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| <h1>Source code for gnomad.resources.config</h1><div class="highlight"><pre> | ||
| <span></span><span class="sd">"""Configuration for loading resources."""</span> | ||
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| <span class="kn">import</span> <span class="nn">logging</span> | ||
| <span class="kn">import</span> <span class="nn">os</span> | ||
| <span class="kn">from</span> <span class="nn">enum</span> <span class="kn">import</span> <span class="n">Enum</span> | ||
| <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span> | ||
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| <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span> | ||
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| <div class="viewcode-block" id="GnomadPublicResourceSource"><a class="viewcode-back" href="../../../api_reference/resources/config.html#gnomad.resources.config.GnomadPublicResourceSource">[docs]</a><span class="k">class</span> <span class="nc">GnomadPublicResourceSource</span><span class="p">(</span><span class="n">Enum</span><span class="p">):</span> | ||
| <span class="w"> </span><span class="sd">"""Sources for public gnomAD resources."""</span> | ||
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| <span class="n">GNOMAD</span> <span class="o">=</span> <span class="s2">"gnomAD"</span> | ||
| <span class="n">GOOGLE_CLOUD_PUBLIC_DATASETS</span> <span class="o">=</span> <span class="s2">"Google Cloud Public Datasets"</span> | ||
| <span class="n">REGISTRY_OF_OPEN_DATA_ON_AWS</span> <span class="o">=</span> <span class="s2">"Registry of Open Data on AWS"</span> | ||
| <span class="n">AZURE_OPEN_DATASETS</span> <span class="o">=</span> <span class="s2">"Azure Open Datasets"</span></div> | ||
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| <div class="viewcode-block" id="get_default_public_resource_source"><a class="viewcode-back" href="../../../api_reference/resources/config.html#gnomad.resources.config.get_default_public_resource_source">[docs]</a><span class="k">def</span> <span class="nf">get_default_public_resource_source</span><span class="p">()</span> <span class="o">-></span> <span class="n">Union</span><span class="p">[</span><span class="n">GnomadPublicResourceSource</span><span class="p">,</span> <span class="nb">str</span><span class="p">]:</span> | ||
| <span class="w"> </span><span class="sd">"""</span> | ||
| <span class="sd"> Get the default source for public gnomAD resources.</span> | ||
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| <span class="sd"> The default source is determined by...</span> | ||
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| <span class="sd"> - If the ``GNOMAD_DEFAULT_PUBLIC_RESOURCE_SOURCE`` environment variable is set, use the source configured there.</span> | ||
| <span class="sd"> - Otherwise, if Hail determines that is is running in a cloud provider's Spark environment, use the source from that cloud provider.</span> | ||
| <span class="sd"> For example, use Azure Open Datasets if running on an Azure HDInsight cluster.</span> | ||
| <span class="sd"> - Otherwise, use Google Cloud Public Datasets.</span> | ||
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| <span class="sd"> :returns: Default resource source</span> | ||
| <span class="sd"> """</span> | ||
| <span class="n">default_source_from_env</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s2">"GNOMAD_DEFAULT_PUBLIC_RESOURCE_SOURCE"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> | ||
| <span class="k">if</span> <span class="n">default_source_from_env</span><span class="p">:</span> | ||
| <span class="c1"># Convert to a GnomadPublicResourceSource enum if possible</span> | ||
| <span class="k">try</span><span class="p">:</span> | ||
| <span class="n">default_source</span> <span class="o">=</span> <span class="n">GnomadPublicResourceSource</span><span class="p">(</span><span class="n">default_source_from_env</span><span class="p">)</span> | ||
| <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span> | ||
| <span class="s2">"Using configured source for gnomAD resources: </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">default_source</span><span class="o">.</span><span class="n">value</span> | ||
| <span class="p">)</span> | ||
| <span class="k">return</span> <span class="n">default_source</span> | ||
| <span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span> | ||
| <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span> | ||
| <span class="s2">"Using configured custom source for gnomAD resources: </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> | ||
| <span class="n">default_source_from_env</span><span class="p">,</span> | ||
| <span class="p">)</span> | ||
| <span class="k">return</span> <span class="n">default_source_from_env</span> | ||
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| <span class="k">try</span><span class="p">:</span> | ||
| <span class="kn">from</span> <span class="nn">hail.utils</span> <span class="kn">import</span> <span class="n">guess_cloud_spark_provider</span> | ||
| <span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span> | ||
| <span class="k">pass</span> | ||
| <span class="k">else</span><span class="p">:</span> | ||
| <span class="n">cloud_spark_provider</span> <span class="o">=</span> <span class="n">guess_cloud_spark_provider</span><span class="p">()</span> | ||
| <span class="n">default_resource_sources_by_provider</span> <span class="o">=</span> <span class="p">{</span> | ||
| <span class="s2">"dataproc"</span><span class="p">:</span> <span class="n">GnomadPublicResourceSource</span><span class="o">.</span><span class="n">GOOGLE_CLOUD_PUBLIC_DATASETS</span><span class="p">,</span> | ||
| <span class="s2">"hdinsight"</span><span class="p">:</span> <span class="n">GnomadPublicResourceSource</span><span class="o">.</span><span class="n">AZURE_OPEN_DATASETS</span><span class="p">,</span> | ||
| <span class="p">}</span> | ||
| <span class="k">if</span> <span class="n">cloud_spark_provider</span><span class="p">:</span> | ||
| <span class="k">try</span><span class="p">:</span> | ||
| <span class="n">default_source_from_provider</span> <span class="o">=</span> <span class="n">default_resource_sources_by_provider</span><span class="p">[</span> | ||
| <span class="n">cloud_spark_provider</span> | ||
| <span class="p">]</span> | ||
| <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span> | ||
| <span class="s2">"Using default source for gnomAD resources based on cloud"</span> | ||
| <span class="s2">" provider: </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> | ||
| <span class="n">default_source_from_provider</span><span class="p">,</span> | ||
| <span class="p">)</span> | ||
| <span class="k">return</span> <span class="n">default_source_from_provider</span> | ||
| <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span> | ||
| <span class="k">pass</span> | ||
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| <span class="k">return</span> <span class="n">GnomadPublicResourceSource</span><span class="o">.</span><span class="n">GOOGLE_CLOUD_PUBLIC_DATASETS</span></div> | ||
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| <span class="k">class</span> <span class="nc">_GnomadPublicResourceConfiguration</span><span class="p">:</span> | ||
| <span class="w"> </span><span class="sd">"""Configuration for public gnomAD resources."""</span> | ||
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| <span class="n">_source</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">GnomadPublicResourceSource</span><span class="p">,</span> <span class="nb">str</span><span class="p">,</span> <span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span> | ||
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| <span class="nd">@property</span> | ||
| <span class="k">def</span> <span class="nf">source</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-></span> <span class="n">Union</span><span class="p">[</span><span class="n">GnomadPublicResourceSource</span><span class="p">,</span> <span class="nb">str</span><span class="p">]:</span> | ||
| <span class="w"> </span><span class="sd">"""</span> | ||
| <span class="sd"> Get the source for public gnomAD resource files.</span> | ||
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| <span class="sd"> This is used to determine which URLs gnomAD resources will be loaded from.</span> | ||
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| <span class="sd"> :returns: Source name or path to root of resources directory</span> | ||
| <span class="sd"> """</span> | ||
| <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_source</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> | ||
| <span class="bp">self</span><span class="o">.</span><span class="n">_source</span> <span class="o">=</span> <span class="n">get_default_public_resource_source</span><span class="p">()</span> | ||
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| <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_source</span> | ||
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| <span class="nd">@source</span><span class="o">.</span><span class="n">setter</span> | ||
| <span class="k">def</span> <span class="nf">source</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">GnomadPublicResourceSource</span><span class="p">,</span> <span class="nb">str</span><span class="p">])</span> <span class="o">-></span> <span class="kc">None</span><span class="p">:</span> | ||
| <span class="w"> </span><span class="sd">"""</span> | ||
| <span class="sd"> Set the default source for resource files.</span> | ||
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| <span class="sd"> This is used to determine which URLs gnomAD resources will be loaded from.</span> | ||
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| <span class="sd"> :param source: Source name or path to root of resources directory</span> | ||
| <span class="sd"> """</span> | ||
| <span class="bp">self</span><span class="o">.</span><span class="n">_source</span> <span class="o">=</span> <span class="n">source</span> | ||
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| <span class="n">gnomad_public_resource_configuration</span> <span class="o">=</span> <span class="n">_GnomadPublicResourceConfiguration</span><span class="p">()</span> | ||
| </pre></div> | ||
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