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Filter SV by custom driver annotations in oncoprint and study page
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Bas Leenknegt
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Apr 25, 2023
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end-to-end-test/local/specs/custom-driver-annotations-in-study-view.spec.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,116 @@ | ||
| const assert = require('assert'); | ||
| const { waitForNetworkQuiet } = require('../../shared/specUtils'); | ||
| const goToUrlAndSetLocalStorage = require('../../shared/specUtils') | ||
| .goToUrlAndSetLocalStorage; | ||
|
|
||
| const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, ''); | ||
| const STUDY_VIEW_URL = `${CBIOPORTAL_URL}/study/summary?id=study_es_0`; | ||
| const ALTERATION_MENU_BTN = `button[data-test="AlterationFilterButton"]`; | ||
| const SHOW_UNKNOWN_TIER = `input[data-test="ShowUnknownTier"]`; | ||
| const SV_TABLE = `div[data-test="structural variants-table"]`; | ||
| const ANY_ROW = `div[aria-rowindex]`; | ||
| const BRAF_ROW = `div[aria-rowindex="1"]`; | ||
| const GENE_NAME = `div[data-test="geneNameCell"]`; | ||
| const ALTERATIONS_TOTAL = `span[data-test="numberOfAlterations"]`; | ||
| const ALTERATION_CASES = `span[data-test="numberOfAlteredCasesText"]`; | ||
| const SHOW_CLASS_3 = `input[data-test="Class_3"]`; | ||
| const SHOW_CLASS_4 = `input[data-test="Class_4"]`; | ||
| const SHOW_PUTATIVE_DRIVERS = `input[data-test="ShowDriver"]`; | ||
| const SHOW_UNKNOWN_ONCOGENICITY = `input[data-test="ShowUnknownOncogenicity"]`; | ||
|
|
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| describe('custom driver annotations feature in study view', function() { | ||
| describe('structural variants', () => { | ||
| beforeEach(() => { | ||
| goToUrlAndSetLocalStorage(STUDY_VIEW_URL, true); | ||
| waitForNetworkQuiet(); | ||
| }); | ||
|
|
||
| it('shows all structural variants', () => { | ||
| $(SV_TABLE) | ||
| .$(BRAF_ROW) | ||
| .waitForDisplayed(); | ||
| assert($(SV_TABLE).$$(ANY_ROW).length === 21); | ||
| let geneName = $(SV_TABLE) | ||
| .$(BRAF_ROW) | ||
| .$(GENE_NAME) | ||
| .getText(); | ||
| assert(geneName === 'BRAF'); | ||
| const alterations = $(SV_TABLE) | ||
| .$(BRAF_ROW) | ||
| .$(ALTERATIONS_TOTAL); | ||
| assert(alterations.getText() === '36'); | ||
| const alterationCases = $(SV_TABLE) | ||
| .$(BRAF_ROW) | ||
| .$(ALTERATION_CASES) | ||
| .getText(); | ||
| assert(alterationCases === '35'); | ||
| }); | ||
|
|
||
| it('can exclude unknown (and NULL) driver tiers', () => { | ||
| $(ALTERATION_MENU_BTN).click(); | ||
| $(SHOW_UNKNOWN_TIER).waitForDisplayed(5000); | ||
| assert($(SHOW_UNKNOWN_TIER).isSelected()); | ||
| $(SHOW_UNKNOWN_TIER).click(); | ||
| $(SV_TABLE) | ||
| .$(BRAF_ROW) | ||
| .waitForDisplayed(); | ||
| assert($(SV_TABLE).$$(ANY_ROW).length === 10); | ||
| const alterations = $(SV_TABLE) | ||
| .$(BRAF_ROW) | ||
| .$(ALTERATIONS_TOTAL) | ||
| .getText(); | ||
| assert(alterations === '1'); | ||
| const brafCases = $(SV_TABLE) | ||
| .$(BRAF_ROW) | ||
| .$(ALTERATION_CASES) | ||
| .getText(); | ||
| assert(brafCases === '1'); | ||
| }); | ||
|
|
||
| it('can exclude custom driver tiers', () => { | ||
| $(ALTERATION_MENU_BTN).click(); | ||
| $(SHOW_UNKNOWN_TIER).waitForDisplayed(5000); | ||
| assert($(SHOW_UNKNOWN_TIER).isSelected()); | ||
| $(SHOW_UNKNOWN_TIER).click(); | ||
|
|
||
| assert($(SHOW_CLASS_3).isSelected()); | ||
| $(SHOW_CLASS_3).click(); | ||
|
|
||
| assert($(SHOW_CLASS_4).isSelected()); | ||
| $(SHOW_CLASS_4).click(); | ||
|
|
||
| $(SV_TABLE) | ||
| .$(ANY_ROW) | ||
| .waitForDisplayed(); | ||
|
|
||
| assert($(SV_TABLE).$$(ANY_ROW).length === 5); | ||
| assert(getAllGeneNames() === 'ALK,EGFR,EML4,ERG,TMPRSS2'); | ||
| }); | ||
|
|
||
| it('can exclude custom drivers', () => { | ||
| $(ALTERATION_MENU_BTN).click(); | ||
| $(SHOW_UNKNOWN_TIER).waitForDisplayed(5000); | ||
|
|
||
| assert($(SHOW_PUTATIVE_DRIVERS).isSelected()); | ||
| $(SHOW_PUTATIVE_DRIVERS).click(); | ||
|
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| assert($(SHOW_UNKNOWN_ONCOGENICITY).isSelected()); | ||
| $(SHOW_UNKNOWN_ONCOGENICITY).click(); | ||
|
|
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| $(SV_TABLE) | ||
| .$(ANY_ROW) | ||
| .waitForDisplayed(); | ||
|
|
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| assert($(SV_TABLE).$$(ANY_ROW).length === 2); | ||
| assert(getAllGeneNames() === 'NCOA4,RET'); | ||
| }); | ||
| }); | ||
| }); | ||
|
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| function getAllGeneNames() { | ||
| return $(SV_TABLE) | ||
| .$$(ANY_ROW) | ||
| .map(e => e.$(GENE_NAME).getText()) | ||
| .sort() | ||
| .join(); | ||
| } |
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