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move sync to async for all remote tests #4920

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merged 19 commits into from
Jul 17, 2024
Merged

move sync to async for all remote tests #4920

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e40e032
move sync to async
bemijonathan Jun 6, 2024
4e7897c
move all customTabs to async
bemijonathan Jun 12, 2024
f5fdab1
move all customTabs to async
bemijonathan Jun 12, 2024
402bc05
move all expressionComparison to async
bemijonathan Jun 12, 2024
91e5ac2
move all genomicEvolotion to async
bemijonathan Jun 12, 2024
b29c5f4
move all groupComparison to async
bemijonathan Jun 12, 2024
28e7949
move all groupComparison to async
bemijonathan Jun 12, 2024
58e6005
move all results.logic to async
bemijonathan Jun 12, 2024
58b528c
move all redirect to async
bemijonathan Jun 12, 2024
a78d8bb
move all quickSearch to async
bemijonathan Jun 12, 2024
3e8b495
convert plots to async
bemijonathan Jun 12, 2024
06a5693
move all patient.spec.js to async
bemijonathan Jun 13, 2024
6281704
move all oncoprinter.spec.js to async
bemijonathan Jun 13, 2024
2d9eb2b
retest and refactor few changes
bemijonathan Jun 24, 2024
f0dd1b7
Adjust window size to fix custom tabs spec tests
alisman Jul 15, 2024
2d21302
added some wait time and retest
bemijonathan Jul 17, 2024
92fe4b3
retest and refactor few changes
bemijonathan Jul 17, 2024
514ae50
fix results logic
bemijonathan Jul 17, 2024
1adafee
fix: await in results logic
bemijonathan Jul 17, 2024
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256 changes: 159 additions & 97 deletions end-to-end-test/remote/specs/core/customTabs.spec.js
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236 changes: 115 additions & 121 deletions end-to-end-test/remote/specs/core/expressionComparison.spec.js
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Original file line number Diff line number Diff line change
@@ -1,35 +1,27 @@
var assert = require('assert');
var expect = require('chai').expect;
const assert = require('assert');

var {
const {
getElement,
goToUrlAndSetLocalStorage,
clickQueryByGeneButton,
useExternalFrontend,
useNetlifyDeployPreview,
setInputText,
waitForNumberOfStudyCheckboxes,
clickModifyStudySelectionButton,
waitForOncoprint,
setDropdownOpen,
jq,
waitForNetworkQuiet,
getElementByTestHandle,
setServerConfiguration,
} = require('../../../shared/specUtils');
clickElement,
} = require('../../../shared/specUtils_Async');

const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, '');

var searchInputSelector = 'div[data-test=study-search] input[type=text]';

function expressionDataAvailable() {
return $(
'span=mRNA Expression. Select one of the profiles below:'
const expressionDataAvailable = async () => {
return (
await getElement(
'span=mRNA Expression. Select one of the profiles below:'
)
).isExisting();
}
};

describe('plots tab expression data with rule configuration', function() {
before(() => {
goToUrlAndSetLocalStorage(CBIOPORTAL_URL);
before(async () => {
await goToUrlAndSetLocalStorage(CBIOPORTAL_URL);

setServerConfiguration({
enable_cross_study_expression: `
Expand All @@ -38,193 +30,195 @@ describe('plots tab expression data with rule configuration', function() {
});
});

it('For multi study query, if all studies are pan_can then we CAN compare expression in plots', () => {
it('For multi study query, if all studies are pan_can then we CAN compare expression in plots', async () => {
const url = `/results/plots?cancer_study_list=acc_tcga_pan_can_atlas_2018%2Cchol_tcga_pan_can_atlas_2018&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Cgistic&case_set_id=all&gene_list=CDKN2A%2520MDM2&geneset_list=%20&tab_index=tab_visualize&Action=Submit`;
goToUrlAndSetLocalStorage(CBIOPORTAL_URL + url);
await goToUrlAndSetLocalStorage(CBIOPORTAL_URL + url);

waitForNetworkQuiet();
$('.Select-arrow-zone').click();
$('.Select-option').waitForExist();
$('.Select-option=mRNA').isExisting();
await waitForNetworkQuiet();
await clickElement('.Select-arrow-zone');
await (await getElement('.Select-option')).waitForExist();
await (await getElement('.Select-option=mRNA')).isExisting();

assert.equal(
$(
'div=Expression data cannot be compared across the selected studies.'
await (
await getElement(
'div=Expression data cannot be compared across the selected studies.'
)
).isExisting(),
false
);
});

it('For multi study query that is NOT all pan_can, no expression data in plots', () => {
it('For multi study query that is NOT all pan_can, no expression data in plots', async () => {
const url = `/results/plots?cancer_study_list=acc_tcga_pan_can_atlas_2018%2Cchol_tcga&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Cgistic&case_set_id=all&gene_list=CDKN2A%2520MDM2&geneset_list=%20&tab_index=tab_visualize&Action=Submit`;
goToUrlAndSetLocalStorage(CBIOPORTAL_URL + url);
waitForNetworkQuiet();
$('.Select-arrow-zone').click();
$('.Select-option=Mutation').waitForExist();
assert.equal($('.Select-option=mRNA').isExisting(), false);
await goToUrlAndSetLocalStorage(CBIOPORTAL_URL + url);
await waitForNetworkQuiet();
await clickElement('.Select-arrow-zone');
await (await getElement('.Select-option=Mutation')).waitForExist();
assert.equal(
await (await getElement('.Select-option=mRNA')).isExisting(),
false
);

assert.equal(
$(
'div=Expression data cannot be compared across the selected studies.'
await (
await getElement(
'div=Expression data cannot be compared across the selected studies.'
)
).isExisting(),
true
);
});

it('For single study, NOT pan_can, there is expression available in plots', () => {
it('For single study, NOT pan_can, there is expression available in plots', async () => {
const url = `/results/plots?cancer_study_list=chol_tcga&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Cgistic&case_set_id=all&gene_list=CDKN2A%2520MDM2&geneset_list=%20&tab_index=tab_visualize&Action=Submit`;
goToUrlAndSetLocalStorage(CBIOPORTAL_URL + url);
waitForNetworkQuiet();
$('.Select-arrow-zone').click();
$('.Select-option=Mutation').waitForExist();
assert.equal($('.Select-option=mRNA').isExisting(), true);
await goToUrlAndSetLocalStorage(CBIOPORTAL_URL + url);
await waitForNetworkQuiet();
await clickElement('.Select-arrow-zone');
await (await getElement('.Select-option=Mutation')).waitForExist();
assert.equal(
await (await getElement('.Select-option=mRNA')).isExisting(),
true
);

assert.equal(
$(
'div=Expression data cannot be compared across the selected studies.'
await (
await getElement(
'div=Expression data cannot be compared across the selected studies.'
)
).isExisting(),
false
);
});
});

describe('plots tab expression data without rule configuration', function() {
before(() => {
goToUrlAndSetLocalStorage(CBIOPORTAL_URL);
before(async () => {
await goToUrlAndSetLocalStorage(CBIOPORTAL_URL);

setServerConfiguration({
enable_cross_study_expression: undefined,
});
});

it('for multi study query that is NOT all pan_can, expression data is NOT available in plots', () => {
it('for multi study query that is NOT all pan_can, expression data is NOT available in plots', async () => {
const url = `/results/plots?cancer_study_list=acc_tcga_pan_can_atlas_2018%2Cchol_tcga&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Cgistic&case_set_id=all&gene_list=CDKN2A%2520MDM2&geneset_list=%20&tab_index=tab_visualize&Action=Submit`;
goToUrlAndSetLocalStorage(CBIOPORTAL_URL + url);
waitForNetworkQuiet();
await goToUrlAndSetLocalStorage(CBIOPORTAL_URL + url);
await waitForNetworkQuiet();

browser.execute(() => {
await browser.execute(() => {
window.globalStores.appStore.serverConfig.enable_cross_study_expression = undefined;
});

$('.Select-arrow-zone').click();
$('.Select-option=Mutation').waitForExist();
assert.equal($('.Select-option=mRNA').isExisting(), false);
await clickElement('.Select-arrow-zone');
await (await getElement('.Select-option=Mutation')).waitForExist();
assert.equal(
await (await getElement('.Select-option=mRNA')).isExisting(),
false
);

$(
'div=Expression data cannot be compared across the selected studies.'
await (
await getElement(
'div=Expression data cannot be compared across the selected studies.'
)
).isExisting();
});
});

describe('expression data in query form', function() {
beforeEach(() => {
goToUrlAndSetLocalStorage(CBIOPORTAL_URL);
beforeEach(async () => {
await goToUrlAndSetLocalStorage(CBIOPORTAL_URL);

setServerConfiguration({
enable_cross_study_expression: `
(studies)=>studies.filter(s=>/pan_can_atlas/.test(s.studyId) === false).length === 0
`,
});

waitForNetworkQuiet();
await waitForNetworkQuiet();
});

after(() => {
setServerConfiguration({});
});

it('For single study with expression data, we can see expression data', () => {
$('.studyItem_sarc_tcga_pub').click();
getElementByTestHandle('queryByGeneButton').click();
assert.equal(expressionDataAvailable(), true);
it('For single study with expression data, we can see expression data', async () => {
await clickElement('.studyItem_sarc_tcga_pub');
await clickElement('[data-test="queryByGeneButton"]');
assert.equal(await expressionDataAvailable(), true);
});

it("For single study without expression data, we AREN'T offered expression data", () => {
$('.studyItem_chol_nccs_2013').click();

getElementByTestHandle('queryByGeneButton').click();
assert.equal(expressionDataAvailable(), false);
it("For single study without expression data, we AREN'T offered expression data", async () => {
await clickElement('.studyItem_chol_nccs_2013');
await clickElement('[data-test="queryByGeneButton"]');
assert.equal(await expressionDataAvailable(), false);
});

it("For two studies with expression data (only one pancan) we AREN'T offered expression data", () => {
$('.studyItem_sarc_tcga_pub').click();
$('.studyItem_chol_tcga_pan_can_atlas_2018').click();

getElementByTestHandle('queryByGeneButton').click();

assert.equal(expressionDataAvailable(), false);
it("For two studies with expression data (only one pancan) we AREN'T offered expression data", async () => {
await clickElement('.studyItem_sarc_tcga_pub');
await clickElement('.studyItem_chol_tcga_pan_can_atlas_2018');
await clickElement('[data-test="queryByGeneButton"]');
assert.equal(await expressionDataAvailable(), false);
});

it('For two studies (both pan can) with expression data we ARE offered expression data', () => {
$('.studyItem_brca_tcga_pan_can_atlas_2018').click();
$('.studyItem_chol_tcga_pan_can_atlas_2018').click();

getElementByTestHandle('queryByGeneButton').click();

assert.equal(expressionDataAvailable(), true);
it('For two studies (both pan can) with expression data we ARE offered expression data', async () => {
await clickElement('.studyItem_brca_tcga_pan_can_atlas_2018');
await clickElement('.studyItem_chol_tcga_pan_can_atlas_2018');
await (await getElementByTestHandle('queryByGeneButton')).click();
assert.equal(await expressionDataAvailable(), true);
});
});

describe('cross study expression data without configuration rule', () => {
beforeEach(() => {
goToUrlAndSetLocalStorage(CBIOPORTAL_URL);
beforeEach(async () => {
await goToUrlAndSetLocalStorage(CBIOPORTAL_URL);

browser.execute(() => {
await browser.execute(() => {
window.globalStores.appStore.serverConfig.enable_cross_study_expression = undefined;
});
});

it('without configuration rule, no multi study expression', () => {
$('.studyItem_brca_tcga_pan_can_atlas_2018').click();
$('.studyItem_chol_tcga_pan_can_atlas_2018').click();

getElementByTestHandle('queryByGeneButton').click();

assert.equal(expressionDataAvailable(), false);
it('without configuration rule, no multi study expression', async () => {
await clickElement('.studyItem_brca_tcga_pan_can_atlas_2018');
await clickElement('.studyItem_chol_tcga_pan_can_atlas_2018');
await (await getElementByTestHandle('queryByGeneButton')).click();
assert.equal(await expressionDataAvailable(), false);
});

it('without configuration rule, single study expression available', () => {
$('.studyItem_brca_tcga_pan_can_atlas_2018').click();
$('.studyItem_chol_tcga_pan_can_atlas_2018').click();

getElementByTestHandle('queryByGeneButton').click();

assert.equal(expressionDataAvailable(), false);
it('without configuration rule, single study expression available', async () => {
await clickElement('.studyItem_brca_tcga_pan_can_atlas_2018');
await clickElement('.studyItem_chol_tcga_pan_can_atlas_2018');
await (await getElementByTestHandle('queryByGeneButton')).click();
assert.equal(await expressionDataAvailable(), false);
});
});

describe('custom expression comparison rule', () => {
beforeEach(() => {
goToUrlAndSetLocalStorage(CBIOPORTAL_URL);
beforeEach(async () => {
await goToUrlAndSetLocalStorage(CBIOPORTAL_URL);
setServerConfiguration({
enable_cross_study_expression:
'(studies)=>studies.filter(s=>/gbm_cptac_2021/.test(s.studyId)).length > 0',
});
});

it('with all pancan, expression NOT available', () => {
$('.studyItem_brca_tcga_pan_can_atlas_2018').click();
$('.studyItem_chol_tcga_pan_can_atlas_2018').click();

getElementByTestHandle('queryByGeneButton').click();

assert.equal(expressionDataAvailable(), false);
it('with all pancan, expression NOT available', async () => {
await clickElement('.studyItem_brca_tcga_pan_can_atlas_2018');
await clickElement('.studyItem_chol_tcga_pan_can_atlas_2018');
await (await getElementByTestHandle('queryByGeneButton')).click();
assert.equal(await expressionDataAvailable(), false);
});

it('configuration rule is satisfied and expression available across study', () => {
$('.studyItem_chol_tcga').click();
$('.studyItem_gbm_cptac_2021').click();

getElementByTestHandle('queryByGeneButton').click();

assert.equal(expressionDataAvailable(), true);
it('configuration rule is satisfied and expression available across study', async () => {
await clickElement('.studyItem_chol_tcga');
await clickElement('.studyItem_gbm_cptac_2021');
await (await getElementByTestHandle('queryByGeneButton')).click();
assert.equal(await expressionDataAvailable(), true);
});

it('single study still has expression despite rule', () => {
$('.studyItem_chol_tcga_pan_can_atlas_2018').click();

getElementByTestHandle('queryByGeneButton').click();

assert.equal(expressionDataAvailable(), true);
it('single study still has expression despite rule', async () => {
await clickElement('.studyItem_chol_tcga_pan_can_atlas_2018');
await (await getElementByTestHandle('queryByGeneButton')).click();
assert.equal(await expressionDataAvailable(), true);
});
});
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