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annotate Sphinx/source/users/lua.rst @ 235:17f8eda5fccb TomasZubiri/documented-some-parameter-types-expected-1553029141048
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author | Tomas Zubiri <me@tomaszubiri.com> |
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date | Tue, 19 Mar 2019 20:59:05 +0000 |
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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 | |
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127 The parameters: |
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128 |
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129 * ``uri`` specifies the resource being accessed, do not include URL schema, hostname or port. (For example: '/instances' ) |
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130 |
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131 * ``body`` is a json-formatted string containing the body of a POST or PUT request. (For example: '{"Keep":"StudyDate"}' ) |
0 | 132 |
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133 * ``builtin`` is an optional Boolean that specifies whether the request targets only the built-in REST API of Orthanc (if set to ``true``), or the full the REST API after being tainted by plugins (if set to ``false``). |
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134 |
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135 For example: |
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136 |
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137 RestApiPost('/instances/5af318ac-78fb-47ff-b0b0-0df18b0588e0/anonymize', '{}') |
0 | 138 |
139 General-purpose functions | |
140 ^^^^^^^^^^^^^^^^^^^^^^^^^ | |
141 | |
142 The Lua engine of Orthanc contain several general-purpose ancillary | |
143 functions: | |
144 | |
145 * ``PrintRecursive(v)`` recursively prints the content of a `Lua table | |
146 <http://www.lua.org/pil/2.5.html>`__ to the log file of Orthanc. | |
147 * ``ParseJson(s)`` converts a string encoded in the `JSON format | |
148 <https://en.wikipedia.org/wiki/JSON>`__ to a Lua table. | |
149 * ``DumpJson(v, keepStrings)`` encodes a Lua table as a JSON string. | |
150 Setting the optional argument ``keepStrings`` (available from | |
151 release 0.9.5) to ``true`` prevents the automatic conversion of | |
152 strings to integers. | |
153 * ``GetOrthancConfiguration()`` returns a Lua table containing the | |
154 content of the :ref:`configuration files <configuration>` of | |
155 Orthanc. | |
156 | |
157 | |
158 Similarly to the functions to :ref:`call the REST API of Orthanc | |
159 <lua-rest>`, several functions are available to make generic HTTP | |
160 requests to Web services: | |
161 | |
90 | 162 * ``HttpGet(url, headers)`` |
163 * ``HttpPost(url, body, headers)`` | |
164 * ``HttpPut(url, body, headers)`` | |
165 * ``HttpDelete(url, headers)`` | |
0 | 166 * ``SetHttpCredentials(username, password)`` can be used to setup the |
167 HTTP credentials. | |
168 | |
91 | 169 The ``headers`` argument is optional and has been added in release |
170 1.2.1. It allows to set the HTTP headers for the HTTP client request. | |
0 | 171 |
172 .. _lua-origin: | |
173 | |
174 Origin of the instances | |
175 ^^^^^^^^^^^^^^^^^^^^^^^ | |
176 | |
177 Whenever Orthanc decides whether it should should store a new instance | |
178 (cf. the ``ReceivedInstanceFilter()`` callback), or whenever it has | |
179 actually stored a new instance (cf. the ``OnStoredInstance`` | |
180 callback), an ``origin`` parameter is provided. This parameter is a | |
181 `Lua table <http://www.lua.org/pil/2.5.html>`__ that describes from | |
182 which Orthanc subsystem the new instance comes from. | |
183 | |
184 There are 4 possible subsystems, that can be distinguished according | |
185 to the value of ``origin["RequestOrigin"]``: | |
186 | |
187 * ``RestApi``: The instance originates from some HTTP request to the REST | |
188 API. In this case, the ``RemoteIp`` and ``Username`` fields are | |
189 available in ``origin``. They respectively describe the IP address | |
190 of the HTTP client, and the username that was used for HTTP | |
191 authentication (as defined in the ``RegisteredUsers`` | |
192 :ref:`configuration variable <configuration>`). | |
193 * ``DicomProtocol``: The instance originates from a DICOM C-Store. | |
194 The fields ``RemoteIp``, ``RemoteAet`` and ``CalledAet`` | |
195 respectively provide the IP address of the DICOM SCU (client), the | |
196 application entity title of the DICOM SCU client, and the | |
197 application entity title of the Orthanc SCP server. The | |
198 ``CalledAet`` can be used for :ref:`advanced auto-routing scenarios | |
199 <lua-auto-routing>`, when a single instance of Orthanc acts as a | |
200 proxy for several DICOM SCU clients. | |
201 * ``Lua``: The instance originates from a Lua script. | |
202 * ``Plugins``: The instance originates from a plugin. | |
203 | |
204 | |
205 .. _lua-filter-dicom: | |
206 | |
75 | 207 Filtering incoming DICOM instances |
0 | 208 ---------------------------------- |
209 | |
210 .. highlight:: lua | |
211 | |
212 Each time a DICOM instance is received by Orthanc (either through the | |
213 DICOM protocol or through the REST API), the | |
214 ``ReceivedInstanceFilter()`` Lua function is invoked. If this callback | |
215 returns ``true``, the instance is accepted for storage. If it returns | |
216 ``false``, the instance is discarded. This mechanism can be used to | |
217 filter the incoming DICOM instances. Here is an example of a Lua | |
218 filter that only allows incoming instances of MR modality:: | |
219 | |
220 function ReceivedInstanceFilter(dicom, origin) | |
221 -- Only allow incoming MR images | |
222 if dicom.Modality == 'MR' then | |
223 return true | |
224 else | |
225 return false | |
226 end | |
227 end | |
228 | |
229 The argument dicom corresponds to a `Lua table | |
230 <http://www.lua.org/pil/2.5.html>`__ (i.e. an associative array) that | |
231 contains the DICOM tags of the incoming instance. For debugging | |
232 purpose, you can print this structure as follows:: | |
233 | |
234 function ReceivedInstanceFilter(dicom, origin) | |
235 PrintRecursive(dicom) | |
236 -- Accept all incoming instances (default behavior) | |
237 return true | |
238 end | |
239 | |
240 The argument ``origin`` is :ref:`documented separately <lua-origin>`. | |
241 | |
242 | |
243 .. _lua-filter-rest: | |
244 | |
75 | 245 Filtering incoming REST requests |
0 | 246 -------------------------------- |
247 | |
248 .. highlight:: lua | |
249 | |
250 Lua scripting can be used to control the access to the various URI of | |
251 the REST API. Each time an incoming HTTP request is received, the | |
252 ``IncomingHttpRequestFilter()`` Lua function is called. The access to | |
253 the resource is granted if and only if this callback script returns | |
254 ``true``. | |
255 | |
256 This mechanism can be used to implement fine-grained `access control | |
25 | 257 lists <https://en.wikipedia.org/wiki/Access_control_list>`__. Here is |
0 | 258 an example of a Lua script that limits POST, PUT and DELETE requests |
259 to an user that is called "admin":: | |
260 | |
261 function IncomingHttpRequestFilter(method, uri, ip, username, httpHeaders) | |
262 -- Only allow GET requests for non-admin users | |
263 | |
264 if method == 'GET' then | |
265 return true | |
266 elseif username == 'admin' then | |
267 return true | |
268 else | |
269 return false | |
270 end | |
271 end | |
272 | |
273 Here is a description of the arguments of this Lua callback: | |
274 | |
275 * ``method``: The HTTP method (GET, POST, PUT or DELETE). | |
276 * ``uri``: The path to the resource (e.g. ``/tools/generate-uid``). | |
277 * ``ip``: The IP address of the host that has issued the HTTP request (e.g. ``127.0.0.1``). | |
278 * ``username``: If HTTP Basic Authentication is enabled in the | |
279 :ref:`configuration file <configuration>`, the name of the user that | |
280 has issued the HTTP request (as defined in the ``RegisteredUsers`` | |
281 configuration variable). If the authentication is disabled, this | |
282 argument is set to the empty string. | |
283 * ``httpHeaders``: The HTTP headers of the incoming request. This | |
284 argument is available since Orthanc 1.0.1. It is useful if the | |
285 authentication should be achieved through tokens, for instance | |
286 against a `LDAP | |
287 <https://en.wikipedia.org/wiki/Lightweight_Directory_Access_Protocol>`__ | |
288 or `OAuth2 <https://en.wikipedia.org/wiki/OAuth>`__ server. | |
289 | |
290 | |
291 .. _lua-auto-routing: | |
292 | |
75 | 293 Auto-routing of DICOM images |
0 | 294 ---------------------------- |
295 | |
296 .. highlight:: lua | |
297 | |
298 Since release 0.8.0, the routing of DICOM flows can be very easily | |
299 automated with Orthanc. All you have to do is to declare your | |
300 destination modality in the :ref:`configuration file <configuration>` | |
301 (section ``DicomModalities``), then to create and install a Lua | |
302 script. For instance, here is a sample script:: | |
303 | |
304 function OnStoredInstance(instanceId, tags, metadata) | |
305 Delete(SendToModality(instanceId, 'sample')) | |
306 end | |
307 | |
308 If this script is loaded into Orthanc, whenever a new DICOM instance | |
309 is received by Orthanc, it will be routed to the modality whose | |
310 symbolic name is ``sample`` (through a Store-SCU command), then it | |
311 will be removed from Orthanc. In other words, this is a **one-liner | |
312 script to implement DICOM auto-routing**. | |
313 | |
314 Very importantly, thanks to this feature, you do not have to use the | |
315 REST API or to create external scripts in order to automate simple | |
316 imaging flows. The scripting engine is entirely contained inside the | |
317 Orthanc core system. | |
318 | |
319 Thanks to Lua expressiveness, you can also implement conditional | |
320 auto-routing. For instance, if you wish to route only patients whose | |
321 name contains "David", you would simply write:: | |
322 | |
323 function OnStoredInstance(instanceId, tags, metadata) | |
324 -- Extract the value of the "PatientName" DICOM tag | |
325 local patientName = string.lower(tags['PatientName']) | |
326 | |
327 if string.find(patientName, 'david') ~= nil then | |
328 -- Only route patients whose name contains "David" | |
329 Delete(SendToModality(instanceId, 'sample')) | |
330 | |
331 else | |
332 -- Delete the patients that are not called "David" | |
333 Delete(instanceId) | |
334 end | |
335 end | |
336 | |
337 Besides ``SendToModality()``, a mostly identical function with the | |
338 same arguments called ``SendToPeer()`` can be used to route instances | |
339 to :ref:`Orthanc peers <peers>`. It is also possible to modify the | |
340 received instances before routing them. For instance, here is how you | |
341 would replace the ``StationName`` DICOM tag:: | |
342 | |
343 function OnStoredInstance(instanceId, tags, metadata) | |
344 -- Ignore the instances that result from a modification to avoid | |
345 -- infinite loops | |
346 if (metadata['ModifiedFrom'] == nil and | |
347 metadata['AnonymizedFrom'] == nil) then | |
348 | |
349 -- The tags to be replaced | |
350 local replace = {} | |
351 replace['StationName'] = 'My Medical Device' | |
352 | |
353 -- The tags to be removed | |
354 local remove = { 'MilitaryRank' } | |
355 | |
356 -- Modify the instance, send it, then delete the modified instance | |
357 Delete(SendToModality(ModifyInstance(instanceId, replace, remove, true), 'sample')) | |
358 | |
359 -- Delete the original instance | |
360 Delete(instanceId) | |
361 end | |
362 end | |
363 | |
364 | |
75 | 365 Important remarks about auto-routing |
366 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
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367 |
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368 The ``SendToModality()``, ``SendToPeer()``, ``ModifyInstance()`` and |
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369 ``Delete()`` functions are for the most basic cases of auto-routing |
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370 (implying a single DICOM instance, and possibly a basic modification |
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371 of this instance). The ``ModifyInstance()`` function `could also lead |
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372 to problems |
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373 <https://groups.google.com/d/msg/orthanc-users/hmv2y-LgKm8/oMAuGJWMBgAJ>`__ |
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374 if it deals with tags wrongly interpreted as numbers by Lua. |
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375 |
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376 For more evolved auto-routing scenarios, remember that Lua scripts |
191 | 377 :ref:`have full access to the REST API of Orthanc <lua-rest>`. This is |
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378 illustrated by the ``AutoroutingModification.lua`` sample available in |
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379 the source distribution of Orthanc:: |
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380 |
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381 function OnStoredInstance(instanceId, tags, metadata, origin) |
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382 -- Ignore the instances that result from the present Lua script to |
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383 -- avoid infinite loops |
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384 if origin['RequestOrigin'] ~= 'Lua' then |
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385 |
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386 -- The tags to be replaced |
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387 local replace = {} |
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388 replace['StationName'] = 'My Medical Device' |
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389 replace['0031-1020'] = 'Some private tag' |
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390 |
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391 -- The tags to be removed |
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392 local remove = { 'MilitaryRank' } |
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393 |
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394 -- Modify the instance |
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395 local command = {} |
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396 command['Replace'] = replace |
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397 command['Remove'] = remove |
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398 local modifiedFile = RestApiPost('/instances/' .. instanceId .. '/modify', DumpJson(command, true)) |
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399 |
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400 -- Upload the modified instance to the Orthanc database so that |
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401 -- it can be sent by Orthanc to other modalities |
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402 local modifiedId = ParseJson(RestApiPost('/instances/', modifiedFile)) ['ID'] |
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403 |
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404 -- Send the modified instance to another modality |
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405 RestApiPost('/modalities/sample/store', modifiedId) |
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406 |
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407 -- Delete the original and the modified instances |
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408 RestApiDelete('/instances/' .. instanceId) |
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409 RestApiDelete('/instances/' .. modifiedId) |
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410 end |
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411 end |
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412 |
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413 Also note that :ref:`other callbacks are available <lua-callbacks>` |
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414 (``OnStablePatient()``, ``OnStableStudy()`` and ``OnStableSeries()``) |
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415 to react to other events than the reception of a single instance |
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416 with ``OnStoredInstance()``. |
75 | 417 |
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418 .. _lua-fix-cfind: |
75 | 419 |
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420 Fixing C-Find requests |
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421 ---------------------- |
75 | 422 |
423 :ref:`C-Find requests <dicom-find>` are sometimes interpreted | |
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424 differently by different DICOM servers (e.g. the ``*`` wildcard, as |
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425 `reported by users |
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426 <https://groups.google.com/d/msg/orthanc-users/3g7V7kqr3g0/IREL88RWAwAJ>`__), |
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427 and sometimes a querying modality might set unexpected DICOM tags |
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428 (cf. `this real-world example |
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429 <https://groups.google.com/d/msg/orthanc-users/PLWKqVVaXLs/n_0x4vKhAgAJ>`__). In |
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430 such situations, it is possible to dynamically fix incoming or |
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431 outgoing C-Find queries using a Lua script. |
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432 |
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433 Sanitizing incoming C-Find requests can be done by implementing the |
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434 ``IncomingFindRequestFilter(query, origin)`` callback that is called |
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435 whenever the Orthanc C-Find SCP is queried by a remote modality. For |
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436 instance, here is Lua script to remove a private tag that is specified |
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437 by some manufacturer:: |
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438 |
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439 function IncomingFindRequestFilter(query, origin) |
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440 -- First display the content of the C-Find query |
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441 PrintRecursive(query) |
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442 PrintRecursive(origin) |
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443 |
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444 -- Remove the "PrivateCreator" tag from the query |
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445 local v = query |
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446 v['5555,0010'] = nil |
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447 |
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448 return v |
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449 end |
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450 |
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451 The ``origin`` argument contains information about which modality has |
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452 issued the request. |
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453 |
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454 Note that the ``IncomingFindRequestFilter`` callback is not applied to |
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455 C-Find requests targeting :ref:`modality worklists |
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456 <worklists-plugin>`. Since Orthanc 1.4.2, the corresponding |
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457 ``IncomingWorklistRequestFilter`` callback can be used to sanitize |
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458 C-FIND requests against worklists:: |
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459 |
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460 function IncomingWorklistRequestFilter(query, origin) |
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461 PrintRecursive(query) |
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462 PrintRecursive(origin) |
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463 |
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464 -- Implements the same behavior as the "FilterIssuerAet" |
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465 -- option of the sample worklist plugin |
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466 query['0040,0100'][1]['0040,0001'] = origin['RemoteAet'] |
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467 |
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468 return query |
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469 end |
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470 |
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471 Similarly, the callback ``OutgoingFindRequestFilter(query, modality)`` |
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472 is invoked whenever Orthanc acts as a C-Find SCU, which gives the |
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473 opportunity to dynamically fix outgoing C-Find requests before they |
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474 are actually sent to the queried modality. For instance, here is a |
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475 sample Lua callback that would replace asterisk wildcards (i.e. ``*``) |
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476 by an empty string for any query/retrieve issued by Orthanc (including |
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477 from Orthanc Explorer):: |
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478 |
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479 function OutgoingFindRequestFilter(query, modality) |
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480 for key, value in pairs(query) do |
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481 if value == '*' then |
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482 query[key] = '' |
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483 end |
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484 end |
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485 |
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486 return query |
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487 end |