Mercurial > hg > orthanc-book
annotate Sphinx/source/users/advanced-rest.rst @ 936:5491953f7492
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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
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| date | Sun, 16 Apr 2023 16:55:46 +0200 |
| parents | a5e7e7001316 |
| children | 0b89127439b1 |
| rev | line source |
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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 | |
| 933 | 91 response to the asynchronous creation of archive. As of Orthanc |
| 92 1.12.0, 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 | |
| 933 | 142 re-submission after a delay. As of Orthanc 1.12.0, 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 |
| 933 | 151 <https://hg.orthanc-server.com/orthanc-tests/file/Orthanc-1.12.0/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 |
| 933 | 224 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.12.0/OrthancServer/Sources/ServerJobs/ArchiveJob.cpp>`__ |
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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 |
| 933 | 233 As of Orthanc 1.12.0, only the creation of a ZIP or a DICOMDIR archive |
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234 produces such "outputs". |
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235 |
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236 |
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237 .. _pdf: |
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238 |
| 310 | 239 Attaching PDF file as DICOM series |
| 240 ---------------------------------- | |
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241 |
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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. |
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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 |
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254 .. code-block:: bash |
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255 |
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256 # create the json data, with the BASE64 data embedded in it |
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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 |
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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 |
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263 Using powershell: |
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264 |
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265 .. code-block:: perl |
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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 |
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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' |
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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 |
| 907 | 282 And here's another sample `using python |
| 283 <https://bitbucket.org/osimis/orthanc-setup-samples/src/master/python-samples/attach-pdf-to-study.py>`__. | |
| 284 | |
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285 Please note that the ``/tools/create-dicom`` API call will return the |
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286 Orthanc instance ID of the newly created DICOM resource. |
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287 |
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288 You can use the ``/instances/.../pdf`` URI to retrieve an embedded PDF |
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289 file. |
| 228 | 290 |
| 291 | |
| 596 | 292 .. _private-tags: |
| 293 | |
| 294 Creating DICOM instance with private tags | |
| 295 ----------------------------------------- | |
| 296 | |
| 297 .. highlight:: json | |
| 298 | |
| 299 The ``/tools/create-dicom`` URI can be used to create DICOM instances | |
| 300 containing private tags. Those private tags must first be defined in | |
| 301 the ``Dictionary`` configuration option of Orthanc. Importantly, the | |
| 302 ``xxxx,0010`` tag must be defined to register the private creator, | |
| 303 where ``xxxx`` is the private group of interest. Here is a sample:: | |
| 304 | |
| 305 { | |
| 306 "Dictionary" : { | |
| 906 | 307 "0405,0010" : [ "LO", "PrivateCreatorForMyCompany", 1, 1, "My Company" ], // reserve 0405,10xx for "My Company" |
| 308 "0405,1001" : [ "ST", "MyPrivateXMLTag", 1, 1, "My Company" ] // all tags from "My Company" must start with 0405,10xx | |
| 596 | 309 } |
| 310 } | |
| 311 | |
| 312 Once Orthanc is started using this configuration file, it is possible | |
| 313 to create a DICOM instance using the following POST body on | |
| 314 ``/tools/create-dicom``:: | |
| 315 | |
| 316 { | |
| 905 | 317 "PrivateCreator" : "My Company", // private creator here |
| 596 | 318 "Tags" : |
| 319 { | |
| 320 "PatientName" : "Love^Sarah", | |
| 321 "PatientID" : "7", | |
| 905 | 322 "PrivateCreatorForMyCompany" : "My Company", // and here ! |
| 323 "MyPrivateXMLTag" : "<xml><test>Testing</test></xml>" | |
| 596 | 324 } |
| 325 } | |
| 326 | |
| 905 | 327 Which then gives this in Orthanc UI: |
| 328 | |
| 329 .. image:: ../images/PrivateTagsInCreateDicom.png | |
| 330 :align: center | |
| 331 :width: 400px | |
| 332 | |
| 808 | 333 Rob Oakes provides more a `detailed explanation about how to use |
| 334 private tags with Orthanc | |
| 335 <https://oak-tree.tech/blog/soandor-orthanc-private-headers>`__ on | |
| 336 Oak-Tree's homepage. | |
| 228 | 337 |
| 808 | 338 |
| 228 | 339 .. _prometheus: |
| 340 | |
| 341 Instrumentation with Prometheus | |
| 342 ------------------------------- | |
| 343 | |
| 344 .. highlight:: text | |
| 345 | |
| 346 Orthanc publishes its metrics according to the `text-based format of | |
| 347 Prometheus | |
| 348 <https://prometheus.io/docs/instrumenting/exposition_formats/#text-based-format>`__ | |
| 349 (check also the `OpenMetrics project <https://openmetrics.io/>`__), onto | |
| 350 the ``/tools/metrics-prometheus`` URI of the REST API. For instance:: | |
| 351 | |
| 352 $ curl http://localhost:8042/tools/metrics-prometheus | |
| 927 | 353 orthanc_count_instances 21741 1680083638028 |
| 354 orthanc_count_patients 86 1680083638028 | |
| 355 orthanc_count_series 239 1680083638028 | |
| 356 orthanc_count_studies 93 1680083638028 | |
| 357 orthanc_dicom_cache_count 2 1680083630571 | |
| 358 orthanc_dicom_cache_size 0.00191688538 1680083630571 | |
| 359 orthanc_disk_size_mb 16855.9629 1680083638028 | |
| 360 orthanc_jobs_completed 10 1680083638028 | |
| 361 orthanc_jobs_failed 0 1680083638028 | |
| 362 orthanc_jobs_pending 0 1680083638028 | |
| 363 orthanc_jobs_running 0 1680083638028 | |
| 364 orthanc_jobs_success 10 1680083638028 | |
| 365 orthanc_last_change 81062 1680083638028 | |
| 366 orthanc_rest_api_active_requests 1 1680083638027 | |
| 367 orthanc_rest_api_duration_ms 77 1680083630549 | |
| 368 orthanc_storage_create_duration_ms 2 1680083630565 | |
| 369 orthanc_storage_read_duration_ms 2 1680083630557 | |
| 370 orthanc_store_dicom_duration_ms 7 1680083630570 | |
| 371 orthanc_uncompressed_size_mb 16855.9629 1680083638028 | |
| 372 orthanc_up_time_s 64 1680083638028 | |
| 228 | 373 |
| 374 | |
| 375 .. highlight:: bash | |
| 376 | |
| 377 Note that the collection of metrics can be statically disabled by | |
| 378 setting the :ref:`global configuration option <configuration>` | |
| 379 ``MetricsEnabled`` to ``false``, or dynamically disabled by PUT-ing | |
| 380 ``0`` on ``/tools/metrics``:: | |
| 381 | |
| 382 $ curl http://localhost:8042/tools/metrics | |
| 383 1 | |
| 384 $ curl http://localhost:8042/tools/metrics -X PUT -d '0' | |
| 385 $ curl http://localhost:8042/tools/metrics | |
| 386 0 | |
| 387 | |
| 388 | |
| 389 .. highlight:: yaml | |
| 390 | |
| 391 Here is a sample configuration for Prometheus (in the `YAML format | |
| 392 <https://en.wikipedia.org/wiki/YAML>`__):: | |
| 393 | |
| 394 scrape_configs: | |
| 395 - job_name: 'orthanc' | |
| 396 scrape_interval: 10s | |
| 397 metrics_path: /tools/metrics-prometheus | |
| 398 basic_auth: | |
| 399 username: orthanc | |
| 400 password: orthanc | |
| 401 static_configs: | |
| 402 - targets: ['192.168.0.2:8042'] | |
| 403 | |
| 404 .. highlight:: bash | |
| 405 | |
| 406 Obviously, make sure to adapt this sample with your actual IP | |
| 407 address. Thanks to Docker, you can easily start a Prometheus server by | |
| 408 writing this configuration to, say, ``/tmp/prometheus.yml``, then | |
| 409 type:: | |
| 410 | |
|
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411 $ sudo run -p 9090:9090 -v /tmp/prometheus.yml:/etc/prometheus/prometheus.yml --rm prom/prometheus:v2.7.0 |