Mercurial > hg > orthanc-book
annotate Sphinx/source/users/advanced-rest.rst @ 906:6057a8beee07
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author | Alain Mazy <am@osimis.io> |
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date | Fri, 06 Jan 2023 16:05:36 +0100 |
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1 .. _rest-advanced: |
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2 |
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3 Advanced features of the REST API |
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4 ================================= |
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5 |
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6 .. contents:: |
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7 :depth: 3 |
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8 |
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9 This section of the Orthanc Book is a complement to the description of |
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10 the :ref:`REST API of Orthanc <rest>`. It explains some advanced uses |
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11 of the API. |
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12 |
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13 |
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14 .. _jobs: |
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15 |
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16 Jobs |
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17 ---- |
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18 |
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19 Since Orthanc 1.4.0, a jobs engine is embedded within Orthanc. Jobs |
854 | 20 are high-level tasks to be processed by Orthanc. Jobs can be started |
21 synchronously or asynchronously (see the section below). All Jobs, | |
22 no matter how they were started, are first added | |
227 | 23 to a queue of pending tasks, and Orthanc will simultaneously execute a |
24 fixed number of jobs (check out :ref:`configuration option | |
25 <configuration>` ``ConcurrentJobs``). Once the jobs have been | |
26 processed, they are tagged as successful or failed, and kept in a | |
27 history (the size of this history is controlled by the | |
28 ``JobsHistorySize`` option). | |
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29 |
227 | 30 By default, Orthanc saves the jobs into its database (check out the |
855 | 31 ``SaveJobs`` option). Jobs are saved within 100ms after their creation, |
32 and then, the whole jobs list, with their updated status, is saved every 10 seconds and when | |
854 | 33 Orthanc stops. If Orthanc is stopped then relaunched, the jobs whose |
34 processing was not finished are automatically put into the queue of | |
35 pending tasks or resumed if they were being processed when Orthanc stopped, | |
36 regardless of whether they were started synchronously or asynchronously | |
37 (see the section below). The command-line option ``--no-jobs`` can also be used to | |
798 | 38 prevent the loading of jobs from the database upon the launch of |
39 Orthanc. | |
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40 |
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41 Note that the queue of pending jobs has no size limit. |
227 | 42 |
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43 .. _jobs-synchronicity: |
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44 |
227 | 45 Synchronous vs. asynchronous calls |
46 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
47 | |
48 Some calls to the REST API of Orthanc need time to be executed, and | |
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49 thus result in adding a job to the processing queue. This notably |
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50 includes the following URIs: |
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51 |
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52 * :ref:`Modifying and anonymizing <anonymization>` DICOM instances. |
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53 * Creating ZIP or media archives. |
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54 * C-Move SCU (``/queries/.../retrieve``). |
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55 * C-Store SCU (``/modalities/.../store``). |
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56 * Sending to an Orthanc peer (``/peers/.../store``). |
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57 * :ref:`Split/merge <split-merge>`. |
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58 * Sending images using the :ref:`transfers accelerator <transfers>` plugin. |
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59 |
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60 Such REST API calls can be configured to be executed in a synchronous |
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61 or an asynchronous mode: |
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62 |
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63 * **Synchronous calls** wait for the end of the execution of their |
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64 associated job. This is in general the default behavior. |
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65 * **Asynchronous calls** end immediately and return a handle to their |
227 | 66 associated job. It is up to the caller to monitor the execution by |
67 calling the jobs API (e.g. to know whether the job has finished its | |
68 execution). | |
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69 |
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70 The choice between synchronous and asynchronous modes is done by |
227 | 71 setting the ``Synchronous`` field (or indifferently the |
72 ``Asynchronous`` field) in the POST body of the call to the REST | |
73 API. Note that the :ref:`transfers accelerator <transfers>` only runs | |
74 in asynchronous mode. | |
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75 |
227 | 76 An integer number (possibly negative) can be specified in the |
77 ``Priority`` field of the POST body. Jobs with higher priority will be | |
78 executed first. By default, the priority is set to zero. | |
79 | |
80 Despite being more complex to handle, the asynchronous mode is highly | |
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81 recommended for jobs whose execution time can last over a dozen of |
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82 seconds (typically, the creation of an archive if |
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83 ``SynchronousZipStream`` :ref:`configuration option <configuration>` |
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84 is set to ``false``, or a network transfer). Indeed, synchronous |
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85 calls can be affected by timeouts in the HTTP protocol if they last |
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86 too long. |
227 | 87 |
850 | 88 When generating archives asynchronously, you should take care of |
89 the ``MediaArchiveSize`` configuration that defines the maximum | |
90 number of ZIP/media archives that are maintained by Orthanc, as a | |
91 response to the asynchronous creation of archive. As of Orthanc | |
872 | 92 1.11.2, this value is ``1`` by default ! |
227 | 93 |
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94 .. _jobs-monitoring: |
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95 |
227 | 96 Monitoring jobs |
97 ^^^^^^^^^^^^^^^ | |
98 | |
99 .. highlight:: bash | |
100 | |
101 The list of all jobs can be retrieved as follows:: | |
102 | |
103 $ curl http://localhost:8042/jobs | |
104 [ "e0d12aac-47eb-454f-bb7f-9857931e2904" ] | |
105 | |
106 Full details about each job can be retrieved:: | |
107 | |
108 $ curl http://localhost:8042/jobs/e0d12aac-47eb-454f-bb7f-9857931e2904 | |
109 { | |
110 "CompletionTime" : "20190306T095223.753851", | |
111 "Content" : { | |
112 "Description" : "REST API", | |
113 "InstancesCount" : 1, | |
114 "UncompressedSizeMB" : 0 | |
115 }, | |
116 "CreationTime" : "20190306T095223.750666", | |
117 "EffectiveRuntime" : 0.001, | |
118 "ErrorCode" : 0, | |
119 "ErrorDescription" : "Success", | |
120 "ID" : "e0d12aac-47eb-454f-bb7f-9857931e2904", | |
121 "Priority" : 0, | |
122 "Progress" : 100, | |
123 "State" : "Success", | |
124 "Timestamp" : "20190306T095408.556082", | |
125 "Type" : "Archive" | |
126 } | |
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127 |
227 | 128 Note that the ``/jobs?expand`` URI will retrieve this information in |
129 one single REST query. The ``Content`` field contains the parameters | |
130 of the job, and is very specific to the ``Type`` of job. | |
131 | |
132 The ``State`` field can be: | |
133 | |
134 * ``Pending``: The job is waiting to be executed. | |
135 * ``Running``: The job is being executed. The ``Progress`` field will | |
136 be continuously updated to reflect the progression of the execution. | |
137 * ``Success``: The job has finished with success. | |
138 * ``Failure``: The job has finished with failure. Check out the | |
139 ``ErrorCode`` and ``ErrorDescription`` fields for more information. | |
140 * ``Paused``: The job has been paused. | |
141 * ``Retry``: The job has failed internally, and has been scheduled for | |
872 | 142 re-submission after a delay. As of Orthanc 1.11.2, this feature is not |
227 | 143 used by any type of job. |
144 | |
145 In order to wait for the end of an asynchronous call, the caller will | |
847 | 146 typically have to poll the ``/jobs/...`` URI (i.e. make periodic |
227 | 147 calls), waiting for the ``State`` field to become ``Success`` or |
148 ``Failure``. | |
149 | |
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150 Note that the `integration tests of Orthanc |
872 | 151 <https://hg.orthanc-server.com/orthanc-tests/file/Orthanc-1.11.2/Tests/Toolbox.py>`__ |
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152 give an example about how to monitor a job in Python using the REST |
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153 API (cf. function ``MonitorJob()``). |
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154 |
227 | 155 |
833 | 156 .. _jobs-priority: |
157 | |
158 Jobs priority | |
159 ^^^^^^^^^^^^^ | |
160 | |
161 When executing jobs, Orthanc will pick the jobs with the highest ``Priority`` | |
162 from the pending job list. An integer value is a valid ``Priority``. You may | |
163 also use negative number to lower the priority below the default one (``0``). | |
164 | |
165 Pending jobs are not ordered in the API response but they are picked up in the right order. | |
166 | |
167 | |
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168 .. _jobs-controlling: |
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169 |
227 | 170 Interacting with jobs |
171 ^^^^^^^^^^^^^^^^^^^^^ | |
172 | |
173 Given the ID of some job, one can: | |
174 | |
175 * Cancel the job by POST-ing to ``/jobs/.../cancel``. | |
176 * Pause the job by POST-ing to ``/jobs/.../pause``. | |
177 * Resume a job in ``Paused`` state by POST-ing to ``/jobs/.../resume``. | |
178 * Retry a job in ``Failed`` state by POST-ing to ``/jobs/.../resubmit``. | |
179 | |
180 The related state machine is depicted in the `implementation notes | |
449 | 181 <https://hg.orthanc-server.com/orthanc/raw-file/default/OrthancServer/Resources/ImplementationNotes/JobsEngineStates.pdf>`__. |
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182 |
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183 |
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184 Example: Asynchronous generation of an archive |
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185 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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186 |
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187 .. highlight:: bash |
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188 |
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189 Sucessful jobs are associated with a set of so-called "outputs" that |
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190 can be attached to the job. |
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191 |
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192 Here is a sample bash session to ask Orthanc to generate a ZIP |
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193 archive, then to download it locally:: |
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194 |
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195 $ curl http://localhost:8042/studies/27f7126f-4f66fb14-03f4081b-f9341db2-53925988/archive -d '{"Asynchronous":true}' |
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196 { |
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197 "ID" : "82cc02d1-03fe-41f9-be46-a308d16ea94a", |
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198 "Path" : "/jobs/82cc02d1-03fe-41f9-be46-a308d16ea94a" |
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199 } |
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200 $ curl http://localhost:8042/jobs/82cc02d1-03fe-41f9-be46-a308d16ea94a |
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201 { |
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202 "CompletionTime" : "20200817T144700.401777", |
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203 "Content" : { |
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204 "Description" : "REST API", |
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205 "InstancesCount" : 232, |
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206 "UncompressedSizeMB" : 64 |
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207 }, |
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208 "CreationTime" : "20200817T144658.011824", |
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209 "EffectiveRuntime" : 2.3879999999999999, |
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210 "ErrorCode" : 0, |
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211 "ErrorDescription" : "Success", |
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212 "ID" : "82cc02d1-03fe-41f9-be46-a308d16ea94a", |
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213 "Priority" : 0, |
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214 "Progress" : 100, |
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215 "State" : "Success", |
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216 "Timestamp" : "20200817T144705.770825", |
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217 "Type" : "Archive" |
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218 } |
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219 $ curl http://localhost:8042/jobs/82cc02d1-03fe-41f9-be46-a308d16ea94a/archive > a.zip |
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220 |
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221 Note how we retrieve the content of the archive by accessing the |
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222 ``archive`` output of the job (check out the virtual method |
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223 ``IJob::GetOutput()`` from the `source code |
872 | 224 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.11.2/OrthancServer/Sources/ServerJobs/ArchiveJob.cpp>`__ |
487
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225 of Orthanc). |
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226 |
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227 Here is the corresponding sequence of commands to generate a DICOMDIR |
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228 media:: |
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229 |
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230 $ curl http://localhost:8042/studies/27f7126f-4f66fb14-03f4081b-f9341db2-53925988/media -d '{"Asynchronous":true}' |
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231 $ curl http://localhost:8042/jobs/6332be8a-0052-44fb-8cc2-ac959aeccad9/archive > a.zip |
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232 |
872 | 233 As of Orthanc 1.11.2, only the creation of a ZIP or a DICOMDIR archive |
516
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234 produces such "outputs". |
487
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235 |
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236 |
224
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237 .. _pdf: |
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238 |
310 | 239 Attaching PDF file as DICOM series |
240 ---------------------------------- | |
224
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241 |
226
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242 Among many different types of data, DICOM files can be used to store |
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243 PDF files. The ``/tools/create-dicom`` URI can be used to upload a PDF |
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244 file to Orthanc. The following scripts perform such a *DICOM-ization*; |
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245 They convert the ``HelloWorld2.pdf`` file to base64, then perform a |
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246 ``POST`` request with JSON data containing the converted payload. |
225
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247 |
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248 Importantly, the ``Parent`` field of the ``POST`` body can be set to |
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249 the :ref:`Orthanc identifier of some study <orthanc-ids>` in order to |
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250 attach the newly-created PDF series to the given parent study. |
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251 |
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252 Using bash: |
227 | 253 |
297
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254 .. code-block:: bash |
225
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255 |
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256 # create the json data, with the BASE64 data embedded in it |
545
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257 (echo -n '{"Parent": "b6e8436b-c5835b7b-cecc9576-0483e165-ab5c710b", "Tags" : {"Modality" : "CT"}, "Content" : "data:application/pdf;base64,'; base64 HelloWorld2.pdf; echo '"}') > /tmp/foo |
225
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258 |
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259 # upload it to Orthanc |
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260 cat /tmp/foo | curl -H "Content-Type: application/json" -d @- http://localhost:8042/tools/create-dicom |
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261 |
227 | 262 |
297
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263 Using powershell: |
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264 |
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265 .. code-block:: perl |
225
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266 |
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267 # create the BASE64 string data |
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268 $fileInBase64 = $([Convert]::ToBase64String((gc -Path "HelloWorld2.pdf" -Encoding Byte))) |
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269 |
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270 # create the json data |
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271 $params = @{Tags = @{PatientName = "Benjamino";Modality = "CT"};Content= "data:application/pdf;base64,$fileInBase64"} |
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272 |
376 | 273 # disabling the progress bar makes the Invoke-RestMethod call MUCH faster |
297
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274 $ProgressPreference = 'SilentlyContinue' |
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275 |
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276 # upload it to Orthanc |
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277 $reply = Invoke-RestMethod http://localhost:8042/tools/create-dicom -Method POST -Body ($params|ConvertTo-Json) -ContentType 'application/json' |
225
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278 |
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279 # display the result |
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280 Write-Host "The instance can be retrieved in PDF at http://localhost:8042$($reply.Path)/pdf" |
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281 |
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282 Please note that the ``/tools/create-dicom`` API call will return the |
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283 Orthanc instance ID of the newly created DICOM resource. |
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284 |
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285 You can use the ``/instances/.../pdf`` URI to retrieve an embedded PDF |
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286 file. |
228 | 287 |
288 | |
596 | 289 .. _private-tags: |
290 | |
291 Creating DICOM instance with private tags | |
292 ----------------------------------------- | |
293 | |
294 .. highlight:: json | |
295 | |
296 The ``/tools/create-dicom`` URI can be used to create DICOM instances | |
297 containing private tags. Those private tags must first be defined in | |
298 the ``Dictionary`` configuration option of Orthanc. Importantly, the | |
299 ``xxxx,0010`` tag must be defined to register the private creator, | |
300 where ``xxxx`` is the private group of interest. Here is a sample:: | |
301 | |
302 { | |
303 "Dictionary" : { | |
906 | 304 "0405,0010" : [ "LO", "PrivateCreatorForMyCompany", 1, 1, "My Company" ], // reserve 0405,10xx for "My Company" |
305 "0405,1001" : [ "ST", "MyPrivateXMLTag", 1, 1, "My Company" ] // all tags from "My Company" must start with 0405,10xx | |
596 | 306 } |
307 } | |
308 | |
309 Once Orthanc is started using this configuration file, it is possible | |
310 to create a DICOM instance using the following POST body on | |
311 ``/tools/create-dicom``:: | |
312 | |
313 { | |
905 | 314 "PrivateCreator" : "My Company", // private creator here |
596 | 315 "Tags" : |
316 { | |
317 "PatientName" : "Love^Sarah", | |
318 "PatientID" : "7", | |
905 | 319 "PrivateCreatorForMyCompany" : "My Company", // and here ! |
320 "MyPrivateXMLTag" : "<xml><test>Testing</test></xml>" | |
596 | 321 } |
322 } | |
323 | |
905 | 324 Which then gives this in Orthanc UI: |
325 | |
326 .. image:: ../images/PrivateTagsInCreateDicom.png | |
327 :align: center | |
328 :width: 400px | |
329 | |
808 | 330 Rob Oakes provides more a `detailed explanation about how to use |
331 private tags with Orthanc | |
332 <https://oak-tree.tech/blog/soandor-orthanc-private-headers>`__ on | |
333 Oak-Tree's homepage. | |
228 | 334 |
808 | 335 |
228 | 336 .. _prometheus: |
337 | |
338 Instrumentation with Prometheus | |
339 ------------------------------- | |
340 | |
341 .. highlight:: text | |
342 | |
343 Orthanc publishes its metrics according to the `text-based format of | |
344 Prometheus | |
345 <https://prometheus.io/docs/instrumenting/exposition_formats/#text-based-format>`__ | |
346 (check also the `OpenMetrics project <https://openmetrics.io/>`__), onto | |
347 the ``/tools/metrics-prometheus`` URI of the REST API. For instance:: | |
348 | |
349 $ curl http://localhost:8042/tools/metrics-prometheus | |
350 orthanc_count_instances 1 1551868380543 | |
351 orthanc_count_patients 1 1551868380543 | |
352 orthanc_count_series 1 1551868380543 | |
353 orthanc_count_studies 1 1551868380543 | |
354 orthanc_disk_size_mb 0.0135002136 1551868380543 | |
355 orthanc_jobs_completed 1 1551868380543 | |
356 orthanc_jobs_failed 0 1551868380543 | |
357 orthanc_jobs_pending 0 1551868380543 | |
358 orthanc_jobs_running 0 1551868380543 | |
359 orthanc_jobs_success 1 1551868380543 | |
360 orthanc_rest_api_active_requests 1 1551868380543 | |
361 orthanc_rest_api_duration_ms 0 1551868094265 | |
362 orthanc_storage_create_duration_ms 0 1551865919315 | |
363 orthanc_storage_read_duration_ms 0 1551865943752 | |
364 orthanc_store_dicom_duration_ms 5 1551865919319 | |
365 orthanc_uncompressed_size_mb 0.0135002136 1551868380543 | |
366 | |
367 | |
368 .. highlight:: bash | |
369 | |
370 Note that the collection of metrics can be statically disabled by | |
371 setting the :ref:`global configuration option <configuration>` | |
372 ``MetricsEnabled`` to ``false``, or dynamically disabled by PUT-ing | |
373 ``0`` on ``/tools/metrics``:: | |
374 | |
375 $ curl http://localhost:8042/tools/metrics | |
376 1 | |
377 $ curl http://localhost:8042/tools/metrics -X PUT -d '0' | |
378 $ curl http://localhost:8042/tools/metrics | |
379 0 | |
380 | |
381 | |
382 .. highlight:: yaml | |
383 | |
384 Here is a sample configuration for Prometheus (in the `YAML format | |
385 <https://en.wikipedia.org/wiki/YAML>`__):: | |
386 | |
387 scrape_configs: | |
388 - job_name: 'orthanc' | |
389 scrape_interval: 10s | |
390 metrics_path: /tools/metrics-prometheus | |
391 basic_auth: | |
392 username: orthanc | |
393 password: orthanc | |
394 static_configs: | |
395 - targets: ['192.168.0.2:8042'] | |
396 | |
397 .. highlight:: bash | |
398 | |
399 Obviously, make sure to adapt this sample with your actual IP | |
400 address. Thanks to Docker, you can easily start a Prometheus server by | |
401 writing this configuration to, say, ``/tmp/prometheus.yml``, then | |
402 type:: | |
403 | |
363
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404 $ sudo run -p 9090:9090 -v /tmp/prometheus.yml:/etc/prometheus/prometheus.yml --rm prom/prometheus:v2.7.0 |