Mercurial > hg > orthanc-book
view Sphinx/source/users/docker-osimis.rst @ 1013:ab270400aae1
python: overriding core API
| author | Alain Mazy <am@osimis.io> |
|---|---|
| date | Tue, 09 Jan 2024 11:50:17 +0100 |
| parents | 5df222ddd7d1 |
| children | 7f21ad59dffb b00f7426db52 |
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.. _docker-osimis: .. highlight:: bash osimis/orthanc Docker images ============================ .. contents:: :depth: 3 .. warning:: Starting from the ``22.6.1`` release, we are providing 2 types of images: - the default image with the usual tag: e.g ``22.6.1`` - the full image with a e.g ``22.6.1-full`` tag The default image is suitable for 99.9% of users. You should use the full image only if you need to use one of these: - the Azure Blob storage plugin - the Google Cloud storage plugin - the ODBC plugin with SQL Server (msodbcsql18 is preinstalled) .. 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 at any time. Introduction ------------ Our commercial partner `Osimis <https://www.osimis.io>`__ `publishes separated Docker images <https://hub.docker.com/r/osimis/orthanc>`__. 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://github.com/orthanc-server/orthanc-setup-samples/src>`__ contains lots of examples on how to use these images. In particular, `this example <https://github.com/orthanc-server/orthanc-setup-samples/tree/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://github.com/orthanc-server/orthanc-builder/blob/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 - ``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 :ref:`control memory usage <scalability-memory>` - ``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 <https://groups.google.com/g/orthanc-users/c/EXjTq2ZU1vw/m/02CwW1jzAQAJ>`__ 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 ------------------- .. 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://github.com/orthanc-server/orthanc-builder/blob/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. Healthcheck probe ----------------- In version 21.10.0, the `/probes/test-aliveness.py <https://github.com/orthanc-server/orthanc-builder/blob/master/docker/orthanc/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 <https://github.com/orthanc-server/orthanc-setup-samples/src/8016d140a237a892db703aac4782307c46732847/docker/tls-mutual-auth/docker-compose.yml#lines-51>`__ 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** | ``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" | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Housekeeper** | ``HOUSEKEEPER_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "Housekeeper": { | | | | "Enable": true | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **DelayedDeletion** | ``DELAYED_DELETION_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "DelayedDeletion": { | | | | "Enable": true | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **MultitenantDicom** | ``MULTITENANT_DICOM_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Wsi** | ``WSI_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Odbc** | ``ODBC_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "Odbc": { | | | | "EnableIndex": true, | | | | "EnableStorage": false, | | | | "IndexConnectionString": "MUST BE DEFINED", | | | | "StorageConnectionString": "MUST BE DEFINED" | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Tcia** | ``TCIA_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "Tcia": { | | | | "Enable": true | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Indexer** | ``INDEXER_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "Indexer": { | | | | "Enable": true | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Neuro** | ``NEURO_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "Neuro": { | | | | "Enable": true | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **AzureBlobStorage** | ``AZURE_BLOB_STORAGE_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "AzureBlobStorage": { | | | | "ConnectionString": "MUST BE DEFINED BY YOU", | | | | "ContainerName": "MUST BE DEFINED BY YOU" | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **AwsS3Storage** | ``AWS_S3_STORAGE_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "AwsS3Storage": { | | | | "BucketName": "MUST BE DEFINED BY YOU", | | | | "Region": "MUST BE DEFINED BY YOU" | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **GoogleCloudStorage** | ``GOOGLE_CLOUD_STORAGE_PLUGIN_ENABLED`` | .. code-block:: json | | | | | | | | { | | | | "GoogleCloudStorage": { | | | | "ServiceAccountFile": "MUST BE DEFINED BY YOU", | | | | "BucketName": "MUST BE DEFINED BY YOU" | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **OrthancExplorer2** | ``ORTHANC_EXPLORER_2_ENABLED`` | .. code-block:: json | | | Note: enabled by default | | | | | { | | | | "OrthancExplorer2": { | | | | "Enable": true, | | | | "IsDefaultOrthancUI": false | | | | } | | | | } | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **VolView** | ``VOLVIEW_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ | **Ohif** | ``OHIF_PLUGIN_ENABLED`` | | +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+ Under the hood -------------- The source code that is used to generate the image can be found `here <https://github.com/orthanc-server/orthanc-builder/blob/master/docker/orthanc/Dockerfile>`__. The Python script that is used at startup can be found `here <https://github.com/orthanc-server/orthanc-builder/blob/master/docker/orthanc/generateConfiguration.py>`__