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annotate Sphinx/source/users/advanced-rest.rst @ 693:650100457193
SynchronousZipStream
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
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| date | Thu, 03 Jun 2021 21:26:40 +0200 |
| parents | 17c1ff4e6ae4 |
| children | 8a247c645ac6 |
| 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 |
| 227 | 20 are high-level tasks to be processed by Orthanc. Jobs are first added |
| 21 to a queue of pending tasks, and Orthanc will simultaneously execute a | |
| 22 fixed number of jobs (check out :ref:`configuration option | |
| 23 <configuration>` ``ConcurrentJobs``). Once the jobs have been | |
| 24 processed, they are tagged as successful or failed, and kept in a | |
| 25 history (the size of this history is controlled by the | |
| 26 ``JobsHistorySize`` option). | |
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27 |
| 227 | 28 By default, Orthanc saves the jobs into its database (check out the |
| 29 ``SaveJobs`` option). If Orthanc is stopped then relaunched, the jobs | |
| 30 whose processing was not finished are automatically put into the queue | |
| 31 of pending tasks. The command-line option ``--no-jobs`` can also be | |
| 32 used to prevent the loading of jobs from the database upon the launch | |
| 33 of Orthanc. | |
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34 |
| 227 | 35 Note that the queue of pending jobs has a maximum size (check out the |
| 36 ``LimitJobs`` option). When this limit is reached, the addition of new | |
| 37 jobs is blocked until some job finishes. | |
| 38 | |
| 39 | |
| 40 | |
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41 .. _jobs-synchronicity: |
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42 |
| 227 | 43 Synchronous vs. asynchronous calls |
| 44 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 45 | |
| 46 Some calls to the REST API of Orthanc need time to be executed, and | |
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47 thus result in adding a job to the processing queue. This notably |
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48 includes the following URIs: |
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49 |
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50 * :ref:`Modifying and anonymizing <anonymization>` DICOM instances. |
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51 * Creating ZIP or media archives. |
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52 * C-Move SCU (``/queries/.../retrieve``). |
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53 * C-Store SCU (``/modalities/.../store``). |
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54 * Sending to an Orthanc peer (``/peers/.../store``). |
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55 * :ref:`Split/merge <split-merge>`. |
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56 * Sending images using the :ref:`transfers accelerator <transfers>` plugin. |
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57 |
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58 Such REST API calls can be configured to be executed in a synchronous |
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59 or an asynchronous mode: |
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60 |
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61 * **Synchronous calls** wait for the end of the execution of their |
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62 associated job. This is in general the default behavior. |
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63 * **Asynchronous calls** end immediately and return a handle to their |
| 227 | 64 associated job. It is up to the caller to monitor the execution by |
| 65 calling the jobs API (e.g. to know whether the job has finished its | |
| 66 execution). | |
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67 |
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68 The choice between synchronous and asynchronous modes is done by |
| 227 | 69 setting the ``Synchronous`` field (or indifferently the |
| 70 ``Asynchronous`` field) in the POST body of the call to the REST | |
| 71 API. Note that the :ref:`transfers accelerator <transfers>` only runs | |
| 72 in asynchronous mode. | |
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73 |
| 227 | 74 An integer number (possibly negative) can be specified in the |
| 75 ``Priority`` field of the POST body. Jobs with higher priority will be | |
| 76 executed first. By default, the priority is set to zero. | |
| 77 | |
| 78 Despite being more complex to handle, the asynchronous mode is highly | |
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79 recommended for jobs whose execution time can last over a dozen of |
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80 seconds (typically, the creation of an archive if |
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81 ``SynchronousZipStream`` :ref:`configuration option <configuration>` |
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82 is set to ``false``, or a network transfer). Indeed, synchronous |
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83 calls can be affected by timeouts in the HTTP protocol if they last |
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84 too long. |
| 227 | 85 |
| 86 | |
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87 .. _jobs-monitoring: |
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88 |
| 227 | 89 Monitoring jobs |
| 90 ^^^^^^^^^^^^^^^ | |
| 91 | |
| 92 .. highlight:: bash | |
| 93 | |
| 94 The list of all jobs can be retrieved as follows:: | |
| 95 | |
| 96 $ curl http://localhost:8042/jobs | |
| 97 [ "e0d12aac-47eb-454f-bb7f-9857931e2904" ] | |
| 98 | |
| 99 Full details about each job can be retrieved:: | |
| 100 | |
| 101 $ curl http://localhost:8042/jobs/e0d12aac-47eb-454f-bb7f-9857931e2904 | |
| 102 { | |
| 103 "CompletionTime" : "20190306T095223.753851", | |
| 104 "Content" : { | |
| 105 "Description" : "REST API", | |
| 106 "InstancesCount" : 1, | |
| 107 "UncompressedSizeMB" : 0 | |
| 108 }, | |
| 109 "CreationTime" : "20190306T095223.750666", | |
| 110 "EffectiveRuntime" : 0.001, | |
| 111 "ErrorCode" : 0, | |
| 112 "ErrorDescription" : "Success", | |
| 113 "ID" : "e0d12aac-47eb-454f-bb7f-9857931e2904", | |
| 114 "Priority" : 0, | |
| 115 "Progress" : 100, | |
| 116 "State" : "Success", | |
| 117 "Timestamp" : "20190306T095408.556082", | |
| 118 "Type" : "Archive" | |
| 119 } | |
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120 |
| 227 | 121 Note that the ``/jobs?expand`` URI will retrieve this information in |
| 122 one single REST query. The ``Content`` field contains the parameters | |
| 123 of the job, and is very specific to the ``Type`` of job. | |
| 124 | |
| 125 The ``State`` field can be: | |
| 126 | |
| 127 * ``Pending``: The job is waiting to be executed. | |
| 128 * ``Running``: The job is being executed. The ``Progress`` field will | |
| 129 be continuously updated to reflect the progression of the execution. | |
| 130 * ``Success``: The job has finished with success. | |
| 131 * ``Failure``: The job has finished with failure. Check out the | |
| 132 ``ErrorCode`` and ``ErrorDescription`` fields for more information. | |
| 133 * ``Paused``: The job has been paused. | |
| 134 * ``Retry``: The job has failed internally, and has been scheduled for | |
| 678 | 135 re-submission after a delay. As of Orthanc 1.9.3, this feature is not |
| 227 | 136 used by any type of job. |
| 137 | |
| 138 In order to wait for the end of an asynchronous call, the caller will | |
| 139 typically have to poll the ``/jobs/...` URI (i.e. make periodic | |
| 140 calls), waiting for the ``State`` field to become ``Success`` or | |
| 141 ``Failure``. | |
| 142 | |
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143 Note that the `integration tests of Orthanc |
| 678 | 144 <https://hg.orthanc-server.com/orthanc-tests/file/Orthanc-1.9.3/Tests/Toolbox.py>`__ |
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145 give an example about how to monitor a job in Python using the REST |
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146 API (cf. function ``MonitorJob()``). |
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147 |
| 227 | 148 |
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149 .. _jobs-controlling: |
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150 |
| 227 | 151 Interacting with jobs |
| 152 ^^^^^^^^^^^^^^^^^^^^^ | |
| 153 | |
| 154 Given the ID of some job, one can: | |
| 155 | |
| 156 * Cancel the job by POST-ing to ``/jobs/.../cancel``. | |
| 157 * Pause the job by POST-ing to ``/jobs/.../pause``. | |
| 158 * Resume a job in ``Paused`` state by POST-ing to ``/jobs/.../resume``. | |
| 159 * Retry a job in ``Failed`` state by POST-ing to ``/jobs/.../resubmit``. | |
| 160 | |
| 161 The related state machine is depicted in the `implementation notes | |
| 449 | 162 <https://hg.orthanc-server.com/orthanc/raw-file/default/OrthancServer/Resources/ImplementationNotes/JobsEngineStates.pdf>`__. |
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163 |
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164 |
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165 Example: Asynchronous generation of an archive |
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166 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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167 |
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168 .. highlight:: bash |
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169 |
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170 Sucessful jobs are associated with a set of so-called "outputs" that |
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171 can be attached to the job. |
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172 |
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173 Here is a sample bash session to ask Orthanc to generate a ZIP |
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174 archive, then to download it locally:: |
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175 |
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176 $ curl http://localhost:8042/studies/27f7126f-4f66fb14-03f4081b-f9341db2-53925988/archive -d '{"Asynchronous":true}' |
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177 { |
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178 "ID" : "82cc02d1-03fe-41f9-be46-a308d16ea94a", |
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179 "Path" : "/jobs/82cc02d1-03fe-41f9-be46-a308d16ea94a" |
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180 } |
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181 $ curl http://localhost:8042/jobs/82cc02d1-03fe-41f9-be46-a308d16ea94a |
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182 { |
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183 "CompletionTime" : "20200817T144700.401777", |
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184 "Content" : { |
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185 "Description" : "REST API", |
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186 "InstancesCount" : 232, |
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187 "UncompressedSizeMB" : 64 |
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188 }, |
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189 "CreationTime" : "20200817T144658.011824", |
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190 "EffectiveRuntime" : 2.3879999999999999, |
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191 "ErrorCode" : 0, |
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192 "ErrorDescription" : "Success", |
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193 "ID" : "82cc02d1-03fe-41f9-be46-a308d16ea94a", |
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194 "Priority" : 0, |
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195 "Progress" : 100, |
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196 "State" : "Success", |
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197 "Timestamp" : "20200817T144705.770825", |
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198 "Type" : "Archive" |
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199 } |
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200 $ curl http://localhost:8042/jobs/82cc02d1-03fe-41f9-be46-a308d16ea94a/archive > a.zip |
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201 |
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202 Note how we retrieve the content of the archive by accessing the |
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203 ``archive`` output of the job (check out the virtual method |
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204 ``IJob::GetOutput()`` from the `source code |
| 678 | 205 <https://hg.orthanc-server.com/orthanc/file/Orthanc-1.9.3/OrthancServer/Sources/ServerJobs/ArchiveJob.cpp>`__ |
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206 of Orthanc). |
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207 |
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208 Here is the corresponding sequence of commands to generate a DICOMDIR |
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209 media:: |
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210 |
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211 $ curl http://localhost:8042/studies/27f7126f-4f66fb14-03f4081b-f9341db2-53925988/media -d '{"Asynchronous":true}' |
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212 $ curl http://localhost:8042/jobs/6332be8a-0052-44fb-8cc2-ac959aeccad9/archive > a.zip |
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213 |
| 678 | 214 As of Orthanc 1.9.3, only the creation of a ZIP or a DICOMDIR archive |
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215 produces such "outputs". |
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216 |
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217 |
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218 .. _pdf: |
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219 |
| 310 | 220 Attaching PDF file as DICOM series |
| 221 ---------------------------------- | |
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222 |
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223 Among many different types of data, DICOM files can be used to store |
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224 PDF files. The ``/tools/create-dicom`` URI can be used to upload a PDF |
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225 file to Orthanc. The following scripts perform such a *DICOM-ization*; |
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226 They convert the ``HelloWorld2.pdf`` file to base64, then perform a |
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227 ``POST`` request with JSON data containing the converted payload. |
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228 |
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229 Importantly, the ``Parent`` field of the ``POST`` body can be set to |
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230 the :ref:`Orthanc identifier of some study <orthanc-ids>` in order to |
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231 attach the newly-created PDF series to the given parent study. |
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232 |
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233 Using bash: |
| 227 | 234 |
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235 .. code-block:: bash |
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236 |
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237 # create the json data, with the BASE64 data embedded in it |
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238 (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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239 |
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240 # upload it to Orthanc |
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241 cat /tmp/foo | curl -H "Content-Type: application/json" -d @- http://localhost:8042/tools/create-dicom |
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242 |
| 227 | 243 |
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244 Using powershell: |
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245 |
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246 .. code-block:: perl |
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247 |
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248 # create the BASE64 string data |
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249 $fileInBase64 = $([Convert]::ToBase64String((gc -Path "HelloWorld2.pdf" -Encoding Byte))) |
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250 |
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251 # create the json data |
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252 $params = @{Tags = @{PatientName = "Benjamino";Modality = "CT"};Content= "data:application/pdf;base64,$fileInBase64"} |
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253 |
| 376 | 254 # disabling the progress bar makes the Invoke-RestMethod call MUCH faster |
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255 $ProgressPreference = 'SilentlyContinue' |
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256 |
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257 # upload it to Orthanc |
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258 $reply = Invoke-RestMethod http://localhost:8042/tools/create-dicom -Method POST -Body ($params|ConvertTo-Json) -ContentType 'application/json' |
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259 |
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260 # display the result |
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261 Write-Host "The instance can be retrieved in PDF at http://localhost:8042$($reply.Path)/pdf" |
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262 |
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263 Please note that the ``/tools/create-dicom`` API call will return the |
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264 Orthanc instance ID of the newly created DICOM resource. |
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265 |
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266 You can use the ``/instances/.../pdf`` URI to retrieve an embedded PDF |
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267 file. |
| 228 | 268 |
| 269 | |
| 596 | 270 .. _private-tags: |
| 271 | |
| 272 Creating DICOM instance with private tags | |
| 273 ----------------------------------------- | |
| 274 | |
| 275 .. highlight:: json | |
| 276 | |
| 277 The ``/tools/create-dicom`` URI can be used to create DICOM instances | |
| 278 containing private tags. Those private tags must first be defined in | |
| 279 the ``Dictionary`` configuration option of Orthanc. Importantly, the | |
| 280 ``xxxx,0010`` tag must be defined to register the private creator, | |
| 281 where ``xxxx`` is the private group of interest. Here is a sample:: | |
| 282 | |
| 283 { | |
| 284 "Dictionary" : { | |
| 285 "0405,0010" : [ "LO", "Private data element", 1, 1, "RawDataStore" ], | |
| 286 "0405,1001" : [ "ST", "XML", 1, 1, "RawDataStore" ] | |
| 287 } | |
| 288 } | |
| 289 | |
| 290 Once Orthanc is started using this configuration file, it is possible | |
| 291 to create a DICOM instance using the following POST body on | |
| 292 ``/tools/create-dicom``:: | |
| 293 | |
| 294 { | |
| 295 "PrivateCreator" : "RawDataStore", | |
| 296 "Tags" : | |
| 297 { | |
| 298 "PatientName" : "Love^Sarah", | |
| 299 "PatientID" : "7", | |
| 300 "0405,0010" : "RawDataStore", | |
| 301 "0405,1001" : "<xml><test>Testing</test></xml>" | |
| 302 } | |
| 303 } | |
| 304 | |
| 228 | 305 |
| 306 .. _prometheus: | |
| 307 | |
| 308 Instrumentation with Prometheus | |
| 309 ------------------------------- | |
| 310 | |
| 311 .. highlight:: text | |
| 312 | |
| 313 Orthanc publishes its metrics according to the `text-based format of | |
| 314 Prometheus | |
| 315 <https://prometheus.io/docs/instrumenting/exposition_formats/#text-based-format>`__ | |
| 316 (check also the `OpenMetrics project <https://openmetrics.io/>`__), onto | |
| 317 the ``/tools/metrics-prometheus`` URI of the REST API. For instance:: | |
| 318 | |
| 319 $ curl http://localhost:8042/tools/metrics-prometheus | |
| 320 orthanc_count_instances 1 1551868380543 | |
| 321 orthanc_count_patients 1 1551868380543 | |
| 322 orthanc_count_series 1 1551868380543 | |
| 323 orthanc_count_studies 1 1551868380543 | |
| 324 orthanc_disk_size_mb 0.0135002136 1551868380543 | |
| 325 orthanc_jobs_completed 1 1551868380543 | |
| 326 orthanc_jobs_failed 0 1551868380543 | |
| 327 orthanc_jobs_pending 0 1551868380543 | |
| 328 orthanc_jobs_running 0 1551868380543 | |
| 329 orthanc_jobs_success 1 1551868380543 | |
| 330 orthanc_rest_api_active_requests 1 1551868380543 | |
| 331 orthanc_rest_api_duration_ms 0 1551868094265 | |
| 332 orthanc_storage_create_duration_ms 0 1551865919315 | |
| 333 orthanc_storage_read_duration_ms 0 1551865943752 | |
| 334 orthanc_store_dicom_duration_ms 5 1551865919319 | |
| 335 orthanc_uncompressed_size_mb 0.0135002136 1551868380543 | |
| 336 | |
| 337 | |
| 338 .. highlight:: bash | |
| 339 | |
| 340 Note that the collection of metrics can be statically disabled by | |
| 341 setting the :ref:`global configuration option <configuration>` | |
| 342 ``MetricsEnabled`` to ``false``, or dynamically disabled by PUT-ing | |
| 343 ``0`` on ``/tools/metrics``:: | |
| 344 | |
| 345 $ curl http://localhost:8042/tools/metrics | |
| 346 1 | |
| 347 $ curl http://localhost:8042/tools/metrics -X PUT -d '0' | |
| 348 $ curl http://localhost:8042/tools/metrics | |
| 349 0 | |
| 350 | |
| 351 | |
| 352 .. highlight:: yaml | |
| 353 | |
| 354 Here is a sample configuration for Prometheus (in the `YAML format | |
| 355 <https://en.wikipedia.org/wiki/YAML>`__):: | |
| 356 | |
| 357 scrape_configs: | |
| 358 - job_name: 'orthanc' | |
| 359 scrape_interval: 10s | |
| 360 metrics_path: /tools/metrics-prometheus | |
| 361 basic_auth: | |
| 362 username: orthanc | |
| 363 password: orthanc | |
| 364 static_configs: | |
| 365 - targets: ['192.168.0.2:8042'] | |
| 366 | |
| 367 .. highlight:: bash | |
| 368 | |
| 369 Obviously, make sure to adapt this sample with your actual IP | |
| 370 address. Thanks to Docker, you can easily start a Prometheus server by | |
| 371 writing this configuration to, say, ``/tmp/prometheus.yml``, then | |
| 372 type:: | |
| 373 | |
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374 $ sudo run -p 9090:9090 -v /tmp/prometheus.yml:/etc/prometheus/prometheus.yml --rm prom/prometheus:v2.7.0 |