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annotate Sphinx/source/users/docker.rst @ 363:9c28eeab2db6
removed sudo from docker
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 31 Mar 2020 17:27:55 +0200 |
| parents | 011b01ccf52d |
| children | 234de55ed125 |
| rev | line source |
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| 54 | 1 .. _docker: |
| 2 .. highlight:: bash | |
| 3 | |
| 4 | |
| 5 Orthanc for Docker | |
| 6 ================== | |
| 7 | |
| 8 .. contents:: | |
| 9 :depth: 3 | |
| 10 | |
| 11 | |
| 12 Introduction | |
| 13 ------------ | |
| 14 | |
| 15 `Docker images <https://en.wikipedia.org/wiki/Docker_(software)>`__ | |
| 16 for the Orthanc core and its official plugins are freely available on | |
| 17 the `DockerHub platform <https://hub.docker.com/u/jodogne/>`__. The | |
| 18 source code of the corresponding Docker images is available on `GitHub | |
| 19 <https://github.com/jodogne/OrthancDocker>`__. | |
| 20 | |
| 229 | 21 **Note about Orthanc vs. Osimis Docker images:** |
| 22 | |
| 23 * The ``jodogne/orthanc`` and ``jodogne/orthanc-plugins`` Docker | |
| 24 images that are described on this page are always kept in sync with | |
| 25 the latest releases of the Orthanc project, with a basic | |
| 26 configuration system that is inherited from the Debian packages | |
| 27 (i.e. manual edition of the configuration files). | |
| 28 | |
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29 * Our commercial partner `Osimis <https://www.osimis.io>`__ also |
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30 `publishes separated Docker images |
| 229 | 31 <https://osimis.atlassian.net/wiki/spaces/OKB/pages/26738689/How+to+use+osimis+orthanc+Docker+images>`__. |
| 32 These ``osimis/orthanc`` images are used by the technical team of | |
| 33 Osimis in order to provide professional support to their customers, | |
| 34 with a configuration system that can be tuned through environment | |
| 35 variables (which is very handy if using ``docker-compose``). These | |
| 36 images are not necessarily always in sync with the Orthanc project, | |
| 37 but they also include the :ref:`plugins edited by Osimis | |
| 38 <plugins-osimis>`, notably the Osimis Web viewer (that is much more | |
| 39 advanced than the Orthanc Web viewer) and the advanced authorization | |
| 40 plugin. | |
| 41 | |
| 42 **Note for CentOS users:** The Docker environment might be difficult to | |
| 54 | 43 configure on your platform. Hints are available on the `Orthanc Users |
| 44 discussion group | |
| 45 <https://groups.google.com/d/msg/orthanc-users/w-uPAknnRQc/-XhzBGSCAwAJ>`__. | |
| 46 | |
| 47 | |
| 48 Running the Orthanc core | |
| 49 ------------------------ | |
| 50 | |
| 51 The following command will start the core of Orthanc, with all the | |
| 52 plugins disabled:: | |
| 53 | |
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54 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc |
| 54 | 55 |
| 56 Once Orthanc is running, use Mozilla Firefox at URL | |
| 57 http://localhost:8042/ to interact with Orthanc. The default username | |
| 58 is ``orthanc`` and its password is ``orthanc``. | |
| 59 | |
| 60 The command above starts the mainline version of Orthanc, whose | |
| 69 | 61 development is in continuous progress. Do not forget to regularly |
| 62 update the Docker image to benefit from the latest features:: | |
| 63 | |
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64 $ docker pull jodogne/orthanc |
| 69 | 65 |
| 66 If more stability is required, you can select the official release of | |
| 67 Orthanc to be run:: | |
| 54 | 68 |
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69 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.6.0 |
| 54 | 70 |
| 71 Passing additional command-line options (e.g. to make Orthanc verbose) | |
| 72 can be done as follows (note the ``/etc/orthanc`` option that is | |
| 73 required for Orthanc to find its configuration files):: | |
| 74 | |
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75 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc /etc/orthanc --verbose |
| 54 | 76 |
| 77 | |
| 78 Usage, with plugins enabled | |
| 79 --------------------------- | |
| 80 | |
| 81 The following command will run the mainline version of the Orthanc | |
| 82 core, together with its :ref:`Web viewer <webviewer>`, its | |
| 83 :ref:`PostgreSQL support <postgresql>`, its :ref:`DICOMweb | |
| 84 implementation <dicomweb>`, and its :ref:`whole-slide imaging viewer | |
| 85 <wsi>`:: | |
| 86 | |
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87 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins |
| 54 | 88 |
| 89 | |
| 90 Fine-tuning the configuration | |
| 91 ----------------------------- | |
| 92 | |
| 93 For security reasons, you should at least protect your instance of | |
| 94 Orthanc by changing this default user, in the ``RegisteredUsers`` | |
| 95 :ref:`configuration option <configuration>`. You will also probably | |
| 96 need to fine-tune other parameters, notably the list of the DICOM | |
| 97 modalities Orthanc knows about. | |
| 98 | |
| 99 You can generate a custom configuration file for Orthanc as follows:: | |
| 100 | |
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101 $ docker run --rm --entrypoint=cat jodogne/orthanc /etc/orthanc/orthanc.json > /tmp/orthanc.json |
| 54 | 102 |
| 103 Then, edit the just-generated file ``/tmp/orthanc.json`` and restart | |
| 104 Orthanc with your updated configuration:: | |
| 105 | |
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106 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc |
| 54 | 107 |
| 108 | |
| 109 Making the Orthanc database persistent | |
| 110 -------------------------------------- | |
| 111 | |
| 112 The filesystem of Docker containers is volatile (its content is | |
| 113 deleted once the container stops). You can make the Orthanc database | |
| 114 persistent by mapping the ``/var/lib/orthanc/db`` folder of the | |
| 115 container to some path in the filesystem of your Linux host, e.g.:: | |
| 116 | |
| 117 $ mkdir /tmp/orthanc-db | |
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118 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.6.0 |
| 54 | 119 |
| 120 | |
| 121 Whole-slide imaging support | |
| 122 --------------------------- | |
| 123 | |
| 124 The ``orthanc-plugins`` image includes support for :ref:`microscopic | |
| 125 whole-slide imaging (WSI) <wsi>`. For instance, the following command | |
| 126 will start the WSI viewer plugin transparently together with Orthanc:: | |
| 127 | |
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128 $ docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins |
| 54 | 129 |
| 130 Note that we gave the name ``orthanc-wsi`` to this new Docker | |
| 131 container. Then, the Dicomizer command-line tool can be invoked as | |
| 132 follows:: | |
| 133 | |
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134 $ 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 | 135 |
| 136 This command needs a few explanations: | |
| 137 | |
| 138 * ``--link=orthanc-wsi:orthanc`` links the container running the | |
| 139 Dicomizer, to the Docker container running Orthanc that we started | |
| 140 just before. | |
| 141 * ``--entrypoint=OrthancWSIDicomizer`` specifies that the Dicomizer | |
| 142 must be run instead of the Orthanc server. | |
| 143 * ``-v /tmp/Source.tif:/tmp/Source.tif:ro`` maps the source image | |
| 144 ``/tmp/Source.tif`` on the host computer into the Orthanc container | |
| 145 as read-only file ``/tmp/Source.tif``. | |
| 146 * ``--orthanc=http://orthanc:8042/`` instructs the Dicomizer to push | |
| 147 images through the ``--link`` created above. | |
| 148 * ``--username=orthanc --password=orthanc`` correspond to the default | |
| 149 credentials of the ``orthanc-plugins`` image. | |
| 150 | |
| 151 Obviously, you are free to add all the options you wish (check out the | |
| 152 ``--help`` flag to list these options). In particular, the | |
| 153 ``--dataset`` option allows to specify DICOM tags, in the JSON file | |
| 154 format, so as to include them in the resulting DICOM series (the | |
| 155 option ``--sample-dataset`` prints a sample JSON file that has the | |
| 156 expected format). | |
| 157 | |
| 158 If you have a source image that is not a hierarchical TIFF, you must | |
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159 instruct the Dicomizer to use `OpenSlide <https://openslide.org/>`__ |
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160 to decode it by adding the ``--openslide`` option:: |
| 54 | 161 |
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162 $ 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 | 163 |
| 164 | |
| 165 PostgreSQL and Orthanc inside Docker | |
| 166 ------------------------------------ | |
| 167 | |
| 168 It is possible to run both Orthanc and PostgreSQL inside Docker. First, start the official PostgreSQL container:: | |
| 169 | |
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170 $ docker run --name some-postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=pgpassword --rm postgres |
| 54 | 171 |
| 172 Open another shell, and create a database to host the Orthanc database:: | |
| 173 | |
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174 $ 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 | 175 |
| 176 You will have to type the password (cf. the environment variable | |
| 177 ``POSTGRES_PASSWORD`` above that it set to ``pgpassword``). Then, | |
| 178 retrieve the IP and the port of the PostgreSQL container, together | |
| 179 with the default Orthanc configuration file:: | |
| 180 | |
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181 $ docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres |
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182 $ docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres |
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183 $ docker run --rm --entrypoint=cat jodogne/orthanc-plugins /etc/orthanc/orthanc.json > /tmp/orthanc.json |
| 54 | 184 |
| 185 .. highlight:: json | |
| 186 | |
| 187 Add the following section to ``/tmp/orthanc.json`` (adapting the | |
| 188 values Host and Port to what docker inspect said above):: | |
| 189 | |
| 190 "PostgreSQL" : { | |
| 191 "EnableIndex" : true, | |
| 192 "EnableStorage" : true, | |
| 193 "Host" : "172.17.0.38", | |
| 194 "Port" : 5432, | |
| 195 "Database" : "orthanc", | |
| 196 "Username" : "postgres", | |
| 197 "Password" : "pgpassword" | |
| 198 } | |
| 199 | |
| 200 .. highlight:: bash | |
| 201 | |
| 202 Finally, you can start Orthanc:: | |
| 203 | |
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204 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins |
| 54 | 205 |
| 206 | |
| 207 Debugging | |
| 208 --------- | |
| 209 | |
| 176 | 210 .. highlight:: text |
| 211 | |
| 54 | 212 For debugging purpose, you can start an interactive bash session as |
| 213 follows:: | |
| 214 | |
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215 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc |
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216 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins |
| 175 | 217 |
| 176 | 218 For developers and power users, the images ``jodogne/orthanc-debug`` |
| 219 contain the Orthanc core compiled in debug mode (i.e. with runtime | |
| 220 assertions enabled, and including debugging symbols). A ``gdb`` | |
| 177 | 221 command-line session can be started as follows:: |
| 176 | 222 |
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223 $ docker run -i -t --rm --entrypoint=bash --network=host --cap-add=SYS_PTRACE -p 4242:4242 -p 8042:8042 jodogne/orthanc-debug |
| 176 | 224 # gdb --args Orthanc /etc/orthanc/ --verbose |
| 175 | 225 |
| 184 | 226 Exceptions can be automatically caught by launching ``gdb`` as follows:: |
| 227 | |
| 228 # gdb --ex 'catch t' --ex r --ex bt --args ./Orthanc /etc/orthanc/ --verbose | |
| 229 | |
| 176 | 230 Note that: |
| 231 | |
| 232 * The plugins are not available in this image yet. | |
| 233 | |
| 234 * The Orthanc source code can be found in folder ``/root/orthanc``. | |
| 235 | |
| 236 * The build artifacts can be found in folder ``/root/orthanc/Build``. | |
| 237 | |
| 238 * This command launches the mainline version. To start a released version, | |
| 336 | 239 use e.g. ``jodogne/orthanc-debug:1.6.0``. |