import { assert } from 'chai'; import { getCaseViewElt, makeClinicalTrackTooltip, makeGeneticTrackTooltip_getCoverageInformation, makeHeatmapTrackTooltip, } from './TooltipUtils'; import { AnnotatedExtendedAlteration } from '../../../pages/resultsView/ResultsViewPageStore'; import { AlterationTypeConstants } from 'shared/constants'; import $ from 'jquery'; import { MolecularProfile } from 'cbioportal-ts-api-client'; import { getPatientViewUrl, getSampleViewUrl } from '../../api/urls'; import { getServerConfig } from 'config/config'; import ServerConfigDefaults from 'config/serverConfigDefaults'; import { PUTATIVE_DRIVER, PUTATIVE_PASSENGER } from 'shared/lib/StoreUtils'; import { makeGeneticTrackTooltip } from 'shared/components/oncoprint/makeGeneticTrackTooltip'; import { AnnotatedStructuralVariant } from 'shared/model/AnnotatedMutation'; describe('Oncoprint TooltipUtils', () => { describe('getCaseViewElt', () => { it('gives empty result for no input', () => { assert.equal(getCaseViewElt([], false), ''); }); it('shows case id if single input and no linkout', () => { assert.equal( getCaseViewElt( [ { sample: 'sampleID', patient: 'patientID', study_id: 'studyID', }, ], false ), 'sampleID' ); assert.equal( getCaseViewElt( [{ patient: 'patientID', study_id: 'studyID' }], false ), 'patientID' ); }); it('shows link if single input and linkout', () => { let elt = $( getCaseViewElt( [ { sample: 'sampleID', patient: 'patientID', study_id: 'studyID', }, ], true ) ); assert.equal( elt.attr('href'), getSampleViewUrl('studyID', 'sampleID') ); assert.equal(elt.text(), 'sampleID'); elt = $( getCaseViewElt( [{ patient: 'patientID', study_id: 'studyID' }], true ) ); assert.equal( elt.attr('href'), getPatientViewUrl('studyID', 'patientID') ); assert.equal(elt.text(), 'patientID'); }); it('shows number if multiple input and no linkout', () => { assert.equal( getCaseViewElt( [ { sample: 'sampleID', patient: 'patientID', study_id: 'studyID', }, { sample: 'sampleID2', patient: 'patientID2', study_id: 'studyID', }, { sample: 'sampleID3', patient: 'patientID3', study_id: 'studyID', }, ], false ), '3 samples' ); assert.equal( getCaseViewElt( [ { patient: 'patientID', study_id: 'studyID' }, { patient: 'patientID2', study_id: 'studyID' }, { patient: 'patientID3', study_id: 'studyID' }, ], false ), '3 patients' ); }); it('shows link if multiple input and linkout', () => { let elt = $( getCaseViewElt( [ { sample: 'sampleID', patient: 'patientID', study_id: 'studyID', }, { sample: 'sampleID2', patient: 'patientID2', study_id: 'studyID', }, { sample: 'sampleID3', patient: 'patientID3', study_id: 'studyID', }, ], true ) ); assert.equal( elt.attr('href'), getSampleViewUrl('studyID', 'sampleID', [ { patientId: 'patientID', studyId: 'studyID' }, { patientId: 'patientID2', studyId: 'studyID' }, { patientId: 'patientID3', studyId: 'studyID' }, ]) ); assert.equal(elt.text(), 'View these 3 samples'); elt = $( getCaseViewElt( [ { patient: 'patientID', study_id: 'studyID' }, { patient: 'patientID2', study_id: 'studyID' }, { patient: 'patientID3', study_id: 'studyID' }, ], true ) ); assert.equal( elt.attr('href'), getPatientViewUrl('studyID', 'patientID', [ { patientId: 'patientID', studyId: 'studyID' }, { patientId: 'patientID2', studyId: 'studyID' }, { patientId: 'patientID3', studyId: 'studyID' }, ]) ); assert.equal(elt.text(), 'View these 3 patients'); }); }); describe('makeGeneticTrackTooltip', () => { let tooltip: (d: any) => JQuery; beforeAll(() => { tooltip = makeGeneticTrackTooltip(false, () => ({ profile: ({ molecularProfileId: 'profile', name: 'Profile', } as any) as MolecularProfile, profile2: ({ molecularProfileId: 'profile2', name: 'Profile2', } as any) as MolecularProfile, profile3: ({ molecularProfileId: 'profile3', name: 'Profile3', } as any) as MolecularProfile, })); }); function makeMutation( props: Partial ): AnnotatedExtendedAlteration { return { hugoGeneSymbol: 'GENE', proteinChange: 'proteinchange', molecularProfileAlterationType: AlterationTypeConstants.MUTATION_EXTENDED, ...props, } as AnnotatedExtendedAlteration; } function makeStructuralVariant( props: Partial ): AnnotatedStructuralVariant { return { hugoGeneSymbol: 'GENE', site1HugoSymbol: 'GENE', molecularProfileAlterationType: AlterationTypeConstants.STRUCTURAL_VARIANT, variantClass: 'fusion', ...props, } as AnnotatedStructuralVariant; } function makeCna( props: Partial ): AnnotatedExtendedAlteration { return { hugoGeneSymbol: 'GENE', molecularProfileAlterationType: AlterationTypeConstants.COPY_NUMBER_ALTERATION, ...props, } as AnnotatedExtendedAlteration; } function makeMrna( props: Partial ): AnnotatedExtendedAlteration { return { hugoGeneSymbol: 'GENE', molecularProfileAlterationType: AlterationTypeConstants.MRNA_EXPRESSION, ...props, } as AnnotatedExtendedAlteration; } function makeProt( props: Partial ): AnnotatedExtendedAlteration { return { hugoGeneSymbol: 'GENE', molecularProfileAlterationType: AlterationTypeConstants.PROTEIN_LEVEL, ...props, } as AnnotatedExtendedAlteration; } describe('custom driver annotations', () => { it('should show a binary custom driver icon with descriptive title, if theres a binary custom driver annotation', () => { const datum = { sample: 'sample', study_id: '', data: [ makeMutation({ driverFilter: PUTATIVE_DRIVER, driverFilterAnnotation: 'annotation here', }), ], }; const datum2 = { sample: 'sample', study_id: '', data: [ makeMutation({ driverFilter: PUTATIVE_DRIVER, driverFilterAnnotation: 'annotation here', }), ], }; const datum3 = { sample: 'sample', study_id: '', data: [], }; let tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: annotation here']" ).length, 1 ); assert.equal( tooltipOutput.find("img[alt='driver filter']").length, 1, 'should only be one icon' ); assert.isFalse( tooltipOutput.html().indexOf('(1)') > -1, 'theres no (1) because theres only one datum to the tooltip' ); tooltipOutput = tooltip([datum, datum2]); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: annotation here']" ).length, 1, 'mutation appears once' ); assert.equal( tooltipOutput.find("img[alt='driver filter']").length, 1, 'should only be one icon, because mutation appears once in tooltip' ); assert.isTrue( tooltipOutput.html().indexOf('(2)') > -1, 'theres a (2) indicating 2 samples have that mutation' ); tooltipOutput = tooltip([datum, datum3]); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: annotation here']" ).length, 1 ); assert.equal( tooltipOutput.find("img[alt='driver filter']").length, 1, 'should only be one icon' ); assert.isTrue( tooltipOutput.html().indexOf('(1)') > -1, 'theres a (1) indicating 1 sample has that mutation' ); }); it('should show multiple binary custom driver icons with corresponding titles, if there are multiple annotated mutations', () => { const datum = { sample: 'sample', study_id: '', data: [ makeMutation({ driverFilter: PUTATIVE_DRIVER, driverFilterAnnotation: 'annotation 1', }), makeMutation({ driverFilter: PUTATIVE_DRIVER, driverFilterAnnotation: 'annotation 2', }), makeMutation({ driverFilter: PUTATIVE_DRIVER, driverFilterAnnotation: '3 annotation', }), ], }; const datum2 = { sample: 'sample', study_id: '', data: [ makeMutation({ driverFilter: PUTATIVE_DRIVER, driverFilterAnnotation: 'annotation 1', }), makeMutation({ driverFilter: PUTATIVE_DRIVER, driverFilterAnnotation: 'annotation 2', }), makeMutation({ driverFilter: PUTATIVE_DRIVER, driverFilterAnnotation: '3 annotation', }), ], }; const datum3 = { sample: 'sample', study_id: '', data: [], }; let tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: annotation 1']" ).length, 1 ); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: annotation 2']" ).length, 1 ); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: 3 annotation']" ).length, 1 ); assert.equal( tooltipOutput.find("img[alt='driver filter']").length, 3, 'should be three icons' ); assert.isFalse( tooltipOutput.html().indexOf('(1)') > -1, 'theres no (1) because theres only one datum to the tooltip' ); tooltipOutput = tooltip([datum, datum2]); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: annotation 1']" ).length, 1, 'mutation 1 appears once' ); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: annotation 2']" ).length, 1, 'mutation 2 appears once' ); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: 3 annotation']" ).length, 1, 'mutation 3 appears once' ); assert.equal( tooltipOutput.find("img[alt='driver filter']").length, 3, 'should be three icons' ); assert.equal( tooltipOutput.html().match(/\(2\)/g)!.length, 3, 'the string (2) appears thrice, one for each mutation which occurs in 2 data' ); tooltipOutput = tooltip([datum, datum3]); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: annotation 1']" ).length, 1, 'mutation 1 appears once' ); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: annotation 2']" ).length, 1, 'mutation 2 appears once' ); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: 3 annotation']" ).length, 1, 'mutation 3 appears once' ); assert.equal( tooltipOutput.find("img[alt='driver filter']").length, 3, 'should be three icons' ); assert.equal( tooltipOutput.html().match(/\(1\)/g)!.length, 3, 'the string (1) appears thrice, one for each mutation which occurs in 1 data' ); }); it('should not show a binary custom driver icon with descriptive title, if theres a binary annotation of non-driver', () => { const datum = { sample: 'sample', study_id: '', data: [ makeMutation({ driverFilter: PUTATIVE_PASSENGER, driverFilterAnnotation: 'paosidjp', }), makeMutation({ driverFilter: 'Unknown', driverFilterAnnotation: 'asdfas', }), ], }; const tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.find("img[alt='driver filter']").length, 0 ); }); it('should show a tiers custom driver icon with descriptive title, if theres a tiers custom driver annotation', () => { const datum = { sample: 'sample', study_id: '', data: [ makeMutation({ driverTiersFilter: 'tier1', driverTiersFilterAnnotation: 'tier1 mutation', }), ], }; const datum2 = { sample: 'sample', study_id: '', data: [ makeMutation({ driverTiersFilter: 'tier1', driverTiersFilterAnnotation: 'tier1 mutation', }), ], }; const datum3 = { sample: 'sample', study_id: '', data: [], }; let tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.find("img[title='tier1: tier1 mutation']") .length, 1 ); assert.equal( tooltipOutput.find("img[alt='driver tiers filter']").length, 1, 'should only be one icon' ); assert.isFalse( tooltipOutput.html().indexOf('(1)') > -1, 'theres no (1) because theres only one datum to the tooltip' ); tooltipOutput = tooltip([datum, datum2]); assert.equal( tooltipOutput.find("img[title='tier1: tier1 mutation']") .length, 1 ); assert.equal( tooltipOutput.find("img[alt='driver tiers filter']").length, 1, 'should only be one icon, one entry for the mutation' ); assert.isTrue( tooltipOutput.html().indexOf('(2)') > -1, 'theres a (2) indicating 2 samples have that mutation' ); tooltipOutput = tooltip([datum, datum3]); assert.equal( tooltipOutput.find("img[title='tier1: tier1 mutation']") .length, 1 ); assert.equal( tooltipOutput.find("img[alt='driver tiers filter']").length, 1, 'should only be one icon' ); assert.isTrue( tooltipOutput.html().indexOf('(1)') > -1, 'theres a (1) indicating 1 sample has that mutation' ); }); it('should show multiple tiers icons with corresponding titles, if there are multiple annotated mutations', () => { const datum = { sample: 'sample', study_id: '', data: [ makeMutation({ driverTiersFilter: 'tier2', driverTiersFilterAnnotation: 'tier2 mutation', }), makeMutation({ driverTiersFilter: 'tier1', driverTiersFilterAnnotation: 'tier1 mutation', }), makeMutation({ driverTiersFilter: 'tier4', driverTiersFilterAnnotation: 'mutation tier4', }), ], }; const datum2 = { sample: 'sample', study_id: '', data: [ makeMutation({ driverTiersFilter: 'tier2', driverTiersFilterAnnotation: 'tier2 mutation', }), makeMutation({ driverTiersFilter: 'tier1', driverTiersFilterAnnotation: 'tier1 mutation', }), makeMutation({ driverTiersFilter: 'tier4', driverTiersFilterAnnotation: 'mutation tier4', }), ], }; const datum3 = { sample: 'sample', study_id: '', data: [], }; let tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.find("img[title='tier1: tier1 mutation']") .length, 1 ); assert.equal( tooltipOutput.find("img[title='tier2: tier2 mutation']") .length, 1 ); assert.equal( tooltipOutput.find("img[title='tier4: mutation tier4']") .length, 1 ); assert.equal( tooltipOutput.find("img[alt='driver tiers filter']").length, 3, 'should be three icons' ); assert.isFalse( tooltipOutput.html().indexOf('(1)') > -1, 'theres no (1) because theres only one datum to the tooltip' ); tooltipOutput = tooltip([datum, datum2]); assert.equal( tooltipOutput.find("img[title='tier1: tier1 mutation']") .length, 1, 'mutation 1 appears once' ); assert.equal( tooltipOutput.find("img[title='tier2: tier2 mutation']") .length, 1, 'mutation 2 appears once' ); assert.equal( tooltipOutput.find("img[title='tier4: mutation tier4']") .length, 1, 'mutation 3 appears once' ); assert.equal( tooltipOutput.find("img[alt='driver tiers filter']").length, 3, 'should be three icons' ); assert.equal( tooltipOutput.html().match(/\(2\)/g)!.length, 3, 'the string (2) appears thrice, one for each mutation which occurs in 2 data' ); tooltipOutput = tooltip([datum3, datum]); assert.equal( tooltipOutput.find("img[title='tier1: tier1 mutation']") .length, 1, 'mutation 1 appears once' ); assert.equal( tooltipOutput.find("img[title='tier2: tier2 mutation']") .length, 1, 'mutation 2 appears once' ); assert.equal( tooltipOutput.find("img[title='tier4: mutation tier4']") .length, 1, 'mutation 3 appears once' ); assert.equal( tooltipOutput.find("img[alt='driver tiers filter']").length, 3, 'should be three icons' ); assert.equal( tooltipOutput.html().match(/\(1\)/g)!.length, 3, 'the string (1) appears thrice, one for each mutation which occurs in 1 data' ); }); it('should show both binary and tiers custom driver icons, with descriptive titles, if there are both annotations', () => { const datum = { sample: 'sample', study_id: '', data: [ makeMutation({ driverFilter: PUTATIVE_DRIVER, driverFilterAnnotation: 'annotation 1', }), makeMutation({ driverFilter: PUTATIVE_DRIVER, driverFilterAnnotation: 'annotation 2', }), makeMutation({ driverFilter: PUTATIVE_DRIVER, driverFilterAnnotation: '3 annotation', }), makeMutation({ driverFilter: PUTATIVE_PASSENGER, driverFilterAnnotation: 'paosidjp', }), makeMutation({ driverFilter: 'Unknown', driverFilterAnnotation: 'asdfas', }), makeMutation({ driverTiersFilter: 'tier2', driverTiersFilterAnnotation: 'tier2 mutation', }), makeMutation({ driverTiersFilter: 'tier1', driverTiersFilterAnnotation: 'tier1 mutation', }), makeMutation({ driverTiersFilter: 'tier4', driverTiersFilterAnnotation: 'mutation tier4', }), ], }; const tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.find("img[title='tier1: tier1 mutation']") .length, 1 ); assert.equal( tooltipOutput.find("img[title='tier2: tier2 mutation']") .length, 1 ); assert.equal( tooltipOutput.find("img[title='tier4: mutation tier4']") .length, 1 ); assert.equal( tooltipOutput.find("img[alt='driver tiers filter']").length, 3, 'should be three tiers icons' ); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: annotation 1']" ).length, 1 ); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: annotation 2']" ).length, 1 ); assert.equal( tooltipOutput.find( "img[title='Putative_Driver: 3 annotation']" ).length, 1 ); assert.equal( tooltipOutput.find("img[alt='driver filter']").length, 3, 'should be three binary icons' ); }); it('should show neither icon if theres no custom driver annotations', () => { const datum = { sample: 'sample', study_id: '', data: [ makeMutation({ driverFilter: PUTATIVE_PASSENGER, driverFilterAnnotation: 'paosidjp', }), makeMutation({ driverFilter: 'Unknown', driverFilterAnnotation: 'asdfas', }), makeMutation({}), makeMutation({}), ], }; const tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.find("img[alt='driver filter']").length, 0, 'should be no binary icons' ); assert.equal( tooltipOutput.find("img[alt='driver tiers filter']").length, 0, 'should be no tiers icons' ); }); }); describe('germline mutations', () => { it('should show Germline next to every germline mutation, not next to others', () => { const datum = { sample: 'sample', study_id: '', data: [ makeMutation({ mutationStatus: 'germline', proteinChange: 'mutation1', }), makeMutation({ mutationStatus: 'germline', proteinChange: 'mutation2', }), makeMutation({}), ], }; const datum2 = { sample: 'sample', study_id: '', data: [ makeMutation({ mutationStatus: 'germline', proteinChange: 'mutation1', }), makeMutation({ proteinChange: 'mutation2' }), ], }; const datum3 = { sample: 'sample', study_id: '', data: [ makeMutation({ proteinChange: 'mutation1' }), makeMutation({ mutationStatus: 'germline', proteinChange: 'mutation2', }), ], }; let tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.html().match(/Germline/g)!.length, 2 ); assert.isFalse( tooltipOutput.html().indexOf('(1)') > -1, 'theres no (1) because theres only one datum to the tooltip' ); tooltipOutput = tooltip([datum, datum2]); assert.equal( tooltipOutput.html().match(/Germline/g)!.length, 2, 'mutation1 germline, mutation2 germline' ); assert.equal( tooltipOutput.html().match(/\(2\)/g)!.length, 1, 'mutation 1 germline occurs in both data' ); assert.equal( tooltipOutput.html().match(/\(1\)/g)!.length, 3, 'empty mutation, mutation 2 germline, mutation 2 each occur once' ); assert.equal( tooltipOutput.html().match(/mutation2/g)!.length, 2, 'since one is germline and one is not, should appear twice in tooltip' ); tooltipOutput = tooltip([datum, datum3]); assert.equal( tooltipOutput.html().match(/Germline/g)!.length, 2, 'mutation1 germline, mutation2 germline' ); assert.equal( tooltipOutput.html().match(/\(2\)/g)!.length, 1, 'mutation 2 germline occurs in both data' ); assert.equal( tooltipOutput.html().match(/\(1\)/g)!.length, 3, 'empty mutation, mutation 1 germline, mutation 1 each occur once' ); assert.equal( tooltipOutput.html().match(/mutation1/g)!.length, 2, 'since one is germline and one is not, should appear twice in tooltip' ); tooltipOutput = tooltip([datum2, datum3]); assert.equal( tooltipOutput.html().match(/Germline/g)!.length, 2, 'mutation1 germline, mutation2 germline' ); assert.equal( tooltipOutput.html().match(/\(2\)/g), null, 'nothing occurs in both' ); assert.equal( tooltipOutput.html().match(/\(1\)/g)!.length, 4, 'mutation 1 germline, mutation 1, mutation 2 germline, mutation 2 each occur once' ); assert.equal( tooltipOutput.html().match(/mutation1/g)!.length, 2, 'since one is germline and one is not, should appear twice in tooltip' ); assert.equal( tooltipOutput.html().match(/mutation2/g)!.length, 2, 'since one is germline and one is not, should appear twice in tooltip' ); }); }); describe('profiled and not profiled', () => { it("should say 'Not profiled' if 'profiled_in' is empty and 'not_profiled_in' is not", () => { const datum = { sample: 'sample', study_id: '', data: [] as AnnotatedExtendedAlteration[], na: true, profiled_in: [], not_profiled_in: [{ molecularProfileId: 'profile' }], }; let tooltipOutput = tooltip([datum]); assert.isTrue( tooltipOutput .html() .indexOf( 'Not profiled in selected molecular profiles.' ) > -1 ); assert.equal( tooltipOutput.html().match(/\(1\)/g), null, 'doesnt show (1) indicator for only one sample' ); tooltipOutput = tooltip([datum, datum]); assert.isTrue( tooltipOutput .html() .indexOf( 'Not profiled in selected molecular profiles. (2)' ) > -1 ); tooltipOutput = tooltip([datum, datum, datum]); assert.isTrue( tooltipOutput .html() .indexOf( 'Not profiled in selected molecular profiles. (3)' ) > -1 ); }); it("should say 'profiled' if 'not_profiled_in' is empty and 'profiled_in' is not", () => { const datum = { sample: 'sample', study_id: '', data: [] as AnnotatedExtendedAlteration[], na: true, profiled_in: [ { molecularProfileId: 'profile', genePanelId: 'panel' }, ], not_profiled_in: [], }; let tooltipOutput = tooltip([datum]); assert.isTrue( tooltipOutput .html() .indexOf( 'Profiled in all selected molecular profiles.' ) > -1 ); assert.equal( tooltipOutput.html().match(/\(1\)/g), null, 'doesnt show (1) indicator for only one sample' ); tooltipOutput = tooltip([datum, datum]); assert.isTrue( tooltipOutput .html() .indexOf( 'Profiled in all selected molecular profiles. (2)' ) > -1 ); tooltipOutput = tooltip([datum, datum, datum]); assert.isTrue( tooltipOutput .html() .indexOf( 'Profiled in all selected molecular profiles. (3)' ) > -1 ); }); it("should give the correct spread of 'Not profiled' and 'Profiled' over multiple data", () => { const notProfiled = { sample: 'sample', study_id: '', data: [] as AnnotatedExtendedAlteration[], na: true, profiled_in: [], not_profiled_in: [ { molecularProfileId: 'profile' }, { molecularProfileId: 'profile2' }, { molecularProfileId: 'profile3' }, ], }; const profiled = { sample: 'sample', study_id: '', data: [] as AnnotatedExtendedAlteration[], na: true, profiled_in: [ { molecularProfileId: 'profile' }, { molecularProfileId: 'profile2' }, { molecularProfileId: 'profile3' }, ], not_profiled_in: [], }; const datum1 = { sample: 'sample', study_id: '', data: [] as AnnotatedExtendedAlteration[], na: true, profiled_in: [{ molecularProfileId: 'profile' }], not_profiled_in: [ { molecularProfileId: 'profile2' }, { molecularProfileId: 'profile3' }, ], }; const datum2 = { sample: 'sample', study_id: '', data: [] as AnnotatedExtendedAlteration[], na: true, profiled_in: [ { molecularProfileId: 'profile' }, { molecularProfileId: 'profile2' }, ], not_profiled_in: [{ molecularProfileId: 'profile3' }], }; const datum3 = { sample: 'sample', study_id: '', data: [] as AnnotatedExtendedAlteration[], na: true, profiled_in: [ { molecularProfileId: 'profile2' }, { molecularProfileId: 'profile3' }, ], not_profiled_in: [{ molecularProfileId: 'profile' }], }; let tooltipOutput = tooltip([ notProfiled, profiled, notProfiled, ]); assert.isTrue( tooltipOutput .html() .indexOf( 'Not profiled in selected molecular profiles. (2)' ) > -1 ); assert.isTrue( tooltipOutput .html() .indexOf( 'Profiled in all selected molecular profiles. (1)' ) > -1 ); tooltipOutput = tooltip([ notProfiled, profiled, profiled, profiled, ]); assert.isTrue( tooltipOutput .html() .indexOf( 'Not profiled in selected molecular profiles. (1)' ) > -1 ); assert.isTrue( tooltipOutput .html() .indexOf( 'Profiled in all selected molecular profiles. (3)' ) > -1 ); tooltipOutput = tooltip([notProfiled, profiled]); assert.isTrue( tooltipOutput .html() .indexOf( 'Not profiled in selected molecular profiles. (1)' ) > -1 ); assert.isTrue( tooltipOutput .html() .indexOf( 'Profiled in all selected molecular profiles. (1)' ) > -1 ); tooltipOutput = tooltip([ notProfiled, profiled, notProfiled, profiled, profiled, profiled, notProfiled, ]); assert.isTrue( tooltipOutput .html() .indexOf( 'Not profiled in selected molecular profiles. (3)' ) > -1 ); assert.isTrue( tooltipOutput .html() .indexOf( 'Profiled in all selected molecular profiles. (4)' ) > -1 ); tooltipOutput = tooltip([datum1, datum2, datum3]); assert.isTrue( tooltipOutput .html() .indexOf( 'Not profiled in selected molecular profiles.' ) === -1, 'None are profiled in none' ); assert.isTrue( tooltipOutput .html() .indexOf( 'Profiled in all selected molecular profiles.' ) === -1, 'None are profiled in all' ); assert.isTrue( tooltipOutput .html() .indexOf( 'Profiled in: Profile (2), Profile2 (2), Profile3 (1)' ) > -1, 'all the counts are correct (order is arbitrary)' ); assert.isTrue( tooltipOutput .html() .indexOf( 'Not profiled in: Profile2 (1), Profile3 (2), Profile (1)' ) > -1, 'all the counts are correct (order is arbitrary)' ); tooltipOutput = tooltip([ datum1, datum2, datum3, profiled, notProfiled, profiled, ]); // it shows the right number of "not profiled in any" and "profiled in all", and also adds those counts to the specific profile counts assert.isTrue( tooltipOutput .html() .indexOf( 'Not profiled in selected molecular profiles. (1)' ) > -1 ); assert.isTrue( tooltipOutput .html() .indexOf( 'Profiled in all selected molecular profiles. (2)' ) > -1 ); assert.isTrue( tooltipOutput .html() .indexOf( 'Profiled in: Profile (4), Profile2 (4), Profile3 (3)' ) > -1, 'all the counts are correct (order is arbitrary)' ); assert.isTrue( tooltipOutput .html() .indexOf( 'Not profiled in: Profile2 (2), Profile3 (3), Profile (2)' ) > -1, 'all the counts are correct (order is arbitrary)' ); }); }); describe('gene panel information', () => { it('should show the correct gene panel entries in the tooltip, single and multiple data', () => { const datum1 = { sample: 'sample', study_id: '', data: [] as AnnotatedExtendedAlteration[], na: true, profiled_in: [ { molecularProfileId: 'profile', genePanelId: 'panel1', }, { molecularProfileId: 'profile', genePanelId: 'panel2', }, { molecularProfileId: 'profile2', genePanelId: 'panel3', }, ], not_profiled_in: [], }; const datum2 = { sample: 'sample', study_id: '', data: [] as AnnotatedExtendedAlteration[], na: true, profiled_in: [], not_profiled_in: [ { molecularProfileId: 'profile', genePanelId: 'panel1', }, { molecularProfileId: 'profile', genePanelId: 'panel2', }, { molecularProfileId: 'profile2', genePanelId: 'panel3', }, ], }; const datum3 = { sample: 'sample', study_id: '', data: [] as AnnotatedExtendedAlteration[], na: true, profiled_in: [ { molecularProfileId: 'profile', genePanelId: 'panel1', }, { molecularProfileId: 'profile', genePanelId: 'panel2', }, ], not_profiled_in: [ { molecularProfileId: 'profile2', genePanelId: 'panel3', }, ], }; let tooltipOutput = tooltip([datum1]); assert.equal(tooltipOutput.text().match(/panel1/g)!.length, 1); assert.equal(tooltipOutput.text().match(/panel2/g)!.length, 1); assert.equal(tooltipOutput.text().match(/panel3/g)!.length, 1); assert.equal(tooltipOutput.text().match(/\(1\)/g), null); tooltipOutput = tooltip([datum1, datum2]); assert.equal(tooltipOutput.text().match(/panel1/g)!.length, 1); assert.equal(tooltipOutput.text().match(/panel2/g)!.length, 1); assert.equal(tooltipOutput.text().match(/panel3/g)!.length, 1); assert.equal( tooltipOutput.text().match(/panel1 \(1\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/panel2 \(1\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/panel3 \(1\)/g)!.length, 1 ); assert.notEqual( tooltipOutput .find('a:contains("panel1")') .first() .css('color'), 'red' ); assert.notEqual( tooltipOutput .find('a:contains("panel2")') .first() .css('color'), 'red' ); assert.notEqual( tooltipOutput .find('a:contains("panel3")') .first() .css('color'), 'red' ); tooltipOutput = tooltip([datum1, datum3]); assert.equal(tooltipOutput.text().match(/panel1/g)!.length, 1); assert.equal(tooltipOutput.text().match(/panel2/g)!.length, 1); assert.equal(tooltipOutput.text().match(/panel3/g)!.length, 1); assert.equal( tooltipOutput.text().match(/panel1 \(2\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/panel2 \(2\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/panel3 \(1\)/g)!.length, 1 ); assert.notEqual( tooltipOutput .find('a:contains("panel1")') .first() .css('color'), 'red' ); assert.notEqual( tooltipOutput .find('a:contains("panel2")') .first() .css('color'), 'red' ); assert.notEqual( tooltipOutput .find('a:contains("panel3")') .first() .css('color'), 'red' ); tooltipOutput = tooltip([datum3, datum2]); assert.equal(tooltipOutput.text().match(/panel1/g)!.length, 1); assert.equal(tooltipOutput.text().match(/panel2/g)!.length, 1); assert.equal(tooltipOutput.text().match(/panel3/g)!.length, 1); assert.equal( tooltipOutput.text().match(/panel1 \(1\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/panel2 \(1\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/panel3 \(2\)/g)!.length, 1 ); assert.notEqual( tooltipOutput .find('a:contains("panel1")') .first() .css('color'), 'red' ); assert.notEqual( tooltipOutput .find('a:contains("panel2")') .first() .css('color'), 'red' ); assert.equal( tooltipOutput .find('a:contains("panel3")') .first() .css('color'), 'red', 'red because Not profiled in that gene panel' ); tooltipOutput = tooltip([datum3, datum1, datum2]); assert.equal(tooltipOutput.text().match(/panel1/g)!.length, 1); assert.equal(tooltipOutput.text().match(/panel2/g)!.length, 1); assert.equal(tooltipOutput.text().match(/panel3/g)!.length, 1); assert.equal( tooltipOutput.text().match(/panel1 \(2\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/panel2 \(2\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/panel3 \(1\)/g)!.length, 1 ); assert.notEqual( tooltipOutput .find('a:contains("panel1")') .first() .css('color'), 'red' ); assert.notEqual( tooltipOutput .find('a:contains("panel2")') .first() .css('color'), 'red' ); assert.notEqual( tooltipOutput .find('a:contains("panel3")') .first() .css('color'), 'red' ); }); }); describe('genetic alterations', () => { let datum: any; let emptyDatum: any; let tooltipOutput: JQuery; beforeEach(() => { datum = { sample: 'sample', study_id: '', data: [] as AnnotatedExtendedAlteration[], na: false, profiled_in: [], not_profiled_in: [], }; emptyDatum = { sample: 'sample', study_id: '', data: [] as AnnotatedExtendedAlteration[], na: false, profiled_in: [], not_profiled_in: [], }; }); it('single genetic alteration in single case - mutation', () => { datum.data = [makeMutation({ proteinChange: 'PC1' })]; tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.text().match(/Mutation:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC1/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); datum.data = [ makeMutation({ proteinChange: 'PC1' }), makeMutation({ proteinChange: 'PC1' }), ]; tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.text().match(/Mutation:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC1/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); }); it('single genetic alteration in single case - fusion', () => { datum.data = [ makeStructuralVariant({ site2HugoSymbol: 'GENE2', eventInfo: 'GENE-GENE2', }), ]; tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.text().match(/Structural Variant:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/Event Info: GENE-GENE2/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); datum.data = [ makeStructuralVariant({ site2HugoSymbol: 'GENE2', eventInfo: 'GENE-GENE2', }), makeStructuralVariant({ site2HugoSymbol: 'GENE3', eventInfo: 'GENE-GENE3', }), ]; tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.text().match(/Structural Variant:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/Event Info: GENE-GENE2/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); }); it('single genetic alteration in single case - cna', () => { const disp_cna: { [integerCN: string]: string } = { '-2': 'HOMODELETED', '-1': 'HETLOSS', '1': 'GAIN', '2': 'AMPLIFIED', }; for (let i = -2; i <= 2; i++) { datum.data = [makeCna({ value: i })]; tooltipOutput = tooltip([datum]); if (i === 0) { // nothing in tooltip for diploid assert.equal( tooltipOutput .text() .match(/Copy Number Alteration:/g), null ); } else { assert.equal( tooltipOutput .text() .match(/Copy Number Alteration:/g)!.length, 1 ); assert.equal( tooltipOutput .text() .match( new RegExp( `GENE ${disp_cna[i.toString()]}`, 'g' ) )!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); } datum.data = [makeCna({ value: i }), makeCna({ value: i })]; tooltipOutput = tooltip([datum]); if (i === 0) { // nothing in tooltip for diploid assert.equal( tooltipOutput .text() .match(/Copy Number Alteration:/g), null ); } else { assert.equal( tooltipOutput .text() .match(/Copy Number Alteration:/g)!.length, 1 ); assert.equal( tooltipOutput .text() .match( new RegExp( `GENE ${disp_cna[i.toString()]}`, 'g' ) )!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); } } }); it('single genetic alteration in single case - mrna', () => { datum.data = [makeMrna({ alterationSubType: 'high' })]; tooltipOutput = tooltip([datum]); assert.equal(tooltipOutput.text().match(/MRNA:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); datum.data = [ makeMrna({ alterationSubType: 'high' }), makeMrna({ alterationSubType: 'high' }), ]; tooltipOutput = tooltip([datum]); assert.equal(tooltipOutput.text().match(/MRNA:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); datum.data = [makeMrna({ alterationSubType: 'low' })]; tooltipOutput = tooltip([datum]); assert.equal(tooltipOutput.text().match(/MRNA:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE LOW/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); datum.data = [ makeMrna({ alterationSubType: 'low' }), makeMrna({ alterationSubType: 'low' }), ]; tooltipOutput = tooltip([datum]); assert.equal(tooltipOutput.text().match(/MRNA:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE LOW/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); }); it('single genetic alteration in single case - prot', () => { datum.data = [makeProt({ alterationSubType: 'high' })]; tooltipOutput = tooltip([datum]); assert.equal(tooltipOutput.text().match(/PROT:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); datum.data = [ makeProt({ alterationSubType: 'high' }), makeProt({ alterationSubType: 'high' }), ]; tooltipOutput = tooltip([datum]); assert.equal(tooltipOutput.text().match(/PROT:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); datum.data = [makeProt({ alterationSubType: 'low' })]; tooltipOutput = tooltip([datum]); assert.equal(tooltipOutput.text().match(/PROT:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE LOW/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); datum.data = [ makeProt({ alterationSubType: 'low' }), makeProt({ alterationSubType: 'low' }), ]; tooltipOutput = tooltip([datum]); assert.equal(tooltipOutput.text().match(/PROT:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE LOW/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); }); it('single genetic alteration across multiple cases - mutation', () => { datum.data = [makeMutation({ proteinChange: 'PC1' })]; tooltipOutput = tooltip([datum, datum, datum]); assert.equal( tooltipOutput.text().match(/Mutation:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC1\xa0\(3\)/g)!.length, 1 ); tooltipOutput = tooltip([datum, emptyDatum]); assert.equal( tooltipOutput.text().match(/Mutation:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC1\xa0\(1\)/g)!.length, 1 ); }); it('single genetic alteration across multiple cases - fusion', () => { datum.data = [ makeStructuralVariant({ site2HugoSymbol: 'GENE2', eventInfo: 'GENE-GENE2', }), ]; tooltipOutput = tooltip([datum, datum, datum]); assert.equal( tooltipOutput.text().match(/Structural Variant:/g)!.length, 1 ); assert.equal( tooltipOutput .text() .match(/Event Info: GENE-GENE2\xa0\(3\)/g)!.length, 1 ); tooltipOutput = tooltip([datum, emptyDatum]); assert.equal( tooltipOutput.text().match(/Structural Variant:/g)!.length, 1 ); assert.equal( tooltipOutput .text() .match(/Event Info: GENE-GENE2\xa0\(1\)/g)!.length, 1 ); }); it('single genetic alteration across multiple cases - cna', () => { const disp_cna: { [integerCN: string]: string } = { '-2': 'HOMODELETED', '-1': 'HETLOSS', '1': 'GAIN', '2': 'AMPLIFIED', }; for (let i = -2; i <= 2; i++) { datum.data = [makeCna({ value: i })]; tooltipOutput = tooltip([ emptyDatum, datum, datum, datum, datum, ]); if (i === 0) { // nothing in tooltip for diploid assert.equal( tooltipOutput .text() .match(/Copy Number Alteration:/g), null ); } else { assert.equal( tooltipOutput .text() .match(/Copy Number Alteration:/g)!.length, 1 ); assert.equal( tooltipOutput .text() .match( new RegExp( `GENE ${ disp_cna[i.toString()] }\\xa0\\(4\\)`, 'g' ) )!.length, 1 ); } } }); it('single genetic alteration across multiple cases - mrna', () => { datum.data = [makeMrna({ alterationSubType: 'high' })]; tooltipOutput = tooltip([datum, datum]); assert.equal(tooltipOutput.text().match(/MRNA:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH\xa0\(2\)/g)!.length, 1 ); datum.data = [makeMrna({ alterationSubType: 'low' })]; tooltipOutput = tooltip([datum, datum]); assert.equal(tooltipOutput.text().match(/MRNA:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE LOW\xa0\(2\)/g)!.length, 1 ); tooltipOutput = tooltip([emptyDatum, datum]); assert.equal(tooltipOutput.text().match(/MRNA:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE LOW\xa0\(1\)/g)!.length, 1 ); }); it('single genetic alteration across multiple cases - prot', () => { datum.data = [makeProt({ alterationSubType: 'high' })]; tooltipOutput = tooltip([datum, datum, datum, datum, datum]); assert.equal(tooltipOutput.text().match(/PROT:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH\xa0\(5\)/g)!.length, 1 ); datum.data = [makeProt({ alterationSubType: 'low' })]; tooltipOutput = tooltip([datum, datum, datum, datum, datum]); assert.equal(tooltipOutput.text().match(/PROT:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE LOW\xa0\(5\)/g)!.length, 1 ); }); it('multiple alterations of same type in single case - mutation', () => { datum.data = [ makeMutation({ proteinChange: 'PC1' }), makeMutation({ proteinChange: 'PC2' }), ]; tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.text().match(/Mutation:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC1/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC2/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); }); it('multiple alterations of same type in single case - fusion', () => { datum.data = [ makeStructuralVariant({ site2HugoSymbol: 'GENE2', eventInfo: 'GENE-GENE2', }), makeStructuralVariant({ site2HugoSymbol: 'GENE3', eventInfo: 'GENE-GENE3', }), ]; tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.text().match(/Structural Variant:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/Event Info: GENE-GENE2/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/Event Info: GENE-GENE2/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); }); it('multiple alterations of same type in single case - cna', () => { datum.data = [ makeCna({ value: -2 }), makeCna({ value: -1 }), makeCna({ value: 1 }), ]; tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.text().match(/Copy Number Alteration:/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/GENE HOMODELETED/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE HETLOSS/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE GAIN/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); }); it('multiple alterations of same type in single case - mrna', () => { datum.data = [ makeMrna({ alterationSubType: 'high' }), makeMrna({ alterationSubType: 'low' }), makeMrna({ alterationSubType: 'high' }), ]; tooltipOutput = tooltip([datum]); assert.equal(tooltipOutput.text().match(/MRNA:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE LOW/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); }); it('multiple alterations of same type in single case - protein', () => { datum.data = [ makeProt({ alterationSubType: 'low' }), makeProt({ alterationSubType: 'low' }), makeProt({ alterationSubType: 'high' }), ]; tooltipOutput = tooltip([datum]); assert.equal(tooltipOutput.text().match(/PROT:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE LOW/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); }); it('multiple alterations of same type across multiple cases - mutation', () => { datum.data = [ makeMutation({ proteinChange: 'PC1' }), makeMutation({ proteinChange: 'PC2' }), ]; tooltipOutput = tooltip([datum, datum, datum]); assert.equal( tooltipOutput.text().match(/Mutation:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC1\xa0\(3\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC2\xa0\(3\)/g)!.length, 1 ); tooltipOutput = tooltip([datum, emptyDatum]); assert.equal( tooltipOutput.text().match(/Mutation:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC1\xa0\(1\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC2\xa0\(1\)/g)!.length, 1 ); }); it('multiple alterations of same type across multiple cases - fusion', () => { datum.data = [ makeStructuralVariant({ site2HugoSymbol: 'GENE2', eventInfo: 'GENE-GENE2', }), makeStructuralVariant({ site2HugoSymbol: 'GENE3', eventInfo: 'GENE-GENE3', }), ]; tooltipOutput = tooltip([datum, datum, datum, datum]); assert.equal( tooltipOutput.text().match(/Structural Variant:/g)!.length, 1 ); assert.equal( tooltipOutput .text() .match(/Event Info: GENE-GENE2\xa0\(4\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE-GENE3\xa0\(4\)/g)!.length, 1 ); tooltipOutput = tooltip([datum, datum, emptyDatum, emptyDatum]); assert.equal( tooltipOutput.text().match(/Structural Variant:/g)!.length, 1 ); assert.equal( tooltipOutput .text() .match(/Event Info: GENE-GENE2\xa0\(2\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE-GENE3\xa0\(2\)/g)!.length, 1 ); }); it('multiple alterations of same type across multiple cases - cna', () => { datum.data = [ makeCna({ value: -2 }), makeCna({ value: -1 }), makeCna({ value: 1 }), ]; tooltipOutput = tooltip([datum, datum, datum]); assert.equal( tooltipOutput.text().match(/Copy Number Alteration:/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/GENE HOMODELETED\xa0\(3\)/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/GENE HETLOSS\xa0\(3\)/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/GENE GAIN\xa0\(3\)/g)!.length, 1 ); tooltipOutput = tooltip([emptyDatum, emptyDatum, datum]); assert.equal( tooltipOutput.text().match(/Copy Number Alteration:/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/GENE HOMODELETED\xa0\(1\)/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/GENE HETLOSS\xa0\(1\)/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/GENE GAIN\xa0\(1\)/g)!.length, 1 ); }); it('multiple alterations of same type across multiple cases - mrna', () => { datum.data = [ makeMrna({ alterationSubType: 'high' }), makeMrna({ alterationSubType: 'low' }), makeMrna({ alterationSubType: 'high' }), ]; tooltipOutput = tooltip([datum, datum]); assert.equal(tooltipOutput.text().match(/MRNA:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH\xa0\(4\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE LOW\xa0\(2\)/g)!.length, 1 ); tooltipOutput = tooltip([ datum, datum, emptyDatum, emptyDatum, datum, ]); assert.equal(tooltipOutput.text().match(/MRNA:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH\xa0\(6\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE LOW\xa0\(3\)/g)!.length, 1 ); }); it('multiple alterations of same type across multiple cases - protein', () => { datum.data = [ makeProt({ alterationSubType: 'low' }), makeProt({ alterationSubType: 'low' }), makeProt({ alterationSubType: 'high' }), ]; tooltipOutput = tooltip([datum, datum, datum]); assert.equal(tooltipOutput.text().match(/PROT:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH\xa0\(3\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE LOW\xa0\(6\)/g)!.length, 1 ); tooltipOutput = tooltip([datum, emptyDatum]); assert.equal(tooltipOutput.text().match(/PROT:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH\xa0\(1\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE LOW\xa0\(2\)/g)!.length, 1 ); }); it('multiple alterations of different types in single case', () => { datum.data = [ makeMutation({ proteinChange: 'PC1' }), makeMutation({ proteinChange: 'PC2' }), makeStructuralVariant({ site2HugoSymbol: 'GENE2', eventInfo: 'GENE-GENE2', }), makeStructuralVariant({ site2HugoSymbol: 'GENE3', eventInfo: 'GENE-GENE3', }), makeCna({ value: 2 }), makeCna({ value: -2 }), makeMrna({ alterationSubType: 'high' }), makeMrna({ alterationSubType: 'low' }), makeProt({ alterationSubType: 'low' }), ]; tooltipOutput = tooltip([datum]); assert.equal( tooltipOutput.text().match(/Mutation:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC1/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC2/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/Structural Variant:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/Event Info: GENE-GENE2/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/Event Info: GENE-GENE3/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/Copy Number Alteration:/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/GENE AMPLIFIED/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE HOMODELETED/g)!.length, 1 ); assert.equal(tooltipOutput.text().match(/MRNA:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH/g)!.length, 1 ); assert.equal(tooltipOutput.text().match(/PROT:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE LOW/g)!.length, 2 ); // (2 for mrna and protein) assert.equal( tooltipOutput.text().match(/\(\d+\)/g), null, 'no number indicator for single case' ); }); it('multiple alterations of different types across multiple cases', () => { datum.data = [ makeMutation({ proteinChange: 'PC1' }), makeMutation({ proteinChange: 'PC2' }), makeStructuralVariant({ site2HugoSymbol: 'GENE2', eventInfo: 'GENE-GENE2', }), makeStructuralVariant({ site2HugoSymbol: 'GENE3', eventInfo: 'GENE-GENE3', }), makeCna({ value: 2 }), makeCna({ value: -2 }), makeMrna({ alterationSubType: 'high' }), makeMrna({ alterationSubType: 'low' }), makeProt({ alterationSubType: 'low' }), ]; const datum2 = Object.assign({}, emptyDatum, { data: [ makeMutation({ proteinChange: 'PC1' }), makeStructuralVariant({ site2HugoSymbol: 'GENE3', eventInfo: 'GENE-GENE3', }), makeCna({ value: 1 }), makeMrna({ alterationSubType: 'low' }), makeProt({ alterationSubType: 'high' }), makeProt({ alterationSubType: 'low' }), ], }); tooltipOutput = tooltip([ datum, datum, emptyDatum, datum, datum2, ]); assert.equal( tooltipOutput.text().match(/Mutation:/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC1\xa0\(4\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE PC2\xa0\(3\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/Structural Variant:/g)!.length, 1 ); assert.equal( tooltipOutput .text() .match(/Event Info: GENE-GENE2\xa0\(3\)/g)!.length, 1 ); assert.equal( tooltipOutput .text() .match(/Event Info: GENE-GENE3\xa0\(4\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/Copy Number Alteration:/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/GENE AMPLIFIED\xa0\(3\)/g)! .length, 1 ); assert.equal( tooltipOutput.text().match(/GENE GAIN\xa0\(1\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE HOMODELETED\xa0\(3\)/g)! .length, 1 ); assert.equal(tooltipOutput.text().match(/MRNA:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH\xa0\(3\)/g)!.length, 1 ); assert.equal(tooltipOutput.text().match(/PROT:/g)!.length, 1); assert.equal( tooltipOutput.text().match(/GENE HIGH\xa0\(1\)/g)!.length, 1 ); assert.equal( tooltipOutput.text().match(/GENE LOW\xa0\(4\)/g)!.length, 2 ); // (2 for mrna and protein) }); }); }); describe('makeClinicalTrackTooltip', () => { describe('category track tooltip', () => { let trackLabel: string; let trackSpec: any; let tooltip: (dataUnderMouse: any[]) => JQuery; beforeAll(() => { trackLabel = 'label1234'; trackSpec = { key: '', label: trackLabel, description: '', data: [], datatype: 'string' as 'string', }; tooltip = makeClinicalTrackTooltip(trackSpec, false); }); it('should show the given sample id', () => { const sampleTooltipResult = tooltip([ { attr_val_counts: { a: 1 }, attr_val: 'a', sample: 'sampleID', }, ]); assert.isTrue( sampleTooltipResult .html() .indexOf('sampleID') > -1 ); }); it('should show the given patient id', () => { const patientTooltipResult = tooltip([ { attr_val_counts: { a: 1 }, attr_val: 'a', patient: 'patientID', }, ]); assert.isTrue( patientTooltipResult .html() .indexOf('patientID') > -1 ); }); it('should show the correct output for a single value', () => { const tooltipResult = tooltip([ { attr_val_counts: { a: 1 }, attr_val: 'a', sample: 'sampleID', }, ]); assert.isTrue( tooltipResult .html() .indexOf( `label1234: a` ) > -1 ); }); it('should show the correct output for multiple values', () => { const tooltipResult = tooltip([ { attr_val_counts: { a: 1, b: 3 }, attr_val: 'a', sample: 'sampleID', }, ]); assert.isTrue( tooltipResult .html() .indexOf( `label1234:
a: 1 sample
b: 3 samples` ) > -1 ); }); it('should show the correct output for multiple data, single value', () => { const tooltipResult = tooltip([ { attr_val_counts: { a: 1 }, attr_val: 'a', patient: 'patientID', }, { attr_val_counts: { a: 1 }, attr_val: 'a', patient: 'patientID', }, { attr_val_counts: { a: 2 }, attr_val: 'a', patient: 'patientID', }, ]); assert.isTrue( tooltipResult .html() .indexOf( `label1234: a (4 samples)
` ) > -1 ); }); it('should show the correct output for multiple data, multiple values', () => { const tooltip = makeClinicalTrackTooltip(trackSpec, false); const tooltipResult = tooltip([ { attr_val_counts: { a: 1, b: 5 }, attr_val: 'a', patient: 'patientID', }, { attr_val_counts: { a: 1 }, attr_val: 'a', patient: 'patientID', }, { attr_val_counts: { a: 2, b: 1, c: 1 }, attr_val: 'a', patient: 'patientID', }, ]); assert.isTrue( tooltipResult .html() .indexOf( `label1234:
a: 4 samples
b: 6 samples
c: 1 sample` ) > -1 ); }); }); describe('number track tooltip', () => { let trackSpec: any; let tooltip: (dataUnderMouse: any[]) => JQuery; beforeAll(() => { trackSpec = { key: '', label: '', description: '', data: [], datatype: 'number' as 'number', numberRange: [0, 0] as [number, number], numberLogScale: false, }; tooltip = makeClinicalTrackTooltip(trackSpec, false); }); it('should show numerical data rounded to 2 decimal digits', () => { // one data let tooltipResult = tooltip([ { attr_val_counts: { '0.13500013531': 1 }, attr_val: '0.13500013531', sample: 'sampleID', }, ]); assert.isTrue( tooltipResult.html().indexOf('0.14') > -1, 'correct result with no integer part' ); tooltipResult = tooltip([ { attr_val_counts: { '6.100032': 1 }, attr_val: '6.100032', sample: 'sampleID', }, ]); assert.isTrue( tooltipResult.html().indexOf('6.10') > -1, 'correct result with integer part' ); tooltipResult = tooltip([ { attr_val_counts: { '0': 1 }, attr_val: '0', sample: 'sampleID', }, ]); assert.isTrue( tooltipResult.html().indexOf('0') > -1, 'correct result for zero' ); tooltipResult = tooltip([ { attr_val_counts: { '-0.13500013531': 1 }, attr_val: '-0.13500013531', sample: 'sampleID', }, ]); assert.isTrue( tooltipResult.html().indexOf('-0.14') > -1, 'correct result with no integer part, negative' ); tooltipResult = tooltip([ { attr_val_counts: { '-6.100032': 1 }, attr_val: '-6.100032', sample: 'sampleID', }, ]); assert.isTrue( tooltipResult.html().indexOf('-6.10') > -1, 'correct result with integer part, negative' ); // multiple data // more than one data tooltipResult = tooltip([ { attr_val_counts: { '0.13500013531': 1 }, sample: 'sampleID', }, { attr_val_counts: { '0.23500013531': 1 }, sample: 'sampleID', }, { attr_val_counts: { '0.33500013531': 1 }, sample: 'sampleID', }, ]); assert.isTrue( tooltipResult .html() .indexOf('0.24 (average of 3 values)') > -1, 'multiple - correct result with no integer part' ); tooltipResult = tooltip([ { attr_val_counts: { '6.100032': 1 }, sample: 'sampleID' }, { attr_val_counts: { '8.100032': 1 }, sample: 'sampleID' }, ]); assert.isTrue( tooltipResult .html() .indexOf('7.10 (average of 2 values)') > -1, 'multiple - correct result with integer part' ); tooltipResult = tooltip([ { attr_val_counts: { '0': 1 }, sample: 'sampleID' }, { attr_val_counts: { '0': 1 }, sample: 'sampleID' }, { attr_val_counts: { '0': 1 }, sample: 'sampleID' }, { attr_val_counts: { '0': 1 }, sample: 'sampleID' }, ]); assert.isTrue( tooltipResult .html() .indexOf('0 (average of 4 values)') > -1, 'multiple - correct result for zero' ); tooltipResult = tooltip([ { attr_val_counts: { '-0.03500013531': 2, '-0.23500013531': 2, }, sample: 'sampleID', }, ]); assert.isTrue( tooltipResult .html() .indexOf('-0.14 (average of 4 values)') > -1, 'correct result with no integer part, negative' ); tooltipResult = tooltip([ { attr_val_counts: { '-5.100032': 1 }, sample: 'sampleID' }, { attr_val_counts: { '-2.100032': 2 }, sample: 'sampleID' }, ]); assert.isTrue( tooltipResult .html() .indexOf('-3.10 (average of 3 values)') > -1, 'correct result with integer part, negative' ); }); }); }); describe('makeHeatmapTrackTooltip', () => { const tooltip = makeHeatmapTrackTooltip( { molecularAlterationType: 'MRNA_EXPRESSION' } as any, false ); beforeAll(() => { getServerConfig().generic_assay_display_text = ServerConfigDefaults.generic_assay_display_text!; }); it('should show data rounded to 2 decimal digits', () => { // one data let tooltipResult = tooltip([ { profile_data: 0.13500013531, sample: 'sampleID' }, ]); assert.isTrue( tooltipResult.html().indexOf('0.14') > -1, 'correct result with no integer part' ); tooltipResult = tooltip([ { profile_data: 6.100032, sample: 'sampleID' }, ]); assert.isTrue( tooltipResult.html().indexOf('6.10') > -1, 'correct result with integer part' ); tooltipResult = tooltip([{ profile_data: 0, sample: 'sampleID' }]); assert.isTrue( tooltipResult.html().indexOf('0.00') > -1, 'correct result for zero' ); tooltipResult = tooltip([ { profile_data: -0.13500013531, sample: 'sampleID' }, ]); assert.isTrue( tooltipResult.html().indexOf('-0.14') > -1, 'correct result with no integer part, negative' ); tooltipResult = tooltip([ { profile_data: -6.100032, sample: 'sampleID' }, ]); assert.isTrue( tooltipResult.html().indexOf('-6.10') > -1, 'correct result with integer part, negative' ); // more than one data tooltipResult = tooltip([ { profile_data: 0.13500013531, sample: 'sampleID' }, { profile_data: 0.23500013531, sample: 'sampleID' }, { profile_data: 0.33500013531, sample: 'sampleID' }, ]); assert.isTrue( tooltipResult .html() .indexOf('0.24 (average of 3 values)') > -1, 'multiple - correct result with no integer part' ); tooltipResult = tooltip([ { profile_data: 6.100032, sample: 'sampleID' }, { profile_data: 8.100032, sample: 'sampleID' }, ]); assert.isTrue( tooltipResult .html() .indexOf('7.10 (average of 2 values)') > -1, 'multiple - correct result with integer part' ); tooltipResult = tooltip([ { profile_data: 0, sample: 'sampleID' }, { profile_data: 0, sample: 'sampleID' }, { profile_data: 0, sample: 'sampleID' }, { profile_data: 0, sample: 'sampleID' }, ]); assert.isTrue( tooltipResult .html() .indexOf('0.00 (average of 4 values)') > -1, 'multiple - correct result for zero' ); tooltipResult = tooltip([ { profile_data: -0.03500013531, sample: 'sampleID' }, { profile_data: -0.03500013531, sample: 'sampleID' }, { profile_data: -0.23500013531, sample: 'sampleID' }, { profile_data: -0.23500013531, sample: 'sampleID' }, ]); assert.isTrue( tooltipResult .html() .indexOf('-0.14 (average of 4 values)') > -1, 'correct result with no integer part, negative' ); tooltipResult = tooltip([ { profile_data: -6.100032, sample: 'sampleID' }, { profile_data: -2.100032, sample: 'sampleID' }, ]); assert.isTrue( tooltipResult .html() .indexOf('-4.10 (average of 2 values)') > -1, 'correct result with integer part, negative' ); }); it('Should not handle categories for molecular genetic alterations', () => { const tooltipResult = tooltip([ { profile_data: 8, sample: 'sampleID', category: '>8.00' }, ]); assert.isTrue( tooltipResult.html().indexOf('8.00') > -1, 'molecular track - category is ignored when available' ); }); const genericAssayTooltip = makeHeatmapTrackTooltip( { molecularAlterationType: 'GENERIC_ASSAY', genericAssayType: 'TREATMENT_RESPONSE', } as any, false ); it('Should handle categories for generic assay genetic alterations', () => { const tooltipResult = genericAssayTooltip([ { profile_data: 8, sample: 'sampleID', category: '>8.00' }, ]); assert.isTrue( tooltipResult .html() .indexOf('
Treatment Response: >8.00
') > -1, 'generic assay - category is displayed when available' ); }); it('Should handle categories for multiple generic assay genetic alterations', () => { const tooltipResult = genericAssayTooltip([ { profile_data: 8, sample: 'sampleID', category: '>8.00' }, { profile_data: 7, sample: 'sampleID', category: '>7.00' }, ]); assert.isTrue( tooltipResult .html() .indexOf( '
Treatment Response: >8.00, >7.00 (2 data points)
' ) > -1, 'generic assay - multiple categories are displayed when under mouse' ); }); it('Should handle single values and single category for multiple generic assay genetic alterations', () => { const tooltipResult = genericAssayTooltip([ { profile_data: 8, sample: 'sampleID', category: '' }, { profile_data: 7, sample: 'sampleID', category: '>7.00' }, ]); assert.isTrue( tooltipResult .html() .indexOf( '
Treatment Response: 8.00 and >7.00
' ) > -1, 'generic assay - multiple categories are displayed when under mouse' ); }); it('Should handle multiple values and multiple categories for multiple generic assay genetic alterations', () => { const tooltipResult = genericAssayTooltip([ { profile_data: 6, sample: 'sampleID', category: '' }, { profile_data: 8, sample: 'sampleID', category: '' }, { profile_data: 7, sample: 'sampleID', category: '>7.00' }, { profile_data: 7, sample: 'sampleID', category: '>7.00' }, { profile_data: 9, sample: 'sampleID', category: '>9.00' }, ]); assert.isTrue( tooltipResult .html() .indexOf( '
Treatment Response: 7.00 (average of 2 values) and >7.00, >9.00 (3 data points)
' ) > -1, 'generic assay - multiple values and categories (unique) are displayed when under mouse' ); }); }); describe('makeGeneticTrackTooltip_getCoverageInformation', () => { it('gives correct results on undefined input', () => { assert.deepEqual( makeGeneticTrackTooltip_getCoverageInformation( undefined, undefined ), { dispProfiledGenePanelIds: [], dispNotProfiledGenePanelIds: [], dispProfiledIn: undefined, dispNotProfiledIn: undefined, dispAllProfiled: false, dispNotProfiled: false, } ); }); it('gives correct results on empty input', () => { assert.deepEqual( makeGeneticTrackTooltip_getCoverageInformation([], []), { dispProfiledGenePanelIds: [], dispNotProfiledGenePanelIds: [], dispProfiledIn: [], dispNotProfiledIn: [], dispAllProfiled: false, dispNotProfiled: false, } ); }); it('gives correct results with empty profiled_in but no not_profiled_in', () => { assert.deepEqual( makeGeneticTrackTooltip_getCoverageInformation([], undefined), { dispProfiledGenePanelIds: [], dispNotProfiledGenePanelIds: [], dispProfiledIn: [], dispNotProfiledIn: undefined, dispAllProfiled: false, dispNotProfiled: false, } ); }); it('gives correct results with empty not_profiled_in but no profiled_in', () => { assert.deepEqual( makeGeneticTrackTooltip_getCoverageInformation(undefined, []), { dispProfiledGenePanelIds: [], dispNotProfiledGenePanelIds: [], dispProfiledIn: undefined, dispNotProfiledIn: [], dispAllProfiled: false, dispNotProfiled: false, } ); }); it('gives correct results with nonempty profiled_in but no not_profiled_in', () => { assert.deepEqual( makeGeneticTrackTooltip_getCoverageInformation( [{ genePanelId: 'panel', molecularProfileId: 'profile' }], undefined ), { dispProfiledGenePanelIds: ['panel'], dispNotProfiledGenePanelIds: [], dispProfiledIn: ['profile'], dispNotProfiledIn: undefined, dispAllProfiled: false, dispNotProfiled: false, } ); }); it('gives correct results with nonempty not_profiled_in but no profiled_in', () => { assert.deepEqual( makeGeneticTrackTooltip_getCoverageInformation(undefined, [ { molecularProfileId: 'profile' }, ]), { dispProfiledGenePanelIds: [], dispNotProfiledGenePanelIds: [], dispProfiledIn: undefined, dispNotProfiledIn: ['profile'], dispAllProfiled: false, dispNotProfiled: false, } ); }); it('gives correct results with nonempty profiled_in and empty not_profiled_in', () => { assert.deepEqual( makeGeneticTrackTooltip_getCoverageInformation( [{ molecularProfileId: 'profile' }], [] ), { dispProfiledGenePanelIds: [], dispNotProfiledGenePanelIds: [], dispProfiledIn: ['profile'], dispNotProfiledIn: [], dispAllProfiled: true, dispNotProfiled: false, } ); }); it('gives correct results with nonempty not_profiled_in and empty profiled_in', () => { assert.deepEqual( makeGeneticTrackTooltip_getCoverageInformation( [], [{ molecularProfileId: 'profile' }] ), { dispProfiledGenePanelIds: [], dispNotProfiledGenePanelIds: [], dispProfiledIn: [], dispNotProfiledIn: ['profile'], dispAllProfiled: false, dispNotProfiled: true, } ); }); it('gives correct results with nonoverlapping profiled_in and not_profiled_in', () => { assert.deepEqual( makeGeneticTrackTooltip_getCoverageInformation( [{ genePanelId: 'panel', molecularProfileId: 'profile1' }], [{ molecularProfileId: 'profile' }] ), { dispProfiledGenePanelIds: ['panel'], dispNotProfiledGenePanelIds: [], dispProfiledIn: ['profile1'], dispNotProfiledIn: ['profile'], dispAllProfiled: false, dispNotProfiled: false, } ); }); it('gives correct results with overlapping profiled_in and not_profiled_in', () => { assert.deepEqual( makeGeneticTrackTooltip_getCoverageInformation( [{ genePanelId: 'panel', molecularProfileId: 'profile' }], [{ genePanelId: 'panel2', molecularProfileId: 'profile' }] ), { dispProfiledGenePanelIds: ['panel'], dispNotProfiledGenePanelIds: ['panel2'], dispProfiledIn: ['profile'], dispNotProfiledIn: [], dispAllProfiled: true, dispNotProfiled: false, } ); }); }); });