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fix path to DockerHub Osimis
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 19 Apr 2021 09:03:01 +0200
parents 03fd57e8e002
children f4bbb4a7d78a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 .. _docker-osimis:
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2 .. highlight:: bash
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3
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5 Osimis Orthanc Docker images
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6 ============================
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7
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8 .. contents::
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9 :depth: 3
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12 .. warning:: This documentation applies to ``osimis/orthanc`` images from the ``20.4.2`` version.
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13
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14 Note that these images have been re-written in April 2020. The documentation
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15 for older images is still available `here <https://osimis.atlassian.net/wiki/spaces/OKB/pages/26738689/How+to+use+osimis+orthanc+Docker+images#Howtouseosimis/orthancDockerimages>`__
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16
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17 The new images are backward compatible with the previous images except for the
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18 Google Cloud Platform configuration.
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19
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20 However, if you're still using legacy environment variables, you'll get some warning
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21 encouraging you to update to the new namings since the backward compatibility
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22 might be removed one day (currently planed in June 2021).
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23
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24
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25 Introduction
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26 ------------
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27
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28 Our commercial partner `Osimis <https://www.osimis.io>`__
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29 `publishes separated Docker images
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30 <https://hub.docker.com/r/osimis/orthanc>`__
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31 that are used by their technical team in order to provide professional
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32 support to their customers.
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33
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34 These images have been designed to be used with ``docker-compose`` and
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35 provide a configuration system through:
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36
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37 - environment variables
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38 - Docker secrets
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39 - classical configuration files
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40 - a mix of these options
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41
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42 This `repository <https://bitbucket.org/osimis/orthanc-setup-samples/src>`__
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43 contains lots of examples on how to use these images. In particular,
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44 `this example <https://bitbucket.org/osimis/orthanc-setup-samples/src/master/docker/all-usages/docker-compose.yml>`__
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45 shows all the way that can be used to generate the same
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46 configuration in Orthanc.
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47
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48
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49 Environment variables
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50 ---------------------
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51
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52 Any part of the Orthanc configuration file can be configured through an
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53 environment variable. Now that Orthanc and its plugins have hundreds of
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54 configuration parameter, listing all these environment variable would be
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55 too long. That's why we have defined a standard way of naming the variable:
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56
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57 +---------------------------+----------------------------------------------+----------------------------------------------------------------+
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58 | Orthanc configuration | Environment variable | Sample value |
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59 +===========================+==============================================+================================================================+
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60 | StableAge | ORTHANC__STABLE_AGE | ``30`` |
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61 +---------------------------+----------------------------------------------+----------------------------------------------------------------+
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62 | DicomWeb.Root | ORTHANC__DICOM_WEB__ROOT | ``/dicom-web/`` |
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63 +---------------------------+----------------------------------------------+----------------------------------------------------------------+
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64 | DicomWeb.Servers | ORTHANC__DICOM_WEB__SERVERS | ``{"sample": [ "http://127.0.0.1/dicom-web/"]}`` |
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65 +---------------------------+----------------------------------------------+----------------------------------------------------------------+
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66
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67 To find out an environment variable name from an Orthanc setting
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68 (i.e. ``DicomWeb.StudiesMetadata`` is the ``path`` to a setting):
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69
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70 - whenever a word contains a capital letter, insert an underscore ``_`` in front.
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71 ``DicomWeb.StudiesMetadata`` now becomes ``Dicom_Web.Studies_Metadata``
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72 - whenever you go down one level in the JSON configuration, insert
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73 a double underscore ``__``. ``Dicom_Web.Studies_Metadata`` now becomes
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74 ``Dicom_Web__Studies_Metadata``
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75 - capitalize all letters. ``Dicom_Web__Studies_Metadata`` now becomes
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76 ``DICOM_WEB__STUDIES_METADATA``
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77 - add ``ORTHANC__`` in front. ``DICOM_WEB__STUDIES_METADATA`` now becomes
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78 ``ORTHANC__DICOM_WEB__STUDIES_METADATA``
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79
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80 Note that, this automatic rule might fail because of 2 capital letters one after each other in some
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81 Orthanc settings. Therefore, there are some `exceptions <https://bitbucket.org/osimis/orthanc-builder/src/master/docker/orthanc/env-var-non-standards.json>`__ to this rule
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82 that are however quite intuitive.
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83
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84 Special environment variables
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85 -----------------------------
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86
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87 Other environment variables are not related to the Orthanc configuration file
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88 but can be specified to control the way Orthanc is run.
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89
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90 - ``VERBOSE_STARTUP=true`` will allow you to debug the startup process and see
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91 the configuration that has been provided to Orthanc. This setup should be
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92 disabled in production since it might display secret information like passwords
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93 in your logs
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94 - ``VERBOSE_ENABLED=true`` will start Orthanc with the ``--verbose`` option
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95 - ``TRACE_ENABLED=true`` will start Orthanc with the ``--trace`` option
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96 - ``NO_JOBS=true`` will start Orthanc with the ``--no-jobs`` option
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97 - ``UNLOCK=true`` will start Orthanc with the ``--unlock`` option
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98 - ``MALLOC_ARENA_MAX=10`` will :ref:`control memory usage <scalability-memory>`
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99 - ``ORTHANC_JSON`` can be used to pass a JSON "root" configuration (see below).
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100
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101 Configuration files
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102 -------------------
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103
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104 .. highlight:: yaml
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105
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106 Configuration files should be stored in the ``/etc/orthanc/`` folder inside the Docker image.
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107 This is done by building an image thanks to a ``Dockerfile``::
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108
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109 FROM osimis/orthanc
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110 COPY orthanc.json /etc/orthanc/
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111
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112
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113 Configuration files can also be passed as secrets as shown in this ``docker-compose.yml``::
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114
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115 version: "3.3"
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116 services:
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117 orthanc-file-in-secrets:
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118 image: osimis/orthanc
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119 depends_on: [index-db]
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120 ports: ["8201:8042"]
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121 environment:
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122 VERBOSE_STARTUP: "true"
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123
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124 secrets:
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125 - orthanc.secret.json
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126
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127 secrets:
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128 orthanc.secret.json:
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129 file: orthanc.secret.json
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130
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131 Finally, a whole configuration file can be passed as a JSON through the ``ORTHANC_JSON`` environment variable::
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132
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133 version: "3.3"
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134 services:
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135 orthanc-file-in-env-var:
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136 image: osimis/orthanc
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137 depends_on: [index-db]
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138 ports: ["8200:8042"]
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139 environment:
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140 VERBOSE_ENABLED: "true"
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141 OSIMIS_WEB_VIEWER1_PLUGIN_ENABLED: "true"
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142
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143 ORTHANC_JSON: |
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144 {
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145 "Name": "orthanc-file-in-env-var",
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146 "PostgreSQL" : {
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147 "Host": "index-db",
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148 "Password": "pg-password"
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149 },
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150 "RegisteredUsers": {
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151 "demo": "demo"
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152 }
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153 }
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154
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155
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156 Docker secrets
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157 --------------
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158
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159 .. highlight:: yaml
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160
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161 When using your container in a ``Docker Swarm`` or ``Kubernetes`` environment,
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162 it is usually advised to pass sensitive information through ``Docker Secrets``.
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163 For this purpose, any secret whose name is similar to the name of an
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164 environment variable is considered as an environment variable::
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165
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166 version: "3.3"
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167 services:
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168 orthanc-with-direct-secret:
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169 image: osimis/orthanc
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170 depends_on: [index-db]
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171 ports: ["8003:8042"]
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172 environment:
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173 ORTHANC__NAME: "orthanc-with-direct-secret"
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174 VERBOSE_ENABLED: "true"
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175
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176 OSIMIS_WEB_VIEWER1_PLUGIN_ENABLED: "true"
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177
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178 ORTHANC__POSTGRESQL__HOST: "index-db"
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179 ORTHANC__REGISTERED_USERS: |
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180 {"demo": "demo"}
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181
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182 secrets:
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183 - ORTHANC__POSTGRESQL__PASSWORD
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184 secrets:
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185 ORTHANC__POSTGRESQL__PASSWORD:
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186 file: ORTHANC__POSTGRESQL__PASSWORD
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187
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188
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189 Mixing configuration
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190 --------------------
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191
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192 Parts of your configuration can be defined in a configuration file,
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193 another part in an environment variable and yet another in a secret.
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194 If the same setting is defined in multiple location, the latest one
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195 will overwrite the first. Settings are evaluated in this order:
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196
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197 - JSON files from ``/etc/orthanc/``
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198 - JSON files from ``/run/secrets`` (Docker secrets are copied there
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199 by Docker)
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200 - environment variables
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201 - secret environment variables
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202
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203 At this point, if some settings have not been defined yet, some defaults
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204 are applied (see below).
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205
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206
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207 Default configuration
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208 ---------------------
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209
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210 .. highlight:: json
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211
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212 Orthanc and each plugin might have some default settings that might
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213 eventually be different from the defaults included in the Orthanc
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214 executable or the plugin library.
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215
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216 .. below json is copied from orthanc-builder/docker/orthanc/orthanc-defaults.json
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217
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218 Orthanc non-standard defaults::
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219
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220 {
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221 "StorageDirectory" : "/var/lib/orthanc/db",
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222
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223 "RemoteAccessAllowed": true,
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224 "AuthenticationEnabled": true,
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225
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226 "HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt",
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227
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228 "Plugins" : ["/usr/share/orthanc/plugins/"]
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229 }
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230
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231
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232 Default Lua scripts
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233 -------------------
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234
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235 Some Lua scripts are already loaded in the image but are not configured to
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236 be loaded by Orthanc automatically. You'll have to add them to the ``"LuaScripts"``
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237 configuration if you want to use them.
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238
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239 `/lua-scripts/filter-http-tools-reset.lua <https://bitbucket.org/osimis/orthanc-builder/src/master/docker/orthanc/filter-http-tools-reset.lua>`__
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240 can be used to regenerate the ``/tmp/orthanc.json`` configuration file that is loaded by Orthanc every time
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241 you POST to ``/tools/reset``. Note that it declares an ``IncomingHttpRequestFilter``
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242 callback that might conflict with your scripts.
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243
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244
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245 Plugins
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246 -------
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247
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248 Plugins are automatically enabled as soon as you define a setting
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249 in their JSON section or as soon as you define to ``true`` their
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250 specific environment variable.
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251
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252 Below is a list of all plugins, their environment variable and their default configuration
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253 (only when their default configuration is different from the plugin defaults):
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254
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255
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256 .. below table is obtained by running orthanc-builder/docker/orthanc/generatePluginDoc.py
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257
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258
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259 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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260 | Plugin | Environment variable | Default configuration |
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261 +==================================================+==================================================+====================================================================================================+
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262 | **Authorization** | ``AUTHORIZATION_PLUGIN_ENABLED`` | |
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263 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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264 | **ConnectivityChecks** | ``CONNECTIVITY_CHECKS_PLUGIN_ENABLED`` | |
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265 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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266 | **DicomWeb** | ``DICOM_WEB_PLUGIN_ENABLED`` | .. code-block:: json |
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267 | | | |
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268 | | | { |
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269 | | | "DicomWeb": { |
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270 | | | "Enable": true |
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271 | | | } |
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272 | | | } |
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273 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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274 | **Gdcm** | ``GDCM_PLUGIN_ENABLED`` | .. code-block:: json |
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275 | | Note: enabled by default | |
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276 | | | { |
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277 | | | "Gdcm": { |
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278 | | | "Throttling": 4, |
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279 | | | "RestrictTransferSyntaxes": [ |
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280 | | | "1.2.840.10008.1.2.4.90", |
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281 | | | "1.2.840.10008.1.2.4.91", |
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282 | | | "1.2.840.10008.1.2.4.92", |
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283 | | | "1.2.840.10008.1.2.4.93" |
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284 | | | ] |
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285 | | | } |
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286 | | | } |
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287 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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288 | **OrthancWebViewer** | ``ORTHANC_WEB_VIEWER_PLUGIN_ENABLED`` | |
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289 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
549
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290 | **StoneWebViewer** | ``ORTHANC_STONE_VIEWER_PLUGIN_ENABLED`` | |
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291 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
497
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292 | **OsimisWebViewerBasic** | ``OSIMIS_WEB_VIEWER1_PLUGIN_ENABLED`` | |
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293 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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294 | **OsimisWebViewerBasicAlpha** | ``OSIMIS_WEB_VIEWER1_ALPHA_PLUGIN_ENABLED`` | |
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295 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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296 | **PostgreSQL** | ``POSTGRESQL_PLUGIN_ENABLED`` | .. code-block:: json |
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297 | | | |
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298 | | | { |
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299 | | | "PostgreSQL": { |
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300 | | | "EnableIndex": true, |
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301 | | | "EnableStorage": false, |
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302 | | | "Port": 5432, |
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303 | | | "Host": "HOST MUST BE DEFINED", |
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304 | | | "Database": "postgres", |
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305 | | | "Username": "postgres", |
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306 | | | "Password": "postgres", |
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307 | | | "EnableSsl": false, |
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308 | | | "Lock": false |
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309 | | | } |
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310 | | | } |
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311 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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312 | **MySQL** | ``MYSQL_PLUGIN_ENABLED`` | .. code-block:: json |
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313 | | | |
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314 | | | { |
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315 | | | "MySQL": { |
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316 | | | "EnableIndex": true, |
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317 | | | "EnableStorage": false, |
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318 | | | "Port": 3306, |
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319 | | | "Host": "HOST MUST BE DEFINED", |
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320 | | | "Database": "mysql", |
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321 | | | "Username": "root", |
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322 | | | "Password": "mysql", |
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323 | | | "Lock": false |
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324 | | | } |
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325 | | | } |
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326 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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327 | **Python** | ``PYTHON_PLUGIN_ENABLED`` | |
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328 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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329 | **ServeFolders** | ``SERVE_FOLDERS_PLUGIN_ENABLED`` | |
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330 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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331 | **Transfers** | ``TRANSFERS_PLUGIN_ENABLED`` | |
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332 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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333 | **Worklists** | ``WORKLISTS_PLUGIN_ENABLED`` | .. code-block:: json |
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334 | | | |
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335 | | | { |
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336 | | | "Worklists": { |
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337 | | | "Enable": true, |
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338 | | | "Database": "/var/lib/orthanc/worklists" |
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339 | | | } |
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340 | | | } |
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341 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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342 | **Whole-slide imaging** | ``WSI_PLUGIN_ENABLED`` | |
497
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343 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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344 | **Osimis cloud** (synchronization plugin) | ``OSIMIS_CLOUD_PLUGIN_ENABLED`` | |
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345 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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346
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347 Under the hood
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348 --------------
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349
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350 The source code that is used to generate the image can be found `here <https://bitbucket.org/osimis/orthanc-builder/src/master/docker/orthanc/Dockerfile>`__.
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351
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352 The Python script that is used at startup can be found `here <https://bitbucket.org/osimis/orthanc-builder/src/master/docker/orthanc/generateConfiguration.py>`__