Karnak is a DICOM gateway designed for data de-identification and DICOM attribute normalization. It manages continuous DICOM data streams, functioning as a DICOM listener for input and supporting both DICOM and DICOMWeb formats for output.

For detailed usage instructions, refer to the Karnak User Guide.

Application Features

Gateway

• Allow to have multiple destinations for one source.
• A destination can be DICOM or DICOMWeb.
• Provides filtering options for image providers by AE Title and/or hostname to ensure source authenticity.
• Provides filtering options for SOP Class UID to send only specific SOP Class UIDs.
• Use expressions to filter images from the DICOM tag values.

De-identification

• Each destination can be configured with a specific de-identification profile
• Build your own de-identification profile
• Import and export the de-identification profiles to share them with other users.

Build Karnak

Prerequisites:

• JDK 21
• Maven 3

Karnak

Execute the maven command mvn clean install -P production in the root directory of the project.

Run Karnak

To configure and run Karnak with docker, see karnak-docker.

Debug Karnak

Debug in IntelliJ

• Launch the components needed by Karnak (see below "Configure Postgres database with docker")
• Enable Spring and Spring Boot for the project
• Create a Spring Boot launcher from main of StartApplication.java
  • Working Directory must be the mvc directory
  • In VM Options:
    • Add -Djava.library.path="/tmp/dicom-opencv". Note: the tmp folder must be adapted according to your system and dicom-opencv is mandatory as the last folder.
    • Optional: Add -Dvaadin.productionMode=true to enable production mode
  • In Environment variables, add the following values. The following values work with our default configuration define with docker used for the development (see: "Configure locally Postgres database with docker") :
    • Mandatory:
      • ENVIRONMENT=DEV
    • Optional:
      • DB_PASSWORD=5!KAnN@%98%d
      • DB_PORT=5433
      • DB_USER=karnak
      • DB_NAME=karnak
      • DB_HOST=localhost
      • DB_ENCRYPTION_KEY=fsGuSZRIEr$HwlTDPglZg*Vl7WtJCZz6RLvqoMKWSA!
      • KARNAK_ADMIN=admin
      • KARNAK_PASSWORD=admin
      • KARNAK_LOGS_MAX_FILE_SIZE=100MB
      • KARNAK_LOGS_MIN_INDEX=1
      • KARNAK_LOGS_MAX_INDEX=10
      • KARNAK_CLINICAL_LOGS_MAX_FILE_SIZE=100MB
      • KARNAK_CLINICAL_LOGS_MIN_INDEX=1
      • KARNAK_CLINICAL_LOGS_MAX_INDEX=10
      • IDP=undefined
      • OIDC_CLIENT_ID=undefined
      • OIDC_CLIENT_SECRET=undefined
      • OIDC_ISSUER_URI=undefined

Run locally the database and the cache with docker

• Go in the docker folder located in the root project folder.
• To configure third-party components used by karnak, please refer to these links:
  • docker hub postgres
• Adapt the values if necessary (copy .env.example into .env and modify it)
• Execute command:
  • start: docker compose up -d
  • show the logs: docker compose logs -f
  • stop: docker compose down

Docker

Minimum docker version: 20.10

Build with Dockerfile

Go on the root folder and launch the following command:

• Full independent build: docker build -t local/karnak:latest -f Dockerfile .
• Build from compile package:
  • mvn clean install -P production
  • docker build -t local/karnak:latest -f src/main/docker/Dockerfile .

Run image from Docker Hub

See karnak-docker

Docker environment variables

See all the environment variables

Architecture

This project is divided in two parts:

• backend: spring data (entities, repositories, converters, validators), enums, spring configurations, spring security, cache, spring services, models...
• frontend : Vaadin components: logic services, graphic components, views

Identity provider

An OpenID Connect identity provider can be configured by using the environment variables:

• IDP: when this environment variable has the value 'oidc', the following environment variables will configure the OpenID Connect identity provider. Any other value will load the in memory user configuration.
• OIDC_CLIENT_ID: client id of the identity provider
• OIDC_CLIENT_SECRET: client secret of the identity provider
• OIDC_ISSUER_URI: issuer URI of the identity provider

Documentation for API/Endpoints

Workflow

Pipeline