✅ Add e2e/integration testing (#11613)

* Split integration test out

* Add e2e test

* Add E2E test workflow

* Fix profile for e2e tests

* update to run integration and e2e test

* Fix env vars

* fix sonar workflow

Author: haynescd

.github/workflows/core-test.yml

@@ -1,5 +1,19 @@
 name: Core tests
-on: [push, pull_request]
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+    inputs:
+      ref:
+        description: 'Branch or PR to test (default: main)'
+        required: false
+        default: 'main'
+
+permissions:
+      id-token: write   # This is required for requesting the JWT
+      contents: read    # This is required for actions/checkout
+
 jobs:
   build:
     name: Setup and Test
@@ -12,6 +26,9 @@ jobs:
         ports:
           - 3306
         options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=10
+    env:
+      TEST_DB_CLICKHOUSE_PASSWORD: ${{ secrets.TEST_DB_CLICKHOUSE_PASSWORD }}
+      TEST_DB_MYSQL_PASSWORD: ${{ secrets.TEST_DB_MYSQL_PASSWORD }}
     steps:
       - name: 'Checkout cbioportal repo'
         uses: actions/checkout@v2
@@ -64,4 +81,8 @@ jobs:
       - name: 'Run integration tests separately'
         working-directory: ./cbioportal
         run: |
-          mvn -U -Ppublic integration-test -Ddb.test.username=cbio_user -Ddb.test.password=somepassword
+          mvn verify -Pintegration-test
+      - name: 'Run e2e tests separately'
+        working-directory: ./cbioportal
+        run: |
+          mvn verify -Pe2e-test

.github/workflows/security-integration-test.yml

@@ -9,6 +9,9 @@ jobs:
   build:
     name: sonarcloud
     runs-on: ubuntu-latest
+    env:
+      TEST_DB_CLICKHOUSE_PASSWORD: ${{ secrets.TEST_DB_CLICKHOUSE_PASSWORD }}
+      TEST_DB_MYSQL_PASSWORD: ${{ secrets.TEST_DB_MYSQL_PASSWORD }}
     steps:
       - uses: actions/checkout@v2
         with:
@@ -43,8 +46,11 @@ jobs:
       - name: 'Run integration tests'
         run: |
           mvn verify -Pintegration-test
+      - name: 'Run e2e tests'
+        run: |
+          mvn verify -Pe2e-test
       - name: Code Coverage
         env:
           SONAR_TOKEN:  de1b5cc660cd210dde840f492c371da6cc801763
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: mvn sonar:sonar -Pcoverage
+        run: mvn sonar:sonar -Pcoverage

.github/workflows/sonarcloud.yml

@@ -6,39 +6,47 @@ The cBioPortal for Cancer Genomics provides visualization, analysis, and downloa
 
 If you would like to know how to setup a private instance of the portal and/or get set up for developing, see the [documentation](https://docs.cbioportal.org). For details on contributing code changes via pull requests, see our [Contributing document](CONTRIBUTING.md).
 
-If you are interested in coordinating the development of new features, please contact [email protected] or reach out on https://slack.cbioportal.org.
+If you are interested in coordinating the development of new features, please contact <[email protected]> or reach out on <https://slack.cbioportal.org>.
 
 ## 📘 Documentation
+
 See [https://docs.cbioportal.org](https://docs.cbioportal.org)
 
 ## 🤝 License
+
 See [LICENSE](./LICENSE)
 
 ## 💻 Run Backend
+
 cBioPortal consists of several components, please read the [Architecture docs](https://docs.cbioportal.org/architecture-overview/) to figure out what repo would be relevant to edit. If you e.g. only want to make frontend changes, one can directly edit [the frontend repo](https://github.com/cbioportal/cbioportal-frontend) instead. Read the instructions in that repo for more info on how to do frontend development. This repo only contains the backend part. Before editing the backend, it's good to read the [backend code organization](docs/development/Backend-Code-Organization.md).
 
 ### Local Development
 
 This section provides a summary. For Quick Start instructions, or for more additional information, please see [Deploy with Docker](https://docs.cbioportal.org/deployment/docker/)
 
 #### What MySQL database to use
-We recommend to set up a MySQL database automatically using [Docker Compose](https://github.com/cBioPortal/cbioportal-docker-compose). It's useful to know how to do this as it allows you to import any dataset of your choice. For debugging production issues, we also have a database available with all the data on https://cbioportal.org that one can connect to directly. Please reach out on slack to get the credentials.
+
+We recommend to set up a MySQL database automatically using [Docker Compose](https://github.com/cBioPortal/cbioportal-docker-compose). It's useful to know how to do this as it allows you to import any dataset of your choice. For debugging production issues, we also have a database available with all the data on <https://cbioportal.org> that one can connect to directly. Please reach out on slack to get the credentials.
 
 #### Deploy your development image inside Docker Compose
-The easiest option is to deploy your development image directly into the [docker-compose](https://github.com/cBioPortal/cbioportal-docker-compose/blob/5da068f0eb9b4f42db52ab5e91321b26a1826d7a/docker-compose.yml#L6) file. 
+
+The easiest option is to deploy your development image directly into the [docker-compose](https://github.com/cBioPortal/cbioportal-docker-compose/blob/5da068f0eb9b4f42db52ab5e91321b26a1826d7a/docker-compose.yml#L6) file.
 
 1. From the cbioportal repo, build the image:
+
 ```
 docker build -t cbioportal/cbioportal:my-dev-cbioportal-image -f docker/web-and-data/Dockerfile .
 ```
+
 2. From the cbioportal-docker-compose repo, change the [env file](https://github.com/cBioPortal/cbioportal-docker-compose/blob/master/.env) to use your image (e.g. **cbioportal/cbioportal:my-dev-cbioportal-image**).
 
 3. Run the containers.
+
 ```
 docker compose up
 ```
 
-4. The app will be visible at http://localhost:8080.
+4. The app will be visible at <http://localhost:8080>.
 
 For more information, please see [Deploy with Docker](https://docs.cbioportal.org/deployment/docker/#building-cbioportal).
 
@@ -49,6 +57,7 @@ If you want to instead run the cBioPortal web app from the command line please f
 ```
 docker compose -f docker-compose.yml -f dev/open-ports.yml up
 ```
+
 This should open the ports. Now we are ready to run the cBioPortal web app locally. You can compile the backend code with:
 
 ```
@@ -70,7 +79,7 @@ java -Xms2g -Xmx4g \
      org.cbioportal.PortalApplication
 ```
 
-The app should now show up at http://localhost:8080.
+The app should now show up at <http://localhost:8080>.
 
 ### Dev Database
 
@@ -98,35 +107,150 @@ You can then use a JAVA IDE to connect to that port. E.g. in [VSCode](https://co
 }
 ```
 
+## ✅ Testing Overview
+
+This project uses a layered testing strategy that separates **unit**, **integration**, and **end-to-end (E2E)** tests for better clarity and control.
+
+---
+
+### 🧪 Test Layers
+
+| Layer        | Purpose                                                   | Runs by Default? | Tools Used                  |
+|--------------|-----------------------------------------------------------|------------------|-----------------------------|
+| **Unit**     | Test isolated logic (e.g. services, utils)                | ✅ Yes           | JUnit, Mockito              |
+| **Integration** | Test Spring components (e.g. JPA, Repositories) using real databases | 🚫 No            | Spring Boot, Failsafe       |
+| **E2E**       | Test full HTTP endpoints via real HTTP calls             | 🚫 No            | Spring Boot, TestRestTemplate, MockMvc |
+
+---
+
+### 📁 Directory Structure
+
+```
+src/test/java/             → Unit tests (default)
+src/integration/java/      → Integration tests (DB, Spring context)
+src/e2e/java/              → E2E tests (REST API over HTTP)
+```
+
+---
+
+## 🔧 Configuration via Environment Variables
+
+All integration and E2E tests are **configured via environment variables** for test DBs. This avoids hardcoding credentials and allows flexible use in local dev or CI.
+
+### ✅ Supported Environment Variables
+
+| Variable                        | Description                          | Applies To          |
+|----------------------------------|--------------------------------------|---------------------|
+| `TEST_DB_MYSQL_URL`             | JDBC URL for test MySQL              | Integration         |
+| `TEST_DB_MYSQL_USERNAME`        | MySQL username                       | Integration         |
+| `TEST_DB_MYSQL_PASSWORD`        | MySQL password (🔒 required)         | Integration         |
+| `TEST_DB_MYSQL_DRIVER`          | Optional, defaults to MySQL driver   | Integration         |
+| `TEST_DB_CLICKHOUSE_URL`        | JDBC URL for test ClickHouse         | Integration & E2E   |
+| `TEST_DB_CLICKHOUSE_USERNAME`   | ClickHouse username                  | Integration & E2E   |
+| `TEST_DB_CLICKHOUSE_PASSWORD`   | ClickHouse password (🔒 required)    | Integration & E2E   |
+| `TEST_DB_CLICKHOUSE_DRIVER`     | Optional, defaults to ClickHouse driver | Integration & E2E |
+
+> If a variable is marked as required and not set, tests will fail with a helpful error.
+
+---
+
+### 🧪 Running Tests
+
+#### ✅ Run Unit Tests (default)
+
+```bash
+mvn test
+```
+
+---
+
+#### ✅ Run Integration Tests
+
+```bash
+# Set required env vars
+export TEST_DB_MYSQL_PASSWORD=...
+export TEST_DB_CLICKHOUSE_PASSWORD=...
+
+mvn verify -Pintegration-tests
+```
+
+---
+
+#### ✅ Run E2E Tests
+
+```bash
+# Set required env vars
+export TEST_DB_MYSQL_PASSWORD=...
+export TEST_DB_CLICKHOUSE_PASSWORD=...
+
+mvn verify -Pe2e-tests
+```
+
+---
+
+#### 🔍 Test Class Inheritance
+
+All E2E tests should extend:
+
+```java
+public abstract class AbstractE2ETest { ... }
+```
+
+All integration tests (if needed) may use:
+
+```java
+public abstract class AbstractClickhouseIntegrationTest { ... }
+```
+
+These base classes:
+
+- Load the Spring context
+- Register dynamic properties from environment variables using `@DynamicPropertySource`
+- Share default behavior across test suites
+
+---
+
+### 📦 Maven Profile Summary
+
+| Profile           | Purpose               | Command                          |
+|-------------------|-----------------------|----------------------------------|
+| *(default)*       | Unit tests only       | `mvn test`                       |
+| `integration-tests` | Integration tests     | `mvn verify -Pintegration-tests` |
+| `e2e-tests`       | E2E tests              | `mvn verify -Pe2e-tests`         |
+
+---
+
 ## 🌳 Branch Information
 
 | | main branch | upcoming release branch | later release candidate branch |
 | --- | --- | --- | --- |
 | Branch name | [`master`](https://github.com/cBioPortal/cbioportal/tree/master) |  -- |  [`rc`](https://github.com/cBioPortal/cbioportal/tree/rc) |
 | Description | All bug fixes and features not requiring database migrations go here. This code is either already in production or will be released this week | Next release that requires database migrations. Thorough manual product review often takes place for this branch before release | Later releases with features that require database migrations. This is useful to allow merging in new features without affecting the upcoming release. Could be seen as a development branch, but note that only high quality pull requests are merged. That is the feature should be pretty much ready for release after merge. |
-| Live instance | https://www.cbioportal.org / https://master.cbioportal.org | -- | https://rc.cbioportal.org |
-| Live instance version | https://www.cbioportal.org/api/info / https://master.cbioportal.org/api/info | -- | https://rc.cbioportal.org/api/info |
+| Live instance | <https://www.cbioportal.org> / <https://master.cbioportal.org> | -- | <https://rc.cbioportal.org> |
+| Live instance version | <https://www.cbioportal.org/api/info> / <https://master.cbioportal.org/api/info> | -- | <https://rc.cbioportal.org/api/info> |
 | Docker Image | cbioportal/cbioportal:master | --| cbioportal/cbioportal:rc |
 | Kubernetes Config | [production](https://github.com/knowledgesystems/knowledgesystems-k8s-deployment/blob/master/cbioportal/cbioportal_spring_boot.yaml) / [master](https://github.com/knowledgesystems/knowledgesystems-k8s-deployment/blob/master/cbioportal/cbioportal_backend_master.yaml) | -- | [rc](https://github.com/knowledgesystems/knowledgesystems-k8s-deployment/blob/master/cbioportal/cbioportal_backend_rc.yaml) |
 | Status | [![master build status](https://github.com/cbioportal/cbioportal/workflows/Core%20tests/badge.svg)](https://github.com/cBioPortal/cbioportal/actions/workflows/core-test.yml?query=branch%3Amaster) [![master build status](https://github.com/cbioportal/cbioportal/workflows/Integration%20tests/badge.svg)](https://github.com/cBioPortal/cbioportal/actions/workflows/integration-test.yml?query=branch%3Amaster) [![master build status](https://github.com/cbioportal/cbioportal/workflows/Docker%20Image%20CI/badge.svg)](https://github.com/cBioPortal/cbioportal/actions/workflows/dockerimage.yml?query=branch%3Amaster) [![master build status](https://github.com/cbioportal/cbioportal/workflows/Python%20validator/badge.svg)](https://github.com/cBioPortal/cbioportal/actions/workflows/validate-data.yml?query=branch%3Amaster) [![CircleCI](https://circleci.com/gh/cBioPortal/cbioportal/tree/master.svg?style=svg)](https://app.circleci.com/pipelines/github/cBioPortal/cbioportal?branch=master&filter=all) | -- | -- |
 
 ## 🚀 Releases
+
 Release Notes on GitHub:
 
-https://github.com/cBioPortal/cbioportal/releases
+<https://github.com/cBioPortal/cbioportal/releases>
 
 See also the cBioPortal News section for user focused release information:
 
-https://www.cbioportal.org/news
+<https://www.cbioportal.org/news>
 
 Docker Images are available for each tag and branch:
 
-https://hub.docker.com/repository/docker/cbioportal/cbioportal/tags
+<https://hub.docker.com/repository/docker/cbioportal/cbioportal/tags>
 
 ## 👉 Other Repos
+
 Read the [Architecture docs](https://docs.cbioportal.org/2.1-deployment/architecture-overview) to see how these relate:
 
-- https://github.com/cBioPortal/cbioportal-frontend
-- https://github.com/cbioportal/session-service
-- https://github.com/cBioPortal/datahub/
-- https://github.com/cBioPortal/cbioportal-core
+- <https://github.com/cBioPortal/cbioportal-frontend>
+- <https://github.com/cbioportal/session-service>
+- <https://github.com/cBioPortal/datahub/>
+- <https://github.com/cBioPortal/cbioportal-core>