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Merge pull request #4478 from alisman/badgeTest
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Add e2e test for mutation badges/filtering in mutation tab
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@alisman
alisman authored Jan 12, 2023
2 parents 8f46e69 + 327af92 commit a4edc1c
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Showing 2 changed files with 127 additions and 44 deletions.
169 changes: 126 additions & 43 deletions end-to-end-test/remote/specs/core/mutationsTab.spec.js
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
var assert = require('assert');
const { getElementByTestHandle } = require('../../../shared/specUtils');
var waitForOncoprint = require('../../../shared/specUtils').waitForOncoprint;
var setSettingsMenuOpen = require('../../../shared/specUtils')
.setSettingsMenuOpen;
Expand All @@ -8,51 +9,133 @@ var goToUrlAndSetLocalStorage = require('../../../shared/specUtils')
const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, '');

describe('mutations tab', function() {
it('uses VUS filtering', function() {
goToUrlAndSetLocalStorage(
`${CBIOPORTAL_URL}/results/oncoprint?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=acc_tcga_pan_can_atlas_2018&case_set_id=acc_tcga_pan_can_atlas_2018_cnaseq&data_priority=0&gene_list=HSD17B4&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=acc_tcga_pan_can_atlas_2018_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=acc_tcga_pan_can_atlas_2018_mutations&tab_index=tab_visualize`
);
waitForOncoprint(60000);
setSettingsMenuOpen(true);
$('input[data-test="HideVUS"]').click();
setSettingsMenuOpen(false);
$('a.tabAnchor_mutations').waitForExist();
$('a.tabAnchor_mutations').click();
$('[data-test="LazyMobXTable_CountHeader"]').waitForDisplayed();
assert(
$('[data-test="LazyMobXTable_CountHeader"]')
.getHTML(false)
.indexOf('0 Mutations') > -1
);
describe('VUS filtering', () => {
it('uses VUS filtering', function() {
goToUrlAndSetLocalStorage(
`${CBIOPORTAL_URL}/results/oncoprint?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=acc_tcga_pan_can_atlas_2018&case_set_id=acc_tcga_pan_can_atlas_2018_cnaseq&data_priority=0&gene_list=HSD17B4&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=acc_tcga_pan_can_atlas_2018_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=acc_tcga_pan_can_atlas_2018_mutations&tab_index=tab_visualize`
);
waitForOncoprint(60000);
setSettingsMenuOpen(true);
$('input[data-test="HideVUS"]').click();
setSettingsMenuOpen(false);
$('a.tabAnchor_mutations').waitForExist();
$('a.tabAnchor_mutations').click();
$('[data-test="LazyMobXTable_CountHeader"]').waitForDisplayed();
assert(
$('[data-test="LazyMobXTable_CountHeader"]')
.getHTML(false)
.indexOf('0 Mutations') > -1
);
});
it('uses germline filtering', function() {
goToUrlAndSetLocalStorage(
`${CBIOPORTAL_URL}/results/mutations?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=brca_tcga_pub&case_set_id=brca_tcga_pub_cnaseq&data_priority=0&gene_list=BRCA1%2520BRCA2&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=brca_tcga_pub_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=brca_tcga_pub_mutations&tab_index=tab_visualize`
);
$('[data-test="LazyMobXTable_CountHeader"]').waitForDisplayed({
timeout: 10000,
});
assert(
$('[data-test="LazyMobXTable_CountHeader"]')
.getHTML(false)
.indexOf('19 Mutations') > -1,
'unfiltered is 19 mutations'
);

setSettingsMenuOpen(true);
$(
'div[data-test="GlobalSettingsDropdown"] input[data-test="HideGermline"]'
).click();
setSettingsMenuOpen(false);

$('[data-test="LazyMobXTable_CountHeader"]').waitForDisplayed({
timeout: 10000,
});
assert(
$('[data-test="LazyMobXTable_CountHeader"]')
.getHTML(false)
.indexOf('6 Mutations') > -1,
'filtered is 6 mutations'
);
});
});
it('uses germline filtering', function() {
goToUrlAndSetLocalStorage(
`${CBIOPORTAL_URL}/results/mutations?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=brca_tcga_pub&case_set_id=brca_tcga_pub_cnaseq&data_priority=0&gene_list=BRCA1%2520BRCA2&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=brca_tcga_pub_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=brca_tcga_pub_mutations&tab_index=tab_visualize`
);
$('[data-test="LazyMobXTable_CountHeader"]').waitForDisplayed({
timeout: 10000,

describe('alteration badge selectors and filtering', function() {
beforeEach(() => {
goToUrlAndSetLocalStorage(
`${CBIOPORTAL_URL}/results/mutations?cancer_study_list=coadread_tcga_pub&cancer_study_id=coadread_tcga_pub&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic&Z_SCORE_THRESHOLD=2.0&case_set_id=coadread_tcga_pub_nonhypermut&gene_list=TP53&gene_set_choice=user-defined-list&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations&geneset_list=%20&tab_index=tab_visualize&Action=Submit&mutations_gene=KRAS`
);
$('.lollipop-svgnode').waitForDisplayed({
timeout: 10000,
});
});
assert(
$('[data-test="LazyMobXTable_CountHeader"]')
.getHTML(false)
.indexOf('19 Mutations') > -1,
'unfiltered is 19 mutations'
);

setSettingsMenuOpen(true);
$(
'div[data-test="GlobalSettingsDropdown"] input[data-test="HideGermline"]'
).click();
setSettingsMenuOpen(false);

$('[data-test="LazyMobXTable_CountHeader"]').waitForDisplayed({
timeout: 10000,

it('clicking badge filters adjusts mutation table counts', function() {
const getCountText = () => {
return getElementByTestHandle(
'LazyMobXTable_CountHeader'
).getText();
};

assert(
getCountText().includes('98 Mutations'),
'starts with full complement of mutations'
);

// click first missense badge
$('strong=Missense').click();

assert(
getCountText().includes('31 Mutations'),
'reduced by removing missense'
);

// toggle it back on
$('strong=Missense').click();

assert(
getCountText().includes('98 Mutations'),
'full complement restored'
);

$('strong=Splice').click();

assert(
getCountText().includes('97 Mutations'),
'splice filters down'
);

$('strong=Missense').click();

assert(
getCountText().includes('30 Mutations'),
'splice AND missense filters down'
);
});

it('adjusts mutation counts based on driver annotation settings', function() {
getElementByTestHandle('badge-driver')
.$('span=98')
.waitForExist();

setSettingsMenuOpen(true);
getElementByTestHandle('annotateOncoKb').click();
setSettingsMenuOpen(false);

$('.lollipop-svgnode').waitForDisplayed();

getElementByTestHandle('badge-driver')
.$('span=64')
.waitForExist();

setSettingsMenuOpen(true);
getElementByTestHandle('annotateOncoKb').click();
setSettingsMenuOpen(false);

$('.lollipop-svgnode').waitForDisplayed();

getElementByTestHandle('badge-driver')
.$('span=98')
.waitForExist();
});
assert(
$('[data-test="LazyMobXTable_CountHeader"]')
.getHTML(false)
.indexOf('6 Mutations') > -1,
'filtered is 6 mutations'
);
});
});
2 changes: 1 addition & 1 deletion src/pages/resultsView/mutation/DriverAnnotationProteinImpactTypeBadgeSelector.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -174,7 +174,7 @@ export default class DriverAnnotationProteinImpactTypeBadgeSelector extends Prot

if (option.value === DriverVsVusType.DRIVER) {
return (
<span>
<span data-test={'badge-driver'}>
{option.label || option.value}
<span className={styles['driver-annotation-setting']}>
<DefaultTooltip
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