annotate Sphinx/source/users/lua.rst @ 247:325dd3901547

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Sun, 19 May 2019 10:08:52 +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://bitbucket.org/sjodogne/orthanc/src/default/Resources/Samples/Lua/>`__.
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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.
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32 To upload a script stored in the file "``script.lua``" through the
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33 **REST API**, use the following command::
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35 $ curl -X POST http://localhost:8042/tools/execute-script --data-binary @script.lua
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36
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37 Pay attention to the fact that, contrarily to the scripts installed
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38 from the configuration file, the scripts installed through the REST
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39 API are non-persistent: They are discarded after a restart of Orthanc,
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40 which makes them useful for script prototyping. You can also interpret
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41 a single Lua command through the REST API::
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42
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43 $ curl -X POST http://localhost:8042/tools/execute-script --data-binary "print(42)"
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44
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45 *Note:* The ``--data-binary`` cURL option is used instead of
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46 ``--data`` to prevent the interpretation of newlines by cURL, which is
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47 `mandatory for the proper evaluation
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48 <http://stackoverflow.com/questions/3872427/how-to-send-line-break-with-curl>`__ of the possible
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49 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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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 comes 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)``:
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70 Invoked to 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>`.
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73 * ``function IncomingHttpRequestFilter(method, uri, ip, username,
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74 httpHeaders)``: Invoked to known whether a REST request should be
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75 accepted. :ref:`See this section <lua-filter-rest>`.
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76
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77 Some **job-related events** allow to react to :ref:`job <jobs>` completion/failure:
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79 * ``function OnJobSubmitted(jobId)``:
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80 Invoked when a new job has been submitted. Note that this does not
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81 mean the the job execution has started.
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82 * ``function OnJobFailure(jobId)``:
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83 Invoked when a job has failed.
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84 * ``function OnJobSuccess(jobId)``:
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85 Invoked when a job has completed successfully.
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86
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87 Some **DICOM-related events** allow to react to the reception of
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88 new medical images:
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89
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90 * ``function OnStoredInstance(instanceId, tags, metadata, origin)``:
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91 Invoked whenever a new instance has been stored into Orthanc.
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92 This is especially useful for :ref:`lua-auto-routing`. The ``origin``
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93 parameter is :ref:`documented separately <lua-origin>`.
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94 * ``function OnStablePatient(patientId, tags, metadata)``: Invoked
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95 whenever a patient has not received any new instance for a certain
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96 amount of time (cf. the option ``StableAge`` in the
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97 :ref:`configuration file <configuration>`). The :ref:`identifier
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98 <orthanc-ids>` of the patient is provided, together with her DICOM
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99 tags and her :ref:`metadata <metadata>`.
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100 * ``function OnStableSeries(seriesId, tags, metadata)``: Invoked
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101 whenever a series has not received any new instance for a certain
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102 amount of time.
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103 * ``function OnStableStudy(studyId, tags, metadata)``: Invoked
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104 whenever a study has not received any new instance for a certain
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105 amount of time.
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106 * ``function IncomingFindRequestFilter(source, origin)``: Invoked
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107 whenever Orthanc receives an incoming C-Find query through the DICOM
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108 protocol. This allows to inspect the content of the C-Find query,
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109 and possibly modify it if a patch is needed for some manufacturer. A
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110 `sample script is available
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111 <https://bitbucket.org/sjodogne/orthanc/src/default/Resources/Samples/Lua/IncomingFindRequestFilter.lua>`__.
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112
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113 Furthermore, whenever a DICOM association is negotiated for C-Store
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114 SCP, several callbacks are successively invoked to specify which
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115 **transfer syntaxes** are accepted for the association. These
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116 callbacks are listed in `this sample script
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117 <https://bitbucket.org/sjodogne/orthanc/src/default/Resources/Samples/Lua/TransferSyntaxEnable.lua>`__.
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118
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119 *Note:* All of these callbacks are guaranteed to be **invoked in
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120 mutual exclusion**. This implies that Lua scripting in Orthanc does
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121 not support any kind of concurrency.
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122
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123
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124 .. _lua-rest:
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125
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126 Calling the REST API of Orthanc
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127 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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128
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129 Lua scripts have :ref:`full access to the REST API <rest>` of Orthanc
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130 through the following functions:
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131
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132 * ``RestApiGet(uri, builtin)``
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133 * ``RestApiPost(uri, body, builtin)``
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134 * ``RestApiPut(uri, body, builtin)``
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135 * ``RestApiDelete(uri, builtin)``
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136
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137 Here is a description of the parameters:
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138
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139 * ``uri`` specifies the resource being accessed
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140 (e.g. ``/instances``). It must not include the URL schema
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141 (protocol), hostname or port.
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143 * In the context of a POST or PUT request, ``body`` is a string
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144 containing the body of the request
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145 (e.g. ``{"Keep":"StudyDate"}``). This string will often correspond
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146 to a JSON-formatted version of a `Lua table
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147 <http://lua-users.org/wiki/TablesTutorial>`__. The ``DumpJson()``
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148 function (see below) is very useful to achieve this conversion from
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149 a Lua table to a plain string.
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151 * ``builtin`` is an optional Boolean that specifies whether the
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152 request targets only the built-in REST API of Orthanc (if set to
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153 ``true``), or the full the REST API after being tainted by plugins
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154 (if set to ``false``).
235
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155
237
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156 .. highlight:: bash
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157
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158 For instance::
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159
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160 RestApiPost('/instances/5af318ac-78fb-47ff-b0b0-0df18b0588e0/anonymize', '{}')
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161
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162
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163 General-purpose functions
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164 ^^^^^^^^^^^^^^^^^^^^^^^^^
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165
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166 The Lua engine of Orthanc contain several general-purpose ancillary
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167 functions:
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168
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169 * ``PrintRecursive(v)`` recursively prints the content of a `Lua table
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170 <http://www.lua.org/pil/2.5.html>`__ to the log file of Orthanc.
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171 * ``ParseJson(s)`` converts a string encoded in the `JSON format
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172 <https://en.wikipedia.org/wiki/JSON>`__ to a Lua table.
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173 * ``DumpJson(v, keepStrings)`` encodes a Lua table as a JSON string.
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174 Setting the optional argument ``keepStrings`` (available from
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175 release 0.9.5) to ``true`` prevents the automatic conversion of
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176 strings to integers.
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177 * ``GetOrthancConfiguration()`` returns a Lua table containing the
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178 content of the :ref:`configuration files <configuration>` of
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179 Orthanc.
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180
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181
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182 Similarly to the functions to :ref:`call the REST API of Orthanc
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183 <lua-rest>`, several functions are available to make generic HTTP
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184 requests to Web services:
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185
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186 * ``HttpGet(url, headers)``
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187 * ``HttpPost(url, body, headers)``
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188 * ``HttpPut(url, body, headers)``
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189 * ``HttpDelete(url, headers)``
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190 * ``SetHttpCredentials(username, password)`` can be used to setup the
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191 HTTP credentials.
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192
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193 The ``headers`` argument is optional and has been added in release
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194 1.2.1. It allows to set the HTTP headers for the HTTP client request.
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195
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196 .. _lua-origin:
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197
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198 Origin of the instances
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199 ^^^^^^^^^^^^^^^^^^^^^^^
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200
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201 Whenever Orthanc decides whether it should should store a new instance
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202 (cf. the ``ReceivedInstanceFilter()`` callback), or whenever it has
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203 actually stored a new instance (cf. the ``OnStoredInstance``
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204 callback), an ``origin`` parameter is provided. This parameter is a
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205 `Lua table <http://www.lua.org/pil/2.5.html>`__ that describes from
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206 which Orthanc subsystem the new instance comes from.
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207
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208 There are 4 possible subsystems, that can be distinguished according
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209 to the value of ``origin["RequestOrigin"]``:
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210
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211 * ``RestApi``: The instance originates from some HTTP request to the REST
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212 API. In this case, the ``RemoteIp`` and ``Username`` fields are
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213 available in ``origin``. They respectively describe the IP address
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214 of the HTTP client, and the username that was used for HTTP
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215 authentication (as defined in the ``RegisteredUsers``
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216 :ref:`configuration variable <configuration>`).
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217 * ``DicomProtocol``: The instance originates from a DICOM C-Store.
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218 The fields ``RemoteIp``, ``RemoteAet`` and ``CalledAet``
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219 respectively provide the IP address of the DICOM SCU (client), the
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220 application entity title of the DICOM SCU client, and the
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221 application entity title of the Orthanc SCP server. The
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222 ``CalledAet`` can be used for :ref:`advanced auto-routing scenarios
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223 <lua-auto-routing>`, when a single instance of Orthanc acts as a
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224 proxy for several DICOM SCU clients.
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225 * ``Lua``: The instance originates from a Lua script.
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226 * ``Plugins``: The instance originates from a plugin.
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227
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228
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229 .. _lua-filter-dicom:
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230
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231 Filtering incoming DICOM instances
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232 ----------------------------------
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233
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234 .. highlight:: lua
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235
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236 Each time a DICOM instance is received by Orthanc (either through the
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237 DICOM protocol or through the REST API), the
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238 ``ReceivedInstanceFilter()`` Lua function is invoked. If this callback
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239 returns ``true``, the instance is accepted for storage. If it returns
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240 ``false``, the instance is discarded. This mechanism can be used to
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241 filter the incoming DICOM instances. Here is an example of a Lua
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242 filter that only allows incoming instances of MR modality::
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243
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244 function ReceivedInstanceFilter(dicom, origin)
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245 -- Only allow incoming MR images
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246 if dicom.Modality == 'MR' then
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247 return true
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248 else
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249 return false
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250 end
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251 end
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252
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253 The argument dicom corresponds to a `Lua table
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254 <http://www.lua.org/pil/2.5.html>`__ (i.e. an associative array) that
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255 contains the DICOM tags of the incoming instance. For debugging
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256 purpose, you can print this structure as follows::
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257
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258 function ReceivedInstanceFilter(dicom, origin)
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259 PrintRecursive(dicom)
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260 -- Accept all incoming instances (default behavior)
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261 return true
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262 end
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263
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264 The argument ``origin`` is :ref:`documented separately <lua-origin>`.
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265
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266
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267 .. _lua-filter-rest:
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268
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269 Filtering incoming REST requests
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270 --------------------------------
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271
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272 .. highlight:: lua
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273
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274 Lua scripting can be used to control the access to the various URI of
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275 the REST API. Each time an incoming HTTP request is received, the
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276 ``IncomingHttpRequestFilter()`` Lua function is called. The access to
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277 the resource is granted if and only if this callback script returns
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278 ``true``.
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279
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280 This mechanism can be used to implement fine-grained `access control
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281 lists <https://en.wikipedia.org/wiki/Access_control_list>`__. Here is
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282 an example of a Lua script that limits POST, PUT and DELETE requests
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283 to an user that is called "admin"::
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284
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285 function IncomingHttpRequestFilter(method, uri, ip, username, httpHeaders)
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286 -- Only allow GET requests for non-admin users
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287
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288 if method == 'GET' then
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289 return true
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290 elseif username == 'admin' 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 Here is a description of the arguments of this Lua callback:
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298
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299 * ``method``: The HTTP method (GET, POST, PUT or DELETE).
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300 * ``uri``: The path to the resource (e.g. ``/tools/generate-uid``).
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301 * ``ip``: The IP address of the host that has issued the HTTP request (e.g. ``127.0.0.1``).
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302 * ``username``: If HTTP Basic Authentication is enabled in the
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303 :ref:`configuration file <configuration>`, the name of the user that
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304 has issued the HTTP request (as defined in the ``RegisteredUsers``
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305 configuration variable). If the authentication is disabled, this
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306 argument is set to the empty string.
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307 * ``httpHeaders``: The HTTP headers of the incoming request. This
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308 argument is available since Orthanc 1.0.1. It is useful if the
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309 authentication should be achieved through tokens, for instance
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310 against a `LDAP
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311 <https://en.wikipedia.org/wiki/Lightweight_Directory_Access_Protocol>`__
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312 or `OAuth2 <https://en.wikipedia.org/wiki/OAuth>`__ server.
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313
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314
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315 .. _lua-auto-routing:
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316
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317 Auto-routing of DICOM images
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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 Since release 0.8.0, the routing of DICOM flows can be very easily
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323 automated with Orthanc. All you have to do is to declare your
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324 destination modality in the :ref:`configuration file <configuration>`
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325 (section ``DicomModalities``), then to create and install a Lua
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326 script. For instance, here is a sample script::
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327
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328 function OnStoredInstance(instanceId, tags, metadata)
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329 Delete(SendToModality(instanceId, 'sample'))
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330 end
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331
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332 If this script is loaded into Orthanc, whenever a new DICOM instance
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333 is received by Orthanc, it will be routed to the modality whose
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334 symbolic name is ``sample`` (through a Store-SCU command), then it
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335 will be removed from Orthanc. In other words, this is a **one-liner
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336 script to implement DICOM auto-routing**.
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337
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338 Very importantly, thanks to this feature, you do not have to use the
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339 REST API or to create external scripts in order to automate simple
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340 imaging flows. The scripting engine is entirely contained inside the
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341 Orthanc core system.
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342
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343 Thanks to Lua expressiveness, you can also implement conditional
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344 auto-routing. For instance, if you wish to route only patients whose
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345 name contains "David", you would simply write::
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346
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347 function OnStoredInstance(instanceId, tags, metadata)
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348 -- Extract the value of the "PatientName" DICOM tag
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349 local patientName = string.lower(tags['PatientName'])
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350
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351 if string.find(patientName, 'david') ~= nil then
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352 -- Only route patients whose name contains "David"
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353 Delete(SendToModality(instanceId, 'sample'))
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354
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355 else
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356 -- Delete the patients that are not called "David"
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357 Delete(instanceId)
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358 end
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359 end
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360
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361 Besides ``SendToModality()``, a mostly identical function with the
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362 same arguments called ``SendToPeer()`` can be used to route instances
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363 to :ref:`Orthanc peers <peers>`. It is also possible to modify the
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364 received instances before routing them. For instance, here is how you
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365 would replace the ``StationName`` DICOM tag::
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366
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367 function OnStoredInstance(instanceId, tags, metadata)
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368 -- Ignore the instances that result from a modification to avoid
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369 -- infinite loops
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370 if (metadata['ModifiedFrom'] == nil and
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371 metadata['AnonymizedFrom'] == nil) then
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372
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373 -- The tags to be replaced
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374 local replace = {}
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375 replace['StationName'] = 'My Medical Device'
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376
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377 -- The tags to be removed
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378 local remove = { 'MilitaryRank' }
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379
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380 -- Modify the instance, send it, then delete the modified instance
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381 Delete(SendToModality(ModifyInstance(instanceId, replace, remove, true), 'sample'))
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382
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383 -- Delete the original instance
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384 Delete(instanceId)
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385 end
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386 end
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387
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388
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389 Important remarks about auto-routing
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390 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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391
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392 The ``SendToModality()``, ``SendToPeer()``, ``ModifyInstance()`` and
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393 ``Delete()`` functions are for the most basic cases of auto-routing
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394 (implying a single DICOM instance, and possibly a basic modification
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395 of this instance). The ``ModifyInstance()`` function `could also lead
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396 to problems
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397 <https://groups.google.com/d/msg/orthanc-users/hmv2y-LgKm8/oMAuGJWMBgAJ>`__
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398 if it deals with tags wrongly interpreted as numbers by Lua.
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399
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400 For more evolved auto-routing scenarios, remember that Lua scripts
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401 :ref:`have full access to the REST API of Orthanc <lua-rest>`. This is
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402 illustrated by the ``AutoroutingModification.lua`` sample available in
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403 the source distribution of Orthanc::
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404
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405 function OnStoredInstance(instanceId, tags, metadata, origin)
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406 -- Ignore the instances that result from the present Lua script to
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407 -- avoid infinite loops
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408 if origin['RequestOrigin'] ~= 'Lua' then
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409
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410 -- The tags to be replaced
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411 local replace = {}
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412 replace['StationName'] = 'My Medical Device'
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413 replace['0031-1020'] = 'Some private tag'
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414
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415 -- The tags to be removed
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416 local remove = { 'MilitaryRank' }
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417
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418 -- Modify the instance
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419 local command = {}
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420 command['Replace'] = replace
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421 command['Remove'] = remove
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422 local modifiedFile = RestApiPost('/instances/' .. instanceId .. '/modify', DumpJson(command, true))
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423
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424 -- Upload the modified instance to the Orthanc database so that
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425 -- it can be sent by Orthanc to other modalities
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426 local modifiedId = ParseJson(RestApiPost('/instances/', modifiedFile)) ['ID']
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427
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428 -- Send the modified instance to another modality
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429 RestApiPost('/modalities/sample/store', modifiedId)
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430
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431 -- Delete the original and the modified instances
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432 RestApiDelete('/instances/' .. instanceId)
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433 RestApiDelete('/instances/' .. modifiedId)
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434 end
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435 end
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436
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437 Also note that :ref:`other callbacks are available <lua-callbacks>`
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438 (``OnStablePatient()``, ``OnStableStudy()`` and ``OnStableSeries()``)
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439 to react to other events than the reception of a single instance
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440 with ``OnStoredInstance()``.
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441
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442 .. _lua-fix-cfind:
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443
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444 Fixing C-Find requests
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445 ----------------------
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446
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447 :ref:`C-Find requests <dicom-find>` are sometimes interpreted
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448 differently by different DICOM servers (e.g. the ``*`` wildcard, as
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449 `reported by users
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450 <https://groups.google.com/d/msg/orthanc-users/3g7V7kqr3g0/IREL88RWAwAJ>`__),
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451 and sometimes a querying modality might set unexpected DICOM tags
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452 (cf. `this real-world example
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453 <https://groups.google.com/d/msg/orthanc-users/PLWKqVVaXLs/n_0x4vKhAgAJ>`__). In
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454 such situations, it is possible to dynamically fix incoming or
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455 outgoing C-Find queries using a Lua script.
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456
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457 Sanitizing incoming C-Find requests can be done by implementing the
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458 ``IncomingFindRequestFilter(query, origin)`` callback that is called
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459 whenever the Orthanc C-Find SCP is queried by a remote modality. For
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460 instance, here is Lua script to remove a private tag that is specified
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461 by some manufacturer::
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462
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463 function IncomingFindRequestFilter(query, origin)
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464 -- First display the content of the C-Find query
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465 PrintRecursive(query)
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466 PrintRecursive(origin)
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467
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468 -- Remove the "PrivateCreator" tag from the query
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469 local v = query
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470 v['5555,0010'] = nil
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471
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472 return v
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473 end
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474
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475 The ``origin`` argument contains information about which modality has
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476 issued the request.
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477
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478 Note that the ``IncomingFindRequestFilter`` callback is not applied to
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479 C-Find requests targeting :ref:`modality worklists
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480 <worklists-plugin>`. Since Orthanc 1.4.2, the corresponding
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481 ``IncomingWorklistRequestFilter`` callback can be used to sanitize
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482 C-FIND requests against worklists::
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483
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484 function IncomingWorklistRequestFilter(query, origin)
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485 PrintRecursive(query)
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486 PrintRecursive(origin)
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487
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488 -- Implements the same behavior as the "FilterIssuerAet"
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489 -- option of the sample worklist plugin
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490 query['0040,0100'][1]['0040,0001'] = origin['RemoteAet']
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491
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492 return query
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493 end
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494
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495 Similarly, the callback ``OutgoingFindRequestFilter(query, modality)``
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496 is invoked whenever Orthanc acts as a C-Find SCU, which gives the
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497 opportunity to dynamically fix outgoing C-Find requests before they
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498 are actually sent to the queried modality. For instance, here is a
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499 sample Lua callback that would replace asterisk wildcards (i.e. ``*``)
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500 by an empty string for any query/retrieve issued by Orthanc (including
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501 from Orthanc Explorer)::
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502
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503 function OutgoingFindRequestFilter(query, modality)
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504 for key, value in pairs(query) do
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505 if value == '*' then
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506 query[key] = ''
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507 end
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508 end
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509
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510 return query
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511 end