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annotate Sphinx/source/users/docker.rst @ 572:b78e8bf4d021
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Sat, 26 Dec 2020 10:59:40 +0100 |
| parents | 090cc988c35e |
| children | eaa6cdfa7ba6 |
| rev | line source |
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| 54 | 1 .. _docker: |
| 2 .. highlight:: bash | |
| 3 | |
| 4 | |
| 5 Orthanc for Docker | |
| 6 ================== | |
| 7 | |
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8 .. toctree:: |
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9 :hidden: |
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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 | |
| 33 (i.e. manual edition of the configuration files). | |
| 34 | |
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35 * Our commercial partner `Osimis <https://www.osimis.io>`__ also |
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36 `publishes separated Docker images |
| 393 | 37 <https://hub.docker.com/repository/docker/osimis/orthanc>`__. |
| 229 | 38 These ``osimis/orthanc`` images are used by the technical team of |
| 39 Osimis in order to provide professional support to their customers, | |
| 40 with a configuration system that can be tuned through environment | |
| 41 variables (which is very handy if using ``docker-compose``). These | |
| 42 images are not necessarily always in sync with the Orthanc project, | |
| 43 but they also include the :ref:`plugins edited by Osimis | |
| 44 <plugins-osimis>`, notably the Osimis Web viewer (that is much more | |
| 45 advanced than the Orthanc Web viewer) and the advanced authorization | |
| 396 | 46 plugin. A :ref:`specific page <docker-osimis>` is available to describe |
| 393 | 47 how these images should be used. |
| 229 | 48 |
| 49 **Note for CentOS users:** The Docker environment might be difficult to | |
| 54 | 50 configure on your platform. Hints are available on the `Orthanc Users |
| 51 discussion group | |
| 52 <https://groups.google.com/d/msg/orthanc-users/w-uPAknnRQc/-XhzBGSCAwAJ>`__. | |
| 53 | |
| 54 | |
| 55 Running the Orthanc core | |
| 56 ------------------------ | |
| 57 | |
| 58 The following command will start the core of Orthanc, with all the | |
| 59 plugins disabled:: | |
| 60 | |
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61 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc |
| 54 | 62 |
| 63 Once Orthanc is running, use Mozilla Firefox at URL | |
| 64 http://localhost:8042/ to interact with Orthanc. The default username | |
| 65 is ``orthanc`` and its password is ``orthanc``. | |
| 66 | |
| 67 The command above starts the mainline version of Orthanc, whose | |
| 69 | 68 development is in continuous progress. Do not forget to regularly |
| 69 update the Docker image to benefit from the latest features:: | |
| 70 | |
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71 $ docker pull jodogne/orthanc |
| 69 | 72 |
| 73 If more stability is required, you can select the official release of | |
| 74 Orthanc to be run:: | |
| 54 | 75 |
| 568 | 76 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.8.2 |
| 54 | 77 |
| 78 Passing additional command-line options (e.g. to make Orthanc verbose) | |
| 79 can be done as follows (note the ``/etc/orthanc`` option that is | |
| 80 required for Orthanc to find its configuration files):: | |
| 81 | |
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82 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc /etc/orthanc --verbose |
| 54 | 83 |
| 84 | |
| 85 Usage, with plugins enabled | |
| 86 --------------------------- | |
| 87 | |
| 88 The following command will run the mainline version of the Orthanc | |
| 89 core, together with its :ref:`Web viewer <webviewer>`, its | |
| 90 :ref:`PostgreSQL support <postgresql>`, its :ref:`DICOMweb | |
| 91 implementation <dicomweb>`, and its :ref:`whole-slide imaging viewer | |
| 92 <wsi>`:: | |
| 93 | |
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94 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins |
| 54 | 95 |
| 365 | 96 Or you can also start a specific version of Orthanc for more stability:: |
| 97 | |
| 568 | 98 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins:1.8.2 |
| 365 | 99 |
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100 If you have an interest in the :ref:`Python plugin <python-plugin>`, |
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101 you can use the ``orthanc-python`` image. The latter image is a |
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102 heavier version of the ``orthanc-plugins`` image, as it embeds the |
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103 Python 3.7 interpreter. Here is how to start this image:: |
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104 |
| 365 | 105 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python |
| 568 | 106 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python:1.8.2 |
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107 |
| 54 | 108 |
| 109 Fine-tuning the configuration | |
| 110 ----------------------------- | |
| 111 | |
| 112 For security reasons, you should at least protect your instance of | |
| 113 Orthanc by changing this default user, in the ``RegisteredUsers`` | |
| 114 :ref:`configuration option <configuration>`. You will also probably | |
| 115 need to fine-tune other parameters, notably the list of the DICOM | |
| 116 modalities Orthanc knows about. | |
| 117 | |
| 118 You can generate a custom configuration file for Orthanc as follows:: | |
| 119 | |
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120 $ docker run --rm --entrypoint=cat jodogne/orthanc /etc/orthanc/orthanc.json > /tmp/orthanc.json |
| 54 | 121 |
| 122 Then, edit the just-generated file ``/tmp/orthanc.json`` and restart | |
| 123 Orthanc with your updated configuration:: | |
| 124 | |
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125 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc |
| 54 | 126 |
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127 *Remark:* These Docker images automatically set the environment |
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128 variable ``MALLOC_ARENA_MAX`` to ``5`` in order to :ref:`control |
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129 memory usage <scalability-memory>`. This default setting can be |
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130 overriden by providing the option ``-e MALLOC_ARENA_MAX=1`` when |
| 386 | 131 invoking ``docker run`` (the value ``0`` corresponds to the default |
| 132 value). | |
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133 |
| 54 | 134 |
| 382 | 135 .. _docker-compose: |
| 136 | |
| 137 Configuration management using Docker Compose | |
| 138 --------------------------------------------- | |
| 139 | |
| 140 Depending on the context, the `Docker Compose tool | |
| 141 <https://docs.docker.com/compose/>`__ might be easier to use than the | |
| 142 plain Docker tool, as it allows replacing long command lines as above, | |
| 143 by plain configuration files. The trick here is to provide the JSON | |
| 144 configuration files to Orthanc as `secrets | |
| 145 <https://docs.docker.com/compose/compose-file/#secrets>`__ (note that | |
| 146 the related option ``configs`` could in theory be better, | |
| 147 unfortunately it is only available to `Docker Swarm | |
| 148 <https://github.com/docker/compose/issues/5110>`__). | |
| 149 | |
| 150 .. highlight:: yml | |
| 151 | |
| 152 First create the ``docker-compose.yml`` file as follows (this one uses | |
| 153 the `YAML file format <https://en.wikipedia.org/wiki/YAML>`__):: | |
| 154 | |
| 155 version: '3.1' # Secrets are only available since this version of Docker Compose | |
| 156 services: | |
| 157 orthanc: | |
| 568 | 158 image: jodogne/orthanc-plugins:1.8.2 |
| 382 | 159 command: /run/secrets/ # Path to the configuration files (stored as secrets) |
| 160 ports: | |
| 402 | 161 - 4242:4242 |
| 382 | 162 - 8042:8042 |
| 163 secrets: | |
| 164 - orthanc.json | |
| 165 secrets: | |
| 166 orthanc.json: | |
| 167 file: orthanc.json | |
| 168 | |
| 169 .. highlight:: json | |
| 170 | |
| 171 Then, place the configuration file ``orthanc.json`` next to the | |
| 172 ``docker-compose.yml`` file. Here is a minimalist ``orthanc.json``:: | |
| 173 | |
| 174 { | |
| 175 "Name" : "Orthanc in Docker", | |
| 176 "RemoteAccessAllowed" : true | |
| 177 } | |
| 178 | |
| 179 .. highlight:: bash | |
| 180 | |
| 181 This single configuration file should contain all the required | |
| 182 configuration options for Orthanc and all its plugins. The container | |
| 183 can then be started as follows:: | |
| 184 | |
| 185 $ docker-compose up | |
| 186 | |
| 187 | |
| 54 | 188 Making the Orthanc database persistent |
| 189 -------------------------------------- | |
| 190 | |
| 191 The filesystem of Docker containers is volatile (its content is | |
| 192 deleted once the container stops). You can make the Orthanc database | |
| 193 persistent by mapping the ``/var/lib/orthanc/db`` folder of the | |
| 194 container to some path in the filesystem of your Linux host, e.g.:: | |
| 195 | |
| 196 $ mkdir /tmp/orthanc-db | |
| 568 | 197 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.8.2 |
| 54 | 198 |
| 199 | |
| 200 Whole-slide imaging support | |
| 201 --------------------------- | |
| 202 | |
| 203 The ``orthanc-plugins`` image includes support for :ref:`microscopic | |
| 204 whole-slide imaging (WSI) <wsi>`. For instance, the following command | |
| 205 will start the WSI viewer plugin transparently together with Orthanc:: | |
| 206 | |
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207 $ docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins |
| 54 | 208 |
| 209 Note that we gave the name ``orthanc-wsi`` to this new Docker | |
| 210 container. Then, the Dicomizer command-line tool can be invoked as | |
| 211 follows:: | |
| 212 | |
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213 $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.tif:/tmp/Source.tif:ro jodogne/orthanc-plugins --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ /tmp/Source.tif |
| 54 | 214 |
| 215 This command needs a few explanations: | |
| 216 | |
| 217 * ``--link=orthanc-wsi:orthanc`` links the container running the | |
| 218 Dicomizer, to the Docker container running Orthanc that we started | |
| 219 just before. | |
| 220 * ``--entrypoint=OrthancWSIDicomizer`` specifies that the Dicomizer | |
| 221 must be run instead of the Orthanc server. | |
| 222 * ``-v /tmp/Source.tif:/tmp/Source.tif:ro`` maps the source image | |
| 223 ``/tmp/Source.tif`` on the host computer into the Orthanc container | |
| 224 as read-only file ``/tmp/Source.tif``. | |
| 225 * ``--orthanc=http://orthanc:8042/`` instructs the Dicomizer to push | |
| 226 images through the ``--link`` created above. | |
| 227 * ``--username=orthanc --password=orthanc`` correspond to the default | |
| 228 credentials of the ``orthanc-plugins`` image. | |
| 229 | |
| 230 Obviously, you are free to add all the options you wish (check out the | |
| 231 ``--help`` flag to list these options). In particular, the | |
| 232 ``--dataset`` option allows to specify DICOM tags, in the JSON file | |
| 233 format, so as to include them in the resulting DICOM series (the | |
| 234 option ``--sample-dataset`` prints a sample JSON file that has the | |
| 235 expected format). | |
| 236 | |
| 237 If you have a source image that is not a hierarchical TIFF, you must | |
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238 instruct the Dicomizer to use `OpenSlide <https://openslide.org/>`__ |
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239 to decode it by adding the ``--openslide`` option:: |
| 54 | 240 |
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241 $ docker run -t -i --rm --link=orthanc-wsi:orthanc --entrypoint=OrthancWSIDicomizer -v /tmp/Source.svs:/tmp/Source.svs:ro jodogne/orthanc-plugins --username=orthanc --password=orthanc --orthanc=http://orthanc:8042/ --openslide=libopenslide.so /tmp/Source.svs |
| 54 | 242 |
| 243 | |
| 244 PostgreSQL and Orthanc inside Docker | |
| 245 ------------------------------------ | |
| 246 | |
| 247 It is possible to run both Orthanc and PostgreSQL inside Docker. First, start the official PostgreSQL container:: | |
| 248 | |
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249 $ docker run --name some-postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=pgpassword --rm postgres |
| 54 | 250 |
| 251 Open another shell, and create a database to host the Orthanc database:: | |
| 252 | |
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253 $ 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 | 254 |
| 255 You will have to type the password (cf. the environment variable | |
| 256 ``POSTGRES_PASSWORD`` above that it set to ``pgpassword``). Then, | |
| 257 retrieve the IP and the port of the PostgreSQL container, together | |
| 258 with the default Orthanc configuration file:: | |
| 259 | |
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260 $ docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres |
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261 $ docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres |
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262 $ docker run --rm --entrypoint=cat jodogne/orthanc-plugins /etc/orthanc/orthanc.json > /tmp/orthanc.json |
| 54 | 263 |
| 264 .. highlight:: json | |
| 265 | |
| 266 Add the following section to ``/tmp/orthanc.json`` (adapting the | |
| 267 values Host and Port to what docker inspect said above):: | |
| 268 | |
| 269 "PostgreSQL" : { | |
| 270 "EnableIndex" : true, | |
| 271 "EnableStorage" : true, | |
| 272 "Host" : "172.17.0.38", | |
| 273 "Port" : 5432, | |
| 274 "Database" : "orthanc", | |
| 275 "Username" : "postgres", | |
| 276 "Password" : "pgpassword" | |
| 277 } | |
| 278 | |
| 279 .. highlight:: bash | |
| 280 | |
| 281 Finally, you can start Orthanc:: | |
| 282 | |
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283 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins |
| 54 | 284 |
| 285 | |
| 286 Debugging | |
| 287 --------- | |
| 288 | |
| 176 | 289 .. highlight:: text |
| 290 | |
| 54 | 291 For debugging purpose, you can start an interactive bash session as |
| 292 follows:: | |
| 293 | |
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294 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc |
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295 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins |
| 175 | 296 |
| 176 | 297 For developers and power users, the images ``jodogne/orthanc-debug`` |
| 298 contain the Orthanc core compiled in debug mode (i.e. with runtime | |
| 299 assertions enabled, and including debugging symbols). A ``gdb`` | |
| 177 | 300 command-line session can be started as follows:: |
| 176 | 301 |
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302 $ docker run -i -t --rm --entrypoint=bash --network=host --cap-add=SYS_PTRACE -p 4242:4242 -p 8042:8042 jodogne/orthanc-debug |
| 176 | 303 # gdb --args Orthanc /etc/orthanc/ --verbose |
| 175 | 304 |
| 184 | 305 Exceptions can be automatically caught by launching ``gdb`` as follows:: |
| 306 | |
| 307 # gdb --ex 'catch t' --ex r --ex bt --args ./Orthanc /etc/orthanc/ --verbose | |
| 308 | |
| 176 | 309 Note that: |
| 310 | |
| 311 * The plugins are not available in this image yet. | |
| 312 | |
| 313 * The Orthanc source code can be found in folder ``/root/orthanc``. | |
| 314 | |
| 315 * The build artifacts can be found in folder ``/root/orthanc/Build``. | |
| 316 | |
| 317 * This command launches the mainline version. To start a released version, | |
| 568 | 318 use e.g. ``jodogne/orthanc-debug:1.8.2``. |