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annotate Sphinx/source/plugins/dicomweb.rst @ 311:0078d465c768

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 04 Feb 2020 17:18:02 +0100
parents bd1f308a5fd2
children 83d822f11e78
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1 .. _dicomweb:
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4 DICOMweb plugin
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5 ===============
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6
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7 .. contents::
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8
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9 This **official** plugin extends Orthanc with support of the `DICOMweb
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10 protocols <https://en.wikipedia.org/wiki/DICOMweb>`__. More precisely,
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11 the plugin introduces a basic, reference implementation of WADO-URI,
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12 WADO-RS, QIDO-RS and STOW-RS, following `DICOM PS3.18
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13 <http://dicom.nema.org/medical/dicom/current/output/html/part18.html>`__.
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14 The plugin simultaneously turns Orthanc into a **DICOMweb server** and
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15 into a **DICOMweb client**.
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17 For general information, check out the `official homepage of the
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18 plugins <http://www.orthanc-server.com/static.php?page=dicomweb>`__.
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20 The full standard is not implemented yet, the supported features are
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21 `tracked in the repository
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22 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Status.txt>`__.
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25 Compilation
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26 -----------
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27
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28 .. highlight:: text
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30 The procedure to compile this plugin is similar of that for the
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31 :ref:`core of Orthanc <compiling>`. The following commands should work
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32 for every UNIX-like distribution (including GNU/Linux)::
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33
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34 $ mkdir Build
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35 $ cd Build
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36 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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37 $ make
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39 The compilation will produce a shared library ``OrthancDicomWeb`` that
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40 contains the DICOMweb plugin. Pre-compiled binaries for Microsoft
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41 Windows `are also available
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42 <http://www.orthanc-server.com/browse.php?path=/plugin-dicom-web>`__,
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43 and are included in the `Windows installers
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44 <https://www.orthanc-server.com/download-windows.php>`__. A package
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45 for `Apple's Mac OS X
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46 <http://localhost/~jodogne/orthanc/static.php?page=download-mac>`__ is
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47 available courtesy of `Osimis <http://osimis.io/>`__.
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48
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49 *Remark:* Some older build instructions are also available in the
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50 `source distribution
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51 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/BuildInstructions.txt>`__.
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52
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54 Installation
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55 ------------
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57 .. highlight:: json
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58
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59 You of course first have to :ref:`install Orthanc <binaries>`. Once
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60 Orthanc is installed, you must change the :ref:`configuration file
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61 <configuration>` to tell Orthanc where it can find the plugin: This is
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62 done by properly modifying the ``Plugins`` option. For GNU/Linux, you
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63 could for instance use the following configuration file::
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64
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65 {
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66 "Name" : "MyOrthanc",
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67 [...]
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68 "Plugins" : [
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69 "/home/user/OrthancDicomWeb/Build/libOrthancDicomWeb.so"
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70 ]
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71 }
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72
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73 Or, for Windows::
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74
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75 {
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76 "Name" : "MyOrthanc",
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77 [...]
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78 "Plugins" : [
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79 "c:/Temp/OrthancDicomWeb.dll"
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80 ]
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81 }
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82
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83 Note that the DICOMweb server will share all the parameters of the
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84 Orthanc HTTP server, notably wrt. authentication and HTTPS
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85 encryption. For this reason, you will most probably have to enable the
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86 remote access to the Orthanc HTTP server::
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87
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88 {
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89 [...]
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90 "RemoteAccessEnabled" : true,
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91 [...]
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92 }
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93
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94 Once Orthanc has restarted, the root of the DICOMweb REST API is
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95 accessible at ``http://localhost:8042/dicom-web/``.
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96
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97
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98 Options
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99 -------
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100
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101 Server-related options
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102 ^^^^^^^^^^^^^^^^^^^^^^
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103
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104 .. highlight:: json
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105
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106 There are several configuration options that can be set to fine-tune
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107 the Orthanc DICOMweb server. Here is the full list of the available
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108 options, all of them must be grouped inside the ``DicomWeb`` section of
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109 the Orthanc configuration file::
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110
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111 {
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112 [...]
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113 "DicomWeb" : {
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114 "Enable" : true, // Whether DICOMweb support is enabled
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115 "Root" : "/dicom-web/", // Root URI of the DICOMweb API (for QIDO-RS, STOW-RS and WADO-RS)
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116 "EnableWado" : true, // Whether WADO-URI (previously known as WADO) support is enabled
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117 "WadoRoot" : "/wado", // Root URI of the WADO-URI (aka. WADO) API
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118 "Ssl" : false, // Whether HTTPS should be used for subsequent WADO-RS requests
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119 "QidoCaseSensitive" : true, // For QIDO-RS server, whether search is case sensitive (since release 0.5)
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120 "Host" : "localhost" // Hard-codes the name of the host for subsequent WADO-RS requests (deprecated)
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121 }
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122 }
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123
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124 Furthermore, the global option ``DefaultEncoding`` specifies the
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125 encoding (specific character set) that will be used when answering a
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126 QIDO-RS request. It might be a good idea to set this option to
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127 ``Utf8`` if you are dealing with an international environment.
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128
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129 The following configuration options were present in releases <= 0.6 of the plugin,
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130 but are not used anymore::
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131
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132 {
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133 [...]
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134 "DicomWeb" : {
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135 "StowMaxInstances" : 10, // For STOW-RS client, the maximum number of instances in one single HTTP query (0 = no limit)
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136 "StowMaxSize" : 10, // For STOW-RS client, the maximum size of the body in one single HTTP query (in MB, 0 = no limit)
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137 }
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138 }
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139
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140 These older configuration options were used to limit the size of the
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141 HTTP requests, by issuing multiple calls to STOW-RS (set both options
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142 to 0 to send one single request).
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143
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144
243
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145 **Remark:** The option ``Host`` is deprecated. Starting with release
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146 0.7 of the DICOMweb plugin, its value are computed from the standard
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147 HTTP headers ``Forwarded`` and ``Host``, as provided by the HTTP
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148 clients.
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149
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150
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151
255
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152 .. _dicomweb-client-config:
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153
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154 Client-related options
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155 ^^^^^^^^^^^^^^^^^^^^^^
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156
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157 .. highlight:: json
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158
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159 If you want to connect Orthanc as a client to remote DICOMweb servers
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160 (cf. below), you need to modify the configuration file so as to define
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161 each of them in the option ``DicomWeb.Servers``. The syntax is
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162 identical to the ``OrthancPeers`` option of the :ref:`configuration of
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163 the Orthanc core <configuration>`.
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164
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165 In the most simple case, here is how to instruct Orthanc about the
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166 existence of a password-less DICOMweb server that will be referred to
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167 as "sample" in Orthanc::
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168
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169 {
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170 [...]
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171 "DicomWeb" : {
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172 "Servers" : {
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173 "sample" : [ "http://192.168.1.1/dicom-web/" ]
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174 }
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175 }
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176 }
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177
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178 You are of course free to add as many DICOMweb servers as you need. If
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179 the DICOMweb server is protected by a password (with `HTTP Basic
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180 access authentication
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181 <https://en.wikipedia.org/wiki/Basic_access_authentication>`__)::
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182
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183 {
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184 [...]
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185 "DicomWeb" : {
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186 "Servers" : {
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187 "sample" : [ "http://192.168.1.1/dicom-web/", "username", "password" ]
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188 }
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189 }
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190 }
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191
260
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192 Two important options can be provided for individual remote DICOMweb servers:
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193
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194 * ``HasDelete`` can be set to ``true`` to indicate that the HTTP
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195 DELETE method can be used to delete remote studies/series/instances.
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196 This notably adds a "delete" button on the Web interface of the
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197 DICOMweb client, and creates a route
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198 ``/dicom-web/servers/sample/delete`` in the REST API.
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199
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200 * ``ChunkedTransfers`` must be set to ``false`` if the remote DICOMweb
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201 server does not support `HTTP chunked transfer encoding
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202 <https://en.wikipedia.org/wiki/Chunked_transfer_encoding>`__. Setting
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203 this option to ``true`` is the best choice to reduce memory
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204 consumption. However, it must be set to ``false`` if the remote
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205 DICOMweb server is Orthanc <= 1.5.6, as chunked transfer encoding is
293
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206 only supported starting with Orthanc 1.5.8. Beware setting ``ChunkedTransfers``
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207 to ``true`` utilizes all CPU resources which results in extremely low throughput
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208 as of version 1.0 of the DICOMweb plugin (see
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209 `issue 156 <https://bitbucket.org/sjodogne/orthanc/issues/156/>`__ for status).
260
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210
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211 You'll have to convert the JSON array into a JSON object to set these
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212 options::
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213
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214 {
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215 [...]
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216 "DicomWeb" : {
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217 "Servers" : {
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218 "sample" : {
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219 "Url" : "http://192.168.1.1/dicom-web/",
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220 "Username" : "username",
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221 "Password" : "password",
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222 "HasDelete" : true,
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223 "ChunkedTransfers" : true // Set to "false" if "sample" is Orthanc <= 1.5.6
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224 }
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225 }
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226 }
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227 }
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228
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229
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230 Furthermore, if the DICOMweb server is protected with HTTPS client
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231 authentication, you must provide your client certificate (in the `PEM
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232 format
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233 <https://en.wikipedia.org/wiki/Privacy-enhanced_Electronic_Mail>`__),
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234 your client private key (also in the PEM format), together with the
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235 password protecting the private key::
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236
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237 {
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238 [...]
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239 "DicomWeb" : {
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240 "Servers" : {
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241 "sample" : {
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242 "Url" : "http://192.168.1.1/dicom-web/",
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243 "CertificateFile" : "client.crt",
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244 "CertificateKeyFile" : "client.key",
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245 "CertificateKeyPassword" : "password"
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246 }
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247 }
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248 }
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249 }
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250
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251 Finally, it is also possible to use client authentication with
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252 hardware security modules and smart cards through `PKCS#11
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253 <https://en.wikipedia.org/wiki/PKCS_11>`__ (this feature is only
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254 available is the core of Orthanc was compiled with the
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255 ``-DENABLE_PKCS11=ON`` option in CMake, and if the Orthanc
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256 configuration file has a proper ``Pkcs11`` section)::
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257
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258 {
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259 [...]
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260 "DicomWeb" : {
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261 "Servers" : {
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262 "sample" : {
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263 "Url" : "http://192.168.1.1/dicom-web/",
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264 "Pkcs11" : true
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265 }
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266 }
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267 }
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268 }
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269
260
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270 **Remark:** A :ref:`plugin by Osimis <google>` is available to
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271 dynamically create authenticated connections to Google Cloud Platform.
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272
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273 **Important remark:** When querying a DICOMweb server, Orthanc will
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274 automatically use the global configuration options ``HttpProxy``,
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275 ``HttpTimeout``, ``HttpsVerifyPeers``, ``HttpsCACertificates``, and
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276 ``Pkcs11``. Make sure to adapt them if need be.
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277
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278
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279 Quickstart - DICOMweb client
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280 ----------------------------
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281
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282 Starting with version 1.0 of the DICOMweb plugin, a Web interface is
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283 provided to use Orthanc as a DICOMweb client. Simply click on the
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284 "Open DICOMweb client" button at the bottom of the welcome screen of
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285 :ref:`Orthanc Explorer <orthanc-explorer>`.
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286
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287 Here is a direct link to the DICOMweb client running on our demo
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288 server:
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289 `http://demo.orthanc-server.com/dicom-web/app/client/index.html
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290 <http://demo.orthanc-server.com/dicom-web/app/client/index.html>`__
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291
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292
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293
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294 Quickstart - DICOMweb server
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295 ----------------------------
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296
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297 Once your Orthanc server is properly configured (see above), you can
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298 make REST calls to the API of the DICOMweb server. For demonstration
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299 purpose, this section makes the assumption that the ``VIX`` dataset
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300 provided by `OsiriX <http://www.osirix-viewer.com/datasets/>`__ has
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301 been uploaded to Orthanc.
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302
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303 WADO-URI
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304 ^^^^^^^^
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305
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306 .. highlight:: text
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307
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308 Here is a proper WADO-URI (previously known simply as WADO) request to
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309 render one slice of the VIX dataset as a JPEG image::
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310
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311 http://localhost:8042/wado?objectUID=1.3.12.2.1107.5.1.4.54693.30000006100507010800000005466&requestType=WADO
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312
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313
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314 .. highlight:: bash
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315
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316 The ``objectUID`` corresponds to the ``SOPInstanceUID`` DICOM tag of
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317 some instance in the ``VIX`` dataset. Given the Orthanc identifier of
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318 an instance from VIX
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319 (e.g. ``14b4db2c-065edecb-6a767936-7068293a-92fcb080``), the latter
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320 tag can be obtained from the ``MainDicomTags`` field::
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321
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322 $ curl http://localhost:8042/instances/14b4db2c-065edecb-6a767936-7068293a-92fcb080
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323
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324
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325 QIDO-RS
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326 ^^^^^^^
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327
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328 .. highlight:: bash
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329
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330 Regarding QIDO-RS (querying the content of a remote DICOMweb server),
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331 here is how to obtain the list of studies stored by Orthanc::
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332
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333 $ curl http://localhost:8042/dicom-web/studies
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334
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335 Note that the ``/dicom-web/`` prefix comes from the configuration
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336 option ``Root`` of the ``DicomWeb`` section. Filtering the studies is
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337 possible as follows::
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338
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339 $ curl http://localhost:8042/dicom-web/studies?PatientName=VIX
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340
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341
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342
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343 WADO-RS
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344 ^^^^^^^
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345
311
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346 A study can be retrieved through WADO-RS. Here is a sample using the VIX dataset::
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347
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348 $ curl http://localhost:8042/dicom-web/studies/2.16.840.1.113669.632.20.1211.10000315526/
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349
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350 This answer is a `multipart stream
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351 <https://en.wikipedia.org/wiki/MIME#Multipart_messages>`__ of
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352 ``application/dicom`` DICOM instances, so a Web browser will not be
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353 able to display it (. You will have to use either AJAX (JavaScript) or a
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354 command-line tool (such as cURL).
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355
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356 You can render one individual frame as a plain PNG image as follows::
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357
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358 $ curl http://localhost:8042/dicom-web/studies/2.16.840.1.113669.632.20.1211.10000315526/series/1.3.12.2.1107.5.1.4.54693.30000006100507010800000005268/instances/1.3.12.2.1107.5.1.4.54693.30000006100507010800000005466/frames/1/rendered -H 'accept: image/png'
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359
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360
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361 Other endpoints
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362 ^^^^^^^^^^^^^^^
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363
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364 This page only provides some very basic examples about the use of a
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365 DICOMweb server. Please check out `the full reference of the DICOMweb
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366 API <https://www.dicomstandard.org/dicomweb/>`__ for more information.
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367
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368
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369
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370 .. _dicomweb-client:
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371
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372 REST API of the Orthanc DICOMweb client
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373 ---------------------------------------
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374
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375 Listing the available servers
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376 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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377
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378 .. highlight:: bash
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379
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380 The list of the remote DICOMweb servers that are known to the DICOMweb
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381 plugin can be obtained as follows::
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382
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383 $ curl http://localhost:8042/dicom-web/servers/
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384 [ "sample" ]
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385
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386 In this case, a single server called ``sample`` is configured.
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387
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388
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389 Making a call to QIDO-RS or WADO-RS
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390 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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391
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392 .. highlight:: bash
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393
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394 In Orthanc, the URI ``/{dicom-web-root}/servers/{name}/get`` allows to
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395 make a HTTP GET call against a DICOMweb server. This can be used to
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396 issue a QIDO-RS or WADO-RS command. Orthanc will take care of properly
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397 encoding the URL and authenticating the client. For instance, here is
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398 a sample QIDO-RS search to query all the studies (using a bash
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399 command-line)::
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400
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401 $ curl http://localhost:8042/dicom-web/servers/sample/get -d @- << EOF
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402 {
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403 "Uri" : "/studies"
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404 }
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405 EOF
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406
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407 The result of this call is a JSON document formatted according to the
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408 DICOMweb standard. You do not have to specify the base URL of the
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409 remote DICOMweb server, as it is encoded in the configuration file.
32
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410
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411 As a more advanced example, here is how to search all the series
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412 associated with a given patient name, while requesting to use an XML
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413 format::
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414
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415 $ curl http://localhost:8042/dicom-web/servers/sample/get -d @- << EOF
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416 {
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417 "Uri" : "/series",
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418 "HttpHeaders" : {
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419 "Accept" : "application/dicom+xml"
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420 },
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421 "Arguments" : {
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422 "00100010" : "KNIX"
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423 }
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424 }
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425 EOF
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426
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427 The result of the command above is a `multipart stream
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428 <https://en.wikipedia.org/wiki/MIME#Multipart_messages>`__ of XML
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429 documents describing each series.
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430
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431 Note how all the GET arguments to the QIDO-RS request must be
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432 specified in the ``Arguments`` field. Orthanc will take care of
260
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433 `properly encoding it as an URL
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434 <https://en.wikipedia.org/wiki/Percent-encoding>`__.
32
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435
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436 An user-friendly reference of the features available in QIDO-RS and
33
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437 WADO-RS `can be found on this site <http://www.dicomweb.org/>`__.
32
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438
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439
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440 Sending DICOM resources to a STOW-RS server
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441 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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442
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443 .. highlight:: bash
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444
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445 STOW-RS allows to send local DICOM resources to a remote DICOMweb
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446 server. In Orthanc, the STOW-RS client primitive is available at URI
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447 ``/{dicom-web-root}/servers/{name}/stow``. Here is a sample call::
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448
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449 $ curl http://localhost:8042/dicom-web/servers/sample/stow -X POST -d @- << EOF
32
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450 {
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451 "Resources" : [
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452 "6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"
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453 ]
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454 }
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455 EOF
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456
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457 Note that this primitive takes as its input a list of :ref:`Orthanc
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458 identifiers <orthanc-ids>` corresponding to the resources (patients,
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459 studies, series and/or instances) to be exported.
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460
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461 Additional HTTP headers can be added with an optional ``HttpHeaders``
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462 argument as for QIDO-RS and WADO-RS. This might be useful e.g. for
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463 cookie-based session management.
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464
262
3391edf37359 note for packagers
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465 Internally, this call results in creating an :ref:`Orthanc job <jobs>`
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466 that is executed synchronously (the REST call only returns once the
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467 STOW-RS request is finished). You can run the job in asynchronous
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468 mode as follows::
32
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469
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470 $ curl http://localhost:8042/dicom-web/servers/sample/stow -X POST -d @- << EOF
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471 {
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472 "Resources" : [
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473 "6ca4c9f3-5e895cb3-4d82c6da-09e060fe-9c59f228"
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474 ],
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475 "Synchronous" : false,
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476 "Priority" : 10
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477 }
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478 EOF
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479
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480 {
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481 "ID" : "a7bd2a5c-291d-4ca5-977a-66502cab22a1",
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482 "Path" : ".././../jobs/a7bd2a5c-291d-4ca5-977a-66502cab22a1"
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483 }
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484
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485 Such a call ends immediately, and returns the ID of the job created by
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486 Orthanc. The :ref:`status of the job <jobs-monitoring>` can then be
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487 monitored using the Orthanc REST API.
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488
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489
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490
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491 Retrieving DICOM resources from a WADO-RS server
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492 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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493
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494 .. highlight:: bash
32
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495
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diff changeset
496 Once DICOM resources of interest have been identified through a
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diff changeset
497 QIDO-RS call to a remote DICOMweb server (cf. above), it is
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diff changeset
498 interesting to download them locally with a WADO-RS call. You could do
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diff changeset
499 it manually with a second call to the
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500 ``/{dicom-web-root}/servers/{name}/get`` URI, but Orthanc provides
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501 another primitive ``.../retrieve`` to automate this process, in order
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502 to avoid the manual parsing of the multipart stream.
32
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diff changeset
503
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diff changeset
504 Here is how you would download one study, one series and one instance
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diff changeset
505 whose StudyInstanceUID (0020,000d), SeriesInstanceUID (0020,000e) are
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diff changeset
506 SOPInstanceUID (0008,0018) have been identified through a former
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diff changeset
507 QIDO-RS call::
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diff changeset
508
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509 $ curl http://localhost:8042/dicom-web/servers/sample/retrieve -X POST -d @- << EOF
32
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diff changeset
510 {
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diff changeset
511 "Resources" : [
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512 {
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diff changeset
513 "Study" : "1.3.51.0.1.1.192.168.29.133.1688840.1688819"
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514 },
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515 {
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diff changeset
516 "Study" : "1.3.51.0.1.1.192.168.29.133.1681753.1681732",
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diff changeset
517 "Series" : "1.3.12.2.1107.5.2.33.37097.2012041613040617636372171.0.0.0"
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diff changeset
518 },
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519 {
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diff changeset
520 "Study" : "1.3.51.0.1.1.192.168.29.133.1681753.1681732",
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diff changeset
521 "Series" : "1.3.12.2.1107.5.2.33.37097.2012041612474981424569674.0.0.0",
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diff changeset
522 "Instance" : "1.3.12.2.1107.5.2.33.37097.2012041612485540185869716"
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523 }
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diff changeset
524 ]
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525 }
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526 EOF
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527
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diff changeset
528 Orthanc will reply with the list of the Orthanc identifiers of all the
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diff changeset
529 DICOM instances that were downloaded from the remote server.
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diff changeset
530
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531 Remark 1: Contrarily to the ``.../stow`` URI that uses :ref:`Orthanc
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532 identifiers <orthanc-ids>`, the ``.../retrieve`` URI uses DICOM
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533 identifiers.
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534
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535 Remark 2: The ``HttpHeaders`` and ``Arguments`` arguments are also
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536 available, as for QIDO-RS, to fine-tune the parameters of the WADO-RS
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537 request.
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538
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539 Remark 3: As for QIDO-RS, the request is run synchronously by default.
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540 The ``Synchronous`` and ``Priority`` arguments can be used to
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541 asynchronously run the request.
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542
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543
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544
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545 Additional samples
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546 ------------------
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547
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548 Samples of how to call DICOMweb services from standalone applications
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549 are available for `Python
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550 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/Samples/Python/>`__
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551 and for `JavaScript
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552 <https://bitbucket.org/sjodogne/orthanc-dicomweb/src/default/Resources/Samples/JavaScript>`__.
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553
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554 Integration tests are `available separately
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555 <https://bitbucket.org/sjodogne/orthanc-tests/src/default/Plugins/DicomWeb/Run.py>`__,
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556 and provide samples for more advanced features of the REST API (such
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557 as dynamically adding/updating/removing remote DICOMweb servers using
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558 HTTP PUT and DELETE methods).