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annotate Sphinx/source/users/docker.rst @ 412:969d50e63b17 c-get
first info about c-get
author | Alain Mazy <alain@mazy.be> |
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date | Tue, 12 May 2020 07:38:15 +0200 |
parents | 5ed3e680364e |
children | c95817c254fe |
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 |
393 | 31 <https://hub.docker.com/repository/docker/osimis/orthanc>`__. |
229 | 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 | |
396 | 40 plugin. A :ref:`specific page <docker-osimis>` is available to describe |
393 | 41 how these images should be used. |
229 | 42 |
43 **Note for CentOS users:** The Docker environment might be difficult to | |
54 | 44 configure on your platform. Hints are available on the `Orthanc Users |
45 discussion group | |
46 <https://groups.google.com/d/msg/orthanc-users/w-uPAknnRQc/-XhzBGSCAwAJ>`__. | |
47 | |
48 | |
49 Running the Orthanc core | |
50 ------------------------ | |
51 | |
52 The following command will start the core of Orthanc, with all the | |
53 plugins disabled:: | |
54 | |
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55 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc |
54 | 56 |
57 Once Orthanc is running, use Mozilla Firefox at URL | |
58 http://localhost:8042/ to interact with Orthanc. The default username | |
59 is ``orthanc`` and its password is ``orthanc``. | |
60 | |
61 The command above starts the mainline version of Orthanc, whose | |
69 | 62 development is in continuous progress. Do not forget to regularly |
63 update the Docker image to benefit from the latest features:: | |
64 | |
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65 $ docker pull jodogne/orthanc |
69 | 66 |
67 If more stability is required, you can select the official release of | |
68 Orthanc to be run:: | |
54 | 69 |
392 | 70 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.6.1 |
54 | 71 |
72 Passing additional command-line options (e.g. to make Orthanc verbose) | |
73 can be done as follows (note the ``/etc/orthanc`` option that is | |
74 required for Orthanc to find its configuration files):: | |
75 | |
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76 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc /etc/orthanc --verbose |
54 | 77 |
78 | |
79 Usage, with plugins enabled | |
80 --------------------------- | |
81 | |
82 The following command will run the mainline version of the Orthanc | |
83 core, together with its :ref:`Web viewer <webviewer>`, its | |
84 :ref:`PostgreSQL support <postgresql>`, its :ref:`DICOMweb | |
85 implementation <dicomweb>`, and its :ref:`whole-slide imaging viewer | |
86 <wsi>`:: | |
87 | |
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88 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins |
54 | 89 |
365 | 90 Or you can also start a specific version of Orthanc for more stability:: |
91 | |
392 | 92 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins:1.6.1 |
365 | 93 |
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94 If you have an interest in the :ref:`Python plugin <python-plugin>`, |
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95 you can use the ``orthanc-python`` image. The latter image is a |
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96 heavier version of the ``orthanc-plugins`` image, as it embeds the |
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97 Python 3.7 interpreter. Here is how to start this image:: |
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98 |
365 | 99 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python |
392 | 100 $ docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-python:1.6.1 |
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101 |
54 | 102 |
103 Fine-tuning the configuration | |
104 ----------------------------- | |
105 | |
106 For security reasons, you should at least protect your instance of | |
107 Orthanc by changing this default user, in the ``RegisteredUsers`` | |
108 :ref:`configuration option <configuration>`. You will also probably | |
109 need to fine-tune other parameters, notably the list of the DICOM | |
110 modalities Orthanc knows about. | |
111 | |
112 You can generate a custom configuration file for Orthanc as follows:: | |
113 | |
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114 $ docker run --rm --entrypoint=cat jodogne/orthanc /etc/orthanc/orthanc.json > /tmp/orthanc.json |
54 | 115 |
116 Then, edit the just-generated file ``/tmp/orthanc.json`` and restart | |
117 Orthanc with your updated configuration:: | |
118 | |
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119 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc |
54 | 120 |
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121 *Remark:* These Docker images automatically set the environment |
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122 variable ``MALLOC_ARENA_MAX`` to ``5`` in order to :ref:`control |
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123 memory usage <scalability-memory>`. This default setting can be |
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124 overriden by providing the option ``-e MALLOC_ARENA_MAX=1`` when |
386 | 125 invoking ``docker run`` (the value ``0`` corresponds to the default |
126 value). | |
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127 |
54 | 128 |
382 | 129 .. _docker-compose: |
130 | |
131 Configuration management using Docker Compose | |
132 --------------------------------------------- | |
133 | |
134 Depending on the context, the `Docker Compose tool | |
135 <https://docs.docker.com/compose/>`__ might be easier to use than the | |
136 plain Docker tool, as it allows replacing long command lines as above, | |
137 by plain configuration files. The trick here is to provide the JSON | |
138 configuration files to Orthanc as `secrets | |
139 <https://docs.docker.com/compose/compose-file/#secrets>`__ (note that | |
140 the related option ``configs`` could in theory be better, | |
141 unfortunately it is only available to `Docker Swarm | |
142 <https://github.com/docker/compose/issues/5110>`__). | |
143 | |
144 .. highlight:: yml | |
145 | |
146 First create the ``docker-compose.yml`` file as follows (this one uses | |
147 the `YAML file format <https://en.wikipedia.org/wiki/YAML>`__):: | |
148 | |
149 version: '3.1' # Secrets are only available since this version of Docker Compose | |
150 services: | |
151 orthanc: | |
392 | 152 image: jodogne/orthanc-plugins:1.6.1 |
382 | 153 command: /run/secrets/ # Path to the configuration files (stored as secrets) |
154 ports: | |
402 | 155 - 4242:4242 |
382 | 156 - 8042:8042 |
157 secrets: | |
158 - orthanc.json | |
159 secrets: | |
160 orthanc.json: | |
161 file: orthanc.json | |
162 | |
163 .. highlight:: json | |
164 | |
165 Then, place the configuration file ``orthanc.json`` next to the | |
166 ``docker-compose.yml`` file. Here is a minimalist ``orthanc.json``:: | |
167 | |
168 { | |
169 "Name" : "Orthanc in Docker", | |
170 "RemoteAccessAllowed" : true | |
171 } | |
172 | |
173 .. highlight:: bash | |
174 | |
175 This single configuration file should contain all the required | |
176 configuration options for Orthanc and all its plugins. The container | |
177 can then be started as follows:: | |
178 | |
179 $ docker-compose up | |
180 | |
181 | |
54 | 182 Making the Orthanc database persistent |
183 -------------------------------------- | |
184 | |
185 The filesystem of Docker containers is volatile (its content is | |
186 deleted once the container stops). You can make the Orthanc database | |
187 persistent by mapping the ``/var/lib/orthanc/db`` folder of the | |
188 container to some path in the filesystem of your Linux host, e.g.:: | |
189 | |
190 $ mkdir /tmp/orthanc-db | |
392 | 191 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.6.1 |
54 | 192 |
193 | |
194 Whole-slide imaging support | |
195 --------------------------- | |
196 | |
197 The ``orthanc-plugins`` image includes support for :ref:`microscopic | |
198 whole-slide imaging (WSI) <wsi>`. For instance, the following command | |
199 will start the WSI viewer plugin transparently together with Orthanc:: | |
200 | |
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201 $ docker run -p 4242:4242 -p 8042:8042 --rm --name orthanc-wsi jodogne/orthanc-plugins |
54 | 202 |
203 Note that we gave the name ``orthanc-wsi`` to this new Docker | |
204 container. Then, the Dicomizer command-line tool can be invoked as | |
205 follows:: | |
206 | |
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207 $ 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 | 208 |
209 This command needs a few explanations: | |
210 | |
211 * ``--link=orthanc-wsi:orthanc`` links the container running the | |
212 Dicomizer, to the Docker container running Orthanc that we started | |
213 just before. | |
214 * ``--entrypoint=OrthancWSIDicomizer`` specifies that the Dicomizer | |
215 must be run instead of the Orthanc server. | |
216 * ``-v /tmp/Source.tif:/tmp/Source.tif:ro`` maps the source image | |
217 ``/tmp/Source.tif`` on the host computer into the Orthanc container | |
218 as read-only file ``/tmp/Source.tif``. | |
219 * ``--orthanc=http://orthanc:8042/`` instructs the Dicomizer to push | |
220 images through the ``--link`` created above. | |
221 * ``--username=orthanc --password=orthanc`` correspond to the default | |
222 credentials of the ``orthanc-plugins`` image. | |
223 | |
224 Obviously, you are free to add all the options you wish (check out the | |
225 ``--help`` flag to list these options). In particular, the | |
226 ``--dataset`` option allows to specify DICOM tags, in the JSON file | |
227 format, so as to include them in the resulting DICOM series (the | |
228 option ``--sample-dataset`` prints a sample JSON file that has the | |
229 expected format). | |
230 | |
231 If you have a source image that is not a hierarchical TIFF, you must | |
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232 instruct the Dicomizer to use `OpenSlide <https://openslide.org/>`__ |
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233 to decode it by adding the ``--openslide`` option:: |
54 | 234 |
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235 $ 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 | 236 |
237 | |
238 PostgreSQL and Orthanc inside Docker | |
239 ------------------------------------ | |
240 | |
241 It is possible to run both Orthanc and PostgreSQL inside Docker. First, start the official PostgreSQL container:: | |
242 | |
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243 $ docker run --name some-postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=pgpassword --rm postgres |
54 | 244 |
245 Open another shell, and create a database to host the Orthanc database:: | |
246 | |
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247 $ 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 | 248 |
249 You will have to type the password (cf. the environment variable | |
250 ``POSTGRES_PASSWORD`` above that it set to ``pgpassword``). Then, | |
251 retrieve the IP and the port of the PostgreSQL container, together | |
252 with the default Orthanc configuration file:: | |
253 | |
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254 $ docker inspect --format '{{ .NetworkSettings.IPAddress }}' some-postgres |
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255 $ docker inspect --format '{{ .NetworkSettings.Ports }}' some-postgres |
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256 $ docker run --rm --entrypoint=cat jodogne/orthanc-plugins /etc/orthanc/orthanc.json > /tmp/orthanc.json |
54 | 257 |
258 .. highlight:: json | |
259 | |
260 Add the following section to ``/tmp/orthanc.json`` (adapting the | |
261 values Host and Port to what docker inspect said above):: | |
262 | |
263 "PostgreSQL" : { | |
264 "EnableIndex" : true, | |
265 "EnableStorage" : true, | |
266 "Host" : "172.17.0.38", | |
267 "Port" : 5432, | |
268 "Database" : "orthanc", | |
269 "Username" : "postgres", | |
270 "Password" : "pgpassword" | |
271 } | |
272 | |
273 .. highlight:: bash | |
274 | |
275 Finally, you can start Orthanc:: | |
276 | |
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277 $ docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/orthanc.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins |
54 | 278 |
279 | |
280 Debugging | |
281 --------- | |
282 | |
176 | 283 .. highlight:: text |
284 | |
54 | 285 For debugging purpose, you can start an interactive bash session as |
286 follows:: | |
287 | |
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288 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc |
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289 $ docker run -i -t --rm --entrypoint=bash jodogne/orthanc-plugins |
175 | 290 |
176 | 291 For developers and power users, the images ``jodogne/orthanc-debug`` |
292 contain the Orthanc core compiled in debug mode (i.e. with runtime | |
293 assertions enabled, and including debugging symbols). A ``gdb`` | |
177 | 294 command-line session can be started as follows:: |
176 | 295 |
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296 $ docker run -i -t --rm --entrypoint=bash --network=host --cap-add=SYS_PTRACE -p 4242:4242 -p 8042:8042 jodogne/orthanc-debug |
176 | 297 # gdb --args Orthanc /etc/orthanc/ --verbose |
175 | 298 |
184 | 299 Exceptions can be automatically caught by launching ``gdb`` as follows:: |
300 | |
301 # gdb --ex 'catch t' --ex r --ex bt --args ./Orthanc /etc/orthanc/ --verbose | |
302 | |
176 | 303 Note that: |
304 | |
305 * The plugins are not available in this image yet. | |
306 | |
307 * The Orthanc source code can be found in folder ``/root/orthanc``. | |
308 | |
309 * The build artifacts can be found in folder ``/root/orthanc/Build``. | |
310 | |
311 * This command launches the mainline version. To start a released version, | |
392 | 312 use e.g. ``jodogne/orthanc-debug:1.6.1``. |