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E2E Disease Panels test added opencb#461
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@antonioaltamura
antonioaltamura committed Apr 5, 2022
1 parent 6b601a3 commit c1580b6
Showing 1 changed file with 36 additions and 34 deletions.
70 changes: 36 additions & 34 deletions cypress/integration/004-opencga-variant-browser.spec.js
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Original file line number Diff line number Diff line change
Expand Up @@ -115,33 +115,7 @@ context("4. Variant Browser", () => {
checkResults("variant-browser-grid");
});

it("4.7 Filters. Genomic: Disease Panels", () => {
// Genomic: Disease Panels
// TODO decomment once opencga error 'URI Too Long' is fixed
// disease-panel-filter select + button
// cy.get("disease-panel-filter").find(" a").contains("Childhood onset dystonia or chorea or related movement disorder").click({force:true}) // URI too long
// cy.get("disease-panel-filter").find(" a").contains("Amelogenesis imperfecta").click({force:true})
// cy.get("div.search-button-wrapper button").click();
//
// checkResultsOrNot("variant-browser-grid")

// NOTE Covid19... is the first URI too long
/* cy.get("disease-panel-filter div.dropdown-menu a").each(el => {
// cannot use cy.wrap(el) here. disease-panel-filter div.dropdown-menu is refreshed on click on buttons and DOM refs are broken (https://github.com/cypress-io/cypress/issues/7306)
const id = el.attr("id");
cy.get("#" + id).should("exist").click({force: true});
//cy.wrap(el).should("exist").click({force: true});
cy.get("div.search-button-wrapper button").click();
checkResultsOrNot("variant-browser-grid");
cy.wait(2000);
cy.get("opencga-active-filters button[data-filter-name='panel']").click();
});*/
});

it("4.8 Filters. Genomic: Gene Biotype", () => {
it("4.7 Filters. Genomic: Gene Biotype", () => {
// Genomic: Gene Biotype
cy.get("biotype-filter button").click();
cy.get("biotype-filter input[type='search']").type("protein"); // typing protein_coding using autocomplete
Expand All @@ -153,7 +127,7 @@ context("4. Variant Browser", () => {
checkResults("variant-browser-grid");
});

it("4.9 Filters. Genomic: Variant", () => {
it("4.8 Filters. Genomic: Variant", () => {
// Genomic: Variant type cy.get('.magic-checkbox-wrapper > :nth-child(1) > label')
cy.get("variant-type-filter input[value='SNV'] + label").click({force: true});
cy.get("div.search-button-wrapper button").click();
Expand All @@ -162,15 +136,15 @@ context("4. Variant Browser", () => {
checkResults("variant-browser-grid");
});

it("4.10 Filters. Consequence type: LoF", () => {
it("4.9 Filters. Consequence type: LoF", () => {
// Consequence type: SO Term - LoF Enabled
cy.get("variant-browser-filter a[data-cy-section-title='ConsequenceType']").click();
cy.get("consequence-type-select-filter input[value='Loss-of-Function (LoF)'").click({force: true});
cy.get("div.search-button-wrapper button").click();
checkResults("variant-browser-grid");
});

it("4.11 Filters. Consequence type: Missense", () => {
it("4.10 Filters. Consequence type: Missense", () => {
// Consequence type: SO Term - Use example: Missense
cy.get("consequence-type-select-filter button").click();
cy.get("consequence-type-select-filter input[type='search']").type("miss"); // typing missense using autocomplete
Expand All @@ -182,7 +156,7 @@ context("4. Variant Browser", () => {
checkResults("variant-browser-grid");
});

it("4.12 Filters. Population Frequency: 1000 Genomes - AFR < 0.0001 AND EUR > 0.0001", () => {
it("4.11 Filters. Population Frequency: 1000 Genomes - AFR < 0.0001 AND EUR > 0.0001", () => {
// Population Frequency: 1000 Genomes - AFR < 0.0001 AND EUR > 0.0001
cy.get("variant-browser-filter a[data-cy-section-title='PopulationFrequency']").click();
cy.get("population-frequency-filter i[data-cy='pop-freq-toggle-1kG_phase3']").click();
Expand All @@ -199,7 +173,7 @@ context("4. Variant Browser", () => {
checkResults("variant-browser-grid");
});

it("4.13 Filters. Population Frequency: gnomAD - Set all < 0.00001", () => {
it("4.12 Filters. Population Frequency: gnomAD - Set all < 0.00001", () => {
// Population Frequency: gnomAD - Set all < 0.00001
cy.get("population-frequency-filter i[data-cy='pop-freq-toggle-GNOMAD_GENOMES']").click();
cy.get("population-frequency-filter div[data-cy='pop-freq-codes-wrapper-GNOMAD_GENOMES']").should("be.visible");
Expand All @@ -210,9 +184,37 @@ context("4. Variant Browser", () => {
checkResults("variant-browser-grid");
});

it("4.14 Filters. Clinical and Disease: Clinical Annotation: Pathogenic", () => {
// Clinical and Disease: ClinVar Accessions. Use example: Pathogenic
it("4.13 Filters. Clinical: Disease Panels", () => {
cy.get("variant-browser-filter a[data-cy-section-title='Clinical']").click();

// Clinical: Disease Panels
cy.get("disease-panel-filter").find(" a").contains("Childhood onset dystonia or chorea or related movement disorder").click({force: true}); // URI too long
cy.get("disease-panel-filter").find(" a").contains("Amelogenesis imperfecta").click({force: true});
cy.get("div.search-button-wrapper button").click();

checkResultsOrNot("variant-browser-grid");

// Test ALL Panels
// NOTE Covid19... is the first URI too long
/* cy.get("disease-panel-filter select-field-filter").within(() => {
cy.get("a").each(el => {
// cannot use cy.wrap(el) here. disease-panel-filter div.dropdown-menu is refreshed on click on buttons and DOM refs are broken (https://github.com/cypress-io/cypress/issues/7306)
const id = el.attr("id");
console.log("el", el);
cy.get("#" + id).should("exist").click({force: true});
// cy.wrap(el).should("exist").click({force: true});
cy.get("div.search-button-wrapper button").click();
checkResultsOrNot("variant-browser-grid");
cy.wait(2000);
cy.get("opencga-active-filters button[data-filter-name='panel']").click();
});
});*/
});

it("4.14 Filters. Clinical and Disease: Clinical Annotation: Pathogenic", () => {
// Clinical: ClinVar Accessions. Use example: Pathogenic
cy.get("clinical-annotation-filter div[data-cy='clinical-significance'] button.dropdown-toggle").click();
cy.get("clinical-annotation-filter div[data-cy='clinical-significance'] .dropdown-menu").contains("Pathogenic").click();
cy.get("div.search-button-wrapper button").click();
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