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Instruction

This instruction will show you how to build and start a few docker containers for enabling the DCCN DICOM dataflow.

The containers are organised in the following sub-directories:

  • docker/base: basic container with pre-installed tools/libraries/packages/modules
  • docker/orthanc: the Orthanc server
  • docker/wlbroker: the DICOM worklist broker
  • docker/cal2wl: the cron job converting calendar bookings to DICOM worklist

They are orchestrated by the docker-compose file docker/docker-compose-dicomdf.yml.

requirements of the docker host

  • sufficient space on directory /scratch/data_dicom, for Orthanc database and DICOM worklist.
  • access to the project storage, i.e. the /project directory
  • accepting inbound connectivity via ports: 8042, 4042 and 1234

configuration

Prepare environment variables by copying the env.example file to .env; and modify the values accordingly.

The files to be configured properly are:

  • docker/cal2wl/config.yml

    In the file docker/cal2wl/config.yml, change the connections accordingly in order to access the lab-booking events in the DCCN project database.

  • docker/cal2wl/cron/crontab

    In the file docker/cal2wl/cron/crontab, you may adjust how often the lab-booking events in calendar are converted into DICOM worklist.

build the containers

Copy the env.example to .env and modify the environment variables in .env accordingly.

For building the containers, you will make use of the following variables:

  • DOCKER_REGISTRY: the docker registry endpoint used to form the prefix of the image name.
  • DOCKER_IMAGE_TAG: the docker image tag.
  • ORTHANC_VERSION: the Orthanc version based on which the orthac container image.
  • ORTHANC_BUILD: the build number of the orthanc container image.
  • TG_TOOLSET_TAG: the tag of the tg-toolset-golang from which the dicom_worklist program is built and included in the cal2wl container.
$ docker-compose build --force-rm

run the containers

For running the containers, you will make use of the following variables in the .env file:

  • DOCKER_REGISTRY and DOCKER_IMAGE_TAG: these two variables together determine the image to be used for the cal2wl and wlbroker containers.
  • ORTHANC_VERSION and ORTHANC_BUILD: these two variables together determine the image to be used for the orthanc container.
  • VOL_ORTHANC_CONFIG: path or name of the Orthanc configuration volume. It is bind-mounted to /var/lib/orthanc/etc in the Orthanc container.
  • VOL_ORTHANC_LOG: path or name of the Orthanc log volume. It is bind-mounted to /var/lib/orthanc/log in the Orthanc container.
  • VOL_ORTHANC_DB: path or name of the Orthanc data volume. It is bind-mounted to /var/lib/orthanc/db in the Orthanc container.
  • VOL_ORTHANC_IDX: path or name of the Orthanc data index volume. It is bind-mounted to /var/lib/orthanc/idx in the Orthanc container.
  • VOL_WLBROKER: path or name of the workload list storage volume. It is bind-mounted to /data/wlbroker in the cal2wl and wlbroker containers.
  • VOL_CAL2WL_CONFIG: path or name of the cal2wl configuration volume. It is bind-mounted to /opt/config in the cal2wl container.

Start up docker containers using the following command:

$ docker-compose -f docker-compose up -d

If the services are started successfully, the host should export three TCP ports. They are 8042 for Orthanc web front-end, 4042 for Orthanc's DICOM interface, and 1234 for DICOM worklist service.