feat(integration): Add initial "integration tests" (#3121)

* initial commit

* initial 2

* Update integration-tests.yml

* Update integration-tests.yml

* update

* disable webkit for now

* add principles

* add group ficture

* updates

* Delete integration-tests/tests/utils/test-helpers.ts

* rename authenticatedPage to pageWithACreatedUser

* Update README.md

* break test

* if that didn't break it, does this?

* update

* now it should pass again

* upda

* increase timeout

* Update playwright.config.ts

* Update registration.spec.ts

* code review

* fix

* update

* Update group.fixture.ts

* Update submission-flow.spec.ts

* Update playwright.config.ts

* tab

* fix baseurl

* add baseurl

* Update playwright.config.ts

* refactor

* refactor

* try deleting extra config file

* add type decl

.github/workflows/integration-tests.yml

@@ -0,0 +1,107 @@
+name: Integration tests
+on:
+  workflow_dispatch:
+  pull_request:
+    paths:
+      - "backend/**"
+      - "keycloak/**"
+      - "kubernetes/**"
+      - "website/**"
+      - "deploy.py"
+      - "integration-tests/**"
+      - ".github/scripts/**"
+      - ".github/workflows/**"
+  push:
+    branches:
+      - main
+jobs:
+  integration-tests:
+    permissions:
+      packages: read
+      contents: read
+      checks: read
+      actions: read # Required by workflow-telemetry-action
+    runs-on: ubuntu-latest
+    timeout-minutes: 45
+    env:
+      sha: ${{ github.event.pull_request.head.sha || github.sha }}
+    steps:
+      - name: Shorten sha
+        run: echo "sha=${sha::7}" >> $GITHUB_ENV
+      - name: Collect Workflow Telemetry
+        uses: catchpoint/workflow-telemetry-action@v2
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Install k3d
+        run: |
+          curl -s https://raw.githubusercontent.com/rancher/k3d/main/install.sh | bash
+          k3d version
+      - uses: azure/setup-helm@v4
+      - name: Create k3d cluster
+        run: |
+          ./deploy.py --verbose cluster
+      - name: Deploy with helm
+        run: |
+          ./deploy.py --verbose helm --branch ${{ github.ref_name }} --sha ${{ env.sha }} --for-e2e --enablePreprocessing
+      - uses: actions/setup-node@v4
+        with:
+          node-version-file: ./website/.nvmrc
+      - name: Cache .npm
+        uses: actions/cache@v4
+        with:
+          path: ~/.npm
+          key: ${{ runner.os }}-node-${{ hashFiles('integration-tests/**/package-lock.json') }}
+      - name: Install dependencies
+        run: cd integration-tests && npm i
+      - name: Get Installed Playwright Version
+        id: playwright-version
+        run: cd integration-tests && echo "PLAYWRIGHT_VERSION=$(node -e "console.log(require('./package-lock.json').packages['node_modules/@playwright/test'].version)")" >> $GITHUB_ENV
+      - name: Cache Playwright Browsers
+        uses: actions/cache@v4
+        id: playwright-cache
+        with:
+          path: ~/.cache/ms-playwright
+          key: ${{ runner.os }}-playwright-${{ env.PLAYWRIGHT_VERSION }}
+      - name: Install Playwright Browsers and System Dependencies
+        run: cd integration-tests && npx playwright install --with-deps
+        if: steps.playwright-cache.outputs.cache-hit != 'true'
+      - name: Install only System Dependencies
+        run: cd website && npx playwright install-deps
+        if: steps.playwright-cache.outputs.cache-hit == 'true'
+      - name: Wait for the pods to be ready
+        run: ./.github/scripts/wait_for_pods_to_be_ready.py --timeout 190
+      - name: Sleep for 10 secs
+        run: sleep 10
+      - name: Run Integration test
+        run: |
+          set -o pipefail
+          cd integration-tests && npx playwright test 2>&1 | tee output.txt
+          EXIT_CODE=$?
+          echo '```' >> $GITHUB_STEP_SUMMARY
+          sed -n '/Running [0-9]\+ tests/,$p' output.txt >> $GITHUB_STEP_SUMMARY
+          echo '```' >> $GITHUB_STEP_SUMMARY
+          exit $EXIT_CODE
+      - uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: playwright-report
+          path: integration-tests/playwright-report/
+          retention-days: 30
+      - name: List running pods
+        if: ${{ !cancelled() }}
+        run: kubectl get pods --all-namespaces
+      - name: Describe pods
+        if: ${{ !cancelled() }}
+        run: kubectl describe pods -l app=loculus
+      - name: Show events
+        if: ${{ !cancelled() }}
+        run: kubectl get events
+      - name: Save logs from all containers to file
+        if: ${{ !cancelled() }}
+        run: ./.github/scripts/collect_kubernetes_logs.sh
+      - name: Upload Kubernetes logs
+        if: ${{ !cancelled() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: kubernetes-logs
+          path: kubernetes_logs/

.gitignore

@@ -22,3 +22,6 @@ temp/
 
 .aider*
 .env
+
+logs/
+__pycache__/

integration-tests/.gitignore

@@ -0,0 +1,5 @@
+node_modules/
+/test-results/
+/playwright-report/
+/blob-report/
+/playwright/.cache/

integration-tests/README.md

@@ -0,0 +1,15 @@
+# Integration tests
+
+These are tests of the full Loculus system, following sequences through submission to preprocessing to release.
+
+## Principles
+
+Here are some current guiding principles for these tests:
+- Only use facilities users could use (primarily browser interaction), rather than setting things up with backend calls. This makes it easy for others to understand the tests because they can follow them in the browser.
+- All tests should be able to run in parallel. Mostly this can be carried out by creating a separate user/group for each test.
+
+
+## Fixtures
+There are some fixtures to help with the development of tests:
+- `pageWithACreatedUser` creates a user account and logs into it
+- `pageWithGroup` inherits from `pageWithACreatedUser` and in addition creates a group for the user

integration-tests/package.json

@@ -0,0 +1,16 @@
+{
+  "name": "integration_tests",
+  "version": "1.0.0",
+  "main": "index.js",
+  "scripts": {},
+  "keywords": [],
+  "author": "",
+  "license": "ISC",
+  "description": "",
+  "devDependencies": {
+    "@playwright/test": "^1.48.2",
+    "@types/node": "^22.8.3",
+    "@types/uuid": "^10.0.0",
+    "uuid": "^11.0.2"
+  }
+}

integration-tests/playwright.config.ts

@@ -0,0 +1,45 @@
+import { defineConfig, devices } from '@playwright/test';
+
+/**
+ * Read environment variables from file.
+ * https://github.com/motdotla/dotenv
+ */
+// import dotenv from 'dotenv';
+// import path from 'path';
+// dotenv.config({ path: path.resolve(__dirname, '.env') });
+
+/**
+ * See https://playwright.dev/docs/test-configuration.
+ */
+export default defineConfig({
+  testDir: './tests',
+  /* Run tests in files in parallel */
+  fullyParallel: true,
+  /* Fail the build on CI if you accidentally left test.only in the source code. */
+  forbidOnly: !!process.env.CI,
+  /* Retry on CI only */
+  retries: process.env.CI ? 2 : 0,
+  /* Reporter to use. See https://playwright.dev/docs/test-reporters */
+  reporter: 'html',
+  /* Shared settings for all the projects below. See https://playwright.dev/docs/api/class-testoptions. */
+  use: {
+    /* Base URL to use in actions like `await page.goto('/')`. */
+   baseURL: 'http://localhost:3000',
+
+    /* Collect trace when retrying the failed test. See https://playwright.dev/docs/trace-viewer */
+    trace: 'on-first-retry',
+  },
+
+  /* Configure projects for major browsers */
+  projects: [
+    {
+      name: 'chromium',
+      use: { ...devices['Desktop Chrome'] },
+    },
+
+    {
+      name: 'firefox',
+      use: { ...devices['Desktop Firefox'] },
+    }
+  ]
+});

integration-tests/start-server.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+ ../deploy.py cluster --delete
+ ../deploy.py cluster
+ ../deploy.py helm --for-e2e --enablePreprocessing
+ python ../.github/scripts/wait_for_pods_to_be_ready.py

integration-tests/tests/fixtures/auth.fixture.ts

@@ -0,0 +1,31 @@
+import { test as base, Page } from '@playwright/test';
+
+import { v4 as uuidv4 } from 'uuid';
+import { AuthPage } from '../pages/auth.page';
+import { TestAccount } from '../types/auth.types';
+
+type TestFixtures = {
+  pageWithACreatedUser: Page;
+  testAccount: TestAccount;
+};
+
+export const test = base.extend<TestFixtures>({
+  testAccount: async ({}, use) => {
+    const testAccount : TestAccount = {
+      username: `test_user_${uuidv4().slice(0, 8)}`,
+      password: 'password',
+      email: `test_${uuidv4().slice(0, 8)}@test.com`,
+      firstName: 'Test',
+      lastName: 'User',
+      organization: 'Test University'
+    };
+    await use(testAccount);
+  },
+
+  pageWithACreatedUser: async ({ page, testAccount }, use) => {
+    const authPage = new AuthPage(page);
+    await authPage.createAccount(testAccount);
+    await use(page);
+    await authPage.logout();
+  },
+});