Mercurial > hg > orthanc-book
annotate Sphinx/source/users/docker.rst @ 1102:4f3709b36f8a
clarifying docker
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
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| date | Fri, 16 Aug 2024 10:50:55 +0200 |
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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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11 docker-orthancteam.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 | |
| 1102 | 27 |
| 28 .. _docker-jodogne-vs-orthanc-team: | |
| 29 | |
| 30 Orthanc vs. Orthanc Team Docker images | |
| 31 -------------------------------------- | |
| 32 | |
| 33 Two different flavors of Docker images for Orthanc are available: | |
| 229 | 34 |
| 35 * The ``jodogne/orthanc`` and ``jodogne/orthanc-plugins`` Docker | |
| 36 images that are described on this page are always kept in sync with | |
| 37 the latest releases of the Orthanc project, with a basic | |
| 38 configuration system that is inherited from the Debian packages | |
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39 (i.e., manual edition of the configuration files). This is also |
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40 where the new experimental features from `Sébastien Jodogne's |
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41 research team at UCLouvain <https://orthanc.uclouvain.be/>`__ are |
| 1102 | 42 initially released. The binaries used in these images correspond to |
| 43 the Linux Standard Base binaries. The default user interface is the | |
| 44 built-in **Orthanc Explorer**. These images are most useful to | |
| 45 **software developers and researchers**. | |
| 229 | 46 |
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47 * Our commercial partner `Orthanc Team <https://orthanc.team/>`__ also |
| 1102 | 48 `publishes separate Docker images |
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49 <https://hub.docker.com/r/orthancteam/orthanc>`__. These |
| 1102 | 50 ``orthancteam/orthanc`` images are used by the technical team of the |
| 51 Orthanc Team company in order to provide professional support to | |
| 52 their customers, with a configuration system that can be tuned using | |
| 53 **environment variables** (which is very handy if using Docker | |
| 54 Compose or Kubernetes). The binaries used in these images are | |
| 55 compiled from scratch. The default user interface is the **Orthanc | |
| 56 Explorer 2** :ref:`plugin <orthanc-explorer-2>`. A :ref:`specific | |
| 57 page <docker-orthancteam>` is available to describe how these images | |
| 58 should be used. These images are targeted at **ops teams**. | |
| 229 | 59 |
| 60 **Note for CentOS users:** The Docker environment might be difficult to | |
| 54 | 61 configure on your platform. Hints are available on the `Orthanc Users |
| 62 discussion group | |
| 63 <https://groups.google.com/d/msg/orthanc-users/w-uPAknnRQc/-XhzBGSCAwAJ>`__. | |
| 64 | |
| 65 | |
| 66 Running the Orthanc core | |
| 67 ------------------------ | |
| 68 | |
| 69 The following command will start the core of Orthanc, with all the | |
| 70 plugins disabled:: | |
| 71 | |
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72 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc |
| 54 | 73 |
| 74 Once Orthanc is running, use Mozilla Firefox at URL | |
| 75 http://localhost:8042/ to interact with Orthanc. The default username | |
| 76 is ``orthanc`` and its password is ``orthanc``. | |
| 77 | |
| 78 The command above starts the mainline version of Orthanc, whose | |
| 69 | 79 development is in continuous progress. Do not forget to regularly |
| 80 update the Docker image to benefit from the latest features:: | |
| 81 | |
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82 $ docker pull jodogne/orthanc |
| 69 | 83 |
| 84 If more stability is required, you can select the official release of | |
| 85 Orthanc to be run:: | |
| 54 | 86 |
| 1075 | 87 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.4 |
| 54 | 88 |
| 89 Passing additional command-line options (e.g. to make Orthanc verbose) | |
| 90 can be done as follows (note the ``/etc/orthanc`` option that is | |
| 91 required for Orthanc to find its configuration files):: | |
| 92 | |
| 1075 | 93 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.12.4 /etc/orthanc --verbose |
| 54 | 94 |
| 95 | |
| 96 Usage, with plugins enabled | |
| 97 --------------------------- | |
| 98 | |
| 99 The following command will run the mainline version of the Orthanc | |
| 100 core, together with its :ref:`Web viewer <webviewer>`, its | |
| 101 :ref:`PostgreSQL support <postgresql>`, its :ref:`DICOMweb | |
| 102 implementation <dicomweb>`, and its :ref:`whole-slide imaging viewer | |
| 103 <wsi>`:: | |
| 104 | |
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105 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins |
| 54 | 106 |
| 365 | 107 Or you can also start a specific version of Orthanc for more stability:: |
| 108 | |
| 1075 | 109 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins:1.12.4 |
| 365 | 110 |
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111 If you have an interest in the :ref:`Python plugin <python-plugin>`, |
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112 you can use the ``orthanc-python`` image. The latter image is a |
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113 heavier version of the ``orthanc-plugins`` image, as it embeds the |
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114 Python 3.7 interpreter. Here is how to start this image:: |
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115 |
| 365 | 116 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python |
| 1075 | 117 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python:1.12.4 |
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118 |
| 54 | 119 |
| 120 Fine-tuning the configuration | |
| 121 ----------------------------- | |
| 122 | |
| 123 For security reasons, you should at least protect your instance of | |
| 124 Orthanc by changing this default user, in the ``RegisteredUsers`` | |
| 125 :ref:`configuration option <configuration>`. You will also probably | |
| 126 need to fine-tune other parameters, notably the list of the DICOM | |
| 127 modalities Orthanc knows about. | |
| 128 | |
| 129 You can generate a custom configuration file for Orthanc as follows:: | |
| 130 | |
| 1075 | 131 $ docker run --rm --entrypoint=cat jodogne/orthanc:1.12.4 /etc/orthanc/orthanc.json > /tmp/orthanc.json |
| 54 | 132 |
| 133 Then, edit the just-generated file ``/tmp/orthanc.json`` and restart | |
| 134 Orthanc with your updated configuration:: | |
| 135 | |
| 1075 | 136 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc:1.12.4 |
| 54 | 137 |
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138 *Remark:* These Docker images automatically set the environment |
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139 variable ``MALLOC_ARENA_MAX`` to ``5`` in order to :ref:`control |
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140 memory usage <scalability-memory>`. This default setting can be |
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141 overriden by providing the option ``-e MALLOC_ARENA_MAX=1`` when |
| 386 | 142 invoking ``docker run`` (the value ``0`` corresponds to the default |
| 143 value). | |
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144 |
| 54 | 145 |
| 382 | 146 .. _docker-compose: |
| 147 | |
| 148 Configuration management using Docker Compose | |
| 149 --------------------------------------------- | |
| 150 | |
| 151 Depending on the context, the `Docker Compose tool | |
| 152 <https://docs.docker.com/compose/>`__ might be easier to use than the | |
| 153 plain Docker tool, as it allows replacing long command lines as above, | |
| 154 by plain configuration files. The trick here is to provide the JSON | |
| 155 configuration files to Orthanc as `secrets | |
| 156 <https://docs.docker.com/compose/compose-file/#secrets>`__ (note that | |
| 157 the related option ``configs`` could in theory be better, | |
| 158 unfortunately it is only available to `Docker Swarm | |
| 159 <https://github.com/docker/compose/issues/5110>`__). | |
| 160 | |
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161 .. highlight:: yaml |
| 382 | 162 |
| 163 First create the ``docker-compose.yml`` file as follows (this one uses | |
| 164 the `YAML file format <https://en.wikipedia.org/wiki/YAML>`__):: | |
| 165 | |
| 166 version: '3.1' # Secrets are only available since this version of Docker Compose | |
| 167 services: | |
| 168 orthanc: | |
| 1075 | 169 image: jodogne/orthanc-plugins:1.12.4 |
| 382 | 170 command: /run/secrets/ # Path to the configuration files (stored as secrets) |
| 171 ports: | |
| 402 | 172 - 4242:4242 |
| 382 | 173 - 8042:8042 |
| 174 secrets: | |
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175 - orthanc.json |
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176 environment: |
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177 - ORTHANC_NAME=HelloWorld |
| 382 | 178 secrets: |
| 179 orthanc.json: | |
| 180 file: orthanc.json | |
| 181 | |
| 182 .. highlight:: json | |
| 183 | |
| 184 Then, place the configuration file ``orthanc.json`` next to the | |
| 185 ``docker-compose.yml`` file. Here is a minimalist ``orthanc.json``:: | |
| 186 | |
| 187 { | |
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188 "Name" : "${ORTHANC_NAME} in Docker Compose", |
| 382 | 189 "RemoteAccessAllowed" : true |
| 190 } | |
| 191 | |
| 192 .. highlight:: bash | |
| 193 | |
| 194 This single configuration file should contain all the required | |
| 195 configuration options for Orthanc and all its plugins. The container | |
| 196 can then be started as follows:: | |
| 197 | |
| 198 $ docker-compose up | |
| 199 | |
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200 Note how the `environment variable |
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201 <https://docs.docker.com/compose/environment-variables/>`__ |
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202 ``ORTHANC_NAME`` has been used in order to easily adapt the |
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203 configuration of Orthanc. This results from the fact that Orthanc |
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204 injects :ref:`environment variables <orthanc-environment-variables>` |
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205 once reading the content of its configuration files (since Orthanc |
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206 1.5.0). |
| 382 | 207 |
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208 |
| 54 | 209 Making the Orthanc database persistent |
| 210 -------------------------------------- | |
| 211 | |
| 212 The filesystem of Docker containers is volatile (its content is | |
| 213 deleted once the container stops). You can make the Orthanc database | |
| 214 persistent by mapping the ``/var/lib/orthanc/db`` folder of the | |
| 215 container to some path in the filesystem of your Linux host, e.g.:: | |
| 216 | |
| 217 $ mkdir /tmp/orthanc-db | |
| 1075 | 218 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.12.4 |
| 54 | 219 |
| 220 | |
| 221 Whole-slide imaging support | |
| 222 --------------------------- | |
| 223 | |
| 224 The ``orthanc-plugins`` image includes support for :ref:`microscopic | |
| 225 whole-slide imaging (WSI) <wsi>`. For instance, the following command | |
| 226 will start the WSI viewer plugin transparently together with Orthanc:: | |
| 227 | |
| 1075 | 228 $ docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins:1.12.4 |
| 54 | 229 |
| 230 Note that we gave the name ``orthanc-wsi`` to this new Docker | |
| 231 container. Then, the Dicomizer command-line tool can be invoked as | |
| 232 follows:: | |
| 233 | |
| 1075 | 234 $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.tif:/tmp/Source.tif:ro jodogne/orthanc-plugins:1.12.4 --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ /tmp/Source.tif |
| 54 | 235 |
| 236 This command needs a few explanations: | |
| 237 | |
| 238 * ``--link=orthanc-wsi:orthanc`` links the container running the | |
| 239 Dicomizer, to the Docker container running Orthanc that we started | |
| 240 just before. | |
| 241 * ``--entrypoint=OrthancWSIDicomizer`` specifies that the Dicomizer | |
| 242 must be run instead of the Orthanc server. | |
| 243 * ``-v /tmp/Source.tif:/tmp/Source.tif:ro`` maps the source image | |
| 244 ``/tmp/Source.tif`` on the host computer into the Orthanc container | |
| 245 as read-only file ``/tmp/Source.tif``. | |
| 246 * ``--orthanc=http://orthanc:8042/`` instructs the Dicomizer to push | |
| 247 images through the ``--link`` created above. | |
| 248 * ``--username=orthanc --password=orthanc`` correspond to the default | |
| 249 credentials of the ``orthanc-plugins`` image. | |
| 250 | |
| 251 Obviously, you are free to add all the options you wish (check out the | |
| 252 ``--help`` flag to list these options). In particular, the | |
| 253 ``--dataset`` option allows to specify DICOM tags, in the JSON file | |
| 254 format, so as to include them in the resulting DICOM series (the | |
| 255 option ``--sample-dataset`` prints a sample JSON file that has the | |
| 256 expected format). | |
| 257 | |
| 258 If you have a source image that is not a hierarchical TIFF, you must | |
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259 instruct the Dicomizer to use `OpenSlide <https://openslide.org/>`__ |
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260 to decode it by adding the ``--openslide`` option:: |
| 54 | 261 |
| 1075 | 262 $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.svs:/tmp/Source.svs:ro jodogne/orthanc-plugins:1.12.4 --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ --openslide=libopenslide.so /tmp/Source.svs |
| 54 | 263 |
| 264 | |
| 265 PostgreSQL and Orthanc inside Docker | |
| 266 ------------------------------------ | |
| 267 | |
| 268 It is possible to run both Orthanc and PostgreSQL inside Docker. First, start the official PostgreSQL container:: | |
| 269 | |
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270 $ docker run --name some-postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=pgpassword --rm postgres |
| 54 | 271 |
| 272 Open another shell, and create a database to host the Orthanc database:: | |
| 273 | |
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274 $ 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 | 275 |
| 276 You will have to type the password (cf. the environment variable | |
| 277 ``POSTGRES_PASSWORD`` above that it set to ``pgpassword``). Then, | |
| 278 retrieve the IP and the port of the PostgreSQL container, together | |
| 279 with the default Orthanc configuration file:: | |
| 280 | |
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281 $ docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres |
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282 $ docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres |
| 1075 | 283 $ docker run --rm --entrypoint=cat jodogne/orthanc-plugins:1.12.4 /etc/orthanc/orthanc.json > /tmp/orthanc.json |
| 54 | 284 |
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285 .. highlight:: text |
| 54 | 286 |
| 287 Add the following section to ``/tmp/orthanc.json`` (adapting the | |
| 288 values Host and Port to what docker inspect said above):: | |
| 289 | |
| 290 "PostgreSQL" : { | |
| 291 "EnableIndex" : true, | |
| 292 "EnableStorage" : true, | |
| 293 "Host" : "172.17.0.38", | |
| 294 "Port" : 5432, | |
| 295 "Database" : "orthanc", | |
| 296 "Username" : "postgres", | |
| 297 "Password" : "pgpassword" | |
| 298 } | |
| 299 | |
| 300 .. highlight:: bash | |
| 301 | |
| 302 Finally, you can start Orthanc:: | |
| 303 | |
| 1075 | 304 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins:1.12.4 |
| 54 | 305 |
| 306 | |
| 307 Debugging | |
| 308 --------- | |
| 309 | |
| 176 | 310 .. highlight:: text |
| 311 | |
| 54 | 312 For debugging purpose, you can start an interactive bash session as |
| 313 follows:: | |
| 314 | |
| 1075 | 315 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc:1.12.4 |
| 316 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins:1.12.4 |