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annotate Sphinx/source/users/lua.rst @ 105:268ec482f051
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| author | amazy |
|---|---|
| date | Thu, 13 Jul 2017 13:05:54 +0200 |
| parents | e83da2f99e45 |
| children | b879a6274065 |
| rev | line source |
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| 0 | 1 .. _lua: |
| 2 | |
| 3 Server-side scripting with Lua | |
| 4 ============================== | |
| 5 | |
| 6 .. contents:: | |
| 7 | |
| 8 Since release 0.5.2, Orthanc supports server-side scripting through | |
| 25 | 9 the `Lua <https://en.wikipedia.org/wiki/Lua_(programming_language)>`__ |
| 0 | 10 scripting language. Thanks to this major feature, Orthanc can be tuned |
| 11 to specific medical workflows without being driven by an external | |
| 12 script. This page summarizes the possibilities of Orthanc server-side | |
| 13 scripting. | |
| 14 | |
| 15 Many other examples are `available in the source distribution | |
| 16 <https://bitbucket.org/sjodogne/orthanc/src/default/Resources/Samples/Lua/>`__. | |
| 17 | |
| 18 | |
| 75 | 19 Installing a Lua script |
| 0 | 20 ----------------------- |
| 21 | |
| 22 .. highlight:: bash | |
| 23 | |
| 24 A custom Lua script can be installed either by the :ref:`configuration | |
| 25 file <configuration>`, or by uploading it | |
| 26 through the :ref:`REST API <rest-samples>`. | |
| 27 | |
| 28 To install it by the **configuration file** method, you just have to | |
| 29 specify the path to the file containing the Lua script in the | |
| 30 ``LuaScripts`` variable. | |
| 31 | |
| 32 To upload a script stored in the file "``script.lua``" through the | |
| 33 **REST API**, use the following command:: | |
| 34 | |
| 35 $ curl -X POST http://localhost:8042/tools/execute-script --data-binary @script.lua | |
| 36 | |
| 37 Pay attention to the fact that, contrarily to the scripts installed | |
| 38 from the configuration file, the scripts installed through the REST | |
| 39 API are non-persistent: They are discarded after a restart of Orthanc, | |
| 40 which makes them useful for script prototyping. You can also interpret | |
| 41 a single Lua command through the REST API:: | |
| 42 | |
| 43 $ curl -X POST http://localhost:8042/tools/execute-script --data-binary "print(42)" | |
| 44 | |
| 45 *Note:* The ``--data-binary`` cURL option is used instead of | |
| 46 ``--data`` to prevent the interpretation of newlines by cURL, which is | |
| 47 `mandatory for the proper evaluation | |
| 25 | 48 <http://stackoverflow.com/questions/3872427/how-to-send-line-break-with-curl>`__ of the possible |
| 0 | 49 comments inside the Lua script. |
| 50 | |
| 51 | |
| 52 Lua API | |
| 53 ------- | |
| 54 | |
| 55 | |
| 56 .. _lua-callbacks: | |
| 57 | |
| 58 Callbacks to react to events | |
| 59 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 60 | |
| 61 The Lua engine of Orthanc comes invokes the following callbacks that | |
| 62 are triggered on various events. Here are the **generic events**: | |
| 63 | |
| 64 * ``function Initialize()``: Invoked as soon as the Orthanc server is started. | |
| 65 * ``function Finalize()``: Invoked just before the Orthanc server is stopped. | |
| 66 | |
| 67 Some **permission-related events** allow to filter incoming requests: | |
| 68 | |
| 69 * ``function ReceivedInstanceFilter(dicom, origin)``: | |
| 70 Invoked to known whether an incoming DICOM instance should be | |
| 71 accepted. :ref:`See this section <lua-filter-dicom>`. The ``origin`` | |
| 72 parameter is :ref:`documented separately <lua-origin>`. | |
| 73 * ``function IncomingHttpRequestFilter(method, uri, ip, username, | |
| 74 httpHeaders)``: Invoked to known whether a REST request should be | |
| 75 accepted. :ref:`See this section <lua-filter-rest>`. | |
| 76 | |
| 77 Some **DICOM-related events** allow to react to the reception of | |
| 78 new medical images: | |
| 79 | |
| 80 * ``function OnStoredInstance(instanceId, tags, metadata, origin)``: | |
| 81 Invoked whenever a new instance has been stored into Orthanc. | |
| 82 This is especially useful for :ref:`lua-auto-routing`. The ``origin`` | |
| 83 parameter is :ref:`documented separately <lua-origin>`. | |
| 84 * ``function OnStablePatient(patientId, tags, metadata)``: Invoked | |
| 85 whenever a patient has not received any new instance for a certain | |
| 86 amount of time (cf. the option ``StableAge`` in the | |
| 87 :ref:`configuration file <configuration>`). The :ref:`identifier | |
| 88 <orthanc-ids>` of the patient is provided, together with her DICOM | |
| 78 | 89 tags and her :ref:`metadata <metadata>`. |
| 0 | 90 * ``function OnStableSeries(seriesId, tags, metadata)``: Invoked |
| 91 whenever a series has not received any new instance for a certain | |
| 92 amount of time. | |
| 93 * ``function OnStableStudy(studyId, tags, metadata)``: Invoked | |
| 94 whenever a study has not received any new instance for a certain | |
| 95 amount of time. | |
| 96 * ``function IncomingFindRequestFilter(source, origin)``: Invoked | |
| 97 whenever Orthanc receives an incoming C-Find query through the DICOM | |
| 98 protocol. This allows to inspect the content of the C-Find query, | |
| 99 and possibly modify it if a patch is needed for some manufacturer. A | |
| 100 `sample script is available | |
| 101 <https://bitbucket.org/sjodogne/orthanc/src/default/Resources/Samples/Lua/IncomingFindRequestFilter.lua>`__. | |
| 102 | |
|
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103 Furthermore, whenever a DICOM association is negotiated for C-Store |
| 0 | 104 SCP, several callbacks are successively invoked to specify which |
| 105 **transfer syntaxes** are accepted for the association. These | |
| 106 callbacks are listed in `this sample script | |
| 107 <https://bitbucket.org/sjodogne/orthanc/src/default/Resources/Samples/Lua/TransferSyntaxEnable.lua>`__. | |
| 108 | |
| 109 *Note:* All of these callbacks are guaranteed to be **invoked in | |
| 110 mutual exclusion**. This implies that Lua scripting in Orthanc does | |
| 111 not support any kind of concurrency. | |
| 112 | |
| 113 | |
| 114 .. _lua-rest: | |
| 115 | |
| 116 Calling the REST API of Orthanc | |
| 117 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 118 | |
| 119 Lua scripts have :ref:`full access to the REST API <rest>` of Orthanc | |
| 120 through the following functions: | |
| 121 | |
| 122 * ``RestApiGet(uri, builtin)`` | |
| 123 * ``RestApiPost(uri, body, builtin)`` | |
| 124 * ``RestApiPut(uri, body, builtin)`` | |
| 125 * ``RestApiDelete(uri, builtin)`` | |
| 126 | |
| 127 The ``uri`` arguments specifies the URI against which to make the | |
| 128 request, and ``body`` is a string containing the body of POST/PUT | |
| 129 request. The ``builtin`` parameter is an optional Boolean that | |
| 130 specifies whether the request targets only the built-in REST API of | |
| 131 Orthanc (if set to ``true``), or the full the REST API after being | |
| 132 tainted by the plugins (if set to ``false``). | |
| 133 | |
| 134 | |
| 135 General-purpose functions | |
| 136 ^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 137 | |
| 138 The Lua engine of Orthanc contain several general-purpose ancillary | |
| 139 functions: | |
| 140 | |
| 141 * ``PrintRecursive(v)`` recursively prints the content of a `Lua table | |
| 142 <http://www.lua.org/pil/2.5.html>`__ to the log file of Orthanc. | |
| 143 * ``ParseJson(s)`` converts a string encoded in the `JSON format | |
| 144 <https://en.wikipedia.org/wiki/JSON>`__ to a Lua table. | |
| 145 * ``DumpJson(v, keepStrings)`` encodes a Lua table as a JSON string. | |
| 146 Setting the optional argument ``keepStrings`` (available from | |
| 147 release 0.9.5) to ``true`` prevents the automatic conversion of | |
| 148 strings to integers. | |
| 149 * ``GetOrthancConfiguration()`` returns a Lua table containing the | |
| 150 content of the :ref:`configuration files <configuration>` of | |
| 151 Orthanc. | |
| 152 | |
| 153 | |
| 154 Similarly to the functions to :ref:`call the REST API of Orthanc | |
| 155 <lua-rest>`, several functions are available to make generic HTTP | |
| 156 requests to Web services: | |
| 157 | |
| 90 | 158 * ``HttpGet(url, headers)`` |
| 159 * ``HttpPost(url, body, headers)`` | |
| 160 * ``HttpPut(url, body, headers)`` | |
| 161 * ``HttpDelete(url, headers)`` | |
| 0 | 162 * ``SetHttpCredentials(username, password)`` can be used to setup the |
| 163 HTTP credentials. | |
| 164 | |
| 91 | 165 The ``headers`` argument is optional and has been added in release |
| 166 1.2.1. It allows to set the HTTP headers for the HTTP client request. | |
| 0 | 167 |
| 168 .. _lua-origin: | |
| 169 | |
| 170 Origin of the instances | |
| 171 ^^^^^^^^^^^^^^^^^^^^^^^ | |
| 172 | |
| 173 Whenever Orthanc decides whether it should should store a new instance | |
| 174 (cf. the ``ReceivedInstanceFilter()`` callback), or whenever it has | |
| 175 actually stored a new instance (cf. the ``OnStoredInstance`` | |
| 176 callback), an ``origin`` parameter is provided. This parameter is a | |
| 177 `Lua table <http://www.lua.org/pil/2.5.html>`__ that describes from | |
| 178 which Orthanc subsystem the new instance comes from. | |
| 179 | |
| 180 There are 4 possible subsystems, that can be distinguished according | |
| 181 to the value of ``origin["RequestOrigin"]``: | |
| 182 | |
| 183 * ``RestApi``: The instance originates from some HTTP request to the REST | |
| 184 API. In this case, the ``RemoteIp`` and ``Username`` fields are | |
| 185 available in ``origin``. They respectively describe the IP address | |
| 186 of the HTTP client, and the username that was used for HTTP | |
| 187 authentication (as defined in the ``RegisteredUsers`` | |
| 188 :ref:`configuration variable <configuration>`). | |
| 189 * ``DicomProtocol``: The instance originates from a DICOM C-Store. | |
| 190 The fields ``RemoteIp``, ``RemoteAet`` and ``CalledAet`` | |
| 191 respectively provide the IP address of the DICOM SCU (client), the | |
| 192 application entity title of the DICOM SCU client, and the | |
| 193 application entity title of the Orthanc SCP server. The | |
| 194 ``CalledAet`` can be used for :ref:`advanced auto-routing scenarios | |
| 195 <lua-auto-routing>`, when a single instance of Orthanc acts as a | |
| 196 proxy for several DICOM SCU clients. | |
| 197 * ``Lua``: The instance originates from a Lua script. | |
| 198 * ``Plugins``: The instance originates from a plugin. | |
| 199 | |
| 200 | |
| 201 .. _lua-filter-dicom: | |
| 202 | |
| 75 | 203 Filtering incoming DICOM instances |
| 0 | 204 ---------------------------------- |
| 205 | |
| 206 .. highlight:: lua | |
| 207 | |
| 208 Each time a DICOM instance is received by Orthanc (either through the | |
| 209 DICOM protocol or through the REST API), the | |
| 210 ``ReceivedInstanceFilter()`` Lua function is invoked. If this callback | |
| 211 returns ``true``, the instance is accepted for storage. If it returns | |
| 212 ``false``, the instance is discarded. This mechanism can be used to | |
| 213 filter the incoming DICOM instances. Here is an example of a Lua | |
| 214 filter that only allows incoming instances of MR modality:: | |
| 215 | |
| 216 function ReceivedInstanceFilter(dicom, origin) | |
| 217 -- Only allow incoming MR images | |
| 218 if dicom.Modality == 'MR' then | |
| 219 return true | |
| 220 else | |
| 221 return false | |
| 222 end | |
| 223 end | |
| 224 | |
| 225 The argument dicom corresponds to a `Lua table | |
| 226 <http://www.lua.org/pil/2.5.html>`__ (i.e. an associative array) that | |
| 227 contains the DICOM tags of the incoming instance. For debugging | |
| 228 purpose, you can print this structure as follows:: | |
| 229 | |
| 230 function ReceivedInstanceFilter(dicom, origin) | |
| 231 PrintRecursive(dicom) | |
| 232 -- Accept all incoming instances (default behavior) | |
| 233 return true | |
| 234 end | |
| 235 | |
| 236 The argument ``origin`` is :ref:`documented separately <lua-origin>`. | |
| 237 | |
| 238 | |
| 239 .. _lua-filter-rest: | |
| 240 | |
| 75 | 241 Filtering incoming REST requests |
| 0 | 242 -------------------------------- |
| 243 | |
| 244 .. highlight:: lua | |
| 245 | |
| 246 Lua scripting can be used to control the access to the various URI of | |
| 247 the REST API. Each time an incoming HTTP request is received, the | |
| 248 ``IncomingHttpRequestFilter()`` Lua function is called. The access to | |
| 249 the resource is granted if and only if this callback script returns | |
| 250 ``true``. | |
| 251 | |
| 252 This mechanism can be used to implement fine-grained `access control | |
| 25 | 253 lists <https://en.wikipedia.org/wiki/Access_control_list>`__. Here is |
| 0 | 254 an example of a Lua script that limits POST, PUT and DELETE requests |
| 255 to an user that is called "admin":: | |
| 256 | |
| 257 function IncomingHttpRequestFilter(method, uri, ip, username, httpHeaders) | |
| 258 -- Only allow GET requests for non-admin users | |
| 259 | |
| 260 if method == 'GET' then | |
| 261 return true | |
| 262 elseif username == 'admin' then | |
| 263 return true | |
| 264 else | |
| 265 return false | |
| 266 end | |
| 267 end | |
| 268 | |
| 269 Here is a description of the arguments of this Lua callback: | |
| 270 | |
| 271 * ``method``: The HTTP method (GET, POST, PUT or DELETE). | |
| 272 * ``uri``: The path to the resource (e.g. ``/tools/generate-uid``). | |
| 273 * ``ip``: The IP address of the host that has issued the HTTP request (e.g. ``127.0.0.1``). | |
| 274 * ``username``: If HTTP Basic Authentication is enabled in the | |
| 275 :ref:`configuration file <configuration>`, the name of the user that | |
| 276 has issued the HTTP request (as defined in the ``RegisteredUsers`` | |
| 277 configuration variable). If the authentication is disabled, this | |
| 278 argument is set to the empty string. | |
| 279 * ``httpHeaders``: The HTTP headers of the incoming request. This | |
| 280 argument is available since Orthanc 1.0.1. It is useful if the | |
| 281 authentication should be achieved through tokens, for instance | |
| 282 against a `LDAP | |
| 283 <https://en.wikipedia.org/wiki/Lightweight_Directory_Access_Protocol>`__ | |
| 284 or `OAuth2 <https://en.wikipedia.org/wiki/OAuth>`__ server. | |
| 285 | |
| 286 | |
| 287 .. _lua-auto-routing: | |
| 288 | |
| 75 | 289 Auto-routing of DICOM images |
| 0 | 290 ---------------------------- |
| 291 | |
| 292 .. highlight:: lua | |
| 293 | |
| 294 Since release 0.8.0, the routing of DICOM flows can be very easily | |
| 295 automated with Orthanc. All you have to do is to declare your | |
| 296 destination modality in the :ref:`configuration file <configuration>` | |
| 297 (section ``DicomModalities``), then to create and install a Lua | |
| 298 script. For instance, here is a sample script:: | |
| 299 | |
| 300 function OnStoredInstance(instanceId, tags, metadata) | |
| 301 Delete(SendToModality(instanceId, 'sample')) | |
| 302 end | |
| 303 | |
| 304 If this script is loaded into Orthanc, whenever a new DICOM instance | |
| 305 is received by Orthanc, it will be routed to the modality whose | |
| 306 symbolic name is ``sample`` (through a Store-SCU command), then it | |
| 307 will be removed from Orthanc. In other words, this is a **one-liner | |
| 308 script to implement DICOM auto-routing**. | |
| 309 | |
| 310 Very importantly, thanks to this feature, you do not have to use the | |
| 311 REST API or to create external scripts in order to automate simple | |
| 312 imaging flows. The scripting engine is entirely contained inside the | |
| 313 Orthanc core system. | |
| 314 | |
| 315 Thanks to Lua expressiveness, you can also implement conditional | |
| 316 auto-routing. For instance, if you wish to route only patients whose | |
| 317 name contains "David", you would simply write:: | |
| 318 | |
| 319 function OnStoredInstance(instanceId, tags, metadata) | |
| 320 -- Extract the value of the "PatientName" DICOM tag | |
| 321 local patientName = string.lower(tags['PatientName']) | |
| 322 | |
| 323 if string.find(patientName, 'david') ~= nil then | |
| 324 -- Only route patients whose name contains "David" | |
| 325 Delete(SendToModality(instanceId, 'sample')) | |
| 326 | |
| 327 else | |
| 328 -- Delete the patients that are not called "David" | |
| 329 Delete(instanceId) | |
| 330 end | |
| 331 end | |
| 332 | |
| 333 Besides ``SendToModality()``, a mostly identical function with the | |
| 334 same arguments called ``SendToPeer()`` can be used to route instances | |
| 335 to :ref:`Orthanc peers <peers>`. It is also possible to modify the | |
| 336 received instances before routing them. For instance, here is how you | |
| 337 would replace the ``StationName`` DICOM tag:: | |
| 338 | |
| 339 function OnStoredInstance(instanceId, tags, metadata) | |
| 340 -- Ignore the instances that result from a modification to avoid | |
| 341 -- infinite loops | |
| 342 if (metadata['ModifiedFrom'] == nil and | |
| 343 metadata['AnonymizedFrom'] == nil) then | |
| 344 | |
| 345 -- The tags to be replaced | |
| 346 local replace = {} | |
| 347 replace['StationName'] = 'My Medical Device' | |
| 348 | |
| 349 -- The tags to be removed | |
| 350 local remove = { 'MilitaryRank' } | |
| 351 | |
| 352 -- Modify the instance, send it, then delete the modified instance | |
| 353 Delete(SendToModality(ModifyInstance(instanceId, replace, remove, true), 'sample')) | |
| 354 | |
| 355 -- Delete the original instance | |
| 356 Delete(instanceId) | |
| 357 end | |
| 358 end | |
| 359 | |
| 360 | |
| 75 | 361 Important remarks about auto-routing |
| 362 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
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363 |
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364 The ``SendToModality()``, ``SendToPeer()``, ``ModifyInstance()`` and |
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365 ``Delete()`` functions are for the most basic cases of auto-routing |
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366 (implying a single DICOM instance, and possibly a basic modification |
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367 of this instance). The ``ModifyInstance()`` function `could also lead |
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368 to problems |
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369 <https://groups.google.com/d/msg/orthanc-users/hmv2y-LgKm8/oMAuGJWMBgAJ>`__ |
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370 if it deals with tags wrongly interpreted as numbers by Lua. |
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371 |
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372 For more evolved auto-routing scenarios, remember that Lua scripts |
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373 :ref:`have full to the REST API of Orthanc <lua-rest>`. This is |
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374 illustrated by the ``AutoroutingModification.lua`` sample available in |
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375 the source distribution of Orthanc:: |
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376 |
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377 function OnStoredInstance(instanceId, tags, metadata, origin) |
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378 -- Ignore the instances that result from the present Lua script to |
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379 -- avoid infinite loops |
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380 if origin['RequestOrigin'] ~= 'Lua' then |
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381 |
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382 -- The tags to be replaced |
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383 local replace = {} |
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384 replace['StationName'] = 'My Medical Device' |
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385 replace['0031-1020'] = 'Some private tag' |
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386 |
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387 -- The tags to be removed |
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388 local remove = { 'MilitaryRank' } |
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389 |
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390 -- Modify the instance |
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391 local command = {} |
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392 command['Replace'] = replace |
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393 command['Remove'] = remove |
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394 local modifiedFile = RestApiPost('/instances/' .. instanceId .. '/modify', DumpJson(command, true)) |
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395 |
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396 -- Upload the modified instance to the Orthanc database so that |
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397 -- it can be sent by Orthanc to other modalities |
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398 local modifiedId = ParseJson(RestApiPost('/instances/', modifiedFile)) ['ID'] |
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399 |
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400 -- Send the modified instance to another modality |
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401 RestApiPost('/modalities/sample/store', modifiedId) |
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402 |
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403 -- Delete the original and the modified instances |
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404 RestApiDelete('/instances/' .. instanceId) |
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405 RestApiDelete('/instances/' .. modifiedId) |
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406 end |
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407 end |
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408 |
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409 Also note that :ref:`other callbacks are available <lua-callbacks>` |
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410 (``OnStablePatient()``, ``OnStableStudy()`` and ``OnStableSeries()``) |
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411 to react to other events than the reception of a single instance |
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412 with ``OnStoredInstance()``. |
| 75 | 413 |
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414 .. _lua-fix-cfind: |
| 75 | 415 |
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416 Fixing C-Find requests |
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417 ---------------------- |
| 75 | 418 |
| 419 :ref:`C-Find requests <dicom-find>` are sometimes interpreted | |
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420 differently by different DICOM servers (e.g. the ``*`` wildcard, as |
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421 `reported by users |
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422 <https://groups.google.com/d/msg/orthanc-users/3g7V7kqr3g0/IREL88RWAwAJ>`__), |
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423 and sometimes a querying modality might set unexpected DICOM tags |
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424 (cf. `this real-world example |
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425 <https://groups.google.com/d/msg/orthanc-users/PLWKqVVaXLs/n_0x4vKhAgAJ>`__). In |
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426 such situations, it is possible to dynamically fix incoming or |
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427 outgoing C-Find queries using a Lua script. |
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428 |
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429 Fixing incoming C-Find requests can be done by implementing the |
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430 ``IncomingFindRequestFilter(query, origin)`` callback that is called |
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431 whenever the Orthanc C-Find SCP is queried by a remote modality. For |
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432 instance, here is Lua script to remove a private tag that is specified |
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433 by some manufacturer:: |
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434 |
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435 function IncomingFindRequestFilter(query, origin) |
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436 -- First display the content of the C-Find query |
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437 PrintRecursive(query) |
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438 PrintRecursive(origin) |
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439 |
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440 -- Remove the "PrivateCreator" tag from the query |
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441 local v = query |
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442 v['5555,0010'] = nil |
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443 |
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444 return v |
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445 end |
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446 |
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447 The ``origin`` argument contains information about which modality has |
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448 issued the request. |
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449 |
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450 Note that, as of Orthanc 1.2.1, the ``IncomingFindRequestFilter`` is |
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451 not applied to C-Find requests targeting the Modality Worklists plugin. |
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452 This might be fixed in a `future release <https://bitbucket.org/sjodogne/orthanc/issues/57/c-find-matching-refactoring-required>`__. |
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453 |
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454 Similarly, the callback ``OutgoingFindRequestFilter(query, modality)`` |
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455 is invoked whenever Orthanc acts as a C-Find SCU, which gives the |
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456 opportunity to dynamically fix outgoing C-Find requests before they |
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457 are actually sent to the queried modality. For instance, here is a |
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458 sample Lua callback that would replace asterisk wildcards (i.e. ``*``) |
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459 by an empty string for any query/retrieve issued by Orthanc (including |
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460 from Orthanc Explorer):: |
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461 |
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462 function OutgoingFindRequestFilter(query, modality) |
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463 for key, value in pairs(query) do |
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464 if value == '*' then |
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465 query[key] = '' |
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466 end |
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467 end |
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468 |
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469 return query |
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470 end |