WIPP REST API

A Java Spring Boot application for managing WIPP data and workflows. The API follows the HATEOAS architecture using the HAL format.

Requirements

Requirements for development environment setup.

Java environment

• Java JDK 21
• Maven version compatible with Java 21

Database

• MongoDB (Supported versions: 3.6 to 7.0)

Identity and Access Management

• Keycloak 11.0.2
• Default dev configuration expects Keycloak at http://localhost:8081/auth (see wipp-backend-application/src/main/resources/application.properties. Sample Docker run command: docker run -p 8081:8080 -e KEYCLOAK_USER=admin -e KEYCLOAK_PASSWORD=admin quay.io/keycloak/keycloak:11.0.2 (see https://www.keycloak.org/getting-started/getting-started-docker)
• Import WIPP realm available in folder docs/auth-acl
• RBAC-ACLs descriptions available in file docs/auth-acl/acl.md

Kubernetes cluster

• For development purposes, a single-node cluster can be easily installed using Minikube or Docker for Mac on macOS
• We are using Argo Workflows to manage workflows on a Kubernetes cluster, a minimal installation of the Argo Server and Controller can be set up using the following commands:

kubectl apply -f https://github.com/argoproj/argo-workflows/releases/download/v3.5.5/quick-start-minimal.yaml

Please follow the instructions for version 3.5.5 here to:

• install the Argo binary

Data storage

• Create a WIPP-plugins folder in your home directory for data storage (dev Maven profile is expecting the data folder location to be $HOME/WIPP-plugins)
• Create the WIPP data storage Persistent Volume (PV) and Persistent Volume Claim (PVC) in your Kubernetes cluster following the templates for hostPath PV and PVC available in the WIPP repository:
  • path of hostPath in hostPath-wippdata-volume.yaml should be modified to match path of WIPP-plugins folder created above
  • storage of capacity is set to 100Gi by default, this value can be modified in hostPath-wippdata-volume.yaml and hostPath-wippdata-pvc.yaml
  • run hostPath-deploy.sh to setup the WIPP data PV and PVC

Local backend import option
Default root folder configuration for the local backend import of images collections is:

• ${user.home}/WIPP-plugins/local-import in dev profile and
• /data/WIPP-plugins/local-import in prod profile

This default configuration can be changed in wipp-backend-application/pom.xml (property storage.local.import) when running locally or in the deployment manifest when running in a Kubernetes cluster (an additional volume needs to be mounted if the new location is not in the WIPP root data folder).

Data conversion

• WIPP uses the bioformats2raw and raw2ometiff converters to convert images to tiled pyramidal OME TIFF format, which require Blosc to be installed:
  • https://github.com/Blosc/c-blosc for compilation and installation instructions

Compiling

mvn clean install

Running

cd wipp-backend-application
mvn spring-boot:run

• The WIPP REST API will be launched with the dev profile and available at http://localhost:8080/api

• Swagger API documentation will be available at:

• http://localhost:8080/api/swagger-ui/index.html (Swagger UI) and,

• http://localhost:8080/api/v3/api-docs (OpenAPI spec)

Docker packaging

docker build --no-cache . -t wipp_backend

For a Docker deployment of WIPP on a Kubernetes cluster, scripts and configuration files are available in the WIPP repository.

Deployment

1. Create a .env file in the root of the repository, using sample-env as an example.
2. Configure kubectl with a kubeconfig pointing to the correct Kubernetes cluster. Optionally, pass the location of the kubeconfig file in the .env. This value defaults to the standard kubeconfig location.
3. Run the script using: ./deploy.sh.

Application Performance Monitoring (APM)

The Elastic APM Java agent is integrated into the Docker image as an optional setting. The Elastic APM agent will push metrics to an APM server, which feeds into Elasticsearch and Kibana. Configuration of the Elastic APM Java Agent to connect to the APM server is controlled via environment variables. These variables are optional if Elastic APM is not needed.

Environment Variable	Description
ELASTIC_APM_SERVICE_NAME	Service name tag attached to all metrics sent.
ELASTIC_APM_SERVER_URLS	Url of Elastic APM server.
ELASTIC_APM_APPLICATION_PACKAGES	(Optional) Determines stack trace frame. Multiple packages can be set.
ELASTIC_APM_SECRET_TOKEN	(Optional) Secret token for Elastic APM server.

WIPP Development flow

We are following the Gitflow branching model for the WIPP development.

Contributing

Please follow the Contributing guidelines

Disclaimer/License

NIST Disclaimer/License