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annotate Sphinx/source/users/lua.rst @ 610:ec8a9bcf1cdf

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removing list of freelancers
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 01 Feb 2021 12:04:35 +0100
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1 .. _lua:
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2
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3 Server-side scripting with Lua
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4 ==============================
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5
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6 .. contents::
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7
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8 Since release 0.5.2, Orthanc supports server-side scripting through
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9 the `Lua <https://en.wikipedia.org/wiki/Lua_(programming_language)>`__
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10 scripting language. Thanks to this major feature, Orthanc can be tuned
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11 to specific medical workflows without being driven by an external
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12 script. This page summarizes the possibilities of Orthanc server-side
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13 scripting.
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14
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15 Many other examples are `available in the source distribution
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16 <https://hg.orthanc-server.com/orthanc/file/default/OrthancServer/Resources/Samples/Lua/>`__.
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17
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18 A more expressive alternative to Lua scripts is provided by
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19 :ref:`Python plugins <python-plugins>`.
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20
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21
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22 Installing a Lua script
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23 -----------------------
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24
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25 .. highlight:: bash
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27 A custom Lua script can be installed either by the :ref:`configuration
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28 file <configuration>`, or by uploading it
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29 through the :ref:`REST API <rest-samples>`.
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30
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31 To install it by the **configuration file** method, you just have to
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32 specify the path to the file containing the Lua script in the
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33 ``LuaScripts`` variable. A comma-separated list of paths can be
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34 specified to install multiple scripts.
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35
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36 To upload a script stored in the file "``script.lua``" through the
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37 **REST API**, use the following command::
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38
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39 $ curl -X POST http://localhost:8042/tools/execute-script --data-binary @script.lua
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40
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41 Pay attention to the fact that, contrarily to the scripts installed
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42 from the configuration file, the scripts installed through the REST
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43 API are non-persistent: They are discarded after a restart of Orthanc,
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44 which makes them useful for script prototyping. You can also interpret
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45 a single Lua command through the REST API::
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46
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47 $ curl -X POST http://localhost:8042/tools/execute-script --data-binary "print(42)"
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48
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49 *Note:* The ``--data-binary`` cURL option is used instead of
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50 ``--data`` to prevent the interpretation of newlines by cURL, which is
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51 `mandatory for the proper evaluation
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52 <https://stackoverflow.com/questions/3872427/how-to-send-line-break-with-curl>`__
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53 of the possible comments inside the Lua script.
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55 Lua API
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56 -------
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59 .. _lua-callbacks:
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60
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61 Callbacks to react to events
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62 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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63
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64 The Lua engine of Orthanc invokes the following callbacks that
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65 are triggered on various events. Here are the **generic events**:
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66
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67 * ``function Initialize()``: Invoked as soon as the Orthanc server is started.
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68 * ``function Finalize()``: Invoked just before the Orthanc server is stopped.
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69
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70 Some **permission-related events** allow to filter incoming requests:
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71
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72 * ``function ReceivedInstanceFilter(dicom, origin, info)``: Invoked to
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73 known whether an incoming DICOM instance should be
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74 accepted. :ref:`See this section <lua-filter-dicom>`. The ``origin``
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75 parameter is :ref:`documented separately <lua-origin>`. The ``info``
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76 parameter contains additional information and was added in Orthanc
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77 1.6.1.
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78 * ``function IncomingHttpRequestFilter(method, uri, ip, username,
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79 httpHeaders)``: Invoked to known whether a REST request should be
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80 accepted. :ref:`See this section <lua-filter-rest>`.
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81
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82 Some **job-related events** allow to react to :ref:`job <jobs>` completion/failure:
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83
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84 * ``function OnJobSubmitted(jobId)``:
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85 Invoked when a new job has been submitted. Note that this does not
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86 mean the the job execution has started.
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87 * ``function OnJobFailure(jobId)``:
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88 Invoked when a job has failed.
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89 * ``function OnJobSuccess(jobId)``:
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90 Invoked when a job has completed successfully.
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91
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92 Some **DICOM-related events** allow to react to the reception of
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93 new medical images:
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94
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95 * ``function OnStoredInstance(instanceId, tags, metadata, origin)``:
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96 Invoked whenever a new instance has been stored into Orthanc.
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97 This is especially useful for :ref:`lua-auto-routing`. The ``origin``
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98 parameter is :ref:`documented separately <lua-origin>`.
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99 * ``function OnStablePatient(patientId, tags, metadata)``: Invoked
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100 whenever a patient has not received any new instance for a certain
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101 amount of time (cf. the option ``StableAge`` in the
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102 :ref:`configuration file <configuration>`). The :ref:`identifier
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103 <orthanc-ids>` of the patient is provided, together with her DICOM
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104 tags and her :ref:`metadata <metadata>`.
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105 * ``function OnStableSeries(seriesId, tags, metadata)``: Invoked
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106 whenever a series has not received any new instance for a certain
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107 amount of time.
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108 * ``function OnStableStudy(studyId, tags, metadata)``: Invoked
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109 whenever a study has not received any new instance for a certain
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110 amount of time.
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111 * ``function IncomingFindRequestFilter(source, origin)``: Invoked
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112 whenever Orthanc receives an incoming C-Find query through the DICOM
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113 protocol. This allows to inspect the content of the C-Find query,
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114 and possibly modify it if a patch is needed for some manufacturer. A
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115 `sample script is available
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116 <https://hg.orthanc-server.com/orthanc/file/default/OrthancServer/Resources/Samples/Lua/IncomingFindRequestFilter.lua>`__.
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117
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118 Some other **resource-related events** are available:
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119
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120 * ``function OnDeletedPatient(patientId)``: Invoked when a patient has
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121 been removed from the Orthanc database (new in Orthanc 1.6.0).
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122 * ``function OnDeletedStudy(studyId)``: Invoked when a study has been
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123 removed from the Orthanc database (new in Orthanc 1.6.0).
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124 * ``function OnDeletedSeries(seriesId)``: Invoked when a series has
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125 been removed from the Orthanc database (new in Orthanc 1.6.0).
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126 * ``function OnDeletedInstance(instanceId)``: Invoked when a instance
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127 has been removed from the Orthanc database (new in Orthanc 1.6.0).
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128 * ``function OnUpdatedPatient(patientId)``: Invoked when some metadata
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129 or some attachment associated with the given patient has been
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130 updated (new in Orthanc 1.6.0).
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131 * ``function OnUpdatedStudy(studyId)``: Invoked when some metadata or
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132 some attachment associated with the given study has been updated
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133 (new in Orthanc 1.6.0).
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134 * ``function OnUpdatedSeries(seriesId)``: Invoked when some metadata
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135 or some attachment associated with the given series has been updated
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136 (new in Orthanc 1.6.0).
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137 * ``function OnUpdatedInstance(instanceId)``: Invoked when some
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138 metadata or some attachment associated with the given instance has
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139 been updated (new in Orthanc 1.6.0).
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141 Furthermore, in versions of Orthanc <= 1.8.2, whenever a DICOM
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142 association is negotiated for C-Store SCP, several callbacks are
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143 successively invoked to specify which **transfer syntaxes** are
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144 accepted for the association. These callbacks are listed in `this
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145 sample script
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146 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.8.2/OrthancServer/Resources/Samples/Lua/TransferSyntaxEnable.lua>`__.
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147 These callbacks were removed in Orthanc 1.9.0.
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148
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149 *Note:* All of these callbacks are guaranteed to be **invoked in
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150 mutual exclusion**. This implies that Lua scripting in Orthanc does
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151 not support any kind of concurrency.
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152
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153 If a callback is specified multiple times in separate scripts, the
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154 event handler of the latest loaded script is used.
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155
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156
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157 .. _lua-rest:
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158
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159 Calling the REST API of Orthanc
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160 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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161
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162 Lua scripts have :ref:`full access to the REST API <rest>` of Orthanc
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163 through the following functions:
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164
252
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165 * ``RestApiGet(uri, builtin, headers)``
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166 * ``RestApiPost(uri, body, builtin, headers)``
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167 * ``RestApiPut(uri, body, builtin, headers)``
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168 * ``RestApiDelete(uri, builtin, headers)``
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169
237
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170 Here is a description of the parameters:
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171
237
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172 * ``uri`` specifies the resource being accessed
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173 (e.g. ``/instances``). It must not include the URL schema
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174 (protocol), hostname or port.
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175
237
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176 * In the context of a POST or PUT request, ``body`` is a string
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177 containing the body of the request
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178 (e.g. ``{"Keep":"StudyDate"}``). This string will often correspond
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179 to a JSON-formatted version of a `Lua table
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180 <http://lua-users.org/wiki/TablesTutorial>`__. The ``DumpJson()``
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181 function (see below) is very useful to achieve this conversion from
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182 a Lua table to a plain string.
235
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183
237
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184 * ``builtin`` is an optional Boolean that specifies whether the
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185 request targets only the built-in REST API of Orthanc (if set to
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186 ``true``), or the full the REST API after being tainted by plugins
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187 (if set to ``false``).
235
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188
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189 * ``headers`` is an optional argument and was added in release
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190 1.5.7. It allows to provide the REST API endpoint with HTTP headers.
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191
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192 .. highlight:: bash
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193
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194 For instance::
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195
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196 RestApiPost('/instances/5af318ac-78fb-47ff-b0b0-0df18b0588e0/anonymize', '{}')
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197
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198
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199 General-purpose functions
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200 ^^^^^^^^^^^^^^^^^^^^^^^^^
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201
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202 The Lua engine of Orthanc contain several general-purpose ancillary
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203 functions:
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204
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205 * ``PrintRecursive(v)`` recursively prints the content of a `Lua table
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206 <http://www.lua.org/pil/2.5.html>`__ to the log file of Orthanc.
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207 * ``ParseJson(s)`` converts a string encoded in the `JSON format
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208 <https://en.wikipedia.org/wiki/JSON>`__ to a Lua table.
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209 * ``DumpJson(v, keepStrings)`` encodes a Lua table as a JSON string.
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210 Setting the optional argument ``keepStrings`` (available from
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211 release 0.9.5) to ``true`` prevents the automatic conversion of
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212 strings to integers.
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213 * ``GetOrthancConfiguration()`` returns a Lua table containing the
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214 content of the :ref:`configuration files <configuration>` of
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215 Orthanc.
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216
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217
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218 Similarly to the functions to :ref:`call the REST API of Orthanc
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219 <lua-rest>`, several functions are available to make generic HTTP
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220 requests to Web services:
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221
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222 * ``HttpGet(url, headers)``
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223 * ``HttpPost(url, body, headers)``
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224 * ``HttpPut(url, body, headers)``
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225 * ``HttpDelete(url, headers)``
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226 * ``SetHttpCredentials(username, password)`` can be used to setup the
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227 HTTP credentials.
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228
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229 The ``headers`` argument is optional and was added in release
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230 1.2.1. It allows to set the HTTP headers for the HTTP client request.
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231
283
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232 Example::
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233
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234 local preview = RestApiGet('/instances/' .. instanceId .. '/preview')
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235 local headers = {
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236 ["content-type"] = "image/png",
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237 }
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238 HttpPost("http://localhost/my-web-service/instance-preview", preview, headers)
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239
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240 .. _lua-origin:
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241
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242 Origin of the instances
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243 ^^^^^^^^^^^^^^^^^^^^^^^
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244
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245 Whenever Orthanc decides whether it should should store a new instance
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246 (cf. the ``ReceivedInstanceFilter()`` callback), or whenever it has
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247 actually stored a new instance (cf. the ``OnStoredInstance``
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248 callback), an ``origin`` parameter is provided. This parameter is a
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249 `Lua table <http://www.lua.org/pil/2.5.html>`__ that describes from
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250 which Orthanc subsystem the new instance comes from.
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251
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252 There are 4 possible subsystems, that can be distinguished according
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253 to the value of ``origin["RequestOrigin"]``:
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254
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255 * ``RestApi``: The instance originates from some HTTP request to the REST
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256 API. In this case, the ``RemoteIp`` and ``Username`` fields are
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257 available in ``origin``. They respectively describe the IP address
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258 of the HTTP client, and the username that was used for HTTP
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259 authentication (as defined in the ``RegisteredUsers``
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260 :ref:`configuration variable <configuration>`).
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261 * ``DicomProtocol``: The instance originates from a DICOM C-Store.
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262 The fields ``RemoteIp``, ``RemoteAet`` and ``CalledAet``
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263 respectively provide the IP address of the DICOM SCU (client), the
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264 application entity title of the DICOM SCU client, and the
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265 application entity title of the Orthanc SCP server. The
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266 ``CalledAet`` can be used for :ref:`advanced auto-routing scenarios
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267 <lua-auto-routing>`, when a single instance of Orthanc acts as a
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268 proxy for several DICOM SCU clients.
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269 * ``Lua``: The instance originates from a Lua script.
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270 * ``Plugins``: The instance originates from a plugin.
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271
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272
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273 .. _lua-filter-dicom:
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274
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275 Filtering incoming DICOM instances
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276 ----------------------------------
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277
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278 .. highlight:: lua
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279
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280 Each time a DICOM instance is received by Orthanc (either through the
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281 DICOM protocol or through the REST API), the
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282 ``ReceivedInstanceFilter()`` Lua function is invoked. If this callback
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283 returns ``true``, the instance is accepted for storage. If it returns
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284 ``false``, the instance is discarded. This mechanism can be used to
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285 filter the incoming DICOM instances. Here is an example of a Lua
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286 filter that only allows incoming instances of MR modality::
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287
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288 function ReceivedInstanceFilter(dicom, origin, info)
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289 -- Only allow incoming MR images
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290 if dicom.Modality == 'MR' then
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291 return true
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292 else
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293 return false
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294 end
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295 end
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296
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297 The argument ``dicom`` corresponds to a `Lua table
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298 <http://www.lua.org/pil/2.5.html>`__ (i.e. an associative array) that
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299 contains the DICOM tags of the incoming instance. For debugging
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300 purpose, you can print this structure as follows::
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301
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302 function ReceivedInstanceFilter(dicom, origin, info)
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303 PrintRecursive(dicom)
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304 -- Accept all incoming instances (default behavior)
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305 return true
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306 end
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307
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308 The argument ``origin`` is :ref:`documented separately <lua-origin>`.
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309
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310 The argument ``info`` was introduced in Orthanc 1.6.1. It contains
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311 some additional information about the received DICOM instance,
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312 notably:
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313
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314 * ``HasPixelData`` is ``true`` iff. the Pixel Data (7FE0,0010) tag is
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315 present.
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316 * ``TransferSyntaxUID`` contains the transfer syntax UID of the
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317 dataset of the instance (if applicable).
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318
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319
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320 .. _lua-filter-rest:
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321
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322 Filtering incoming REST requests
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323 --------------------------------
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324
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325 .. highlight:: lua
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326
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327 Lua scripting can be used to control the access to the various URI of
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328 the REST API. Each time an incoming HTTP request is received, the
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329 ``IncomingHttpRequestFilter()`` Lua function is called. The access to
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330 the resource is granted if and only if this callback script returns
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331 ``true``.
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332
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333 This mechanism can be used to implement fine-grained `access control
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334 lists <https://en.wikipedia.org/wiki/Access_control_list>`__. Here is
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335 an example of a Lua script that limits POST, PUT and DELETE requests
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336 to an user that is called "admin"::
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337
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338 function IncomingHttpRequestFilter(method, uri, ip, username, httpHeaders)
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339 -- Only allow GET requests for non-admin users
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340
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341 if method == 'GET' then
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342 return true
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343 elseif username == 'admin' then
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344 return true
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345 else
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346 return false
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347 end
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348 end
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349
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350 Here is a description of the arguments of this Lua callback:
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351
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352 * ``method``: The HTTP method (GET, POST, PUT or DELETE).
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353 * ``uri``: The path to the resource (e.g. ``/tools/generate-uid``).
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354 * ``ip``: The IP address of the host that has issued the HTTP request (e.g. ``127.0.0.1``).
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355 * ``username``: If HTTP Basic Authentication is enabled in the
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356 :ref:`configuration file <configuration>`, the name of the user that
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357 has issued the HTTP request (as defined in the ``RegisteredUsers``
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358 configuration variable). If the authentication is disabled, this
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359 argument is set to the empty string.
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360 * ``httpHeaders``: The HTTP headers of the incoming request. This
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361 argument is available since Orthanc 1.0.1. It is useful if the
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362 authentication should be achieved through tokens, for instance
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363 against a `LDAP
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364 <https://en.wikipedia.org/wiki/Lightweight_Directory_Access_Protocol>`__
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365 or `OAuth2 <https://en.wikipedia.org/wiki/OAuth>`__ server.
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366
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367
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368 .. _lua-auto-routing:
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369
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370 Auto-routing of DICOM images
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371 ----------------------------
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372
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373 .. highlight:: lua
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374
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375 Since release 0.8.0, the routing of DICOM flows can be very easily
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376 automated with Orthanc. All you have to do is to declare your
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377 destination modality in the :ref:`configuration file <configuration>`
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378 (section ``DicomModalities``), then to create and install a Lua
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379 script. For instance, here is a sample script::
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380
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381 function OnStoredInstance(instanceId, tags, metadata)
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382 Delete(SendToModality(instanceId, 'sample'))
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383 end
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384
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385 If this script is loaded into Orthanc, whenever a new DICOM instance
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386 is received by Orthanc, it will be routed to the modality whose
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387 symbolic name is ``sample`` (through a Store-SCU command), then it
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388 will be removed from Orthanc. In other words, this is a **one-liner
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389 script to implement DICOM auto-routing**.
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390
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391 Very importantly, thanks to this feature, you do not have to use the
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392 REST API or to create external scripts in order to automate simple
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393 imaging flows. The scripting engine is entirely contained inside the
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394 Orthanc core system.
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395
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396 Thanks to Lua expressiveness, you can also implement conditional
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397 auto-routing. For instance, if you wish to route only patients whose
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398 name contains "David", you would simply write::
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399
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400 function OnStoredInstance(instanceId, tags, metadata)
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401 -- Extract the value of the "PatientName" DICOM tag
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402 local patientName = string.lower(tags['PatientName'])
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403
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404 if string.find(patientName, 'david') ~= nil then
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405 -- Only route patients whose name contains "David"
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406 Delete(SendToModality(instanceId, 'sample'))
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407
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408 else
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409 -- Delete the patients that are not called "David"
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410 Delete(instanceId)
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411 end
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412 end
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413
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414 Besides ``SendToModality()``, a mostly identical function with the
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415 same arguments called ``SendToPeer()`` can be used to route instances
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416 to :ref:`Orthanc peers <peers>`. It is also possible to modify the
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417 received instances before routing them. For instance, here is how you
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418 would replace the ``StationName`` DICOM tag::
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419
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420 function OnStoredInstance(instanceId, tags, metadata)
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421 -- Ignore the instances that result from a modification to avoid
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422 -- infinite loops
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423 if (metadata['ModifiedFrom'] == nil and
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424 metadata['AnonymizedFrom'] == nil) then
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425
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426 -- The tags to be replaced
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427 local replace = {}
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428 replace['StationName'] = 'My Medical Device'
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429
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430 -- The tags to be removed
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431 local remove = { 'MilitaryRank' }
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432
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433 -- Modify the instance, send it, then delete the modified instance
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434 Delete(SendToModality(ModifyInstance(instanceId, replace, remove, true), 'sample'))
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435
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436 -- Delete the original instance
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437 Delete(instanceId)
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438 end
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439 end
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440
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441
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442 Important remarks about auto-routing
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443 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
19
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444
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445 The ``SendToModality()``, ``SendToPeer()``, ``ModifyInstance()`` and
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446 ``Delete()`` functions are for the most basic cases of auto-routing
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447 (implying a single DICOM instance, and possibly a basic modification
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448 of this instance). The ``ModifyInstance()`` function `could also lead
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449 to problems
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450 <https://groups.google.com/d/msg/orthanc-users/hmv2y-LgKm8/oMAuGJWMBgAJ>`__
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451 if it deals with tags wrongly interpreted as numbers by Lua.
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452
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453 For more evolved auto-routing scenarios, remember that Lua scripts
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454 :ref:`have full access to the REST API of Orthanc <lua-rest>`. This is
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455 illustrated by the ``AutoroutingModification.lua`` sample available in
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456 the source distribution of Orthanc::
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457
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458 function OnStoredInstance(instanceId, tags, metadata, origin)
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459 -- Ignore the instances that result from the present Lua script to
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460 -- avoid infinite loops
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461 if origin['RequestOrigin'] ~= 'Lua' then
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462
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463 -- The tags to be replaced
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464 local replace = {}
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465 replace['StationName'] = 'My Medical Device'
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466 replace['0031-1020'] = 'Some private tag'
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467
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468 -- The tags to be removed
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469 local remove = { 'MilitaryRank' }
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470
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471 -- Modify the instance
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472 local command = {}
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473 command['Replace'] = replace
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474 command['Remove'] = remove
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475 local modifiedFile = RestApiPost('/instances/' .. instanceId .. '/modify', DumpJson(command, true))
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476
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477 -- Upload the modified instance to the Orthanc database so that
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478 -- it can be sent by Orthanc to other modalities
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479 local modifiedId = ParseJson(RestApiPost('/instances/', modifiedFile)) ['ID']
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480
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481 -- Send the modified instance to another modality
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482 RestApiPost('/modalities/sample/store', modifiedId)
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483
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484 -- Delete the original and the modified instances
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485 RestApiDelete('/instances/' .. instanceId)
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486 RestApiDelete('/instances/' .. modifiedId)
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487 end
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488 end
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489
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490 Also note that :ref:`other callbacks are available <lua-callbacks>`
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491 (``OnStablePatient()``, ``OnStableStudy()`` and ``OnStableSeries()``)
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492 to react to other events than the reception of a single instance
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493 with ``OnStoredInstance()``.
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494
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495 .. _lua-fix-cfind:
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496
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497 Fixing C-Find requests
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498 ----------------------
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499
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500 :ref:`C-Find requests <dicom-find>` are sometimes interpreted
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501 differently by different DICOM servers (e.g. the ``*`` wildcard, as
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502 `reported by users
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503 <https://groups.google.com/d/msg/orthanc-users/3g7V7kqr3g0/IREL88RWAwAJ>`__),
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504 and sometimes a querying modality might set unexpected DICOM tags
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505 (cf. `this real-world example
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506 <https://groups.google.com/d/msg/orthanc-users/PLWKqVVaXLs/n_0x4vKhAgAJ>`__). In
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507 such situations, it is possible to dynamically fix incoming or
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508 outgoing C-Find queries using a Lua script.
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509
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510 Sanitizing incoming C-Find requests can be done by implementing the
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511 ``IncomingFindRequestFilter(query, origin)`` callback that is called
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512 whenever the Orthanc C-Find SCP is queried by a remote modality. For
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513 instance, here is Lua script to remove a private tag that is specified
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514 by some manufacturer::
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515
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516 function IncomingFindRequestFilter(query, origin)
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517 -- First display the content of the C-Find query
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518 PrintRecursive(query)
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519 PrintRecursive(origin)
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520
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521 -- Remove the "PrivateCreator" tag from the query
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522 local v = query
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523 v['5555,0010'] = nil
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524
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525 return v
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526 end
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527
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528 The ``origin`` argument contains information about which modality has
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529 issued the request.
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530
443
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531 Note that this callback allows you to modify the incoming request
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532 but will not modify the list of tags that Orthanc will return.
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533
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534 Also note that the ``IncomingFindRequestFilter`` callback is not applied to
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535 C-Find requests targeting :ref:`modality worklists
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536 <worklists-plugin>`. Since Orthanc 1.4.2, the corresponding
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diff changeset
537 ``IncomingWorklistRequestFilter`` callback can be used to sanitize
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538 C-FIND requests against worklists::
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539
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diff changeset
540 function IncomingWorklistRequestFilter(query, origin)
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541 PrintRecursive(query)
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diff changeset
542 PrintRecursive(origin)
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diff changeset
543
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544 -- Implements the same behavior as the "FilterIssuerAet"
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545 -- option of the sample worklist plugin
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diff changeset
546 query['0040,0100'][1]['0040,0001'] = origin['RemoteAet']
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547
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diff changeset
548 return query
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diff changeset
549 end
105
268ec482f051 IncomingFindRequestFilter not applied to worklist plugin
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550
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551
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552 Similarly, the callback ``OutgoingFindRequestFilter(query, modality)``
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553 is invoked whenever Orthanc acts as a C-Find SCU, which gives the
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554 opportunity to dynamically fix outgoing C-Find requests before they
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555 are actually sent to the queried modality. For instance, here is a
48c7d2eb98da Fixing C-Find requests
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556 sample Lua callback that would replace asterisk wildcards (i.e. ``*``)
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557 by an empty string for any query/retrieve issued by Orthanc (including
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558 from Orthanc Explorer)::
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559
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560 function OutgoingFindRequestFilter(query, modality)
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561 for key, value in pairs(query) do
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562 if value == '*' then
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563 query[key] = ''
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564 end
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565 end
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566
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567 return query
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568 end