osirixfoundation/karnak repository overview

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.

Karnak documentation⁠ is available online.

⁠Application Features

⁠Gateway

• Allows to build 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:

• JDK 14
• Maven 3
• Package dcm4che20
• Package weasis-dicom-tools
• Code formatter: google-java-format⁠

Use the following commands to build the two dependencies (dcm4che20 and weasis-dicom-tools):

⁠dcm4che20

1. git clone https://github.com/nroduit/dcm4che20.git
2. git checkout image
3. mvn source:jar install

⁠weasis-dicom-tools

1. git clone https://github.com/nroduit/weasis-dicom-tools.git
2. git checkout dcm4che6
3. mvn clean install

⁠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"
  • 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_ID_TYPES=pid
      • 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

  Note: the tmp folder must be adapted according to your system and the dicom-opencv must the last folder.

⁠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:
  • docker hub postgres⁠
  • docker hub mainzelliste⁠
• 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 mvc/src/main/docker/Dockerfile .

⁠Run image from Docker Hub

See karnak-docker⁠

⁠Docker environment variables

See environment variables⁠

⁠Architecture

This project provides two modules:

• karnak-data: the data model for persistence of the gateway configuration
• karnak-mvc: the services and UI for updating the data model

⁠Workflow

⁠Pipeline