osimis/orthanc Docker images¶

Introduction¶

Our commercial partner Osimis publishes separated Docker images. These images have been designed to be used with docker-compose and provide a configuration system through:

• environment variables
• Docker secrets
• classical configuration files
• a mix of these options

This repository contains lots of examples on how to use these images. In particular, this example shows all the way that can be used to generate the same configuration in Orthanc.

Environment variables¶

Any part of the Orthanc configuration file can be configured through an environment variable. Now that Orthanc and its plugins have hundreds of configuration parameter, listing all these environment variable would be too long. That’s why we have defined a standard way of naming the variable:

To find out an environment variable name from an Orthanc setting (i.e. DicomWeb.StudiesMetadata is the path to a setting):

• whenever a word contains a capital letter, insert an underscore _ in front. DicomWeb.StudiesMetadata now becomes Dicom_Web.Studies_Metadata
• whenever you go down one level in the JSON configuration, insert a double underscore __. Dicom_Web.Studies_Metadata now becomes Dicom_Web__Studies_Metadata
• capitalize all letters. Dicom_Web__Studies_Metadata now becomes DICOM_WEB__STUDIES_METADATA
• add ORTHANC__ in front. DICOM_WEB__STUDIES_METADATA now becomes ORTHANC__DICOM_WEB__STUDIES_METADATA

Note that, this automatic rule might fail because of 2 capital letters one after each other in some Orthanc settings. Therefore, there are some exceptions to this rule that are however quite intuitive.

Special environment variables¶

Other environment variables are not related to the Orthanc configuration file but can be specified to control the way Orthanc is run.

• VERBOSE_STARTUP=true will allow you to debug the startup process and see the configuration that has been provided to Orthanc. This setup should be disabled in production since it might display secret information like passwords in your logs
• VERBOSE_ENABLED=true will start Orthanc with the --verbose option
• TRACE_ENABLED=true will start Orthanc with the --trace option
• NO_JOBS=true will start Orthanc with the --no-jobs option
• LOGDIR=/logs will start Orthanc with the --logdir=/logs option (introduced in 21.9.1)
• LOGFILE=/logs will start Orthanc with the --logfile=/logs/orthanc.log option (introduced in 21.9.1)
• MALLOC_ARENA_MAX=10 will control memory usage
• ORTHANC_JSON can be used to pass a JSON “root” configuration (see below).
• BEFORE_ORTHANC_STARTUP_SCRIPT can be used to run a custom script before starting Orthanc.
• FORCE_HOST_ID and GENERATE_HOST_ID_IF_MISSING can be used to control the content of /etc/hostid (introduced in 22.9.1). DCMTK calls gethostid() when generating DICOM UIDs (used, e.g, in modifications/anonymizations). When /etc/hostid is missing, the system tries to generate it from the IP of the system. On some system, in particular circumstances, we have observed that the system performs a DNS query to get the IP of the system. This DNS can timeout (after multiple with retries) and, in particular cases, we have observed a delay of 40 seconds to generate a single DICOM UID in Orthanc. Therefore, if /etc/hostid is missing, the startup script creates it and fill it with a random number (default behaviour). This behaviour can still be deactivated by defining GENERATE_HOST_ID_IF_MISSING=false. The host id can also be forced by defining FORCE_HOST_ID.

Configuration files¶

Configuration files should be stored in the /etc/orthanc/ folder inside the Docker image. This is done by building an image thanks to a Dockerfile:

FROM osimis/orthanc
COPY orthanc.json /etc/orthanc/

Configuration files can also be passed as secrets as shown in this docker-compose.yml:

version: "3.3"
  services:
    orthanc-file-in-secrets:
      image: osimis/orthanc
      depends_on: [index-db]
      ports: ["8201:8042"]
      environment:
        VERBOSE_STARTUP: "true"

      secrets:
        - orthanc.secret.json

  secrets:
    orthanc.secret.json:
      file: orthanc.secret.json

Finally, a whole configuration file can be passed as a JSON through the ORTHANC_JSON environment variable:

version: "3.3"
  services:
    orthanc-file-in-env-var:
      image: osimis/orthanc
      depends_on: [index-db]
      ports: ["8200:8042"]
      environment:
        VERBOSE_ENABLED: "true"
        OSIMIS_WEB_VIEWER1_PLUGIN_ENABLED: "true"

        ORTHANC_JSON: |
          {
            "Name": "orthanc-file-in-env-var",
            "PostgreSQL" : {
              "Host": "index-db",
              "Password": "pg-password"
            },
            "RegisteredUsers": {
              "demo": "demo"
            }
          }

Docker secrets¶

When using your container in a Docker Swarm or Kubernetes environment, it is usually advised to pass sensitive information through Docker Secrets. For this purpose, any secret whose name is similar to the name of an environment variable is considered as an environment variable:

version: "3.3"
  services:
    orthanc-with-direct-secret:
      image: osimis/orthanc
      depends_on: [index-db]
      ports: ["8003:8042"]
      environment:
        ORTHANC__NAME: "orthanc-with-direct-secret"
        VERBOSE_ENABLED: "true"

        OSIMIS_WEB_VIEWER1_PLUGIN_ENABLED: "true"

        ORTHANC__POSTGRESQL__HOST: "index-db"
        ORTHANC__REGISTERED_USERS: |
          {"demo": "demo"}

    secrets:
      - ORTHANC__POSTGRESQL__PASSWORD
  secrets:
    ORTHANC__POSTGRESQL__PASSWORD:
      file: ORTHANC__POSTGRESQL__PASSWORD

Mixing configuration¶

Parts of your configuration can be defined in a configuration file, another part in an environment variable and yet another in a secret. If the same setting is defined in multiple location, the latest one will overwrite the first. Settings are evaluated in this order:

• JSON files from /etc/orthanc/
• JSON files from /run/secrets (Docker secrets are copied there by Docker)
• environment variables
• secret environment variables

At this point, if some settings have not been defined yet, some defaults are applied (see below).

Default configuration¶

Orthanc and each plugin might have some default settings that might eventually be different from the defaults included in the Orthanc executable or the plugin library.

Orthanc non-standard defaults:

{
  "StorageDirectory" : "/var/lib/orthanc/db",

  "RemoteAccessAllowed": true,
  "AuthenticationEnabled": true,

  "HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt",

  "Plugins" : ["/usr/share/orthanc/plugins/"]
}

Default Lua scripts¶

Some Lua scripts are already loaded in the image but are not configured to be loaded by Orthanc automatically. You’ll have to add them to the "LuaScripts" configuration if you want to use them.

/lua-scripts/filter-http-tools-reset.lua can be used to regenerate the /tmp/orthanc.json configuration file that is loaded by Orthanc every time you POST to /tools/reset. Note that it declares an IncomingHttpRequestFilter callback that might conflict with your scripts.

Healthcheck probe¶

In version 21.10.0, the /probes/test-aliveness.py script has been added in order to perform healthchecks. Check the doc in the script itself for more details. A sample configuration is also available in this sample

Plugins¶

Plugins are automatically enabled as soon as you define a setting in their JSON section or as soon as you define to true their specific environment variable.

Below is a list of all plugins, their environment variable and their default configuration (only when their default configuration is different from the plugin defaults):

{
  "DicomWeb": {
    "Enable": true
  }
}

{
  "Gdcm": {
    "Throttling": 4,
    "RestrictTransferSyntaxes": [
      "1.2.840.10008.1.2.4.90",
      "1.2.840.10008.1.2.4.91",
      "1.2.840.10008.1.2.4.92",
      "1.2.840.10008.1.2.4.93"
    ]
  }
}

{
  "PostgreSQL": {
    "EnableIndex": true,
    "EnableStorage": false,
    "Port": 5432,
    "Host": "HOST MUST BE DEFINED",
    "Database": "postgres",
    "Username": "postgres",
    "Password": "postgres",
    "EnableSsl": false,
    "Lock": false
  }
}

{
  "MySQL": {
    "EnableIndex": true,
    "EnableStorage": false,
    "Port": 3306,
    "Host": "HOST MUST BE DEFINED",
    "Database": "mysql",
    "Username": "root",
    "Password": "mysql",
    "Lock": false
  }
}

{
  "Worklists": {
    "Enable": true,
    "Database": "/var/lib/orthanc/worklists"
  }
}

{
  "Housekeeper": {
    "Enable": true
  }
}

{
  "DelayedDeletion": {
    "Enable": true
  }
}

{
  "Odbc": {
    "EnableIndex": true,
    "EnableStorage": false,
    "IndexConnectionString": "MUST BE DEFINED",
    "StorageConnectionString": "MUST BE DEFINED"
  }
}

{
  "Tcia": {
    "Enable": true
  }
}

{
  "Indexer": {
    "Enable": true
  }
}

{
  "Neuro": {
    "Enable": true
  }
}

{
  "AzureBlobStorage": {
    "ConnectionString": "MUST BE DEFINED BY YOU",
    "ContainerName": "MUST BE DEFINED BY YOU"
  }
}

{
  "AwsS3Storage": {
    "BucketName": "MUST BE DEFINED BY YOU",
    "Region": "MUST BE DEFINED BY YOU"
  }
}

{
  "GoogleCloudStorage": {
    "ServiceAccountFile": "MUST BE DEFINED BY YOU",
    "BucketName": "MUST BE DEFINED BY YOU"
  }
}

{
  "OrthancExplorer2": {
    "Enable": true,
    "IsDefaultOrthancUI": false
  }
}

Under the hood¶

The source code that is used to generate the image can be found here.

The Python script that is used at startup can be found here