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annotate Sphinx/source/users/docker.rst @ 995:5c8d2250b361
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| author | Alain Mazy <am@osimis.io> |
|---|---|
| date | Wed, 06 Dec 2023 09:12:28 +0100 |
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| 54 | 1 .. _docker: |
| 2 .. highlight:: bash | |
| 3 | |
| 4 | |
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5 jodogne/orthanc Docker images |
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6 ============================= |
| 54 | 7 |
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8 .. toctree:: |
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9 :hidden: |
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10 |
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11 docker-osimis.rst |
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13 |
| 54 | 14 .. contents:: |
| 15 :depth: 3 | |
| 16 | |
| 17 | |
| 18 Introduction | |
| 19 ------------ | |
| 20 | |
| 21 `Docker images <https://en.wikipedia.org/wiki/Docker_(software)>`__ | |
| 22 for the Orthanc core and its official plugins are freely available on | |
| 23 the `DockerHub platform <https://hub.docker.com/u/jodogne/>`__. The | |
| 24 source code of the corresponding Docker images is available on `GitHub | |
| 25 <https://github.com/jodogne/OrthancDocker>`__. | |
| 26 | |
| 229 | 27 **Note about Orthanc vs. Osimis Docker images:** |
| 28 | |
| 29 * The ``jodogne/orthanc`` and ``jodogne/orthanc-plugins`` Docker | |
| 30 images that are described on this page are always kept in sync with | |
| 31 the latest releases of the Orthanc project, with a basic | |
| 32 configuration system that is inherited from the Debian packages | |
| 759 | 33 (i.e. manual edition of the configuration files). These images are |
| 34 most useful to **software developers and researchers**. | |
| 229 | 35 |
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36 * Our commercial partner `Osimis <https://www.osimis.io>`__ also |
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37 `publishes separated Docker images |
| 759 | 38 <https://hub.docker.com/r/osimis/orthanc>`__. These |
| 39 ``osimis/orthanc`` images are used by the technical team of Osimis | |
| 40 in order to provide professional support to their customers, with a | |
| 41 configuration system that can be tuned through **environment | |
| 42 variables** (which is very handy if using ``docker-compose`` or | |
| 43 Kubernetes). These images are not necessarily always in sync with | |
| 44 the Orthanc project, but they also include the :ref:`plugins edited | |
| 45 by Osimis <plugins-osimis>`, notably the Osimis Web viewer (that is | |
| 46 much more advanced than the Orthanc Web viewer) and the advanced | |
| 47 authorization plugin. A :ref:`specific page <docker-osimis>` is | |
| 48 available to describe how these images should be used. These images | |
| 49 are targeted at **ops teams**. | |
| 229 | 50 |
| 51 **Note for CentOS users:** The Docker environment might be difficult to | |
| 54 | 52 configure on your platform. Hints are available on the `Orthanc Users |
| 53 discussion group | |
| 54 <https://groups.google.com/d/msg/orthanc-users/w-uPAknnRQc/-XhzBGSCAwAJ>`__. | |
| 55 | |
| 56 | |
| 57 Running the Orthanc core | |
| 58 ------------------------ | |
| 59 | |
| 60 The following command will start the core of Orthanc, with all the | |
| 61 plugins disabled:: | |
| 62 | |
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63 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc |
| 54 | 64 |
| 65 Once Orthanc is running, use Mozilla Firefox at URL | |
| 66 http://localhost:8042/ to interact with Orthanc. The default username | |
| 67 is ``orthanc`` and its password is ``orthanc``. | |
| 68 | |
| 69 The command above starts the mainline version of Orthanc, whose | |
| 69 | 70 development is in continuous progress. Do not forget to regularly |
| 71 update the Docker image to benefit from the latest features:: | |
| 72 | |
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73 $ docker pull jodogne/orthanc |
| 69 | 74 |
| 75 If more stability is required, you can select the official release of | |
| 76 Orthanc to be run:: | |
| 54 | 77 |
| 963 | 78 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.1 |
| 54 | 79 |
| 80 Passing additional command-line options (e.g. to make Orthanc verbose) | |
| 81 can be done as follows (note the ``/etc/orthanc`` option that is | |
| 82 required for Orthanc to find its configuration files):: | |
| 83 | |
| 963 | 84 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.1 /etc/orthanc --verbose |
| 54 | 85 |
| 86 | |
| 87 Usage, with plugins enabled | |
| 88 --------------------------- | |
| 89 | |
| 90 The following command will run the mainline version of the Orthanc | |
| 91 core, together with its :ref:`Web viewer <webviewer>`, its | |
| 92 :ref:`PostgreSQL support <postgresql>`, its :ref:`DICOMweb | |
| 93 implementation <dicomweb>`, and its :ref:`whole-slide imaging viewer | |
| 94 <wsi>`:: | |
| 95 | |
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96 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins |
| 54 | 97 |
| 365 | 98 Or you can also start a specific version of Orthanc for more stability:: |
| 99 | |
| 963 | 100 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins:1.12.1 |
| 365 | 101 |
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102 If you have an interest in the :ref:`Python plugin <python-plugin>`, |
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103 you can use the ``orthanc-python`` image. The latter image is a |
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104 heavier version of the ``orthanc-plugins`` image, as it embeds the |
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105 Python 3.7 interpreter. Here is how to start this image:: |
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106 |
| 365 | 107 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python |
| 963 | 108 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python:1.12.1 |
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109 |
| 54 | 110 |
| 111 Fine-tuning the configuration | |
| 112 ----------------------------- | |
| 113 | |
| 114 For security reasons, you should at least protect your instance of | |
| 115 Orthanc by changing this default user, in the ``RegisteredUsers`` | |
| 116 :ref:`configuration option <configuration>`. You will also probably | |
| 117 need to fine-tune other parameters, notably the list of the DICOM | |
| 118 modalities Orthanc knows about. | |
| 119 | |
| 120 You can generate a custom configuration file for Orthanc as follows:: | |
| 121 | |
| 963 | 122 $ docker run --rm --entrypoint=cat jodogne/orthanc:1.12.1 /etc/orthanc/orthanc.json > /tmp/orthanc.json |
| 54 | 123 |
| 124 Then, edit the just-generated file ``/tmp/orthanc.json`` and restart | |
| 125 Orthanc with your updated configuration:: | |
| 126 | |
| 963 | 127 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc:1.12.1 |
| 54 | 128 |
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129 *Remark:* These Docker images automatically set the environment |
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130 variable ``MALLOC_ARENA_MAX`` to ``5`` in order to :ref:`control |
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131 memory usage <scalability-memory>`. This default setting can be |
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132 overriden by providing the option ``-e MALLOC_ARENA_MAX=1`` when |
| 386 | 133 invoking ``docker run`` (the value ``0`` corresponds to the default |
| 134 value). | |
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135 |
| 54 | 136 |
| 382 | 137 .. _docker-compose: |
| 138 | |
| 139 Configuration management using Docker Compose | |
| 140 --------------------------------------------- | |
| 141 | |
| 142 Depending on the context, the `Docker Compose tool | |
| 143 <https://docs.docker.com/compose/>`__ might be easier to use than the | |
| 144 plain Docker tool, as it allows replacing long command lines as above, | |
| 145 by plain configuration files. The trick here is to provide the JSON | |
| 146 configuration files to Orthanc as `secrets | |
| 147 <https://docs.docker.com/compose/compose-file/#secrets>`__ (note that | |
| 148 the related option ``configs`` could in theory be better, | |
| 149 unfortunately it is only available to `Docker Swarm | |
| 150 <https://github.com/docker/compose/issues/5110>`__). | |
| 151 | |
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152 .. highlight:: yaml |
| 382 | 153 |
| 154 First create the ``docker-compose.yml`` file as follows (this one uses | |
| 155 the `YAML file format <https://en.wikipedia.org/wiki/YAML>`__):: | |
| 156 | |
| 157 version: '3.1' # Secrets are only available since this version of Docker Compose | |
| 158 services: | |
| 159 orthanc: | |
| 963 | 160 image: jodogne/orthanc-plugins:1.12.1 |
| 382 | 161 command: /run/secrets/ # Path to the configuration files (stored as secrets) |
| 162 ports: | |
| 402 | 163 - 4242:4242 |
| 382 | 164 - 8042:8042 |
| 165 secrets: | |
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166 - orthanc.json |
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167 environment: |
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168 - ORTHANC_NAME=HelloWorld |
| 382 | 169 secrets: |
| 170 orthanc.json: | |
| 171 file: orthanc.json | |
| 172 | |
| 173 .. highlight:: json | |
| 174 | |
| 175 Then, place the configuration file ``orthanc.json`` next to the | |
| 176 ``docker-compose.yml`` file. Here is a minimalist ``orthanc.json``:: | |
| 177 | |
| 178 { | |
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179 "Name" : "${ORTHANC_NAME} in Docker Compose", |
| 382 | 180 "RemoteAccessAllowed" : true |
| 181 } | |
| 182 | |
| 183 .. highlight:: bash | |
| 184 | |
| 185 This single configuration file should contain all the required | |
| 186 configuration options for Orthanc and all its plugins. The container | |
| 187 can then be started as follows:: | |
| 188 | |
| 189 $ docker-compose up | |
| 190 | |
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191 Note how the `environment variable |
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192 <https://docs.docker.com/compose/environment-variables/>`__ |
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193 ``ORTHANC_NAME`` has been used in order to easily adapt the |
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194 configuration of Orthanc. This results from the fact that Orthanc |
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195 injects :ref:`environment variables <orthanc-environment-variables>` |
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196 once reading the content of its configuration files (since Orthanc |
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197 1.5.0). |
| 382 | 198 |
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199 |
| 54 | 200 Making the Orthanc database persistent |
| 201 -------------------------------------- | |
| 202 | |
| 203 The filesystem of Docker containers is volatile (its content is | |
| 204 deleted once the container stops). You can make the Orthanc database | |
| 205 persistent by mapping the ``/var/lib/orthanc/db`` folder of the | |
| 206 container to some path in the filesystem of your Linux host, e.g.:: | |
| 207 | |
| 208 $ mkdir /tmp/orthanc-db | |
| 963 | 209 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.12.1 |
| 54 | 210 |
| 211 | |
| 212 Whole-slide imaging support | |
| 213 --------------------------- | |
| 214 | |
| 215 The ``orthanc-plugins`` image includes support for :ref:`microscopic | |
| 216 whole-slide imaging (WSI) <wsi>`. For instance, the following command | |
| 217 will start the WSI viewer plugin transparently together with Orthanc:: | |
| 218 | |
| 963 | 219 $ docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins:1.12.1 |
| 54 | 220 |
| 221 Note that we gave the name ``orthanc-wsi`` to this new Docker | |
| 222 container. Then, the Dicomizer command-line tool can be invoked as | |
| 223 follows:: | |
| 224 | |
| 963 | 225 $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.tif:/tmp/Source.tif:ro jodogne/orthanc-plugins:1.12.1 --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ /tmp/Source.tif |
| 54 | 226 |
| 227 This command needs a few explanations: | |
| 228 | |
| 229 * ``--link=orthanc-wsi:orthanc`` links the container running the | |
| 230 Dicomizer, to the Docker container running Orthanc that we started | |
| 231 just before. | |
| 232 * ``--entrypoint=OrthancWSIDicomizer`` specifies that the Dicomizer | |
| 233 must be run instead of the Orthanc server. | |
| 234 * ``-v /tmp/Source.tif:/tmp/Source.tif:ro`` maps the source image | |
| 235 ``/tmp/Source.tif`` on the host computer into the Orthanc container | |
| 236 as read-only file ``/tmp/Source.tif``. | |
| 237 * ``--orthanc=http://orthanc:8042/`` instructs the Dicomizer to push | |
| 238 images through the ``--link`` created above. | |
| 239 * ``--username=orthanc --password=orthanc`` correspond to the default | |
| 240 credentials of the ``orthanc-plugins`` image. | |
| 241 | |
| 242 Obviously, you are free to add all the options you wish (check out the | |
| 243 ``--help`` flag to list these options). In particular, the | |
| 244 ``--dataset`` option allows to specify DICOM tags, in the JSON file | |
| 245 format, so as to include them in the resulting DICOM series (the | |
| 246 option ``--sample-dataset`` prints a sample JSON file that has the | |
| 247 expected format). | |
| 248 | |
| 249 If you have a source image that is not a hierarchical TIFF, you must | |
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250 instruct the Dicomizer to use `OpenSlide <https://openslide.org/>`__ |
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251 to decode it by adding the ``--openslide`` option:: |
| 54 | 252 |
| 963 | 253 $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.svs:/tmp/Source.svs:ro jodogne/orthanc-plugins:1.12.1 --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ --openslide=libopenslide.so /tmp/Source.svs |
| 54 | 254 |
| 255 | |
| 256 PostgreSQL and Orthanc inside Docker | |
| 257 ------------------------------------ | |
| 258 | |
| 259 It is possible to run both Orthanc and PostgreSQL inside Docker. First, start the official PostgreSQL container:: | |
| 260 | |
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261 $ docker run --name some-postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=pgpassword --rm postgres |
| 54 | 262 |
| 263 Open another shell, and create a database to host the Orthanc database:: | |
| 264 | |
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265 $ docker run -it --link some-postgres:postgres --rm postgres sh -c 'echo "CREATE DATABASE orthanc;" | exec psql -h "$POSTGRES_PORT_5432_TCP_ADDR" -p "$POSTGRES_PORT_5432_TCP_PORT" -U postgres' |
| 54 | 266 |
| 267 You will have to type the password (cf. the environment variable | |
| 268 ``POSTGRES_PASSWORD`` above that it set to ``pgpassword``). Then, | |
| 269 retrieve the IP and the port of the PostgreSQL container, together | |
| 270 with the default Orthanc configuration file:: | |
| 271 | |
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272 $ docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres |
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273 $ docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres |
| 963 | 274 $ docker run --rm --entrypoint=cat jodogne/orthanc-plugins:1.12.1 /etc/orthanc/orthanc.json > /tmp/orthanc.json |
| 54 | 275 |
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276 .. highlight:: text |
| 54 | 277 |
| 278 Add the following section to ``/tmp/orthanc.json`` (adapting the | |
| 279 values Host and Port to what docker inspect said above):: | |
| 280 | |
| 281 "PostgreSQL" : { | |
| 282 "EnableIndex" : true, | |
| 283 "EnableStorage" : true, | |
| 284 "Host" : "172.17.0.38", | |
| 285 "Port" : 5432, | |
| 286 "Database" : "orthanc", | |
| 287 "Username" : "postgres", | |
| 288 "Password" : "pgpassword" | |
| 289 } | |
| 290 | |
| 291 .. highlight:: bash | |
| 292 | |
| 293 Finally, you can start Orthanc:: | |
| 294 | |
| 963 | 295 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins:1.12.1 |
| 54 | 296 |
| 297 | |
| 298 Debugging | |
| 299 --------- | |
| 300 | |
| 176 | 301 .. highlight:: text |
| 302 | |
| 54 | 303 For debugging purpose, you can start an interactive bash session as |
| 304 follows:: | |
| 305 | |
| 963 | 306 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc:1.12.1 |
| 307 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins:1.12.1 | |
| 175 | 308 |
| 176 | 309 For developers and power users, the images ``jodogne/orthanc-debug`` |
| 310 contain the Orthanc core compiled in debug mode (i.e. with runtime | |
| 311 assertions enabled, and including debugging symbols). A ``gdb`` | |
| 177 | 312 command-line session can be started as follows:: |
| 176 | 313 |
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314 $ docker run -i -t --rm --entrypoint=bash --network=host --cap-add=SYS_PTRACE -p 4242:4242 -p 8042:8042 jodogne/orthanc-debug |
| 176 | 315 # gdb --args Orthanc /etc/orthanc/ --verbose |
| 175 | 316 |
| 184 | 317 Exceptions can be automatically caught by launching ``gdb`` as follows:: |
| 318 | |
| 319 # gdb --ex 'catch t' --ex r --ex bt --args ./Orthanc /etc/orthanc/ --verbose | |
| 320 | |
| 176 | 321 Note that: |
| 322 | |
| 323 * The plugins are not available in this image yet. | |
| 324 | |
| 325 * The Orthanc source code can be found in folder ``/root/orthanc``. | |
| 326 | |
| 327 * The build artifacts can be found in folder ``/root/orthanc/Build``. | |
| 328 | |
| 329 * This command launches the mainline version. To start a released version, | |
| 963 | 330 use e.g. ``jodogne/orthanc-debug:1.12.1``. |