annotate Sphinx/source/users/lua.rst @ 402:5ed3e680364e

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date Mon, 27 Apr 2020 10:11:21 +0200
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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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15 Many other examples are `available in the source distribution
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16 <https://hg.orthanc-server.com/orthanc/file/default/Resources/Samples/Lua/>`__.
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18
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19 Installing a Lua script
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20 -----------------------
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21
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22 .. highlight:: bash
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23
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24 A custom Lua script can be installed either by the :ref:`configuration
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25 file <configuration>`, or by uploading it
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26 through the :ref:`REST API <rest-samples>`.
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28 To install it by the **configuration file** method, you just have to
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29 specify the path to the file containing the Lua script in the
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30 ``LuaScripts`` variable. A comma-separated list of paths can be
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31 specified to install multiple scripts.
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33 To upload a script stored in the file "``script.lua``" through the
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34 **REST API**, use the following command::
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36 $ curl -X POST http://localhost:8042/tools/execute-script --data-binary @script.lua
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37
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38 Pay attention to the fact that, contrarily to the scripts installed
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39 from the configuration file, the scripts installed through the REST
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40 API are non-persistent: They are discarded after a restart of Orthanc,
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41 which makes them useful for script prototyping. You can also interpret
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42 a single Lua command through the REST API::
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44 $ curl -X POST http://localhost:8042/tools/execute-script --data-binary "print(42)"
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45
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46 *Note:* The ``--data-binary`` cURL option is used instead of
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47 ``--data`` to prevent the interpretation of newlines by cURL, which is
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48 `mandatory for the proper evaluation
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49 <https://stackoverflow.com/questions/3872427/how-to-send-line-break-with-curl>`__
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50 of the possible comments inside the Lua script.
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52 Lua API
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53 -------
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54
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56 .. _lua-callbacks:
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57
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58 Callbacks to react to events
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59 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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60
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61 The Lua engine of Orthanc invokes the following callbacks that
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62 are triggered on various events. Here are the **generic events**:
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63
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64 * ``function Initialize()``: Invoked as soon as the Orthanc server is started.
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65 * ``function Finalize()``: Invoked just before the Orthanc server is stopped.
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66
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67 Some **permission-related events** allow to filter incoming requests:
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68
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69 * ``function ReceivedInstanceFilter(dicom, origin, info)``: Invoked to
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70 known whether an incoming DICOM instance should be
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71 accepted. :ref:`See this section <lua-filter-dicom>`. The ``origin``
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72 parameter is :ref:`documented separately <lua-origin>`. The ``info``
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73 parameter contains additional information and was added in Orthanc
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74 1.6.1.
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75 * ``function IncomingHttpRequestFilter(method, uri, ip, username,
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76 httpHeaders)``: Invoked to known whether a REST request should be
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77 accepted. :ref:`See this section <lua-filter-rest>`.
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78
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79 Some **job-related events** allow to react to :ref:`job <jobs>` completion/failure:
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81 * ``function OnJobSubmitted(jobId)``:
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82 Invoked when a new job has been submitted. Note that this does not
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83 mean the the job execution has started.
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84 * ``function OnJobFailure(jobId)``:
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85 Invoked when a job has failed.
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86 * ``function OnJobSuccess(jobId)``:
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87 Invoked when a job has completed successfully.
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88
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89 Some **DICOM-related events** allow to react to the reception of
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90 new medical images:
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91
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92 * ``function OnStoredInstance(instanceId, tags, metadata, origin)``:
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93 Invoked whenever a new instance has been stored into Orthanc.
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94 This is especially useful for :ref:`lua-auto-routing`. The ``origin``
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95 parameter is :ref:`documented separately <lua-origin>`.
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96 * ``function OnStablePatient(patientId, tags, metadata)``: Invoked
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97 whenever a patient has not received any new instance for a certain
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98 amount of time (cf. the option ``StableAge`` in the
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99 :ref:`configuration file <configuration>`). The :ref:`identifier
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100 <orthanc-ids>` of the patient is provided, together with her DICOM
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101 tags and her :ref:`metadata <metadata>`.
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102 * ``function OnStableSeries(seriesId, tags, metadata)``: Invoked
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103 whenever a series has not received any new instance for a certain
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104 amount of time.
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105 * ``function OnStableStudy(studyId, tags, metadata)``: Invoked
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106 whenever a study has not received any new instance for a certain
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107 amount of time.
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108 * ``function IncomingFindRequestFilter(source, origin)``: Invoked
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109 whenever Orthanc receives an incoming C-Find query through the DICOM
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110 protocol. This allows to inspect the content of the C-Find query,
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111 and possibly modify it if a patch is needed for some manufacturer. A
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112 `sample script is available
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113 <https://hg.orthanc-server.com/orthanc/file/default/Resources/Samples/Lua/IncomingFindRequestFilter.lua>`__.
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114
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115 Some other **resource-related events** are available:
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116
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117 * ``function OnDeletedPatient(patientId)``: Invoked when a patient has
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118 been removed from the Orthanc database (new in Orthanc 1.6.0).
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119 * ``function OnDeletedStudy(studyId)``: Invoked when a study has been
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120 removed from the Orthanc database (new in Orthanc 1.6.0).
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121 * ``function OnDeletedSeries(seriesId)``: Invoked when a series has
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122 been removed from the Orthanc database (new in Orthanc 1.6.0).
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123 * ``function OnDeletedInstance(instanceId)``: Invoked when a instance
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124 has been removed from the Orthanc database (new in Orthanc 1.6.0).
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125 * ``function OnUpdatedPatient(patientId)``: Invoked when some metadata
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126 or some attachment associated with the given patient has been
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127 updated (new in Orthanc 1.6.0).
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128 * ``function OnUpdatedStudy(studyId)``: Invoked when some metadata or
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129 some attachment associated with the given study has been updated
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130 (new in Orthanc 1.6.0).
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131 * ``function OnUpdatedSeries(seriesId)``: Invoked when some metadata
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132 or some attachment associated with the given series has been updated
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133 (new in Orthanc 1.6.0).
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134 * ``function OnUpdatedInstance(instanceId)``: Invoked when some
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135 metadata or some attachment associated with the given instance has
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136 been updated (new in Orthanc 1.6.0).
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137
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138 Furthermore, whenever a DICOM association is negotiated for C-Store
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139 SCP, several callbacks are successively invoked to specify which
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140 **transfer syntaxes** are accepted for the association. These
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141 callbacks are listed in `this sample script
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142 <https://hg.orthanc-server.com/orthanc/file/default/Resources/Samples/Lua/TransferSyntaxEnable.lua>`__.
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143
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144 *Note:* All of these callbacks are guaranteed to be **invoked in
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145 mutual exclusion**. This implies that Lua scripting in Orthanc does
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146 not support any kind of concurrency.
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147
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148 If a callback is specified multiple times in separate scripts, the
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149 event handler of the latest loaded script is used.
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150
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151
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152 .. _lua-rest:
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153
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154 Calling the REST API of Orthanc
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155 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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156
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157 Lua scripts have :ref:`full access to the REST API <rest>` of Orthanc
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158 through the following functions:
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159
252
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160 * ``RestApiGet(uri, builtin, headers)``
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161 * ``RestApiPost(uri, body, builtin, headers)``
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162 * ``RestApiPut(uri, body, builtin, headers)``
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163 * ``RestApiDelete(uri, builtin, headers)``
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164
237
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165 Here is a description of the parameters:
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166
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167 * ``uri`` specifies the resource being accessed
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168 (e.g. ``/instances``). It must not include the URL schema
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169 (protocol), hostname or port.
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170
237
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171 * In the context of a POST or PUT request, ``body`` is a string
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172 containing the body of the request
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173 (e.g. ``{"Keep":"StudyDate"}``). This string will often correspond
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174 to a JSON-formatted version of a `Lua table
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175 <http://lua-users.org/wiki/TablesTutorial>`__. The ``DumpJson()``
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176 function (see below) is very useful to achieve this conversion from
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177 a Lua table to a plain string.
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178
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179 * ``builtin`` is an optional Boolean that specifies whether the
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180 request targets only the built-in REST API of Orthanc (if set to
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181 ``true``), or the full the REST API after being tainted by plugins
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182 (if set to ``false``).
235
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183
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184 * ``headers`` is an optional argument and was added in release
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185 1.5.7. It allows to provide the REST API endpoint with HTTP headers.
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186
237
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187 .. highlight:: bash
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188
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189 For instance::
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190
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191 RestApiPost('/instances/5af318ac-78fb-47ff-b0b0-0df18b0588e0/anonymize', '{}')
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192
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193
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194 General-purpose functions
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195 ^^^^^^^^^^^^^^^^^^^^^^^^^
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196
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197 The Lua engine of Orthanc contain several general-purpose ancillary
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198 functions:
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199
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200 * ``PrintRecursive(v)`` recursively prints the content of a `Lua table
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201 <http://www.lua.org/pil/2.5.html>`__ to the log file of Orthanc.
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202 * ``ParseJson(s)`` converts a string encoded in the `JSON format
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203 <https://en.wikipedia.org/wiki/JSON>`__ to a Lua table.
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204 * ``DumpJson(v, keepStrings)`` encodes a Lua table as a JSON string.
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205 Setting the optional argument ``keepStrings`` (available from
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206 release 0.9.5) to ``true`` prevents the automatic conversion of
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207 strings to integers.
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208 * ``GetOrthancConfiguration()`` returns a Lua table containing the
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209 content of the :ref:`configuration files <configuration>` of
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210 Orthanc.
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211
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212
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213 Similarly to the functions to :ref:`call the REST API of Orthanc
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214 <lua-rest>`, several functions are available to make generic HTTP
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215 requests to Web services:
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216
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217 * ``HttpGet(url, headers)``
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218 * ``HttpPost(url, body, headers)``
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219 * ``HttpPut(url, body, headers)``
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220 * ``HttpDelete(url, headers)``
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221 * ``SetHttpCredentials(username, password)`` can be used to setup the
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222 HTTP credentials.
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223
252
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224 The ``headers`` argument is optional and was added in release
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225 1.2.1. It allows to set the HTTP headers for the HTTP client request.
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226
283
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227 Example::
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228
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229 local preview = RestApiGet('/instances/' .. instanceId .. '/preview')
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230 local headers = {
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231 ["content-type"] = "image/png",
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232 }
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233 HttpPost("http://localhost/my-web-service/instance-preview", preview, headers)
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234
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235 .. _lua-origin:
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236
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237 Origin of the instances
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238 ^^^^^^^^^^^^^^^^^^^^^^^
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239
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240 Whenever Orthanc decides whether it should should store a new instance
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241 (cf. the ``ReceivedInstanceFilter()`` callback), or whenever it has
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242 actually stored a new instance (cf. the ``OnStoredInstance``
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243 callback), an ``origin`` parameter is provided. This parameter is a
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244 `Lua table <http://www.lua.org/pil/2.5.html>`__ that describes from
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245 which Orthanc subsystem the new instance comes from.
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246
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247 There are 4 possible subsystems, that can be distinguished according
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248 to the value of ``origin["RequestOrigin"]``:
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249
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250 * ``RestApi``: The instance originates from some HTTP request to the REST
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251 API. In this case, the ``RemoteIp`` and ``Username`` fields are
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252 available in ``origin``. They respectively describe the IP address
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253 of the HTTP client, and the username that was used for HTTP
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254 authentication (as defined in the ``RegisteredUsers``
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255 :ref:`configuration variable <configuration>`).
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256 * ``DicomProtocol``: The instance originates from a DICOM C-Store.
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257 The fields ``RemoteIp``, ``RemoteAet`` and ``CalledAet``
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258 respectively provide the IP address of the DICOM SCU (client), the
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259 application entity title of the DICOM SCU client, and the
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260 application entity title of the Orthanc SCP server. The
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261 ``CalledAet`` can be used for :ref:`advanced auto-routing scenarios
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262 <lua-auto-routing>`, when a single instance of Orthanc acts as a
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263 proxy for several DICOM SCU clients.
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264 * ``Lua``: The instance originates from a Lua script.
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265 * ``Plugins``: The instance originates from a plugin.
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266
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267
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268 .. _lua-filter-dicom:
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269
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270 Filtering incoming DICOM instances
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271 ----------------------------------
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272
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273 .. highlight:: lua
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274
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275 Each time a DICOM instance is received by Orthanc (either through the
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276 DICOM protocol or through the REST API), the
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277 ``ReceivedInstanceFilter()`` Lua function is invoked. If this callback
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278 returns ``true``, the instance is accepted for storage. If it returns
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279 ``false``, the instance is discarded. This mechanism can be used to
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280 filter the incoming DICOM instances. Here is an example of a Lua
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281 filter that only allows incoming instances of MR modality::
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282
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283 function ReceivedInstanceFilter(dicom, origin, info)
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284 -- Only allow incoming MR images
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285 if dicom.Modality == 'MR' then
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286 return true
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287 else
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288 return false
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289 end
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290 end
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291
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292 The argument ``dicom`` corresponds to a `Lua table
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293 <http://www.lua.org/pil/2.5.html>`__ (i.e. an associative array) that
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294 contains the DICOM tags of the incoming instance. For debugging
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295 purpose, you can print this structure as follows::
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296
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297 function ReceivedInstanceFilter(dicom, origin, info)
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298 PrintRecursive(dicom)
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299 -- Accept all incoming instances (default behavior)
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300 return true
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301 end
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302
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303 The argument ``origin`` is :ref:`documented separately <lua-origin>`.
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304
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305 The argument ``info`` was introduced in Orthanc 1.6.1. It contains
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306 some additional information about the received DICOM instance,
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307 notably:
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308
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309 * ``HasPixelData`` is ``true`` iff. the Pixel Data (7FE0,0010) tag is
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310 present.
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311 * ``TransferSyntaxUID`` contains the transfer syntax UID of the
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312 dataset of the instance (if applicable).
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313
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314
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315 .. _lua-filter-rest:
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316
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317 Filtering incoming REST requests
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318 --------------------------------
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319
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320 .. highlight:: lua
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321
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322 Lua scripting can be used to control the access to the various URI of
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323 the REST API. Each time an incoming HTTP request is received, the
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324 ``IncomingHttpRequestFilter()`` Lua function is called. The access to
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325 the resource is granted if and only if this callback script returns
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326 ``true``.
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327
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328 This mechanism can be used to implement fine-grained `access control
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329 lists <https://en.wikipedia.org/wiki/Access_control_list>`__. Here is
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330 an example of a Lua script that limits POST, PUT and DELETE requests
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331 to an user that is called "admin"::
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332
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333 function IncomingHttpRequestFilter(method, uri, ip, username, httpHeaders)
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334 -- Only allow GET requests for non-admin users
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335
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336 if method == 'GET' then
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337 return true
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338 elseif username == 'admin' then
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339 return true
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340 else
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341 return false
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342 end
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343 end
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344
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345 Here is a description of the arguments of this Lua callback:
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346
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347 * ``method``: The HTTP method (GET, POST, PUT or DELETE).
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348 * ``uri``: The path to the resource (e.g. ``/tools/generate-uid``).
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349 * ``ip``: The IP address of the host that has issued the HTTP request (e.g. ``127.0.0.1``).
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350 * ``username``: If HTTP Basic Authentication is enabled in the
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351 :ref:`configuration file <configuration>`, the name of the user that
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352 has issued the HTTP request (as defined in the ``RegisteredUsers``
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353 configuration variable). If the authentication is disabled, this
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354 argument is set to the empty string.
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355 * ``httpHeaders``: The HTTP headers of the incoming request. This
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356 argument is available since Orthanc 1.0.1. It is useful if the
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357 authentication should be achieved through tokens, for instance
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358 against a `LDAP
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359 <https://en.wikipedia.org/wiki/Lightweight_Directory_Access_Protocol>`__
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360 or `OAuth2 <https://en.wikipedia.org/wiki/OAuth>`__ server.
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361
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362
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363 .. _lua-auto-routing:
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364
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365 Auto-routing of DICOM images
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366 ----------------------------
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367
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368 .. highlight:: lua
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369
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370 Since release 0.8.0, the routing of DICOM flows can be very easily
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371 automated with Orthanc. All you have to do is to declare your
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372 destination modality in the :ref:`configuration file <configuration>`
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373 (section ``DicomModalities``), then to create and install a Lua
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374 script. For instance, here is a sample script::
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375
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376 function OnStoredInstance(instanceId, tags, metadata)
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377 Delete(SendToModality(instanceId, 'sample'))
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378 end
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379
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380 If this script is loaded into Orthanc, whenever a new DICOM instance
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381 is received by Orthanc, it will be routed to the modality whose
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382 symbolic name is ``sample`` (through a Store-SCU command), then it
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383 will be removed from Orthanc. In other words, this is a **one-liner
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384 script to implement DICOM auto-routing**.
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385
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386 Very importantly, thanks to this feature, you do not have to use the
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387 REST API or to create external scripts in order to automate simple
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388 imaging flows. The scripting engine is entirely contained inside the
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389 Orthanc core system.
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390
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391 Thanks to Lua expressiveness, you can also implement conditional
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392 auto-routing. For instance, if you wish to route only patients whose
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393 name contains "David", you would simply write::
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394
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395 function OnStoredInstance(instanceId, tags, metadata)
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396 -- Extract the value of the "PatientName" DICOM tag
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397 local patientName = string.lower(tags['PatientName'])
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398
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399 if string.find(patientName, 'david') ~= nil then
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400 -- Only route patients whose name contains "David"
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401 Delete(SendToModality(instanceId, 'sample'))
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402
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403 else
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404 -- Delete the patients that are not called "David"
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405 Delete(instanceId)
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406 end
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407 end
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408
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409 Besides ``SendToModality()``, a mostly identical function with the
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410 same arguments called ``SendToPeer()`` can be used to route instances
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411 to :ref:`Orthanc peers <peers>`. It is also possible to modify the
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412 received instances before routing them. For instance, here is how you
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413 would replace the ``StationName`` DICOM tag::
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414
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415 function OnStoredInstance(instanceId, tags, metadata)
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416 -- Ignore the instances that result from a modification to avoid
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417 -- infinite loops
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418 if (metadata['ModifiedFrom'] == nil and
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419 metadata['AnonymizedFrom'] == nil) then
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420
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421 -- The tags to be replaced
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422 local replace = {}
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423 replace['StationName'] = 'My Medical Device'
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424
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425 -- The tags to be removed
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426 local remove = { 'MilitaryRank' }
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427
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428 -- Modify the instance, send it, then delete the modified instance
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429 Delete(SendToModality(ModifyInstance(instanceId, replace, remove, true), 'sample'))
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430
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431 -- Delete the original instance
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432 Delete(instanceId)
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433 end
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434 end
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435
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436
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437 Important remarks about auto-routing
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438 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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439
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440 The ``SendToModality()``, ``SendToPeer()``, ``ModifyInstance()`` and
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441 ``Delete()`` functions are for the most basic cases of auto-routing
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442 (implying a single DICOM instance, and possibly a basic modification
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443 of this instance). The ``ModifyInstance()`` function `could also lead
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444 to problems
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445 <https://groups.google.com/d/msg/orthanc-users/hmv2y-LgKm8/oMAuGJWMBgAJ>`__
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446 if it deals with tags wrongly interpreted as numbers by Lua.
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447
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448 For more evolved auto-routing scenarios, remember that Lua scripts
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449 :ref:`have full access to the REST API of Orthanc <lua-rest>`. This is
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450 illustrated by the ``AutoroutingModification.lua`` sample available in
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451 the source distribution of Orthanc::
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452
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453 function OnStoredInstance(instanceId, tags, metadata, origin)
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454 -- Ignore the instances that result from the present Lua script to
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455 -- avoid infinite loops
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456 if origin['RequestOrigin'] ~= 'Lua' then
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457
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458 -- The tags to be replaced
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459 local replace = {}
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460 replace['StationName'] = 'My Medical Device'
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461 replace['0031-1020'] = 'Some private tag'
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462
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463 -- The tags to be removed
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464 local remove = { 'MilitaryRank' }
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465
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466 -- Modify the instance
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467 local command = {}
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468 command['Replace'] = replace
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469 command['Remove'] = remove
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470 local modifiedFile = RestApiPost('/instances/' .. instanceId .. '/modify', DumpJson(command, true))
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471
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472 -- Upload the modified instance to the Orthanc database so that
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473 -- it can be sent by Orthanc to other modalities
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474 local modifiedId = ParseJson(RestApiPost('/instances/', modifiedFile)) ['ID']
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475
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476 -- Send the modified instance to another modality
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477 RestApiPost('/modalities/sample/store', modifiedId)
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478
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479 -- Delete the original and the modified instances
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480 RestApiDelete('/instances/' .. instanceId)
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481 RestApiDelete('/instances/' .. modifiedId)
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482 end
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483 end
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484
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485 Also note that :ref:`other callbacks are available <lua-callbacks>`
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486 (``OnStablePatient()``, ``OnStableStudy()`` and ``OnStableSeries()``)
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487 to react to other events than the reception of a single instance
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488 with ``OnStoredInstance()``.
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489
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490 .. _lua-fix-cfind:
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491
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492 Fixing C-Find requests
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493 ----------------------
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494
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495 :ref:`C-Find requests <dicom-find>` are sometimes interpreted
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496 differently by different DICOM servers (e.g. the ``*`` wildcard, as
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497 `reported by users
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498 <https://groups.google.com/d/msg/orthanc-users/3g7V7kqr3g0/IREL88RWAwAJ>`__),
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499 and sometimes a querying modality might set unexpected DICOM tags
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500 (cf. `this real-world example
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501 <https://groups.google.com/d/msg/orthanc-users/PLWKqVVaXLs/n_0x4vKhAgAJ>`__). In
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502 such situations, it is possible to dynamically fix incoming or
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503 outgoing C-Find queries using a Lua script.
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504
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505 Sanitizing incoming C-Find requests can be done by implementing the
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506 ``IncomingFindRequestFilter(query, origin)`` callback that is called
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507 whenever the Orthanc C-Find SCP is queried by a remote modality. For
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508 instance, here is Lua script to remove a private tag that is specified
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509 by some manufacturer::
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510
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511 function IncomingFindRequestFilter(query, origin)
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512 -- First display the content of the C-Find query
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513 PrintRecursive(query)
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514 PrintRecursive(origin)
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515
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516 -- Remove the "PrivateCreator" tag from the query
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517 local v = query
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518 v['5555,0010'] = nil
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519
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520 return v
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521 end
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522
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523 The ``origin`` argument contains information about which modality has
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524 issued the request.
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525
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526 Note that the ``IncomingFindRequestFilter`` callback is not applied to
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527 C-Find requests targeting :ref:`modality worklists
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528 <worklists-plugin>`. Since Orthanc 1.4.2, the corresponding
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529 ``IncomingWorklistRequestFilter`` callback can be used to sanitize
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530 C-FIND requests against worklists::
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531
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532 function IncomingWorklistRequestFilter(query, origin)
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533 PrintRecursive(query)
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534 PrintRecursive(origin)
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535
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536 -- Implements the same behavior as the "FilterIssuerAet"
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537 -- option of the sample worklist plugin
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538 query['0040,0100'][1]['0040,0001'] = origin['RemoteAet']
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539
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540 return query
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541 end
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542
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543 Similarly, the callback ``OutgoingFindRequestFilter(query, modality)``
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544 is invoked whenever Orthanc acts as a C-Find SCU, which gives the
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545 opportunity to dynamically fix outgoing C-Find requests before they
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546 are actually sent to the queried modality. For instance, here is a
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547 sample Lua callback that would replace asterisk wildcards (i.e. ``*``)
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548 by an empty string for any query/retrieve issued by Orthanc (including
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549 from Orthanc Explorer)::
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550
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551 function OutgoingFindRequestFilter(query, modality)
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552 for key, value in pairs(query) do
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553 if value == '*' then
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554 query[key] = ''
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555 end
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556 end
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557
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558 return query
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559 end