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Impl. structural variants table in study view
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,154 @@ | ||
| var assert = require('assert'); | ||
| var goToUrlAndSetLocalStorage = require('../../shared/specUtils') | ||
| .goToUrlAndSetLocalStorage; | ||
| var waitForStudyView = require('../../shared/specUtils').waitForStudyView; | ||
|
|
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| const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, ''); | ||
| // TODO remove feature flag after merge. | ||
| const studyViewUrl = `${CBIOPORTAL_URL}/study/summary?id=study_es_0&featureFlags=STUDY_VIEW_STRUCT_VAR_TABLE`; | ||
| const structVarTable = '//*[@data-test="structural variant pairs-table"]'; | ||
| const filterCheckBox = '[data-test=labeledCheckbox]'; | ||
| const structVarFilterPillTag = '[data-test=pill-tag]'; | ||
| const uncheckedSvIcon = '[data-test=structVarQueryCheckboxUnchecked]'; | ||
| const checkedSvIcon = '[data-test=structVarQueryCheckboxChecked]'; | ||
| const structVarNameCell = '[data-test=structVarNameCell]'; | ||
| const toast = '.Toastify div[role=alert]'; | ||
|
|
||
| describe('study view structural variant table', function() { | ||
| beforeEach(() => { | ||
| goToUrlAndSetLocalStorage(studyViewUrl, true); | ||
| waitForStudyView(); | ||
| }); | ||
|
|
||
| it('adds structural variant to study view filter', () => { | ||
| $(structVarTable) | ||
| .$(filterCheckBox) | ||
| .click(); | ||
| $('[data-test=selectSamplesButton]').waitForExist(); | ||
| $('[data-test=selectSamplesButton]').click(); | ||
| assert($(structVarFilterPillTag).isExisting()); | ||
| }); | ||
|
|
||
| it('shows all checkboxes when row is hovered', () => { | ||
| $(structVarNameCell).waitForExist(); | ||
| const firstSvRowCell = $$(structVarNameCell)[0]; | ||
| assert.equal($$(structVarNameCell)[1].getText(), 'SND1'); | ||
| assert.equal($$(structVarNameCell)[2].getText(), 'BRAF'); | ||
|
|
||
| movePointerWithRetry(firstSvRowCell, () => | ||
| $(uncheckedSvIcon).waitForDisplayed() | ||
| ); | ||
| assert.equal($$(uncheckedSvIcon).length, 3); | ||
| }); | ||
|
|
||
| it('shows only checked checkboxes when row is not hovered', () => { | ||
| $(structVarNameCell).waitForExist(); | ||
| const gene1Cell = $$(structVarNameCell)[1]; | ||
| movePointerWithRetry(gene1Cell, () => | ||
| $(uncheckedSvIcon).waitForDisplayed() | ||
| ); | ||
| assert.equal($$(uncheckedSvIcon).length, 3); | ||
|
|
||
| gene1Cell.waitForClickable(); | ||
| gene1Cell.click(); | ||
|
|
||
| // hover somewhere else: | ||
| movePointerWithRetry($('span=Gene 2'), $(checkedSvIcon).waitForExist()); | ||
|
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| assert.equal($$(uncheckedSvIcon).length, 0); | ||
| assert.equal($$(checkedSvIcon).length, 1); | ||
| }); | ||
|
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||
| it('adds gene1::gene2 to Results View query', () => { | ||
| $(structVarNameCell).waitForExist(); | ||
| const firstSvRowCell = $$(structVarNameCell)[0]; | ||
|
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||
| movePointerWithRetry(firstSvRowCell, () => { | ||
| $$(uncheckedSvIcon)[0].waitForClickable(); | ||
| }); | ||
| const gene1And2Checkbox = $$(uncheckedSvIcon)[0]; | ||
| gene1And2Checkbox.click(); | ||
| $(toast).waitForDisplayed(); | ||
| clearToast(); | ||
|
|
||
| const resultsViewQueryBox = openResultViewQueryBox(); | ||
| assert.equal('SND1: FUSION::BRAF ;', resultsViewQueryBox.getValue()); | ||
| }); | ||
|
|
||
| it('adds gene1::* to Results View query', () => { | ||
| $(structVarNameCell).waitForExist(); | ||
| const gene1Cell = $$(structVarNameCell)[1]; | ||
| movePointerWithRetry(gene1Cell, () => | ||
| $(uncheckedSvIcon).waitForDisplayed() | ||
| ); | ||
| gene1Cell.waitForClickable(); | ||
| gene1Cell.click(); | ||
| $(toast).waitForDisplayed(); | ||
| clearToast(); | ||
|
|
||
| const resultsViewQueryBox = openResultViewQueryBox(); | ||
| assert.equal('SND1: FUSION:: ;', resultsViewQueryBox.getValue()); | ||
| }); | ||
|
|
||
| it('adds *::gene2 to Results View query', () => { | ||
| $(structVarNameCell).waitForExist(); | ||
| const gene2Cell = $$(structVarNameCell)[2]; | ||
| movePointerWithRetry(gene2Cell, () => | ||
| $(uncheckedSvIcon).waitForDisplayed() | ||
| ); | ||
| gene2Cell.waitForClickable(); | ||
| gene2Cell.click(); | ||
| $(toast).waitForDisplayed(); | ||
| clearToast(); | ||
|
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||
| const resultsViewQueryBox = openResultViewQueryBox(); | ||
| assert.equal('BRAF: ::FUSION ;', resultsViewQueryBox.getValue()); | ||
| }); | ||
| }); | ||
|
|
||
| function openResultViewQueryBox() { | ||
| const resultsViewQueryBox = $('[data-test=geneSet]'); | ||
| resultsViewQueryBox.waitForClickable(); | ||
| resultsViewQueryBox.click(); | ||
| return resultsViewQueryBox; | ||
| } | ||
|
|
||
| function clearToast() { | ||
| const toastify = $('.Toastify button'); | ||
| toastify.waitForClickable(); | ||
| toastify.click(); | ||
| browser.pause(100); | ||
| } | ||
|
|
||
| function movePointerTo(element) { | ||
| element.waitForDisplayed(); | ||
| element.scrollIntoView(); | ||
| const x = element.getLocation('x'); | ||
| const y = element.getLocation('y'); | ||
| browser.performActions([ | ||
| { | ||
| type: 'pointer', | ||
| parameters: { pointerType: 'mouse' }, | ||
| actions: [ | ||
| { type: 'pointerMove', duration: 0, x, y }, | ||
| { type: 'pointerMove', duration: 0, x, y }, | ||
| ], | ||
| }, | ||
| ]); | ||
| } | ||
|
|
||
| /** | ||
| * When scrolling to the new location, some tooltips might pop up and interfere. | ||
| * A retry solves this problem: the second time the pointer is already near/at the desired location | ||
| */ | ||
| function movePointerWithRetry(element, isOk) { | ||
| movePointerTo(element); | ||
| try { | ||
| if (isOk()) { | ||
| return; | ||
| } | ||
| } catch (e) { | ||
| // retry | ||
| } | ||
| movePointerTo(element); | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -30,17 +30,17 @@ | |
| "buildBootstrap": "sass --style :compressed src/globalStyles/bootstrap-entry.scss src/globalStyles/prefixed-bootstrap.min.css", | ||
| "heroku-postbuild": "yarn run build && yarn add [email protected] -g", | ||
| "updateAPI": "yarn run fetchAPI && yarn run buildAPI && yarn run updateOncoKbAPI && yarn run updateGenomeNexusAPI", | ||
| "fetchAPILocal": "export CBIOPORTAL_URL=http://localhost:8090 && curl -L -k ${CBIOPORTAL_URL}/api/api-docs | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json && curl -L -k ${CBIOPORTAL_URL}/api/api-docs?group=internal | json | grep -v host | grep -v basePath | grep -v termsOfService > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json", | ||
| "fetchAPI": "./scripts/env_vars.sh && eval \"$(./scripts/env_vars.sh)\" && curl -L -k ${CBIOPORTAL_URL}/api/api-docs | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json && curl -L -k ${CBIOPORTAL_URL}/api/api-docs?group=internal | json | grep -v host | grep -v basePath | grep -v termsOfService > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json", | ||
| "fetchAPILocal": "export CBIOPORTAL_URL=http://localhost:8090 && curl -s -L -k ${CBIOPORTAL_URL}/api/api-docs | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json && curl -s -L -k ${CBIOPORTAL_URL}/api/api-docs?group=internal | json | grep -v host | grep -v basePath | grep -v termsOfService > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json", | ||
| "fetchAPI": "./scripts/env_vars.sh && eval \"$(./scripts/env_vars.sh)\" && curl -s -L -k ${CBIOPORTAL_URL}/api/api-docs | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPI-docs.json && curl -s -L -k ${CBIOPORTAL_URL}/api/api-docs?group=internal | json | grep -v host | grep -v basePath | grep -v termsOfService > packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal-docs.json", | ||
| "buildAPI": "node scripts/generate-api.js packages/cbioportal-ts-api-client/src/generated CBioPortalAPI CBioPortalAPIInternal", | ||
| "updateOncoKbAPI": "yarn run fetchOncoKbAPI && yarn run buildOncoKbAPI", | ||
| "fetchOncoKbAPI": "curl -k https://www.oncokb.org/api/v1/v2/api-docs?group=Public%20APIs | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/oncokb-ts-api-client/src/generated/OncoKbAPI-docs.json", | ||
| "fetchOncoKbAPI": "curl -s -k https://www.oncokb.org/api/v1/v2/api-docs?group=Public%20APIs | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/oncokb-ts-api-client/src/generated/OncoKbAPI-docs.json", | ||
| "buildOncoKbAPI": "node scripts/generate-api.js packages/oncokb-ts-api-client/src/generated OncoKbAPI", | ||
| "updateG2SAPI": "yarn run fetchG2SAPI && yarn run buildG2SAPI", | ||
| "fetchG2SAPI": "curl -k http://g2s.genomenexus.org/v2/api-docs?group=api > packages/genome-nexus-ts-api-client/src/generated/Genome2StructureAPI-docs.json", | ||
| "fetchG2SAPI": "curl -s -k http://g2s.genomenexus.org/v2/api-docs?group=api > packages/genome-nexus-ts-api-client/src/generated/Genome2StructureAPI-docs.json", | ||
| "buildG2SAPI": "node scripts/generate-api.js packages/genome-nexus-ts-api-client/src/generated Genome2StructureAPI", | ||
| "updateGenomeNexusAPI": "yarn run fetchGenomeNexusAPI && yarn run buildGenomeNexusAPI", | ||
| "fetchGenomeNexusAPI": "./scripts/env_vars.sh && eval \"$(./scripts/env_vars.sh)\" && curl -k ${GENOME_NEXUS_URL}/v2/api-docs | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json && curl -k ${GENOME_NEXUS_URL}/v2/api-docs?group=internal | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json", | ||
| "fetchGenomeNexusAPI": "./scripts/env_vars.sh && eval \"$(./scripts/env_vars.sh)\" && curl -s -k ${GENOME_NEXUS_URL}/v2/api-docs | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json && curl -s -k ${GENOME_NEXUS_URL}/v2/api-docs?group=internal | json | grep -v basePath | grep -v termsOfService | grep -v host > packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json", | ||
| "buildGenomeNexusAPI": "node scripts/generate-api.js packages/genome-nexus-ts-api-client/src/generated GenomeNexusAPI GenomeNexusAPIInternal", | ||
| "updateHotspotGenes": "./scripts/get_hotspot_genes.sh > src/shared/static-data/hotspotGenes.json", | ||
| "compileOqlParser": "cd src/shared/lib/oql && pegjs oql-parser.pegjs", | ||
|
|
||
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