@molgenis/vip-report-template 2.7.3 → 3.0.0

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

@@ -1,660 +0,0 @@
-import initialState from '@/store/state';
-import getters from '@/store/getters';
-import { State } from '@/types/State';
-import { GenomeBrowserDb } from '@/types/GenomeBrowserDb';
-import { mock } from 'ts-mockito';
-import { Api, Vcf } from '@molgenis/vip-report-api';
-
-test('samples returns empty array in case of no samples', () => {
-  const testState: State = { ...initialState };
-  expect(getters.samples(testState)).toStrictEqual([]);
-});
-
-test('samples returns array sorted by sample id', () => {
-  const person0: Api.Person = mock<Api.Person>();
-  person0.individualId = 'personC';
-  const sample0: Api.Sample = mock<Api.Sample>();
-  sample0.person = person0;
-  const person1: Api.Person = mock<Api.Person>();
-  person1.individualId = 'personA';
-  const sample1: Api.Sample = mock<Api.Sample>();
-  sample1.person = person1;
-  const person2: Api.Person = mock<Api.Person>();
-  person2.individualId = 'personB';
-  const sample2: Api.Sample = mock<Api.Sample>();
-  sample2.person = person2;
-
-  const samples: Api.PagedItems<Api.Sample> = mock<Api.PagedItems<Api.Sample>>();
-  samples.items = [sample2, sample0, sample1, sample2];
-
-  const testState: State = { ...initialState, samples };
-  expect(getters.samples(testState).map((sample) => sample.person.individualId)).toEqual([
-    'personA',
-    'personB',
-    'personB',
-    'personC'
-  ]);
-});
-
-test('get sample by id returns null in case of no samples', () => {
-  const testState: State = { ...initialState };
-  expect(getters.getSampleById(testState)('MySampleId')).toBe(null);
-});
-
-test('get sample by id returns null in case of unknown sample', () => {
-  const person0: Api.Person = mock<Api.Person>();
-  person0.individualId = 'MySampleId';
-  const sample0: Api.Sample = mock<Api.Sample>();
-  sample0.person = person0;
-
-  const samples: Api.PagedItems<Api.Sample> = mock<Api.PagedItems<Api.Sample>>();
-  samples.items = [sample0];
-
-  const testState: State = { ...initialState, samples };
-  expect(getters.getSampleById(testState)('UnknownSampleId')).toBe(null);
-});
-
-test('get sample by id returns sample in case of known sample', () => {
-  const person0: Api.Person = mock<Api.Person>();
-  person0.individualId = 'MySampleId';
-  const sample0: Api.Sample = mock<Api.Sample>();
-  sample0.person = person0;
-
-  const samples: Api.PagedItems<Api.Sample> = mock<Api.PagedItems<Api.Sample>>();
-  samples.items = [sample0];
-
-  const testState: State = { ...initialState, samples };
-  expect(getters.getSampleById(testState)('MySampleId')).toBe(sample0);
-});
-
-test('get maternal sample for selected sample', () => {
-  const person: Api.Person = mock<Api.Person>();
-  person.individualId = 'sample';
-  person.maternalId = 'sampleMother';
-
-  const sample: Api.Sample = mock<Api.Sample>();
-  sample.person = person;
-
-  const personMother: Api.Person = mock<Api.Person>();
-  personMother.individualId = 'sampleMother';
-  const sampleMother: Api.Sample = mock<Api.Sample>();
-  sampleMother.person = personMother;
-
-  const samples: Api.PagedItems<Api.Sample> = mock<Api.PagedItems<Api.Sample>>();
-  samples.items = [sample, sampleMother];
-
-  const testState: State = { ...initialState, samples, selectedSample: sample };
-  expect(getters.sampleMaternal(testState)).toBe(sampleMother);
-});
-
-test('get maternal sample in case of no selected sample', () => {
-  const person: Api.Person = mock<Api.Person>();
-  person.individualId = 'sample';
-  person.maternalId = 'sampleMother';
-
-  const sample: Api.Sample = mock<Api.Sample>();
-  sample.person = person;
-
-  const personMother: Api.Person = mock<Api.Person>();
-  personMother.individualId = 'sampleMother';
-  const sampleMother: Api.Sample = mock<Api.Sample>();
-  sampleMother.person = personMother;
-
-  const samples: Api.PagedItems<Api.Sample> = mock<Api.PagedItems<Api.Sample>>();
-  samples.items = [sample, sampleMother];
-
-  const testState: State = { ...initialState, samples };
-  expect(getters.sampleMaternal(testState)).toBe(null);
-});
-
-test('get maternal sample in case of no samples', () => {
-  const testState: State = { ...initialState };
-  expect(getters.sampleMaternal(testState)).toBeNull();
-});
-
-test('get maternal sample in case of no samples with a selected sample', () => {
-  const person: Api.Person = mock<Api.Person>();
-  person.individualId = 'sample';
-  person.maternalId = '0';
-
-  const sample: Api.Sample = mock<Api.Sample>();
-  sample.person = person;
-
-  const testState: State = { ...initialState, selectedSample: sample };
-  expect(getters.sampleMaternal(testState)).toBeNull();
-});
-
-test('get maternal sample for selected sample without maternal sample', () => {
-  const person: Api.Person = mock<Api.Person>();
-  person.individualId = 'sample';
-  person.maternalId = '0';
-
-  const sample: Api.Sample = mock<Api.Sample>();
-  sample.person = person;
-
-  const samples: Api.PagedItems<Api.Sample> = mock<Api.PagedItems<Api.Sample>>();
-  samples.items = [sample];
-
-  const testState: State = { ...initialState, samples, selectedSample: sample };
-  expect(getters.sampleMaternal(testState)).toBeNull();
-});
-
-test('get paternal sample for selected sample', () => {
-  const person: Api.Person = mock<Api.Person>();
-  person.individualId = 'sample';
-  person.paternalId = 'sampleFather';
-
-  const sample: Api.Sample = mock<Api.Sample>();
-  sample.person = person;
-
-  const personFather: Api.Person = mock<Api.Person>();
-  personFather.individualId = 'sampleFather';
-  const sampleFather: Api.Sample = mock<Api.Sample>();
-  sampleFather.person = personFather;
-
-  const samples: Api.PagedItems<Api.Sample> = mock<Api.PagedItems<Api.Sample>>();
-  samples.items = [sample, sampleFather];
-
-  const testState: State = { ...initialState, samples, selectedSample: sample };
-  expect(getters.samplePaternal(testState)).toBe(sampleFather);
-});
-
-test('get paternal sample in case of no selected sample', () => {
-  const person: Api.Person = mock<Api.Person>();
-  person.individualId = 'sample';
-  person.paternalId = 'sampleFather';
-
-  const sample: Api.Sample = mock<Api.Sample>();
-  sample.person = person;
-
-  const personFather: Api.Person = mock<Api.Person>();
-  personFather.individualId = 'sampleFather';
-  const sampleFather: Api.Sample = mock<Api.Sample>();
-  sampleFather.person = personFather;
-
-  const samples: Api.PagedItems<Api.Sample> = mock<Api.PagedItems<Api.Sample>>();
-  samples.items = [sample, sampleFather];
-
-  const testState: State = { ...initialState, samples };
-  expect(getters.samplePaternal(testState)).toBeNull();
-});
-
-test('get paternal sample for selected sample without paternal sample', () => {
-  const person: Api.Person = mock<Api.Person>();
-  person.individualId = 'sample';
-  person.paternalId = '0';
-
-  const sample: Api.Sample = mock<Api.Sample>();
-  sample.person = person;
-
-  const personFather: Api.Person = mock<Api.Person>();
-  personFather.individualId = 'sampleFather';
-  const sampleFather: Api.Sample = mock<Api.Sample>();
-  sampleFather.person = personFather;
-
-  const samples: Api.PagedItems<Api.Sample> = mock<Api.PagedItems<Api.Sample>>();
-  samples.items = [sample, sampleFather];
-
-  const testState: State = { ...initialState, samples, selectedSample: sample };
-  expect(getters.samplePaternal(testState)).toBeNull();
-});
-
-test('get paternal sample in case of no samples with a selected sample', () => {
-  const person: Api.Person = mock<Api.Person>();
-  person.individualId = 'sample';
-  person.maternalId = '0';
-
-  const sample: Api.Sample = mock<Api.Sample>();
-  sample.person = person;
-
-  const testState: State = { ...initialState, selectedSample: sample };
-  expect(getters.samplePaternal(testState)).toBeNull();
-});
-
-test('get genomeBrowserDb for NCBI34 assembly', () => {
-  const metadata = mock<Api.Metadata>();
-  metadata.htsFile = mock<Api.HtsFileMetadata>();
-  metadata.htsFile.genomeAssembly = 'NCBI34';
-
-  const testState: State = { ...initialState, metadata: metadata };
-  expect(getters.genomeBrowserDb(testState)).toBe(GenomeBrowserDb.hg16);
-});
-
-test('get genomeBrowserDb for NCBI35 assembly', () => {
-  const metadata = mock<Api.Metadata>();
-  metadata.htsFile = mock<Api.HtsFileMetadata>();
-  metadata.htsFile.genomeAssembly = 'NCBI35';
-
-  const testState: State = { ...initialState, metadata: metadata };
-  expect(getters.genomeBrowserDb(testState)).toBe(GenomeBrowserDb.hg17);
-});
-
-test('get genomeBrowserDb for NCBI36 assembly', () => {
-  const metadata = mock<Api.Metadata>();
-  metadata.htsFile = mock<Api.HtsFileMetadata>();
-  metadata.htsFile.genomeAssembly = 'NCBI36';
-
-  const testState: State = { ...initialState, metadata: metadata };
-  expect(getters.genomeBrowserDb(testState)).toBe(GenomeBrowserDb.hg18);
-});
-
-test('get genomeBrowserDb for GRCh37 assembly', () => {
-  const metadata = mock<Api.Metadata>();
-  metadata.htsFile = mock<Api.HtsFileMetadata>();
-  metadata.htsFile.genomeAssembly = 'GRCh37';
-
-  const testState: State = { ...initialState, metadata: metadata };
-  expect(getters.genomeBrowserDb(testState)).toBe(GenomeBrowserDb.hg19);
-});
-
-test('get genomeBrowserDb for GRCh38 assembly', () => {
-  const metadata = mock<Api.Metadata>();
-  metadata.htsFile = mock<Api.HtsFileMetadata>();
-  metadata.htsFile.genomeAssembly = 'GRCh38';
-
-  const testState: State = { ...initialState, metadata: metadata };
-  expect(getters.genomeBrowserDb(testState)).toBe(GenomeBrowserDb.hg38);
-});
-
-test('get genomeBrowserDb for UNKNOWN assembly', () => {
-  const metadata = mock<Api.Metadata>();
-  metadata.htsFile = mock<Api.HtsFileMetadata>();
-  metadata.htsFile.genomeAssembly = 'UNKNOWN';
-
-  const testState: State = { ...initialState, metadata: metadata };
-  expect(getters.genomeBrowserDb(testState)).toBe(null);
-});
-
-test('get genomeBrowserDb when no metadata available', () => {
-  const testState: State = { ...initialState };
-  expect(getters.genomeBrowserDb(testState)).toBe(null);
-});
-
-test('metadata has consequences', () => {
-  const infoMetadata = mock<Vcf.InfoMetadata>();
-  infoMetadata.id = 'CSQ';
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = { CSQ: infoMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = { ...initialState, metadata: metadata };
-  expect(getters.hasConsequences(testState)).toBe(true);
-});
-
-test('metadata has no consequences', () => {
-  const infoMetadata = mock<Vcf.InfoMetadata>();
-  infoMetadata.id = 'NO_CSQ';
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = { NO_CSQ: infoMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = { ...initialState, metadata: metadata };
-  expect(getters.hasConsequences(testState)).toBe(false);
-});
-
-test('metadata has CAPICE', () => {
-  const infoMetadata = mock<Vcf.InfoMetadata>();
-  infoMetadata.id = 'CAP';
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = { CAP: infoMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = { ...initialState, metadata: metadata };
-  expect(getters.hasCapice(testState)).toBe(true);
-});
-
-test('metadata has no CAPICE', () => {
-  const infoMetadata = mock<Vcf.InfoMetadata>();
-  infoMetadata.id = 'NO_CAP';
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = { NO_CAP: infoMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = { ...initialState, metadata: metadata };
-  expect(getters.hasCapice(testState)).toBe(false);
-});
-
-test('annotations are enabled', () => {
-  const testState: State = { ...initialState, annotations: {} };
-  expect(getters.isAnnotationEnabled(testState)).toBe(true);
-});
-
-test('annotations are disabled', () => {
-  const testState: State = { ...initialState, annotations: null };
-  expect(getters.isAnnotationEnabled(testState)).toBe(false);
-});
-
-test('get existing annotation', () => {
-  const person: Api.Person = mock<Api.Person>();
-  person.individualId = 'sample0';
-  const sample: Api.Sample = mock<Api.Sample>();
-  sample.person = person;
-
-  const record = mock<Vcf.Record>();
-  record.c = '1';
-  record.p = 2;
-  record.r = 'A';
-  record.a = ['C', 'CT'];
-
-  const annotation = {
-    sampleId: 'sample0',
-    chr: '1',
-    pos: 2,
-    ref: 'A',
-    alt: ['C', 'CT'],
-    geneMatch: 'true',
-    class: 'LP',
-    txt: null
-  };
-  const testState: State = {
-    ...initialState,
-    selectedSample: sample,
-    annotations: { 'sample0_1_2_A_C,CT': annotation }
-  };
-  expect(getters.getAnnotation(testState)(record)).toEqual(annotation);
-});
-
-test('get non-existing annotation', () => {
-  const person: Api.Person = mock<Api.Person>();
-  person.individualId = 'sample1';
-  const sample: Api.Sample = mock<Api.Sample>();
-  sample.person = person;
-
-  const record = mock<Vcf.Record>();
-  record.c = '1';
-  record.p = 2;
-  record.r = 'A';
-  record.a = ['C'];
-
-  const annotation = {
-    sampleId: 'sample1',
-    chr: '1',
-    pos: 2,
-    ref: 'A',
-    alt: ['C'],
-    geneMatch: null,
-    class: null,
-    txt: null
-  };
-  const testState: State = {
-    ...initialState,
-    selectedSample: sample,
-    annotations: {}
-  };
-  expect(getters.getAnnotation(testState)(record)).toEqual(annotation);
-});
-
-test('get annotation in case of no annotations', () => {
-  const person: Api.Person = mock<Api.Person>();
-  person.individualId = 'sample0';
-  const sample: Api.Sample = mock<Api.Sample>();
-  sample.person = person;
-
-  const record = mock<Vcf.Record>();
-  record.c = '1';
-  record.p = 2;
-  record.r = 'A';
-  record.a = ['C', 'CT'];
-
-  const testState: State = {
-    ...initialState,
-    selectedSample: sample
-  };
-  expect(() => getters.getAnnotation(testState)(record)).toThrow();
-});
-
-test('get annotation in case of no selected sample', () => {
-  const testState: State = {
-    ...initialState,
-    annotations: {}
-  };
-
-  const record = mock<Vcf.Record>();
-  record.c = '1';
-  record.p = 2;
-  record.r = 'A';
-  record.a = ['C', 'CT'];
-
-  expect(() => getters.getAnnotation(testState)(record)).toThrow();
-});
-
-test('whether records contain phenotype associations', () => {
-  const hpoMetadata = mock<Vcf.InfoMetadata>();
-  hpoMetadata.id = 'HPO';
-
-  const infoMetadata = mock<Vcf.InfoMetadata>();
-  infoMetadata.id = 'CSQ';
-  infoMetadata.nested = { separator: '|', items: [hpoMetadata] };
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = { CSQ: infoMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isRecordsContainPhenotypes(testState)).toEqual(true);
-});
-
-test('whether records contain phenotype associations with VEP without HPO', () => {
-  const infoMetadata = mock<Vcf.InfoMetadata>();
-  infoMetadata.id = 'CSQ';
-  infoMetadata.nested = { separator: '|', items: [] };
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = { CSQ: infoMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isRecordsContainPhenotypes(testState)).toEqual(false);
-});
-
-test('whether records contain MVL annotations', () => {
-  const mvlMetadata = mock<Vcf.InfoMetadata>();
-  mvlMetadata.id = 'VKGL_UMCG';
-
-  const infoMetadata = mock<Vcf.InfoMetadata>();
-  infoMetadata.id = 'CSQ';
-  infoMetadata.nested = { separator: '|', items: [mvlMetadata] };
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = { CSQ: infoMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isRecordsContainMvl(testState)).toEqual(true);
-});
-
-test('whether records contain MVL annotations - false', () => {
-  const infoMetadata = mock<Vcf.InfoMetadata>();
-  infoMetadata.id = 'CSQ';
-  infoMetadata.nested = { separator: '|', items: [] };
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = { CSQ: infoMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isRecordsContainMvl(testState)).toEqual(false);
-});
-
-test('whether records contain MVL annotations - no meta', () => {
-  const testState: State = {
-    ...initialState
-  };
-  expect(getters.isRecordsContainMvl(testState)).toEqual(false);
-});
-
-test('whether records contain MVL annotations - no info meta', () => {
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = {};
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isRecordsContainMvl(testState)).toEqual(false);
-});
-
-test('whether records contain MVL annotations - no nested meta', () => {
-  const infoMetadata = mock<Vcf.InfoMetadata>();
-  infoMetadata.id = 'CSQ';
-  infoMetadata.nested = undefined;
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = { CSQ: infoMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isRecordsContainMvl(testState)).toEqual(false);
-});
-
-test('whether records contain phenotype associations without VEP', () => {
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.info = {};
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isRecordsContainPhenotypes(testState)).toEqual(false);
-});
-
-test('whether records contain inheritance matching information. true.', () => {
-  const formatMetadata = mock<Vcf.FormatMetadata>();
-  formatMetadata.id = 'VIM';
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.format = { VIM: formatMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isSamplesContainInheritance(testState)).toEqual(true);
-});
-
-test('whether records contain inheritance matching information. false.', () => {
-  const formatMetadata = mock<Vcf.FormatMetadata>();
-  formatMetadata.id = 'OTHER';
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.format = { OTHER: formatMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isSamplesContainInheritance(testState)).toEqual(false);
-});
-
-test('whether records contain inheritance matching information. null.', () => {
-  const metadata = null;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isSamplesContainInheritance(testState)).toEqual(false);
-});
-
-test('whether records contain denovo information. true.', () => {
-  const formatMetadata = mock<Vcf.FormatMetadata>();
-  formatMetadata.id = 'VID';
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.format = { VID: formatMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isSamplesContainDenovo(testState)).toEqual(true);
-});
-
-test('whether records contain denovo information. false.', () => {
-  const formatMetadata = mock<Vcf.FormatMetadata>();
-  formatMetadata.id = 'OTHER';
-
-  const recordsMetadata = mock<Vcf.Metadata>();
-  recordsMetadata.format = { OTHER: formatMetadata };
-
-  const metadata = mock<Api.Metadata>();
-  metadata.records = recordsMetadata;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isSamplesContainDenovo(testState)).toEqual(false);
-});
-
-test('whether records contain denovo information. null.', () => {
-  const metadata = null;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isSamplesContainDenovo(testState)).toEqual(false);
-});
-
-test('whether records contain read depth information. null.', () => {
-  const metadata = null;
-
-  const testState: State = {
-    ...initialState,
-    metadata: metadata
-  };
-  expect(getters.isSamplesContainDepth(testState)).toEqual(false);
-});