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new env var for osimis/orthanc
author Alain Mazy <am@osimis.io>
date Wed, 21 Sep 2022 11:00:46 +0200
parents 71e339681c6b
children 815f70009ec2
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1 .. _docker-osimis:
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2 .. highlight:: bash
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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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11 .. warning::
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13 Starting from the ``22.6.1`` release, we are providing 2 types of images:
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14
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15 - the default image with the usual tag: e.g ``22.6.1``
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16 - the full image with a e.g ``22.6.1-full`` tag
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17
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18 The default image is suitable for 99.9% of users.
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19
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20 You should use the full image only if you need to use one of these:
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21
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22 - the Azure Blob storage plugin
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23 - the Google Cloud storage plugin
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24 - the ODBC plugin with SQL Server (msodbcsql18 is preinstalled)
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25
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27 .. warning::
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28 This documentation applies to ``osimis/orthanc`` images from the ``20.4.2`` version.
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29
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30 Note that these images have been re-written in April 2020. The documentation
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31 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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32
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33 The new images are backward compatible with the previous images except for the
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34 Google Cloud Platform configuration.
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35
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36 However, if you're still using legacy environment variables, you'll get some warning
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37 encouraging you to update to the new namings since the backward compatibility
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38 might be removed at any time.
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41 Introduction
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42 ------------
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43
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44 Our commercial partner `Osimis <https://www.osimis.io>`__
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45 `publishes separated Docker images
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46 <https://hub.docker.com/r/osimis/orthanc>`__
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47 that are used by their technical team in order to provide professional
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48 support to their customers.
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49
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50 These images have been designed to be used with ``docker-compose`` and
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51 provide a configuration system through:
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52
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53 - environment variables
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54 - Docker secrets
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55 - classical configuration files
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56 - a mix of these options
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57
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58 This `repository <https://bitbucket.org/osimis/orthanc-setup-samples/src>`__
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59 contains lots of examples on how to use these images. In particular,
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60 `this example <https://bitbucket.org/osimis/orthanc-setup-samples/src/master/docker/all-usages/docker-compose.yml>`__
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61 shows all the way that can be used to generate the same
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62 configuration in Orthanc.
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63
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64
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65 Environment variables
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66 ---------------------
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67
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68 Any part of the Orthanc configuration file can be configured through an
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69 environment variable. Now that Orthanc and its plugins have hundreds of
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70 configuration parameter, listing all these environment variable would be
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71 too long. That's why we have defined a standard way of naming the variable:
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72
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73 +---------------------------+----------------------------------------------+----------------------------------------------------------------+
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74 | Orthanc configuration | Environment variable | Sample value |
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75 +===========================+==============================================+================================================================+
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76 | StableAge | ORTHANC__STABLE_AGE | ``30`` |
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77 +---------------------------+----------------------------------------------+----------------------------------------------------------------+
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78 | DicomWeb.Root | ORTHANC__DICOM_WEB__ROOT | ``/dicom-web/`` |
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79 +---------------------------+----------------------------------------------+----------------------------------------------------------------+
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80 | DicomWeb.Servers | ORTHANC__DICOM_WEB__SERVERS | ``{"sample": [ "http://127.0.0.1/dicom-web/"]}`` |
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81 +---------------------------+----------------------------------------------+----------------------------------------------------------------+
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82
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83 To find out an environment variable name from an Orthanc setting
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84 (i.e. ``DicomWeb.StudiesMetadata`` is the ``path`` to a setting):
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85
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86 - whenever a word contains a capital letter, insert an underscore ``_`` in front.
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87 ``DicomWeb.StudiesMetadata`` now becomes ``Dicom_Web.Studies_Metadata``
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88 - whenever you go down one level in the JSON configuration, insert
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89 a double underscore ``__``. ``Dicom_Web.Studies_Metadata`` now becomes
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90 ``Dicom_Web__Studies_Metadata``
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91 - capitalize all letters. ``Dicom_Web__Studies_Metadata`` now becomes
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92 ``DICOM_WEB__STUDIES_METADATA``
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93 - add ``ORTHANC__`` in front. ``DICOM_WEB__STUDIES_METADATA`` now becomes
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94 ``ORTHANC__DICOM_WEB__STUDIES_METADATA``
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95
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96 Note that, this automatic rule might fail because of 2 capital letters one after each other in some
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97 Orthanc settings. Therefore, there are some `exceptions <https://github.com/orthanc-server/orthanc-builder/blob/master/docker/orthanc/env-var-non-standards.json>`__ to this rule
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98 that are however quite intuitive.
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99
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100 Special environment variables
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101 -----------------------------
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102
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103 Other environment variables are not related to the Orthanc configuration file
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104 but can be specified to control the way Orthanc is run.
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105
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106 - ``VERBOSE_STARTUP=true`` will allow you to debug the startup process and see
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107 the configuration that has been provided to Orthanc. This setup should be
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108 disabled in production since it might display secret information like passwords
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109 in your logs
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110 - ``VERBOSE_ENABLED=true`` will start Orthanc with the ``--verbose`` option
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111 - ``TRACE_ENABLED=true`` will start Orthanc with the ``--trace`` option
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112 - ``NO_JOBS=true`` will start Orthanc with the ``--no-jobs`` option
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113 - ``LOGDIR=/logs`` will start Orthanc with the ``--logdir=/logs`` option (introduced in 21.9.1)
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114 - ``LOGFILE=/logs`` will start Orthanc with the ``--logfile=/logs/orthanc.log`` option (introduced in 21.9.1)
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115 - ``MALLOC_ARENA_MAX=10`` will :ref:`control memory usage <scalability-memory>`
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116 - ``ORTHANC_JSON`` can be used to pass a JSON "root" configuration (see below).
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117 - ``BEFORE_ORTHANC_STARTUP_SCRIPT`` can be used to `run a custom script <https://groups.google.com/g/orthanc-users/c/EXjTq2ZU1vw/m/02CwW1jzAQAJ>`__ before starting Orthanc.
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118 - ``FORCE_HOST_ID`` and ``GENERATE_HOST_ID_IF_MISSING`` can be used to control the content of /etc/hostid (introduced in 22.9.1).
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119 DCMTK calls gethostid() when generating DICOM UIDs (used, e.g, in modifications/anonymizations).
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120 When /etc/hostid is missing, the system tries to generate it from the IP of the system.
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121 On some system, in particular circumstances, we have observed that the system performs a DNS query
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122 to get the IP of the system. This DNS can timeout (after multiple with retries) and, in particular cases,
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123 we have observed a delay of 40 seconds to generate a single DICOM UID in Orthanc.
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124 Therefore, if /etc/hostid is missing, the startup script creates it and fill it with a random number (default behaviour).
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125 This behaviour can still be deactivated by defining ``GENERATE_HOST_ID_IF_MISSING=false``.
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126 The host id can also be forced by defining ``FORCE_HOST_ID``.
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127
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128
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129
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130 Configuration files
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131 -------------------
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132
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133 .. highlight:: yaml
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134
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135 Configuration files should be stored in the ``/etc/orthanc/`` folder inside the Docker image.
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136 This is done by building an image thanks to a ``Dockerfile``::
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137
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138 FROM osimis/orthanc
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139 COPY orthanc.json /etc/orthanc/
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140
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141
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142 Configuration files can also be passed as secrets as shown in this ``docker-compose.yml``::
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143
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144 version: "3.3"
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145 services:
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146 orthanc-file-in-secrets:
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147 image: osimis/orthanc
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148 depends_on: [index-db]
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149 ports: ["8201:8042"]
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150 environment:
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151 VERBOSE_STARTUP: "true"
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152
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153 secrets:
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154 - orthanc.secret.json
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155
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156 secrets:
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157 orthanc.secret.json:
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158 file: orthanc.secret.json
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159
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160 Finally, a whole configuration file can be passed as a JSON through the ``ORTHANC_JSON`` environment variable::
497
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161
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162 version: "3.3"
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163 services:
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164 orthanc-file-in-env-var:
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165 image: osimis/orthanc
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166 depends_on: [index-db]
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167 ports: ["8200:8042"]
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168 environment:
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169 VERBOSE_ENABLED: "true"
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170 OSIMIS_WEB_VIEWER1_PLUGIN_ENABLED: "true"
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171
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172 ORTHANC_JSON: |
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173 {
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174 "Name": "orthanc-file-in-env-var",
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175 "PostgreSQL" : {
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176 "Host": "index-db",
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177 "Password": "pg-password"
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178 },
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179 "RegisteredUsers": {
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180 "demo": "demo"
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181 }
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182 }
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183
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184
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185 Docker secrets
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186 --------------
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187
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188 .. highlight:: yaml
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189
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190 When using your container in a ``Docker Swarm`` or ``Kubernetes`` environment,
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191 it is usually advised to pass sensitive information through ``Docker Secrets``.
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192 For this purpose, any secret whose name is similar to the name of an
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193 environment variable is considered as an environment variable::
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194
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195 version: "3.3"
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196 services:
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197 orthanc-with-direct-secret:
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198 image: osimis/orthanc
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199 depends_on: [index-db]
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200 ports: ["8003:8042"]
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201 environment:
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202 ORTHANC__NAME: "orthanc-with-direct-secret"
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203 VERBOSE_ENABLED: "true"
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204
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205 OSIMIS_WEB_VIEWER1_PLUGIN_ENABLED: "true"
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206
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207 ORTHANC__POSTGRESQL__HOST: "index-db"
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208 ORTHANC__REGISTERED_USERS: |
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209 {"demo": "demo"}
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210
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211 secrets:
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212 - ORTHANC__POSTGRESQL__PASSWORD
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213 secrets:
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214 ORTHANC__POSTGRESQL__PASSWORD:
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215 file: ORTHANC__POSTGRESQL__PASSWORD
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216
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217
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218 Mixing configuration
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219 --------------------
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220
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221 Parts of your configuration can be defined in a configuration file,
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222 another part in an environment variable and yet another in a secret.
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223 If the same setting is defined in multiple location, the latest one
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224 will overwrite the first. Settings are evaluated in this order:
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225
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226 - JSON files from ``/etc/orthanc/``
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227 - JSON files from ``/run/secrets`` (Docker secrets are copied there
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228 by Docker)
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229 - environment variables
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230 - secret environment variables
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231
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232 At this point, if some settings have not been defined yet, some defaults
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233 are applied (see below).
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234
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235
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236 Default configuration
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237 ---------------------
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238
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239 .. highlight:: json
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240
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241 Orthanc and each plugin might have some default settings that might
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242 eventually be different from the defaults included in the Orthanc
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243 executable or the plugin library.
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244
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245 .. below json is copied from orthanc-builder/docker/orthanc/orthanc-defaults.json
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246
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247 Orthanc non-standard defaults::
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248
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249 {
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250 "StorageDirectory" : "/var/lib/orthanc/db",
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251
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252 "RemoteAccessAllowed": true,
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253 "AuthenticationEnabled": true,
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254
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255 "HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt",
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256
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257 "Plugins" : ["/usr/share/orthanc/plugins/"]
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258 }
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259
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260
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261 Default Lua scripts
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262 -------------------
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263
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264 Some Lua scripts are already loaded in the image but are not configured to
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265 be loaded by Orthanc automatically. You'll have to add them to the ``"LuaScripts"``
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266 configuration if you want to use them.
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267
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268 `/lua-scripts/filter-http-tools-reset.lua <https://github.com/orthanc-server/orthanc-builder/blob/master/docker/orthanc/filter-http-tools-reset.lua>`__
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269 can be used to regenerate the ``/tmp/orthanc.json`` configuration file that is loaded by Orthanc every time
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270 you POST to ``/tools/reset``. Note that it declares an ``IncomingHttpRequestFilter``
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271 callback that might conflict with your scripts.
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272
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273 Healthcheck probe
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274 -----------------
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275
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276 In version 21.10.0, the `/probes/test-aliveness.py <https://github.com/orthanc-server/orthanc-builder/blob/master/docker/orthanc/test-aliveness.py>`__
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277 script has been added in order to perform healthchecks. Check the doc in the script itself for more details.
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278 A sample configuration is also available in `this sample <https://bitbucket.org/osimis/orthanc-setup-samples/src/8016d140a237a892db703aac4782307c46732847/docker/tls-mutual-auth/docker-compose.yml#lines-51>`__
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279
497
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280
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281 Plugins
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282 -------
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283
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284 Plugins are automatically enabled as soon as you define a setting
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285 in their JSON section or as soon as you define to ``true`` their
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286 specific environment variable.
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287
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288 Below is a list of all plugins, their environment variable and their default configuration
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289 (only when their default configuration is different from the plugin defaults):
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290
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291
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292 .. below table is obtained by running orthanc-builder/docker/orthanc/generatePluginDoc.py
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293
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294
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295 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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296 | Plugin | Environment variable | Default configuration |
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297 +==================================================+==================================================+====================================================================================================+
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298 | **Authorization** | ``AUTHORIZATION_PLUGIN_ENABLED`` | |
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299 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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300 | **ConnectivityChecks** | ``CONNECTIVITY_CHECKS_PLUGIN_ENABLED`` | |
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301 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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302 | **DicomWeb** | ``DICOM_WEB_PLUGIN_ENABLED`` | .. code-block:: json |
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303 | | | |
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304 | | | { |
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305 | | | "DicomWeb": { |
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306 | | | "Enable": true |
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307 | | | } |
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308 | | | } |
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309 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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310 | **Gdcm** | ``GDCM_PLUGIN_ENABLED`` | .. code-block:: json |
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311 | | Note: enabled by default | |
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312 | | | { |
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313 | | | "Gdcm": { |
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314 | | | "Throttling": 4, |
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315 | | | "RestrictTransferSyntaxes": [ |
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316 | | | "1.2.840.10008.1.2.4.90", |
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317 | | | "1.2.840.10008.1.2.4.91", |
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318 | | | "1.2.840.10008.1.2.4.92", |
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319 | | | "1.2.840.10008.1.2.4.93" |
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320 | | | ] |
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321 | | | } |
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322 | | | } |
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323 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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324 | **OrthancWebViewer** | ``ORTHANC_WEB_VIEWER_PLUGIN_ENABLED`` | |
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325 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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326 | **StoneWebViewer** | ``STONE_WEB_VIEWER_PLUGIN_ENABLED`` | |
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327 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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328 | **OsimisWebViewerBasic** | ``OSIMIS_WEB_VIEWER1_PLUGIN_ENABLED`` | |
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329 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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330 | **OsimisWebViewerBasicAlpha** | ``OSIMIS_WEB_VIEWER1_ALPHA_PLUGIN_ENABLED`` | |
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331 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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332 | **PostgreSQL** | ``POSTGRESQL_PLUGIN_ENABLED`` | .. code-block:: json |
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333 | | | |
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334 | | | { |
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335 | | | "PostgreSQL": { |
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336 | | | "EnableIndex": true, |
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337 | | | "EnableStorage": false, |
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338 | | | "Port": 5432, |
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339 | | | "Host": "HOST MUST BE DEFINED", |
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340 | | | "Database": "postgres", |
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341 | | | "Username": "postgres", |
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342 | | | "Password": "postgres", |
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343 | | | "EnableSsl": false, |
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344 | | | "Lock": false |
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345 | | | } |
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346 | | | } |
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347 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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348 | **MySQL** | ``MYSQL_PLUGIN_ENABLED`` | .. code-block:: json |
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349 | | | |
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350 | | | { |
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351 | | | "MySQL": { |
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352 | | | "EnableIndex": true, |
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353 | | | "EnableStorage": false, |
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354 | | | "Port": 3306, |
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355 | | | "Host": "HOST MUST BE DEFINED", |
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356 | | | "Database": "mysql", |
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357 | | | "Username": "root", |
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358 | | | "Password": "mysql", |
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359 | | | "Lock": false |
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360 | | | } |
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361 | | | } |
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362 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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363 | **Python** | ``PYTHON_PLUGIN_ENABLED`` | |
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364 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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365 | **ServeFolders** | ``SERVE_FOLDERS_PLUGIN_ENABLED`` | |
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366 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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367 | **Transfers** | ``TRANSFERS_PLUGIN_ENABLED`` | |
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368 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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369 | **Worklists** | ``WORKLISTS_PLUGIN_ENABLED`` | .. code-block:: json |
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370 | | | |
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371 | | | { |
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372 | | | "Worklists": { |
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373 | | | "Enable": true, |
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374 | | | "Database": "/var/lib/orthanc/worklists" |
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375 | | | } |
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376 | | | } |
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377 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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378 | **Housekeeper** | ``HOUSEKEEPER_PLUGIN_ENABLED`` | .. code-block:: json |
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379 | | | |
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380 | | | { |
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381 | | | "Housekeeper": { |
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382 | | | "Enable": true |
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383 | | | } |
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384 | | | } |
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385 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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386 | **DelayedDeletion** | ``DELAYED_DELETION_PLUGIN_ENABLED`` | .. code-block:: json |
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387 | | | |
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388 | | | { |
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389 | | | "DelayedDeletion": { |
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390 | | | "Enable": true |
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391 | | | } |
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392 | | | } |
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393 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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394 | **Wsi** | ``WSI_PLUGIN_ENABLED`` | |
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395 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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396 | **Odbc** | ``ODBC_PLUGIN_ENABLED`` | .. code-block:: json |
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397 | | | |
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398 | | | { |
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399 | | | "Odbc": { |
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400 | | | "EnableIndex": true, |
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401 | | | "EnableStorage": false, |
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402 | | | "IndexConnectionString": "MUST BE DEFINED", |
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403 | | | "StorageConnectionString": "MUST BE DEFINED" |
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404 | | | } |
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405 | | | } |
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406 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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407 | **Tcia** | ``TCIA_PLUGIN_ENABLED`` | .. code-block:: json |
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408 | | | |
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409 | | | { |
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410 | | | "Tcia": { |
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411 | | | "Enable": true |
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412 | | | } |
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413 | | | } |
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414 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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415 | **Indexer** | ``INDEXER_PLUGIN_ENABLED`` | .. code-block:: json |
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416 | | | |
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417 | | | { |
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418 | | | "Indexer": { |
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419 | | | "Enable": true |
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420 | | | } |
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421 | | | } |
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422 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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423 | **Neuro** | ``NEURO_PLUGIN_ENABLED`` | .. code-block:: json |
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424 | | | |
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425 | | | { |
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426 | | | "Neuro": { |
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427 | | | "Enable": true |
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428 | | | } |
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429 | | | } |
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430 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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431 | **AzureBlobStorage** | ``AZURE_BLOB_STORAGE_PLUGIN_ENABLED`` | .. code-block:: json |
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432 | | | |
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433 | | | { |
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434 | | | "AzureBlobStorage": { |
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435 | | | "ConnectionString": "MUST BE DEFINED BY YOU", |
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436 | | | "ContainerName": "MUST BE DEFINED BY YOU" |
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437 | | | } |
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438 | | | } |
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439 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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440 | **AwsS3Storage** | ``AWS_S3_STORAGE_PLUGIN_ENABLED`` | .. code-block:: json |
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441 | | | |
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442 | | | { |
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443 | | | "AwsS3Storage": { |
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444 | | | "BucketName": "MUST BE DEFINED BY YOU", |
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445 | | | "Region": "MUST BE DEFINED BY YOU" |
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446 | | | } |
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447 | | | } |
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448 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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449 | **GoogleCloudStorage** | ``GOOGLE_CLOUD_STORAGE_PLUGIN_ENABLED`` | .. code-block:: json |
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450 | | | |
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451 | | | { |
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452 | | | "GoogleCloudStorage": { |
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453 | | | "ServiceAccountFile": "MUST BE DEFINED BY YOU", |
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454 | | | "BucketName": "MUST BE DEFINED BY YOU" |
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455 | | | } |
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456 | | | } |
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457 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
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458 | **OrthancExplorer2** | ``ORTHANC_EXPLORER_2_ENABLED`` | .. code-block:: json |
848
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459 | | Note: enabled by default | |
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460 | | | { |
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461 | | | "OrthancExplorer2": { |
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462 | | | "Enable": true, |
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463 | | | "IsDefaultOrthancUI": false |
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464 | | | } |
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465 | | | } |
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466 +--------------------------------------------------+--------------------------------------------------+----------------------------------------------------------------------------------------------------+
497
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467 Under the hood
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468 --------------
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469
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470 The source code that is used to generate the image can be found `here <https://github.com/orthanc-server/orthanc-builder/blob/master/docker/orthanc/Dockerfile>`__.
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471
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472 The Python script that is used at startup can be found `here <https://github.com/orthanc-server/orthanc-builder/blob/master/docker/orthanc/generateConfiguration.py>`__