Merge pull request #1803 from 4dn-dcic/npm_updates_apr_2023

utku-ozturk · web-flow · commit 1ad3d5986d75 · 2023-05-22T16:38:02.000+03:00
Npm Updates Apr-May 2023
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -6,12 +6,24 @@ fourfront
 Change Log
 ----------
 
+5.3.4
+=====
+
+`PR Npm Updates Apr-May 2023  <https://github.com/4dn-dcic/fourfront/pull/1803>`_
+
+* jsonwebtoken npm package is replaced with jose
+* cypress 10 to 12 migration completed
+* new cypress test for not facet feature added
+* auth0 client/domain grabbed from /auth0_config in cypress tests (old implementation gets them from env. variables)
+
+
 5.3.3
 =====
 
 * updated suggested_enums for processed files
 * updated assay_subclass_short by making a more general FISH at expense of RNA and DNA FISH
 
+
 5.3.2
 =====
 
diff --git a/deploy/post_deploy_testing/cypress.config.js b/deploy/post_deploy_testing/cypress.config.js
@@ -17,5 +17,6 @@ module.exports = defineConfig({
         },
         baseUrl: 'https://data.4dnucleome.org',
         specPattern: 'cypress/e2e/**/*.{js,jsx,ts,tsx}',
+        testIsolation: false
     },
 });
diff --git a/deploy/post_deploy_testing/cypress/e2e/04a_search_views_local.cy.js b/deploy/post_deploy_testing/cypress/e2e/04a_search_views_local.cy.js
@@ -28,14 +28,9 @@ describe('Deployment/CI Search View Tests', function () {
             cy.get('input#field_for_tags.form-control').focus().type('deleted_by_cypress_test').wait(100).end();
 
             // Click Validate button
-            cy.get(".action-buttons-container .btn")
-                .within(function () {
-                    return cy.contains('Validate').click().end().wait(1000);
-                }).end()
-                //Click Submit button
-                .get(".action-buttons-container .btn").within(function () {
-                    return cy.contains('Submit').click().end().wait(1000);
-                }).end();
+            cy.get(".action-buttons-container").as("editButtons");
+            cy.get("@editButtons").find('button.btn').contains('Validate').click().end().wait(1000).end();
+            cy.get("@editButtons").find('button.btn').contains('Submit').click().end().wait(1000).end();
         });
     }
 
@@ -61,9 +56,16 @@ describe('Deployment/CI Search View Tests', function () {
             cy.visit('/pages'); // We should get redirected to ?type=Page
         });
 
-        beforeEach(function(){
+        beforeEach(function () {
             // Ensure we preserve search session cookie for proper ordering.
-            Cypress.Cookies.preserveOnce("searchSessionID");
+            cy.session('preserveCookies', () => {
+                // Ensure we preserve search session cookie for proper ordering.
+                cy.getCookie('searchSessionID').then((cookie) => {
+                    if (cookie) {
+                        cy.setCookie('searchSessionID', cookie.value);
+                    }
+                });
+            });
         });
 
         it('Should redirect to /search/?type=Page correctly', function(){
@@ -384,9 +386,16 @@ describe('Deployment/CI Search View Tests', function () {
             cy.visit('/'); // Start at home page
         });
 
-        beforeEach(function(){
+        beforeEach(function () {
             // Ensure we preserve search session cookie for proper ordering.
-            Cypress.Cookies.preserveOnce("searchSessionID");
+            cy.session('preserveCookies', () => {
+                // Ensure we preserve search session cookie for proper ordering.
+                cy.getCookie('searchSessionID').then((cookie) => {
+                    if (cookie) {
+                        cy.setCookie('searchSessionID', cookie.value);
+                    }
+                });
+            });
         });
 
         it('SearchBox input works, goes to /browse/ on submit', function(){
diff --git a/deploy/post_deploy_testing/cypress/e2e/04b_search_views.cy.js b/deploy/post_deploy_testing/cypress/e2e/04b_search_views.cy.js
@@ -8,9 +8,16 @@ describe('Post-Deployment Search View Tests', function () {
             cy.visit('/search/');
         });
 
-        beforeEach(function(){
+        beforeEach(function () {
             // Ensure we preserve search session cookie for proper ordering.
-            Cypress.Cookies.preserveOnce("searchSessionID");
+            cy.session('preserveCookies', () => {
+                // Ensure we preserve search session cookie for proper ordering.
+                cy.getCookie('searchSessionID').then((cookie) => {
+                    if (cookie) {
+                        cy.setCookie('searchSessionID', cookie.value);
+                    }
+                });
+            });
         });
 
         it('Load as you scroll works for ?type=Item', function () {
@@ -55,9 +62,16 @@ describe('Post-Deployment Search View Tests', function () {
             cy.visit('/search/');
         });
 
-        beforeEach(function(){
+        beforeEach(function () {
             // Ensure we preserve search session cookie for proper ordering.
-            Cypress.Cookies.preserveOnce("searchSessionID");
+            cy.session('preserveCookies', () => {
+                // Ensure we preserve search session cookie for proper ordering.
+                cy.getCookie('searchSessionID').then((cookie) => {
+                    if (cookie) {
+                        cy.setCookie('searchSessionID', cookie.value);
+                    }
+                });
+            });
         });
 
         it('Starting from /search/, typing "olfactory" into searchbox redirects back to search', function () {
diff --git a/deploy/post_deploy_testing/cypress/e2e/07_higlass_display.cy.js b/deploy/post_deploy_testing/cypress/e2e/07_higlass_display.cy.js
@@ -12,6 +12,16 @@ describe("HiGlass Display pages", function(){
 
     context('Higlass Display summary page', function(){
 
+        // testIsolation that is a part of Cypress 12 migration is breaking the current test execution.
+        // Adding "testIsolation: false" into cypress.config.js is the workaround to run tests as it was before, but
+        // it is not a complete solution. So, we added beforeEach to clear cookies and local storage as it is descibed in:
+        // https://docs.cypress.io/guides/references/migration-guide#Simulating-Pre-Test-Isolation-Behavior
+        beforeEach(() => {
+            cy.clearLocalStorage();
+            cy.clearCookies();
+            // other beforeEach logic to restore the expected local storage or cookies needed on the client.
+        });
+
         it('Can visit HiGlass Display collection page without login', function(){
 
             // Visit the page and confirm you can see the table and facet properties.
@@ -58,6 +68,8 @@ describe("HiGlass Display pages", function(){
         var testItemsToDelete = [];
 
         beforeEach(function() {
+            cy.clearLocalStorage();
+            cy.clearCookies();
             // Log in.
             cy.visit('/higlass-view-configs/').login4DN({ 'email': 'ud4dntest@gmail.com', 'useEnvToken' : true }).wait(500);
         });
@@ -119,8 +131,7 @@ describe("HiGlass Display pages", function(){
             cy.visit(draftUrl);
 
             // When the app creates a new HiGlass display, we'll capture the JSON of the POST call.
-            cy.server();
-            cy.route('POST', '/higlass-view-configs/').as('newHiglassDisplay');
+            cy.intercept('POST', '/higlass-view-configs/').as('newHiglassDisplay');
 
             // Ensure HiGlassComponent has loaded (before Clone btn can be clicked w/o errors)
             cy.get('.higlass-instance .react-grid-layout').end()
@@ -131,16 +142,16 @@ describe("HiGlass Display pages", function(){
                 }).end()
                 .get('.alert div').should('contain.text', 'Saved new display.').end()
                 // Inspect POST response.
-                .get('@newHiglassDisplay').then(function (xhr) {
+                .get('@newHiglassDisplay').then(function ({ request, response }) {
 
                     // Expect a 201 response.
-                    expect(xhr.status).to.eq(201);
+                    expect(response.statusCode).to.eq(201);
 
                     // Expect a new uuid.
-                    expect(xhr.responseBody["@graph"][0]["uuid"]).to.not.equal("00000000-1111-0000-1111-000000000002");
+                    expect(response.body["@graph"][0]["uuid"]).to.not.equal("00000000-1111-0000-1111-000000000002");
 
                     // Add the test Item so we can delete it later.
-                    testItemsToDelete.push(xhr.responseBody["@graph"][0]);
+                    testItemsToDelete.push(response.body["@graph"][0]);
                 })
                 .end()
                 // Wait for HiGlass to fully be initialized as well, to avoid __zoom error perhaps.
@@ -159,8 +170,7 @@ describe("HiGlass Display pages", function(){
             cy.visit(draftUrl);
 
             // There will be an AJAX response to a POST for the new Higlass display, so capture it here.
-            cy.server();
-            cy.route('POST', '/higlass-view-configs/').as('newHiglassDisplay');
+            cy.intercept('POST', '/higlass-view-configs/').as('newHiglassDisplay');
 
             // Ensure HiGlassComponent has loaded (before Clone btn can be clicked w/o errors)
             cy.get('.higlass-instance .react-grid-layout').end()
@@ -175,17 +185,17 @@ describe("HiGlass Display pages", function(){
                 .get('.alert div').should('contain.text', 'Saved new display.').end()
 
                 // Inspect the AJAX response so we can capture the new uuid.
-                .get('@newHiglassDisplay').then(function (xhr) {
+                .get('@newHiglassDisplay').then(function ({ request, response }) {
 
                     // Expect a 201 response.
-                    expect(xhr.status).to.eq(201);
+                    expect(response.statusCode).to.eq(201);
 
                     // Expect a new uuid.
-                    expect(xhr.responseBody["@graph"][0]["uuid"]).to.not.equal("00000000-1111-0000-1111-000000000002");
+                    expect(response.body["@graph"][0]["uuid"]).to.not.equal("00000000-1111-0000-1111-000000000002");
 
                     // Add the test uuid so we can delete it later.
-                    testItemsToDelete.push(xhr.responseBody["@graph"][0]);
-                    const newID = xhr.responseBody["@graph"][0]["@id"];
+                    testItemsToDelete.push(response.body["@graph"][0]);
+                    const newID = response.body["@graph"][0]["@id"];
                     expect(newID).to.be.ok;
 
                     // Clicking the SaveAs button should redirect us to the new page
@@ -222,6 +232,12 @@ describe("HiGlass Display pages", function(){
 
     context('Sharing on the Individual Higlass display page', function() {
 
+        // https://docs.cypress.io/guides/references/migration-guide#Simulating-Pre-Test-Isolation-Behavior
+        beforeEach(() => {
+            cy.clearLocalStorage();
+            cy.clearCookies();
+        });
+
         after(function(){
 
             // Edit the higlass display back to draft status.
diff --git a/deploy/post_deploy_testing/cypress/e2e/09a_create_biosample.cy.js b/deploy/post_deploy_testing/cypress/e2e/09a_create_biosample.cy.js
@@ -39,20 +39,11 @@ describe('Biosample create page', function () {
             cy.get('input#field_for_tags.form-control').focus().type('deleted_by_cypress_test').wait(100).end();
 
             // Click Validate button
-            cy.get(".action-buttons-container .btn")
-                .within(function () {
-                    return cy.contains('Validate').click().end().wait(1000);
-                }).end()
-                //Click Submit button
-                .get(".action-buttons-container .btn").within(function () {
-                    return cy.contains('Submit').click().end().wait(500);
-                }).end()
-                //Navigate new biosample data page
-                .get(".action-buttons-container .btn").within(function () {
-                    return cy.contains('Skip').click().end();
-                })
-                .end()
-                .get("h1.page-title").contains("Biosample").wait(3000).end(); // Await until are at Biosample page. Then wait 1s to ensure we have new context.
+            cy.get(".action-buttons-container").as("editButtons");
+            cy.get("@editButtons").find('button.btn').contains('Validate').click().end().wait(1000).end();
+            cy.get("@editButtons").find('button.btn').contains('Submit').click().end().wait(500).end();
+            cy.get("@editButtons").find('button.btn').contains('Skip').click().end();
+            cy.get("h1.page-title").contains("Biosample").wait(3000).end(); // Await until are at Biosample page. Then wait 1s to ensure we have new context.
 
             // Queue for deletion in subsequent test.
             cy.get('script[data-prop-name=context]').then(function($context){
diff --git a/deploy/post_deploy_testing/cypress/support/commands.js b/deploy/post_deploy_testing/cypress/support/commands.js
@@ -25,8 +25,7 @@
 // Cypress.Commands.overwrite("visit", (originalFn, url, options) => { ... })
 
 import _ from 'underscore';
-var jwt = require('jsonwebtoken');
-import { Buffer } from 'buffer';
+const jose = require('jose');
 import { navUserAcctDropdownBtnSelector, navUserAcctLoginBtnSelector } from './variables';
 
 
@@ -86,6 +85,31 @@ const auth0UserIds = {
     'u4dntestcypress@gmail.com': 'google-oauth2|104145819796576369116'
 };
 
+
+Cypress.Commands.add('signJWT', (auth0secret, email, sub) => {
+    cy.request({
+        'url' : '/auth0_config?format=json',
+        'method' : 'GET',
+        'headers' : { 'Accept': "application/json", 'Content-Type': "application/json; charset=UTF-8" },
+        'followRedirect' : true
+    }).then(function (resp) {
+        if (resp.status && resp.status === 200) {
+            const auth0Config = resp.body;
+            const secret = new TextEncoder().encode(auth0secret);
+            const jwt = new jose.SignJWT({ 'email': email, 'email_verified': true });
+            const token = jwt
+                .setProtectedHeader({ alg: 'HS256', typ: 'JWT' })
+                .setIssuedAt()
+                .setIssuer(auth0Config.auth0Domain)
+                .setExpirationTime('1h')
+                .setAudience(auth0Config.auth0Client)
+                .setSubject(sub)
+                .sign(secret);
+            return token;
+        }
+    });
+});
+
 /**
  * This emulates login.js. Perhaps we should adjust login.js somewhat to match this better re: navigate.then(...) .
  */
@@ -124,10 +148,8 @@ Cypress.Commands.add('login4DN', function(options = { 'useEnvToken' : true }){
         }).end();
     }
 
-    let jwt_token = null;
-
     if (options.useEnvToken) {
-        jwt_token = Cypress.env('JWT_TOKEN');
+        const jwt_token = Cypress.env('JWT_TOKEN');
         console.log('ENV TOKEN', jwt_token);
         if (typeof jwt_token === 'string' && jwt_token) {
             console.log('Logging in with token');
@@ -138,35 +160,27 @@ Cypress.Commands.add('login4DN', function(options = { 'useEnvToken' : true }){
     // If no token, we try to generate/impersonate one ourselves
 
     const email = options.email || options.user || Cypress.env('LOGIN_AS_USER') || '4dndcic@gmail.com';
-    const auth0client = Cypress.env('Auth0Client');
     const auth0secret = Cypress.env('Auth0Secret');
 
-    if (!auth0client || !auth0secret) throw new Error('Cannot test login if no Auth0Client & Auth0Secret in ENV vars.');
+    if (!auth0secret) throw new Error('Cannot test login if no Auth0Secret in ENV vars.');
 
     Cypress.log({
         'name' : "Login 4DN",
         'message' : 'Attempting to impersonate-login for ' + email,
         'consoleProps' : ()=>{
-            return { auth0client, auth0secret, email };
+            return { auth0secret, email };
         }
     });
 
     // Generate JWT
-    const jwtPayload = {
-        'email': email,
-        'email_verified': true,
-        'aud': auth0client,
-        "iss": "https://hms-dbmi.auth0.com/",
-        "sub": auth0UserIds[email] || ''
-    };
-
-    jwt_token = jwt.sign(jwtPayload, Buffer.from(auth0secret, 'utf-8'));
-    expect(jwt_token).to.have.length.greaterThan(0);
-    Cypress.log({
-        'name' : "Login 4DN",
-        'message' : 'Generated own JWT with length ' + jwt_token.length,
+    cy.signJWT(auth0secret, email, auth0UserIds[email] || '').then((token) => {
+        expect(token).to.have.length.greaterThan(0);
+        Cypress.log({
+            'name': "Login 4DN",
+            'message': 'Generated own JWT with length ' + token.length,
+        });
+        return performLogin(token);
     });
-    return performLogin(jwt_token);
 
 });
 
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
diff --git a/pyproject.toml b/pyproject.toml
