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| <h1>Source code for apache_beam.io.gcp.dicomclient</h1><div class="highlight"><pre> |
| <span></span><span class="c1">#</span> |
| <span class="c1"># Licensed to the Apache Software Foundation (ASF) under one or more</span> |
| <span class="c1"># contributor license agreements. See the NOTICE file distributed with</span> |
| <span class="c1"># this work for additional information regarding copyright ownership.</span> |
| <span class="c1"># The ASF licenses this file to You under the Apache License, Version 2.0</span> |
| <span class="c1"># (the "License"); you may not use this file except in compliance with</span> |
| <span class="c1"># the License. You may obtain a copy of the License at</span> |
| <span class="c1">#</span> |
| <span class="c1"># http://www.apache.org/licenses/LICENSE-2.0</span> |
| <span class="c1">#</span> |
| <span class="c1"># Unless required by applicable law or agreed to in writing, software</span> |
| <span class="c1"># distributed under the License is distributed on an "AS IS" BASIS,</span> |
| <span class="c1"># WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span> |
| <span class="c1"># See the License for the specific language governing permissions and</span> |
| <span class="c1"># limitations under the License.</span> |
| <span class="c1">#</span> |
| |
| <span class="c1"># pytype: skip-file</span> |
| |
| <span class="kn">from</span> <span class="nn">google.auth</span> <span class="kn">import</span> <span class="n">default</span> |
| <span class="kn">from</span> <span class="nn">google.auth.transport</span> <span class="kn">import</span> <span class="n">requests</span> |
| |
| |
| <div class="viewcode-block" id="DicomApiHttpClient"><a class="viewcode-back" href="../../../../apache_beam.io.gcp.dicomclient.html#apache_beam.io.gcp.dicomclient.DicomApiHttpClient">[docs]</a><span class="k">class</span> <span class="nc">DicomApiHttpClient</span><span class="p">:</span> |
| <span class="w"> </span><span class="sd">"""DICOM api client that talk to api via http request"""</span> |
| <span class="n">healthcare_base_url</span> <span class="o">=</span> <span class="s2">"https://healthcare.googleapis.com/v1"</span> |
| <span class="n">session</span> <span class="o">=</span> <span class="kc">None</span> |
| |
| <div class="viewcode-block" id="DicomApiHttpClient.get_session"><a class="viewcode-back" href="../../../../apache_beam.io.gcp.dicomclient.html#apache_beam.io.gcp.dicomclient.DicomApiHttpClient.get_session">[docs]</a> <span class="k">def</span> <span class="nf">get_session</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">credential</span><span class="p">):</span> |
| <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">:</span> |
| <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span> |
| |
| <span class="c1"># if the credential is not provided, use the default credential.</span> |
| <span class="k">if</span> <span class="ow">not</span> <span class="n">credential</span><span class="p">:</span> |
| <span class="n">credential</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">default</span><span class="p">()</span> |
| <span class="n">new_seesion</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">AuthorizedSession</span><span class="p">(</span><span class="n">credential</span><span class="p">)</span> |
| <span class="bp">self</span><span class="o">.</span><span class="n">session</span> <span class="o">=</span> <span class="n">new_seesion</span> |
| <span class="k">return</span> <span class="n">new_seesion</span></div> |
| |
| <div class="viewcode-block" id="DicomApiHttpClient.qido_search"><a class="viewcode-back" href="../../../../apache_beam.io.gcp.dicomclient.html#apache_beam.io.gcp.dicomclient.DicomApiHttpClient.qido_search">[docs]</a> <span class="k">def</span> <span class="nf">qido_search</span><span class="p">(</span> |
| <span class="bp">self</span><span class="p">,</span> |
| <span class="n">project_id</span><span class="p">,</span> |
| <span class="n">region</span><span class="p">,</span> |
| <span class="n">dataset_id</span><span class="p">,</span> |
| <span class="n">dicom_store_id</span><span class="p">,</span> |
| <span class="n">search_type</span><span class="p">,</span> |
| <span class="n">params</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> |
| <span class="n">credential</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> |
| <span class="w"> </span><span class="sd">"""function for searching a DICOM store"""</span> |
| |
| <span class="c1"># sending request to the REST healthcare api.</span> |
| <span class="n">api_endpoint</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">/projects/</span><span class="si">{}</span><span class="s2">/locations/</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span> |
| <span class="bp">self</span><span class="o">.</span><span class="n">healthcare_base_url</span><span class="p">,</span> <span class="n">project_id</span><span class="p">,</span> <span class="n">region</span><span class="p">)</span> |
| |
| <span class="c1"># base of dicomweb path.</span> |
| <span class="n">dicomweb_path</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">/datasets/</span><span class="si">{}</span><span class="s2">/dicomStores/</span><span class="si">{}</span><span class="s2">/dicomWeb/</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span> |
| <span class="n">api_endpoint</span><span class="p">,</span> <span class="n">dataset_id</span><span class="p">,</span> <span class="n">dicom_store_id</span><span class="p">,</span> <span class="n">search_type</span><span class="p">)</span> |
| |
| <span class="c1"># Make an authenticated API request</span> |
| <span class="n">session</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_session</span><span class="p">(</span><span class="n">credential</span><span class="p">)</span> |
| <span class="n">headers</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"Content-Type"</span><span class="p">:</span> <span class="s2">"application/dicom+json; charset=utf-8"</span><span class="p">}</span> |
| <span class="n">page_size</span> <span class="o">=</span> <span class="mi">500</span> |
| |
| <span class="k">if</span> <span class="n">params</span> <span class="ow">and</span> <span class="s1">'limit'</span> <span class="ow">in</span> <span class="n">params</span><span class="p">:</span> |
| <span class="n">page_size</span> <span class="o">=</span> <span class="n">params</span><span class="p">[</span><span class="s1">'limit'</span><span class="p">]</span> |
| <span class="k">elif</span> <span class="n">params</span><span class="p">:</span> |
| <span class="n">params</span><span class="p">[</span><span class="s1">'limit'</span><span class="p">]</span> <span class="o">=</span> <span class="n">page_size</span> |
| <span class="k">else</span><span class="p">:</span> |
| <span class="n">params</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'limit'</span><span class="p">:</span> <span class="n">page_size</span><span class="p">}</span> |
| |
| <span class="n">offset</span> <span class="o">=</span> <span class="mi">0</span> |
| <span class="n">output</span> <span class="o">=</span> <span class="p">[]</span> |
| <span class="c1"># iterate to get all the results</span> |
| <span class="k">while</span> <span class="kc">True</span><span class="p">:</span> |
| <span class="n">params</span><span class="p">[</span><span class="s1">'offset'</span><span class="p">]</span> <span class="o">=</span> <span class="n">offset</span> |
| <span class="n">response</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">dicomweb_path</span><span class="p">,</span> <span class="n">headers</span><span class="o">=</span><span class="n">headers</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> |
| <span class="n">status</span> <span class="o">=</span> <span class="n">response</span><span class="o">.</span><span class="n">status_code</span> |
| <span class="k">if</span> <span class="n">status</span> <span class="o">!=</span> <span class="mi">200</span><span class="p">:</span> |
| <span class="k">if</span> <span class="n">offset</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> |
| <span class="k">return</span> <span class="p">[],</span> <span class="n">status</span> |
| <span class="n">params</span><span class="p">[</span><span class="s1">'offset'</span><span class="p">]</span> <span class="o">=</span> <span class="n">offset</span> <span class="o">-</span> <span class="mi">1</span> |
| <span class="n">params</span><span class="p">[</span><span class="s1">'limit'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span> |
| <span class="n">response</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">dicomweb_path</span><span class="p">,</span> <span class="n">headers</span><span class="o">=</span><span class="n">headers</span><span class="p">,</span> <span class="n">params</span><span class="o">=</span><span class="n">params</span><span class="p">)</span> |
| <span class="n">check_status</span> <span class="o">=</span> <span class="n">response</span><span class="o">.</span><span class="n">status_code</span> |
| <span class="k">if</span> <span class="n">check_status</span> <span class="o">==</span> <span class="mi">200</span><span class="p">:</span> |
| <span class="c1"># if the number of results equals to page size</span> |
| <span class="k">return</span> <span class="n">output</span><span class="p">,</span> <span class="n">check_status</span> |
| <span class="k">else</span><span class="p">:</span> |
| <span class="c1"># something wrong with the request or server</span> |
| <span class="k">return</span> <span class="p">[],</span> <span class="n">status</span> |
| <span class="n">results</span> <span class="o">=</span> <span class="n">response</span><span class="o">.</span><span class="n">json</span><span class="p">()</span> |
| <span class="n">output</span> <span class="o">+=</span> <span class="n">results</span> |
| <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">results</span><span class="p">)</span> <span class="o"><</span> <span class="n">page_size</span><span class="p">:</span> |
| <span class="c1"># got all the results, return</span> |
| <span class="k">break</span> |
| <span class="n">offset</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">results</span><span class="p">)</span> |
| |
| <span class="k">return</span> <span class="n">output</span><span class="p">,</span> <span class="n">status</span></div> |
| |
| <div class="viewcode-block" id="DicomApiHttpClient.dicomweb_store_instance"><a class="viewcode-back" href="../../../../apache_beam.io.gcp.dicomclient.html#apache_beam.io.gcp.dicomclient.DicomApiHttpClient.dicomweb_store_instance">[docs]</a> <span class="k">def</span> <span class="nf">dicomweb_store_instance</span><span class="p">(</span> |
| <span class="bp">self</span><span class="p">,</span> |
| <span class="n">project_id</span><span class="p">,</span> |
| <span class="n">region</span><span class="p">,</span> |
| <span class="n">dataset_id</span><span class="p">,</span> |
| <span class="n">dicom_store_id</span><span class="p">,</span> |
| <span class="n">dcm_file</span><span class="p">,</span> |
| <span class="n">credential</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> |
| <span class="w"> </span><span class="sd">"""function for storing an instance."""</span> |
| |
| <span class="n">api_endpoint</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">/projects/</span><span class="si">{}</span><span class="s2">/locations/</span><span class="si">{}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span> |
| <span class="bp">self</span><span class="o">.</span><span class="n">healthcare_base_url</span><span class="p">,</span> <span class="n">project_id</span><span class="p">,</span> <span class="n">region</span><span class="p">)</span> |
| |
| <span class="n">dicomweb_path</span> <span class="o">=</span> <span class="s2">"</span><span class="si">{}</span><span class="s2">/datasets/</span><span class="si">{}</span><span class="s2">/dicomStores/</span><span class="si">{}</span><span class="s2">/dicomWeb/studies"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span> |
| <span class="n">api_endpoint</span><span class="p">,</span> <span class="n">dataset_id</span><span class="p">,</span> <span class="n">dicom_store_id</span><span class="p">)</span> |
| |
| <span class="c1"># Make an authenticated API request</span> |
| <span class="n">session</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_session</span><span class="p">(</span><span class="n">credential</span><span class="p">)</span> |
| <span class="n">content_type</span> <span class="o">=</span> <span class="s2">"application/dicom"</span> |
| <span class="n">headers</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"Content-Type"</span><span class="p">:</span> <span class="n">content_type</span><span class="p">}</span> |
| |
| <span class="n">response</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">post</span><span class="p">(</span><span class="n">dicomweb_path</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">dcm_file</span><span class="p">,</span> <span class="n">headers</span><span class="o">=</span><span class="n">headers</span><span class="p">)</span> |
| |
| <span class="k">return</span> <span class="kc">None</span><span class="p">,</span> <span class="n">response</span><span class="o">.</span><span class="n">status_code</span></div></div> |
| </pre></div> |
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