feat: CQDG-865 Add Clinical Data Cypress tests

Ferlab-Ste-Justine · Sep 12, 2024 · 4691f17 · 4691f17
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diff --git a/cypress/e2e/Telechargement/ClinicalDataPageParticipant.cy.ts b/cypress/e2e/Telechargement/ClinicalDataPageParticipant.cy.ts
@@ -0,0 +1,43 @@
+/// <reference types="cypress"/>
+import '../../support/commands';
+import { getDateTime, oneMinute } from '../../support/utils';
+
+const { strDate } = getDateTime();
+
+beforeEach(() => {
+  cy.removeFilesFromFolder(Cypress.config('downloadsFolder'));
+
+  cy.login();
+  cy.visitParticipantEntity('PT0000010');
+  cy.get('[class*="EntityTitle"] button[class*="ant-dropdown-trigger"]').click({force: true});
+});
+
+describe('Page d\'un participant - Télécharger le clinical data', () => {
+  beforeEach(() => {
+    cy.clickAndIntercept('[data-menu-id*="-clinicalData"]', 'POST', '**/file-manifest', 1);
+    cy.waitUntilFile(oneMinute);
+  });
+
+  it('Valider le nom du fichier [CQDG-861]', () => {
+    cy.validateFileName(`cqdg_clinicalData_${strDate.slice(0, 4)}${strDate.slice(4, 6)}${strDate.slice(6, 8)}T*.xlsx`);
+  });
+
+  it('Valider le contenu du fichier [CQDG-861]', () => {
+    cy.validateXlsxFileContent('DownloadClinicalData.json');
+  });
+});
+
+describe('Page d\'un participant - Télécharger le clinical data (family)', () => {
+  beforeEach(() => {
+    cy.clickAndIntercept('[data-menu-id*="-familyClinicalData"]', 'POST', '**/file-manifest', 1);
+    cy.waitUntilFile(oneMinute);
+  });
+
+  it('Valider le nom du fichier [CQDG-861]', () => {
+    cy.validateFileName(`cqdg_familyClinicalData_${strDate.slice(0, 4)}${strDate.slice(4, 6)}${strDate.slice(6, 8)}T*.xlsx`);
+  });
+
+  it('Valider le contenu du fichier [CQDG-861]', () => {
+    cy.validateXlsxFileContent('DownloadClinicalDataFamily.json');
+  });
+});
diff --git a/cypress/e2e/Telechargement/ClinicalDataPageStudy.cy.ts b/cypress/e2e/Telechargement/ClinicalDataPageStudy.cy.ts
@@ -0,0 +1,27 @@
+/// <reference types="cypress"/>
+import '../../support/commands';
+import { getDateTime, oneMinute } from '../../support/utils';
+
+const { strDate } = getDateTime();
+
+beforeEach(() => {
+  cy.removeFilesFromFolder(Cypress.config('downloadsFolder'));
+
+  cy.login();
+  cy.visitStudyEntity('STUDY1', 1);
+  cy.get('[class*="EntityTitle"] button[class*="ant-btn-default"]').eq(0).click({force: true});
+});
+
+describe('Page d\'une étude - Télécharger le clinical data', () => {
+  beforeEach(() => {
+    cy.waitUntilFile(oneMinute);
+  });
+
+  it('Valider le nom du fichier [CQDG-861]', () => {
+    cy.validateFileName(`cqdg_clinicalData_${strDate.slice(0, 4)}${strDate.slice(4, 6)}${strDate.slice(6, 8)}T*.xlsx`);
+  });
+
+  it('Valider le contenu du fichier [CQDG-861]', () => {
+    cy.validateXlsxFileContent('DownloadClinicalDataFamily.json');
+  });
+});
diff --git a/cypress/e2e/Telechargement/ClinicalDataTableauParticipants.cy.ts b/cypress/e2e/Telechargement/ClinicalDataTableauParticipants.cy.ts
@@ -0,0 +1,44 @@
+/// <reference types="cypress"/>
+import '../../support/commands';
+import { getDateTime, oneMinute } from '../../support/utils';
+
+const { strDate } = getDateTime();
+
+beforeEach(() => {
+  cy.removeFilesFromFolder(Cypress.config('downloadsFolder'));
+
+  cy.login();
+  cy.visitDataExploration('participants', '?sharedFilterId=f586eafb-ed2d-4cde-8ac0-c0c44fa2a504');
+  cy.get('div[role="tabpanel"] [class*="ant-table-row"]').eq(0).find('[type="checkbox"]').check({force: true});
+  cy.get('[class*="Header_ProTableHeader"] button[class*="ant-dropdown-trigger"]').eq(1).click({force: true});
+});
+
+describe('Page Data Exploration (Participants) - Télécharger le clinical data', () => {
+  beforeEach(() => {
+    cy.clickAndIntercept('[data-menu-id*="-clinicalData"]', 'POST', '**/file-manifest', 1);
+    cy.waitUntilFile(oneMinute);
+  });
+
+  it('Valider le nom du fichier [CQDG-861]', () => {
+    cy.validateFileName(`cqdg_clinicalData_${strDate.slice(0, 4)}${strDate.slice(4, 6)}${strDate.slice(6, 8)}.xlsx`);
+  });
+
+  it('Valider le contenu du fichier [CQDG-861]', () => {
+    cy.validateXlsxFileContent('DownloadClinicalData.json');
+  });
+});
+
+describe('Page Data Exploration (Participants) - Télécharger le clinical data (family)', () => {
+  beforeEach(() => {
+    cy.clickAndIntercept('[data-menu-id*="-familyClinicalData"]', 'POST', '**/file-manifest', 1);
+    cy.waitUntilFile(oneMinute);
+  });
+
+  it('Valider le nom du fichier [CQDG-861]', () => {
+    cy.validateFileName(`cqdg_familyClinicalData_${strDate.slice(0, 4)}${strDate.slice(4, 6)}${strDate.slice(6, 8)}.xlsx`);
+  });
+
+  it('Valider le contenu du fichier [CQDG-861]', () => {
+    cy.validateXlsxFileContent('DownloadClinicalDataFamily.json');
+  });
+});
diff --git a/cypress/fixtures/DownloadClinicalData.json b/cypress/fixtures/DownloadClinicalData.json
@@ -0,0 +1,36 @@
+{  "content": ["Participant ID",
+              "External Participant ID",
+              "Family ID",
+              "External Family ID",
+              "Relationship to Proband",
+              "Study Name",
+              "Study Code",
+              "Family Type",
+              "Sex",
+              "Ethnicity",
+              "Vital Status",
+              "Affected Status",
+              "Age at Recruitment",
+              "Participant ID",
+              "External Participant ID",
+              "Family ID",
+              "External Family ID",
+              "Relationship to Proband",
+              "Phenotype (HPO)",
+              "Phenotype (Source Text)",
+              "Interpretation",
+              "Age at Phenotype  Participant ID",
+              "External Participant ID",
+              "Family ID",
+              "External Family ID",
+              "Relationship to Proband",
+              "Diagnosis (MONDO)",
+              "Diagnosis (ICD)",
+              "Diagnosis (Source Text)",
+              "Age at Diagnosis  Participant ID",
+              "External Participant ID",
+              "Family ID",
+              "External Family ID",
+              "Family Member ID",
+              "Relationship to Proband"]
+}
diff --git a/cypress/fixtures/DownloadClinicalDataFamily.json b/cypress/fixtures/DownloadClinicalDataFamily.json
@@ -0,0 +1,30 @@
+{  "content": ["Participant ID",
+              "External Participant ID",
+              "Family ID",
+              "External Family ID",
+              "Relationship to Proband",
+              "Study Name",
+              "Study Code",
+              "Family Type",
+              "Sex",
+              "Ethnicity",
+              "Vital Status",
+              "Affected Status",
+              "Age at Recruitment  Participant ID",
+              "External Participant ID",
+              "Family ID",
+              "External Family ID",
+              "Relationship to Proband",
+              "Phenotype (HPO)",
+              "Phenotype (Source Text)",
+              "Interpretation",
+              "Age at Phenotype    Participant ID",
+              "External Participant ID",
+              "Family ID",
+              "External Family ID",
+              "Relationship to Proband",
+              "Diagnosis (MONDO)",
+              "Diagnosis (ICD)",
+              "Diagnosis (Source Text)",
+              "Age at Diagnosis"]
+}
diff --git a/cypress/plugins/index.ts b/cypress/plugins/index.ts
@@ -2,6 +2,7 @@
 /// <reference types="cypress"/>
 import fs, { rmdir } from 'fs';
 import path from 'path';
+import XLSX from 'xlsx';
 
 require('dotenv').config();
 
@@ -20,6 +21,18 @@ module.exports = (on: Cypress.PluginEvents, config: Cypress.ConfigOptions) => {
         });
       });
     },
+    async extractTextFromXLSX(filePath) {
+      const workbook = XLSX.readFile(filePath);
+      let text = '';
+
+      workbook.SheetNames.forEach(sheetName => {
+        const sheet = workbook.Sheets[sheetName];
+        const sheetText = XLSX.utils.sheet_to_csv(sheet);
+        text += sheetText;
+      });
+
+      return text;
+    },
     fileExists(folder) {
       const files = fs.readdirSync(folder);
       const regex = new RegExp('.*');

diff --git a/cypress/support/commands.ts b/cypress/support/commands.ts
@@ -397,6 +397,28 @@ Cypress.Commands.add('validateTotalSelectedQuery', (expectedCount: string|RegExp
   cy.get('[class*="QueryBar_selected"]').find('[class*="QueryBar_total"]').contains(expectedCount).should('exist');
 });
 
+Cypress.Commands.add('validateXlsxFileContent', (fixture: string, replacements?: Replacement[]) => {
+  const arrReplacements = replacements !== undefined ? replacements : [];
+  cy.fixture(fixture).then((expectedData) => {
+    cy.exec(`/bin/ls ${Cypress.config('downloadsFolder')}/*.xlsx`).then((result) => {
+      const filename = result.stdout.trim();
+      cy.task('extractTextFromXLSX', filename).then((file) => {
+        let fileWithData = typeof file === 'string' ? file : '';
+        arrReplacements.forEach((replacement) => {
+          fileWithData = fileWithData.replace(replacement.placeholder, replacement.value);
+        });
+        expectedData.content.forEach((value: any) => {
+          let valueWithData = value;
+          arrReplacements.forEach((replacement) => {
+            valueWithData = valueWithData.replace(replacement.placeholder, replacement.value);
+          });
+          assert.include(fileWithData, valueWithData);
+        });
+      });
+    });
+  });
+});
+
 Cypress.Commands.add('visitAndIntercept', (url: string, methodHTTP: string, routeMatcher: string, nbCalls: number) => {
   cy.intercept(methodHTTP, routeMatcher).as('getRouteMatcher');
 

diff --git a/cypress/support/index.d.ts b/cypress/support/index.d.ts
@@ -38,6 +38,7 @@ declare namespace Cypress {
     validateTableFirstRow(expectedValue: string|RegExp, eq: number, hasCheckbox: boolean = false): cy & CyEventEmitter;
     validateTableResultsCount(expectedCount: string|RegExp, shouldExist: boolean = true): cy & CyEventEmitter;
     validateTotalSelectedQuery(expectedCount: string|RegExp): cy & CyEventEmitter;
+    validateXlsxFileContent(fixture: string, replacements?: Replacement[]): cy & CyEventEmitter;
     visitAndIntercept(url: string, methodHTTP: string, routeMatcher: string, nbCalls: number): cy & CyEventEmitter;
     visitCommunityPage(): cy & CyEventEmitter;
     visitDashboard(): cy & CyEventEmitter;