refactor: Improve Cypress setup and use Cypress commands.js

cypress/integration/index.js

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+export * from './long-running-score.spec';
+export * from './session_all_genes.spec';
+export * from './session_all_celllines.spec';
+export * from './session_all_tissues.spec';
+
+export * from './ordino-video-test.spec';

cypress/integration/long-running-score.spec.js

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+// https://www.youtube.com/watch?v=JZIIf-k852g&t=1s
+it('Long Running Score', function() {
+ cy.visit(Cypress.env('host'));
+ // Login
+ cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click();
+
+ cy.login(); // use Cypress command registerd in Ordino app
+
+ // Show you can select single genes if you wanted
+ cy.scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+ cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+ // wait intentionally a few seconds
+ cy.wait(2000)
+ cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-link]').click();
+
+ // Open Lineup ranking
+ // Define api calls to wait:
+ cy.intercept('/api/tdp/db/publicdb/gene/desc').as('gene_desc');
+ cy.intercept('/api/tdp/db/publicdb/gene/filter?filter_species=human&filter_panel=normal+chromosome+protein+coding+human+genes').as('human_genes');
+ cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click();
+ cy.wait('@gene_desc');
+ cy.wait('@human_genes');
+ cy.waitLineupReadyOrdino(0)
+
+ // Add column
+ cy.get('[data-testid=add-column-button]').click();
+ cy.wait(2000);
+ cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click();
+ cy.select2SingleSelect("data-type", "Relative Copy Number")
+ cy.formSelect("aggregation", "Boxplot")
+ cy.get('[data-testid=primary-dialog-button]').click();
+ cy.checkScoreColLoadedOrdino(0, ['Relative Copy Number', 'Boxplot'], 9)
+
+ // Add column
+ cy.get('[data-testid=add-column-button]').click();
+ cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click();
+ cy.formSelect("aggregation", "Frequency")
+ cy.formSelect("comparison-operator", "> greater than")
+ cy.get(':nth-child(5) > .form-control').clear();
+ cy.get(':nth-child(5) > .form-control').type('4');
+ cy.get('[data-testid=primary-dialog-button]').click();
+ cy.checkScoreColLoadedOrdino(0, ['Frequency > 4'], 10)
+})

cypress/integration/ordino-video-test.spec.js

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+import { cy, it, Cypress } from 'local-cypress';
+
+// https://www.youtube.com/watch?v=JZIIf-k852g&t=1s
+it('ordino video', function() {
+ cy.visit(Cypress.env('host'));
+
+ cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click();
+
+ cy.login(); // use Cypress command registerd in Ordino app
+
+ // Show you can select single genes if you wanted
+ cy.scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+ cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+ // wait intentionally a few seconds
+ cy.wait(2000)
+ cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-link]').click();
+
+ // Open Lineup ranking
+ // Define api calls to wait:
+ cy.intercept('/api/tdp/db/publicdb/gene/desc').as('gene_desc');
+ cy.intercept('/api/tdp/db/publicdb/gene/filter?filter_species=human&filter_panel=normal+chromosome+protein+coding+human+genes').as('human_genes');
+ cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click();
+ cy.wait('@gene_desc');
+ cy.wait('@human_genes');
+ cy.waitLineupReadyOrdino(0)
+
+ // Add column
+ cy.get('[data-testid=add-column-button]').click();
+ cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click();
+ cy.select2MultiSelect("cell-line", "HCC1954")
+ cy.select2MultiSelect("data-type", "Relative Copy Number")
+ cy.get('[data-testid=primary-dialog-button]').click();
+ cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'Relative Copy Number'], 9);
+
+ // Sort by column
+ cy.get('[data-testid=viewWrapper-0] > .view > .inner > .tdp-view > :nth-child(1) > .le > .le-header > .le-thead > section:nth-last-child(-n+1) > .lu-toolbar > .lu-action-sort').click();
+
+ // Show some information
+ cy.get('[data-testid="(un)collapse-button"] > .fas').click();
+ // intentionally wait 1 second
+ cy.wait(1000)
+ // filter with histogram not possible
+ cy.get('[data-testid="(un)collapse-button"] > .fas').click();
+
+ // Add column
+ cy.get('[data-testid=add-column-button]').click();
+ cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click();
+ cy.select2MultiSelect("cell-line", "HCC1954")
+ cy.select2MultiSelect("data-type", "Normalized Gene Expression (TPM Values)")
+ cy.get('[data-testid=primary-dialog-button]').click();
+ cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'Normalized Gene Expression (TPM Values)'], 10)
+
+ // Add column
+ cy.get('[data-testid=add-column-button]').click();
+ cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(5) > span').click();
+ cy.select2MultiSelect("cell-line", "HCC1954")
+ cy.select2MultiSelect("data-type", "DRIVE RSA (ER McDonald III et al., Cell, 2017)")
+ cy.get('[data-testid=primary-dialog-button]').click();
+ cy.checkScoreColLoadedOrdino(0, ['HCC1954', 'DRIVE RSA (ER McDonald III et al., Cell, 2017)'], 11)
+
+ // Invert column
+ // Here the title should be used. For some reason cypress has problmes, because there is a " character in the title. For now I use the data-id
+ cy.get('[data-id="col10"] > .lu-toolbar > .lu-action-more').click();
+ cy.get('.lu-action-data-mapping > span').click();
+ cy.get('.browser-default').select('linear_invert');
+ cy.get('.lu-dialog-buttons > [type="submit"]').click();
+
+ // Add column
+ cy.get('[data-testid=add-column-button]').click();
+ cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click();
+ cy.formSelect("row-1", "Tumor Type")
+ cy.select2MultiSelect("row-1", "breast carcinoma")
+ cy.select2SingleSelect("data-type", "Normalized Gene Expression (TPM Values)")
+ cy.get('[data-testid=primary-dialog-button]').click();
+ cy.checkScoreColLoadedOrdino(0, ['Tumor Type', 'breast carcinoma', 'Normalized Gene Expression (TPM Values)'], 12)
+
+ // Add column
+ cy.get('[data-testid=add-column-button]').click();
+ cy.wait(2000);
+ cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click();
+ cy.select2SingleSelect("data-type", "Relative Copy Number")
+ cy.formSelect("aggregation", "Boxplot")
+ cy.get('[data-testid=primary-dialog-button]').click();
+ cy.checkScoreColLoadedOrdino(0, ['Relative Copy Number', 'Boxplot'], 13)
+
+ // Add column
+ cy.get('[data-testid=add-column-button]').click();
+ cy.get('[data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(2) > span').click();
+ cy.formSelect("aggregation", "Frequency")
+ cy.formSelect("comparison-operator", "> greater than")
+ cy.get(':nth-child(5) > .form-control').clear();
+ cy.get(':nth-child(5) > .form-control').type('4');
+ cy.get('[data-testid=primary-dialog-button]').click();
+ cy.checkScoreColLoadedOrdino(0, ['Frequency > 4'], 14)
+
+ // Select elements and click on detail views
+ cy.waitLineupReadyOrdino(0)
+ cy.get('[data-index="0"] > .lu-renderer-selection').click();
+ cy.get('[data-testid=celllinedb_expression_vs_copynumber]').click();
+ cy.waitTdpNotBusy()
+ cy.waitLineupReadyOrdino(0)
+ cy.wait(2000)
+ // cy.get('[data-index="6"] > .lu-renderer-selection').click();
+ // cy.waitTdpNotBusy()
+ // cy.waitLineupReadyOrdino(0)
+ // cy.wait(2000)
+ cy.get('[data-testid=targetvalidation]').click();
+ cy.waitTdpNotBusy()
+ cy.wait(2000)
+ cy.get('[data-testid=ensembl_org]').click();
+ cy.waitTdpNotBusy()
+ cy.wait(2000)
+ cy.get('[data-testid=copynumbertable]').click();
+ cy.waitTdpNotBusy()
+ cy.wait(2000)
+
+ // Sort and filter columns
+ cy.get('[data-testid=viewWrapper-1] > .view > .inner > .tdp-view > :nth-child(1) > .le > .le-header > .le-thead > section:nth-last-child(-n+1) > .lu-toolbar > .lu-action-sort').click();
+ cy.get('[title="Tumor Type"] > .lu-toolbar > .lu-action-filter').click();
+ cy.get('.lu-dialog-table > :nth-child(1) > :nth-child(2) > div').click();
+ cy.get('.lu-dialog-table > :nth-child(1) > input').uncheck();
+ cy.get(':nth-child(6) > :nth-child(2) > .lu-dialog-filter-table-entry-label').click();
+ cy.get('.lu-dialog-table > :nth-child(6) > input').check();
+ cy.get('.lu-dialog-buttons > [type="submit"]').click();
+
+ // Add column
+ cy.get('[data-testid=viewWrapper-1] [data-testid=side-panel-wrapper] [data-testid=lu-adder-div] [data-testid=add-column-button]').click();
+ cy.get('[data-testid=viewWrapper-1] > .view > .inner > .tdp-view > [data-testid=side-panel-wrapper] > .panel-header > :nth-child(2) > [data-testid=lu-adder-div] > .lu-search > .lu-search-list > :nth-child(2) > ul > :nth-child(1) > span').click();
+ cy.select2MultiSelect("gene-symbol", ["BRCA1", "BRCA2"])
+ cy.select2MultiSelect("data-type", "AA Mutated")
+ cy.get('[data-testid=primary-dialog-button]').click();
+ cy.checkScoreColLoadedOrdino(1, ['BRCA1', 'AA Mutated'], 10)
+ cy.checkScoreColLoadedOrdino(1, ['BRCA2', 'AA Mutated'], 10)
+
+ cy.waitLineupReadyOrdino(1)
+ cy.get('[data-testid=viewWrapper-1] [data-index="0"] > .lu-renderer-selection').click();
+ cy.get('[data-testid=viewWrapper-1] [data-index="12"] > .lu-renderer-selection').click();
+ cy.get('[data-testid=cosmic]').click();
+ // Intentionally wait 2 seconds
+ cy.waitTdpNotBusy()
+ cy.wait(2000)
+ cy.get('[data-testid=show] [data-testid=form-select]').select('687455');
+ // Intentionally wait 2 seconds
+ cy.waitTdpNotBusy()
+ cy.wait(2000)
+ cy.get('[data-testid=ordino_sessions_shortcut-link]').click();
+ cy.get('[data-testid=current-session-sessionscard] [data-testid=ordino0] [data-testid=save-button]').click();
+ cy.get('[data-testid=agree-input]').check();
+ cy.get('[data-testid=primary-dialog-button]').click();
+ cy.get('[data-testid=ordino_sessions_tab] [data-testid=close-button]').click();
+})

cypress/integration/session_all_celllines.spec.js

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+it('Load all Celllines', function() {
+ cy.visit(Cypress.env('host'));
+
+ // Login
+ cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click();
+
+ cy.login(); // use Cypress command registerd in Ordino app
+
+ // Show you can select single genes if you wanted
+ cy.scrollElementIntoCenter('[data-testid=dataset-card-cellline-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+ cy.get('[data-testid=dataset-card-cellline-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+ // wait intentionally a few seconds
+ cy.wait(2000)
+ cy.get('[data-testid=dataset-card-cellline-dataset] [data-testid=human-link]').click();
+
+ // Open Lineup ranking
+ // Define api calls to wait:
+ cy.intercept('/api/tdp/db/publicdb/cellline/desc').as('cellline_desc');
+ cy.intercept('/api/tdp/db/publicdb/cellline/filter?filter_species=human&filter_panel=CCLE').as('human_cellline');
+ cy.get('[data-testid=ccle-button]').click();
+ cy.wait('@cellline_desc');
+ cy.wait('@human_cellline');
+ cy.waitLineupReadyOrdino(0)
+});

cypress/integration/session_all_genes.spec.js

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+it('Load all Genes', function() {
+ cy.visit(Cypress.env('host'));
+
+ // Login
+ cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click();
+
+ cy.login(); // use Cypress command registerd in Ordino app
+
+ // Show you can select single genes if you wanted
+ cy.scrollElementIntoCenter('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+ cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+ // wait intentionally a few seconds
+ cy.wait(2000)
+ cy.get('[data-testid=dataset-card-genes-dataset] [data-testid=human-link]').click();
+
+ // Open Lineup ranking
+ // Define api calls to wait:
+ cy.intercept('/api/tdp/db/publicdb/gene/desc').as('gene_desc');
+ cy.intercept('/api/tdp/db/publicdb/gene/filter?filter_species=human&filter_panel=normal+chromosome+protein+coding+human+genes').as('human_genes');
+ cy.get('[data-testid=normal-chromosome-protein-coding-human-genes-button]').click();
+ cy.wait('@gene_desc');
+ cy.wait('@human_genes');
+ cy.waitLineupReadyOrdino(0)
+});

cypress/integration/session_all_tissues.spec.js

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+it('Load all Tissues', function() {
+ cy.visit(Cypress.env('host'));
+
+ // Login
+ cy.get('[data-testid=ordino-navbar] [data-testid=start-analysis-button]').click();
+
+ cy.login(); // use Cypress command registerd in Ordino app
+
+ // Show you can select single genes if you wanted
+ cy.scrollElementIntoCenter('[data-testid=dataset-card-tissue-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+ cy.get('[data-testid=dataset-card-tissue-dataset] [data-testid=human-tab] [data-testid=ordino-dataset-searchbox] [data-testid=async-paginate-input]').click()
+ // wait intentionally a few seconds
+ cy.wait(2000)
+ cy.get('[data-testid=dataset-card-tissue-dataset] [data-testid=human-link]').click();
+
+ // Open Lineup ranking
+ // Define api calls to wait:
+ cy.intercept('/api/tdp/db/publicdb/tissue/desc').as('tissue_desc');
+ cy.intercept('/api/tdp/db/publicdb/tissue/filter?filter_species=human&filter_panel=TCGA+normals').as('human_tissue');
+ cy.get('[data-testid=tcga-normals-button]').click();
+ cy.wait('@tissue_desc');
+ cy.wait('@human_tissue');
+ cy.waitLineupReadyOrdino(0)
+});