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Handling DICOM SCP requests using a Python plugin
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 10 Jun 2021 18:36:22 +0200 |
| parents | f4bbb4a7d78a |
| children | 7bda641d5d40 |
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.. _docker-osimis: .. highlight:: bash Osimis Orthanc Docker images ============================ .. contents:: :depth: 3 .. warning:: This documentation applies to ``osimis/orthanc`` images from the ``20.4.2`` version. Note that these images have been re-written in April 2020. The documentation for older images is still available `here <https://osimis.atlassian.net/wiki/spaces/OKB/pages/26738689/How+to+use+osimis+orthanc+Docker+images#Howtouseosimis/orthancDockerimages>`__ The new images are backward compatible with the previous images except for the Google Cloud Platform configuration. However, if you're still using legacy environment variables, you'll get some warning encouraging you to update to the new namings since the backward compatibility might be removed one day (currently planed in June 2021). Introduction ------------ Our commercial partner `Osimis <https://www.osimis.io>`__ `publishes separated Docker images <https://hub.docker.com/r/osimis/orthanc>`__ that are used by their technical team in order to provide professional support to their customers. 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 <https://bitbucket.org/osimis/orthanc-setup-samples/src>`__ contains lots of examples on how to use these images. In particular, `this example <https://bitbucket.org/osimis/orthanc-setup-samples/src/master/docker/all-usages/docker-compose.yml>`__ 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: +---------------------------+----------------------------------------------+----------------------------------------------------------------+ | Orthanc configuration | Environment variable | Sample value | +===========================+==============================================+================================================================+ | StableAge | ORTHANC__STABLE_AGE | ``30`` | +---------------------------+----------------------------------------------+----------------------------------------------------------------+ | DicomWeb.Root | ORTHANC__DICOM_WEB__ROOT | ``/dicom-web/`` | +---------------------------+----------------------------------------------+----------------------------------------------------------------+ | DicomWeb.Servers | ORTHANC__DICOM_WEB__SERVERS | ``{"sample": [ "http://127.0.0.1/dicom-web/"]}`` | +---------------------------+----------------------------------------------+----------------------------------------------------------------+ 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 <https://bitbucket.org/osimis/orthanc-builder/src/master/docker/orthanc/env-var-non-standards.json>`__ 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 - ``UNLOCK=true`` will start Orthanc with the ``--unlock`` option - ``MALLOC_ARENA_MAX=10`` will :ref:`control memory usage <scalability-memory>` - ``ORTHANC_JSON`` can be used to pass a JSON "root" configuration (see below). Configuration files ------------------- .. highlight:: yaml 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 -------------- .. highlight:: yaml 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 --------------------- .. highlight:: json 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. .. below json is copied from orthanc-builder/docker/orthanc/orthanc-defaults.json 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 <https://bitbucket.org/osimis/orthanc-builder/src/master/docker/orthanc/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. 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): .. below table is obtained by running orthanc-builder/docker/orthanc/generatePluginDoc.py +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | Plugin | Environment variable | Default configuration | +==================================================+==================================================+====================================================================================================+ | **Authorization** | ``AUTHORIZATION_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **ConnectivityChecks** | ``CONNECTIVITY_CHECKS_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **DicomWeb** | ``DICOM_WEB_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "DicomWeb": { | | | | "Enable": true | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Gdcm** | ``GDCM_PLUGIN_ENABLED`` | .. code-block:: json | | | Note: enabled by default | | | | | { | | | | "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" | | | | ] | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **OrthancWebViewer** | ``ORTHANC_WEB_VIEWER_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **StoneWebViewer** (DICOMweb plugin is required) | ``STONE_WEB_VIEWER_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **OsimisWebViewerBasic** | ``OSIMIS_WEB_VIEWER1_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **OsimisWebViewerBasicAlpha** | ``OSIMIS_WEB_VIEWER1_ALPHA_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **PostgreSQL** | ``POSTGRESQL_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "PostgreSQL": { | | | | "EnableIndex": true, | | | | "EnableStorage": false, | | | | "Port": 5432, | | | | "Host": "HOST MUST BE DEFINED", | | | | "Database": "postgres", | | | | "Username": "postgres", | | | | "Password": "postgres", | | | | "EnableSsl": false, | | | | "Lock": false | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **MySQL** | ``MYSQL_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "MySQL": { | | | | "EnableIndex": true, | | | | "EnableStorage": false, | | | | "Port": 3306, | | | | "Host": "HOST MUST BE DEFINED", | | | | "Database": "mysql", | | | | "Username": "root", | | | | "Password": "mysql", | | | | "Lock": false | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Python** | ``PYTHON_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **ServeFolders** | ``SERVE_FOLDERS_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Transfers** | ``TRANSFERS_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Worklists** | ``WORKLISTS_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "Worklists": { | | | | "Enable": true, | | | | "Database": "/var/lib/orthanc/worklists" | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Whole-slide imaging** | ``WSI_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Osimis cloud** (synchronization plugin) | ``OSIMIS_CLOUD_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ Under the hood -------------- The source code that is used to generate the image can be found `here <https://bitbucket.org/osimis/orthanc-builder/src/master/docker/orthanc/Dockerfile>`__. The Python script that is used at startup can be found `here <https://bitbucket.org/osimis/orthanc-builder/src/master/docker/orthanc/generateConfiguration.py>`__