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Karnak is a DICOM gateway for data de-identification and DICOM attribute normalization.

Karnak manages a continuous DICOM flow with a DICOM listener as input and a DICOM and/or DICOMWeb as output.

For more information, see the online Karnak user guide

⚠️ Security: Karnak is using Logback and is not affected by CVE-2021-44228. CVE-2021-42550 has been fixed since v0.9.9

Application Features

Gateway

  • Allows building mapping between a source and one or more destinations
  • Each destination can be DICOM or DICOMWeb
  • Filter the images providers by AETitle and/or hostname (ot ensure the authenticity of the source)

de-identification

  • Each destination can be configured with a specific de-identification profile
  • Configuration for sending only specific SopClassUIDs
  • Build your own de-identification profile or add modifications to the basic DICOM profile
  • Import and export the de-identification profiles

Build Karnak

Prerequisites:

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-compose, see karnak-docker.

Debug Karnak

Debug in IntelliJ

  • Launch the components needed by Karnak (see below "Configure locally Mainzelliste and Postgres database with docker-compose")
  • 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.
    • 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 Mainzelliste and Postgres database with docker-compose") :
      • Mandatory:
        • ENVIRONMENT=DEV
      • Optional:
        • DB_PASSWORD=5!KAnN@%98%d
        • DB_PORT=5433
        • DB_USER=karnak
        • DB_NAME=karnak
        • DB_HOST=localhost
        • MAINZELLISTE_HOSTNAME=localhost
        • MAINZELLISTE_HTTP_PORT=8083
        • MAINZELLISTE_API_KEY=changeThisApiKey
        • 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

Configure locally Mainzelliste and Postgres database with docker-compose

Minimum docker-compose version: 1.22

  • Go in the docker folder located in the root project folder.
  • To configure third-party components used by karnak, please refer to these links:
  • 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: 19.03

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

Workflow

Pipeline

Workflow