf.InfoMetadata>();
-  symbolInfoMetadata.id = 'Gene_Name';
-
-  const infoMetadata = mock<Vcf.InfoMetadata>();
-  infoMetadata.id = 'ANN';
-  infoMetadata.nested = {
-    separator: '|',
-    items: [effectInfoMetadata, hgvsCInfoMetadata, hgvsPInfoMetadata, symbolInfoMetadata]
-  };
-
-  return infoMetadata;
-}
-
-test('get consequences in case of no info', () => {
-  const recordMetadata = mock<Vcf.Metadata>();
-  recordMetadata.info = {};
-
-  const record = mock<Vcf.Record>();
-  expect(getConsequences(record, recordMetadata)).toEqual({
-    metadata: expectedMetadata,
-    items: []
-  });
-});
-
-test('get consequences in case of no relevant info', () => {
-  const infoMetadata = mock<Vcf.InfoMetadata>();
-  infoMetadata.id = 'NOT_RELEVANT';
-
-  const recordMetadata = mock<Vcf.Metadata>();
-  recordMetadata.info = { NOT_RELEVANT: infoMetadata };
-
-  const record = mock<Vcf.Record>();
-  expect(getConsequences(record, recordMetadata)).toEqual({
-    metadata: expectedMetadata,
-    items: []
-  });
-});
-
-test('get consequences in case of CSQ info', () => {
-  const recordMetadata = mock<Vcf.Metadata>();
-  recordMetadata.info = { CSQ: createCsqInfoMetadata() };
-
-  const record = mock<Vcf.Record>();
-  record.n = {
-    CSQ: [
-      [['intergenic_variant'], 'hgvsC0', 'hgvsP0', 'symbol0'],
-      [['frameshift_variant'], 'hgvsC1', 'hgvsP1', 'symbol1']
-    ]
-  };
-  expect(getConsequences(record, recordMetadata)).toEqual({
-    metadata: expectedMetadata,
-    items: [
-      {
-        alleleIndex: null,
-        effect: ['frameshift_variant'],
-        symbol: 'symbol1',
-        inheritance: [],
-        primary: null,
-        gnomAD: null,
-        hgvsC: 'hgvsC1',
-        hgvsP: 'hgvsP1',
-        incompletePenetrance: false,
-        pubMed: [],
-        clinVar: [],
-        mvl: null,
-        vkgl: null
-      },
-      {
-        alleleIndex: null,
-        effect: ['intergenic_variant'],
-        symbol: 'symbol0',
-        inheritance: [],
-        primary: null,
-        gnomAD: null,
-        hgvsC: 'hgvsC0',
-        hgvsP: 'hgvsP0',
-        incompletePenetrance: false,
-        pubMed: [],
-        clinVar: [],
-        mvl: null,
-        vkgl: null
-      }
-    ]
-  });
-});
-
-test('get consequences in case of CSQ info with extended info', () => {
-  const recordMetadata = mock<Vcf.Metadata>();
-  recordMetadata.info = { CSQ: createCsqInfoMetadataExtended() };
-
-  const record = mock<Vcf.Record>();
-  record.n = {
-    CSQ: [
-      [
-        ['intergenic_variant'],
-        'hgvsC0',
-        'hgvsP0',
-        'symbol0',
-        ['12345678'],
-        ['benign'],
-        'LP',
-        'VUS',
-        0.2345,
-        'HP:123',
-        [],
-        null,
-        1
-      ],
-      [
-        ['frameshift_variant'],
-        'hgvsC1',
-        'hgvsP1',
-        'symbol1',
-        ['12345678', '23456789'],
-        ['likely_pathogenic', 'pathogenic'],
-        'LB',
-        'B',
-        0.1234,
-        'HP:123',
-        [],
-        '1',
-        2
-      ]
-    ]
-  };
-  expect(getConsequences(record, recordMetadata)).toEqual({
-    metadata: expectedMetadata,
-    items: [
-      {
-        alleleIndex: 2,
-        effect: ['frameshift_variant'],
-        symbol: 'symbol1',
-        inheritance: [],
-        primary: '1',
-        gnomAD: 0.1234,
-        hgvsC: 'hgvsC1',
-        hgvsP: 'hgvsP1',
-        incompletePenetrance: false,
-        pubMed: ['12345678', '23456789'],
-        clinVar: ['likely_pathogenic', 'pathogenic'],
-        vkgl: 'B',
-        mvl: 'LB'
-      },
-      {
-        alleleIndex: 1,
-        effect: ['intergenic_variant'],
-        symbol: 'symbol0',
-        inheritance: [],
-        primary: null,
-        gnomAD: 0.2345,
-        hgvsC: 'hgvsC0',
-        hgvsP: 'hgvsP0',
-        incompletePenetrance: false,
-        pubMed: ['12345678'],
-        clinVar: ['benign'],
-        vkgl: 'VUS',
-        mvl: 'LP'
-      }
-    ]
-  });
-});
-
-test('get consequences in case of ANN info', () => {
-  const recordMetadata = mock<Vcf.Metadata>();
-  recordMetadata.info = { ANN: createAnnInfoMetadata() };
-
-  const record = mock<Vcf.Record>();
-  record.n = {
-    ANN: [
-      [['start_lost'], 'hgvsC0', 'hgvsP0', 'symbol0'],
-      [['missense_variant', 'frameshift_variant'], 'hgvsC1', 'hgvsP1', 'symbol1']
-    ]
-  };
-  expect(getConsequences(record, recordMetadata)).toEqual({
-    metadata: expectedMetadata,
-    items: [
-      {
-        alleleIndex: null,
-        effect: ['missense_variant', 'frameshift_variant'],
-        symbol: 'symbol1',
-        inheritance: [],
-        primary: null,
-        gnomAD: null,
-        hgvsC: 'hgvsC1',
-        hgvsP: 'hgvsP1',
-        incompletePenetrance: false,
-        pubMed: [],
-        clinVar: [],
-        mvl: null,
-        vkgl: null
-      },
-      {
-        alleleIndex: null,
-        effect: ['start_lost'],
-        symbol: 'symbol0',
-        inheritance: [],
-        primary: null,
-        gnomAD: null,
-        hgvsC: 'hgvsC0',
-        hgvsP: 'hgvsP0',
-        incompletePenetrance: false,
-        pubMed: [],
-        clinVar: [],
-        mvl: null,
-        vkgl: null
-      }
-    ]
-  });
-});
-
-test('get consequences in case of CSQ and ANN info', () => {
-  const recordMetadata = mock<Vcf.Metadata>();
-  recordMetadata.info = { ANN: createAnnInfoMetadata(), CSQ: createCsqInfoMetadata() };
-
-  const record = mock<Vcf.Record>();
-  record.n = {
-    ANN: [
-      [['start_lost'], 'hgvsC0', 'hgvsP0', 'symbol0'],
-      [['missense_variant', 'frameshift_variant'], 'hgvsC1', 'hgvsP1', 'symbol1']
-    ],
-    CSQ: [[['intergenic_variant'], 'hgvsC2', 'hgvsP2', 'symbol2']]
-  };
-  expect(getConsequences(record, recordMetadata)).toEqual({
-    metadata: expectedMetadata,
-    items: [
-      {
-        alleleIndex: null,
-        effect: ['missense_variant', 'frameshift_variant'],
-        symbol: 'symbol1',
-        inheritance: [],
-        primary: null,
-        gnomAD: null,
-        hgvsC: 'hgvsC1',
-        hgvsP: 'hgvsP1',
-        incompletePenetrance: false,
-        pubMed: [],
-        clinVar: [],
-        mvl: null,
-        vkgl: null
-      },
-      {
-        alleleIndex: null,
-        effect: ['start_lost'],
-        symbol: 'symbol0',
-        inheritance: [],
-        primary: null,
-        gnomAD: null,
-        hgvsC: 'hgvsC0',
-        hgvsP: 'hgvsP0',
-        incompletePenetrance: false,
-        pubMed: [],
-        clinVar: [],
-        mvl: null,
-        vkgl: null
-      },
-      {
-        alleleIndex: null,
-        effect: ['intergenic_variant'],
-        symbol: 'symbol2',
-        inheritance: [],
-        primary: null,
-        gnomAD: null,
-        hgvsC: 'hgvsC2',
-        hgvsP: 'hgvsP2',
-        incompletePenetrance: false,
-        pubMed: [],
-        clinVar: [],
-        mvl: null,
-        vkgl: null
-      }
-    ]
-  });
-});
-
-test('get phenotypes selector in case of VEP annotations with HPO', () => {
-  const recordMetadata = mock<Vcf.Metadata>();
-  recordMetadata.info = { CSQ: createCsqInfoMetadataExtended() };
-
-  expect(getPhenotypesSelector(recordMetadata)).toEqual(['n', 'CSQ', '*', 9]);
-});
-
-test('get phenotypes selector in case of VEP annotations without HPO', () => {
-  const recordMetadata = mock<Vcf.Metadata>();
-  recordMetadata.info = { CSQ: createCsqInfoMetadata() };
-
-  expect(() => getPhenotypesSelector(recordMetadata)).toThrow();
-});
-
-test('get phenotypes selector in case of SnpEff annotations', () => {
-  const recordMetadata = mock<Vcf.Metadata>();
-  recordMetadata.info = { ANN: createAnnInfoMetadata() };
-
-  expect(() => getPhenotypesSelector(recordMetadata)).toThrow();
-});
-
-test('get inheritance modes gene selector in case of VEP annotations with HPO', () => {
-  const recordMetadata = mock<Vcf.Metadata>();
-  recordMetadata.info = { CSQ: createCsqInfoMetadataExtended() };
-
-  expect(getInheritanceModesGeneSelector(recordMetadata)).toEqual(['n', 'CSQ', '*', 10]);
-});
-
-test('get inheritance modes gene selector in case of VEP annotations without HPO', () => {
-  const recordMetadata = mock<Vcf.Metadata>();
-  recordMetadata.info = { CSQ: createCsqInfoMetadata() };
-
-  expect(() => getInheritanceModesGeneSelector(recordMetadata)).toThrow();
-});
-
-test('get inheritance modes gene selector in case of SnpEff annotations', () => {
-  const recordMetadata = mock<Vcf.Metadata>();
-  recordMetadata.info = { ANN: createAnnInfoMetadata() };
-
-  expect(() => getInheritanceModesGeneSelector(recordMetadata)).toThrow();
-});
-
-test('get variant for consequence with allele index', () => {
-  const record = mock<Vcf.Record>();
-  record.c = '1';
-  record.p = 123;
-  record.r = 'A';
-  record.a = ['T', 'TA'];
-  const consequence = mock<Consequence>();
-  consequence.alleleIndex = 2;
-  expect(getVariant(record, consequence)).toEqual({ chr: '1', pos: 123, ref: 'A', alt: 'TA' });
-});
-
-test('get variant for consequence without allele index', () => {
-  const record = mock<Vcf.Record>();
-  record.c = '1';
-  record.p = 123;
-  record.r = 'A';
-  record.a = ['T', 'TA'];
-  const consequence = mock<Consequence>();
-  consequence.alleleIndex = null;
-  expect(getVariant(record, consequence)).toBeNull();
-});

package/tests/unit/store/actions.spec.ts

@@ -1,191 +0,0 @@
-import actions, { setTestApi } from '@/store/actions';
-import { mock, when } from 'ts-mockito';
-import { Api, ApiClient, Vcf } from '@molgenis/vip-report-api';
-import { ActionContext, Commit } from 'vuex';
-import { State } from '@/types/State';
-import initialState from '@/store/state';
-
-const api: ApiClient = mock(ApiClient);
-setTestApi(api);
-
-test('load metadata', async (done) => {
-  const metadata = mock<Api.Metadata>();
-  when(api.getMeta()).thenReturn(new Promise(() => metadata));
-
-  const commit = jest.fn() as Commit;
-  await actions.loadMetadata({ commit } as ActionContext<State, State>);
-  expect(commit).toHaveBeenCalledWith('setMetadata', metadata);
-  done();
-});
-
-test('load samples', async (done) => {
-  const samples = mock<Api.PagedItems<Api.Sample>>();
-  when(api.getSamples()).thenReturn(new Promise(() => samples));
-
-  const commit = jest.fn() as Commit;
-  await actions.loadSamples({ commit } as ActionContext<State, State>);
-  expect(commit).toHaveBeenCalledWith('setSamples', samples);
-  done();
-});
-
-test('load records without params', async (done) => {
-  const records = mock<Api.PagedItems<Vcf.Record>>();
-  when(api.getRecords()).thenReturn(new Promise(() => records));
-
-  const commit = jest.fn() as Commit;
-  await actions.loadRecords({ commit } as ActionContext<State, State>);
-  expect(commit).toHaveBeenCalledWith('setRecords', records);
-  done();
-});
-
-test('load records with params', async (done) => {
-  const records = mock<Api.PagedItems<Vcf.Record>>();
-  const params = {};
-  when(api.getRecords(params)).thenReturn(new Promise(() => records));
-
-  const commit = jest.fn() as Commit;
-  await actions.loadRecords({ commit } as ActionContext<State, State>, params);
-  expect(commit).toHaveBeenCalledWith('setRecords', records);
-  done();
-});
-
-test('select record', async (done) => {
-  const record = mock<Vcf.Record>();
-  const commit = jest.fn() as Commit;
-  actions.selectRecord({ commit } as ActionContext<State, State>, record);
-  expect(commit).toHaveBeenCalledWith('setSelectedRecord', {});
-  done();
-});
-
-test('select sample and load sample phenotypes', async (done) => {
-  const phenotypes = mock<Api.PagedItems<Api.Phenotype>>();
-  const sample: Api.Sample = {
-    person: {
-      familyId: 'MyFamilyId',
-      individualId: 'personC',
-      paternalId: '0',
-      maternalId: '0',
-      sex: 'MALE',
-      affectedStatus: 'AFFECTED'
-    },
-    index: -1,
-    proband: true
-  };
-  const params: Api.Params = {
-    query: {
-      selector: ['subject', 'id'],
-      operator: '==',
-      args: 'personC'
-    }
-  };
-  when(api.getPhenotypes(params)).thenReturn(new Promise(() => phenotypes));
-
-  const commit = jest.fn() as Commit;
-  await actions.selectSample({ commit } as ActionContext<State, State>, sample);
-  expect(commit).toHaveBeenCalledWith('setSelectedSample', sample);
-  expect(commit).toHaveBeenCalledWith('setSelectedSamplePhenotypes', phenotypes);
-  done();
-});
-
-test('enable annotations', async (done) => {
-  const commit = jest.fn() as Commit;
-  actions.enableAnnotations({ commit } as ActionContext<State, State>);
-  expect(commit).toHaveBeenCalledWith('setAnnotations', {});
-  done();
-});
-
-test('disable annotations', async (done) => {
-  const commit = jest.fn() as Commit;
-  actions.disableAnnotations({ commit } as ActionContext<State, State>);
-  expect(commit).toHaveBeenCalledWith('setAnnotations', null);
-  done();
-});
-
-test('import annotations', async (done) => {
-  const annotations = {
-    'sample0_1_2_A_C,CT': {
-      sampleId: 'sample0',
-      chr: '1',
-      pos: 2,
-      ref: 'A',
-      alt: ['C', 'CT'],
-      geneMatch: 'yes',
-      class: 'LP',
-      txt: 'my notes'
-    }
-  };
-  const commit = jest.fn() as Commit;
-  actions.importAnnotations({ commit } as ActionContext<State, State>, annotations);
-  expect(commit).toHaveBeenCalledWith('setAnnotations', annotations);
-  done();
-});
-
-test('upsert annotations', async (done) => {
-  const annotation = {
-    sampleId: 'sample0',
-    chr: '1',
-    pos: 2,
-    ref: 'A',
-    alt: ['C', 'CT'],
-    geneMatch: 'yes',
-    class: 'LP',
-    txt: 'my notes'
-  };
-  const commit = jest.fn() as Commit;
-  const testState: State = { ...initialState, annotations: {} };
-  actions.upsertAnnotation({ state: testState, commit } as ActionContext<State, State>, annotation);
-  expect(commit).toHaveBeenCalledWith('setAnnotations', { 'sample0_1_2_A_C,CT': annotation });
-  done();
-});
-
-test('set filter records by phenotype', async (done) => {
-  const commit = jest.fn() as Commit;
-  actions.setFilterRecordsByPhenotype({ commit } as ActionContext<State, State>, true);
-  expect(commit).toHaveBeenCalledWith('setFilterRecordsByPhenotype', true);
-  done();
-});
-
-test('set filter records by inheritance', async (done) => {
-  const commit = jest.fn() as Commit;
-  actions.setFilterRecordsByInheritance({ commit } as ActionContext<State, State>, true);
-  expect(commit).toHaveBeenCalledWith('setFilterRecordsByInheritance', true);
-  done();
-});
-
-test('set filter records by denovo status', async (done) => {
-  const commit = jest.fn() as Commit;
-  actions.setFilterRecordsByDenovo({ commit } as ActionContext<State, State>, true);
-  expect(commit).toHaveBeenCalledWith('setFilterRecordsByDenovo', true);
-  done();
-});
-
-test('set filter records by read depth', async (done) => {
-  const commit = jest.fn() as Commit;
-  actions.setFilterRecordsByDepth({ commit } as ActionContext<State, State>, true);
-  expect(commit).toHaveBeenCalledWith('setFilterRecordsByDepth', true);
-  done();
-});
-
-test('get vcf gz', async (done) => {
-  expect(await actions.getVcfGz()).not.toBe(null);
-  done();
-});
-
-test('get fasta gz', async (done) => {
-  const commit = jest.fn() as Commit;
-  expect(await actions.getFastaGz({ commit } as ActionContext<State, State>, { contig: '1', pos: 17350500 })).not.toBe(
-    null
-  );
-  done();
-});
-
-test('get genes gz', async (done) => {
-  expect(await actions.getGenesGz()).not.toBe(null);
-  done();
-});
-
-test('get bam', async (done) => {
-  const commit = jest.fn() as Commit;
-  expect(await actions.getBam({ commit } as ActionContext<State, State>, 'Patient')).not.toBe(null);
-  done();
-});