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Application Quality Deployment Guide⚓︎

OIDC Authentication is currently a requirement of this Building Block.

The Application Quality Building Block (BB) supports the evolution of scientific algorithms from research prototypes to production-grade processing workflows. It provides tooling to verify non-functional requirements—code quality, best practices, vulnerability scanning, performance testing—and to manage these checks via pipelines integrated into a typical CI/CD process.

Introduction⚓︎

The Application Quality Building Block provides tooling to encourage best practices in software development and to test (and optimize) the performance of processing workflows in a sandbox environment. It includes:

  • Development Best Practice: Static code analysis, vulnerability scans, best practice checks for open reproducible science.
  • Application Quality Tooling: Container-based tools that can be orchestrated in pipelines (e.g. SonarQube, Bandit, Sphinx, etc.).
  • Application Performance: Tools supporting performance testing and optimisation of processing workflows.

Architecture Overview⚓︎

  • Application Quality Database: Stores definitions of analysis tools, pipelines, and pipeline execution metadata.
  • Application Quality Web Portal: Front-end for pipeline creation, management, and viewing results.
  • Application Quality API: Backend service that provides data to the Web Portal and interacts with the database.
  • Application Quality Engine: Orchestrates pipeline executions. Submits CWL documents to a CWL runner (e.g. Calrissian) for container-based tasks.
  • CWL Runner (Calrissian): Runs each step in containers on Kubernetes.
  • Optional: OpenSearch & OpenSearch Dashboards to store, visualise, and analyze results.

Prerequisites⚓︎

Before deploying the Application Quality Building Block, ensure you have the following:

Component Requirement Documentation Link
Kubernetes Cluster (tested on v1.28) Installation Guide
Helm Version 3.5 or newer Installation Guide
kubectl Configured for cluster access Installation Guide
OIDC Provider An OIDC Provider must be available Deployment Guide
TLS Certificates Managed via cert-manager or manually TLS Certificate Management Guide
Internal TLS Certificates ClusterIssuer for internal certificates Internal TLS Setup

Clone the Deployment Guide Repository:

git clone https://github.com/EOEPCA/deployment-guide
cd deployment-guide/scripts/application-quality

Validate your environment:

bash check-prerequisites.sh

Deployment Steps⚓︎

1. Run the Configuration Script⚓︎

bash configure-application-quality.sh

Configuration Parameters include:

  • INGRESS_HOST: Base domain (e.g. example.org)
  • STORAGE_CLASS: Name of your storage class (e.g. standard, managed-nfs-storage-retain)
  • CLUSTER_ISSUER: Cert-manager issuer name (e.g. letsencrypt-prod)
  • INTERNAL_CLUSTER_ISSUER: Name of the cert-manager ClusterIssuer for internal TLS. (Default: eoepca-ca-clusterissuer)

OIDC Configuration:

OIDC authentication is currently a requirement of this Building Block.

If you choose to enable OIDC authentication, you will be asked to provide. We will configure the clients in a later step, just provide the names for now.

  • APP_QUALITY_CLIENT_ID: OIDC client ID for the Application Quality Building Block. (use application-quality)

2. Apply Secrets⚓︎

bash apply-secrets.sh

3. Deploy via Helm⚓︎

Note: While the Application Quality BB is not yet in the official EOEPCA Helm charts, you can install it directly from the GitHub repository.

  1. Clone the reference repository:
git clone https://github.com/EOEPCA/application-quality.git reference-repo \
  -b reference-deployment
  1. Install with Helm:
helm dependency update reference-repo/helm

helm upgrade -i application-quality reference-repo/helm \
  --namespace application-quality \
  --create-namespace \
  --values generated-values.yaml

4 Create a Keycloak Client⚓︎

Use the create-client.sh script in the /scripts/utils/ directory. This script prompts you for basic details and automatically creates a Keycloak client in your chosen realm:

bash ../utils/create-client.sh

When prompted:

  • Keycloak Admin Username and Password: Enter the credentials of your Keycloak admin user (these are also in ~/.eoepca/state if you have them set).
  • Keycloak base domain: e.g. auth.example.com

  • Realm: Typically eoepca.

  • Confidential Client?: specify true to create a CONFIDENTIAL client

  • Client ID: You should use the client ID you inputted in the configuration script (application-quality).
  • Client name and description: Provide any helpful text (e.g. Application Quality)
  • Client secret: Enter the Client Secret that was generated during the configuration script (check ~/.eoepca/state).
  • Subdomain: Use application-quality.
  • Additional Subdomains: Leave blank.
  • Additional Hosts: Leave blank.

After it completes, you should see a JSON snippet confirming the newly created client.

Validation⚓︎

  1. Run the validation script (validation.sh):
bash validation.sh

This checks that the required pods/services/ingress exist and that the main endpoint returns a 200 status code.

  1. Manual:

To confirm everything is running…

kubectl get all -n application-quality

Usage Instructions⚓︎

1. Accessing the Web Portal⚓︎

  1. Ensure your ingress is configured to route application-quality.${INGRESS_HOST} (or whichever domain) to the Application Quality front-end.
  2. Open a browser at https://application-quality.${INGRESS_HOST}/.
  3. If OIDC is enabled, you’ll see a Login link in the navigation bar. Unauthenticated users can only browse certain read-only features.

2. Authenticating via EOEPCA IAM⚓︎

  1. Click the Login link.
  2. Choose your Identity Provider (local Keycloak account or GitHub, etc.).
  3. Upon successful login, the top nav bar will show your username and a Logout link.

3. Defining & Executing Pipelines⚓︎

A pipeline is a sequence of analysis tools (CWL definitions) that can run on your application’s source code or container. Common examples include:

  • Static code analysis (e.g. flake8, bandit, ruff, SonarQube)
  • Vulnerability scans (e.g. Trivy, Docker image scanning)
  • Performance checks (executing a workflow in a test environment and capturing resource usage)

Manual Execution:

  1. Navigate to Pipelines in the side menu.
  2. Select the pipeline you wish to run, or create a new one that references your analysis tools.
  3. Click the (execute) icon.
  4. Enter Git repository URL/branch.
  5. Click Execute.

View the pipeline’s progress under Monitoring, which shows each stage (tool) as it runs.

4. Inspection of Analysis Tools & Pipelines⚓︎

  1. Analysis Tools → Lists all available tools. Each tool can have a name, version, Docker container reference, etc.
  2. Pipelines → Each pipeline references one or more tools, plus any triggers or environment variables.

5. Viewing Reports & Metrics⚓︎

Once a pipeline finishes, you can see:

  • Reports: Detailed findings from each tool (lint errors, vulnerabilities, performance metrics, coverage, etc.).
  • Monitoring: The pipeline’s timeline, success/failure, logs, etc.

Uninstallation⚓︎

To remove all Application Quality components:

helm uninstall application-quality -n application-quality
kubectl delete namespace application-quality

kubectl delete pvc --all -n application-quality

Further Reading⚓︎