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_sources/curate_gpt.wrappers.bio.rst.txt

@@ -36,6 +36,14 @@ curate\_gpt.wrappers.bio.mediadive\_wrapper module
    :undoc-members:
    :show-inheritance:
 
+curate\_gpt.wrappers.bio.omicsdi\_wrapper module
+------------------------------------------------
+
+.. automodule:: curate_gpt.wrappers.bio.omicsdi_wrapper
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 curate\_gpt.wrappers.bio.reactome\_wrapper module
 -------------------------------------------------
 
@@ -44,6 +52,14 @@ curate\_gpt.wrappers.bio.reactome\_wrapper module
    :undoc-members:
    :show-inheritance:
 
+curate\_gpt.wrappers.bio.uniprot\_wrapper module
+------------------------------------------------
+
+.. automodule:: curate_gpt.wrappers.bio.uniprot_wrapper
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Module contents
 ---------------
 

_sources/curate_gpt.wrappers.rst.txt

@@ -10,7 +10,6 @@ Subpackages
    curate_gpt.wrappers.bio
    curate_gpt.wrappers.clinical
    curate_gpt.wrappers.general
-   curate_gpt.wrappers.genes
    curate_gpt.wrappers.investigation
    curate_gpt.wrappers.legal
    curate_gpt.wrappers.literature

curate_gpt.evaluation.html

@@ -524,7 +524,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="curate_gpt.evaluation.evaluation_datamodel.Task.model_fields">
-<span class="sig-name descname"><span class="pre">model_fields</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">ClassVar[dict[str,</span> <span class="pre">FieldInfo]]</span></em><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'additional_collections':</span> <span class="pre">FieldInfo(annotation=Union[List[str],</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'agent':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default='dae'),</span> <span class="pre">'embedding_model_name':</span> <span class="pre">FieldInfo(annotation=str,</span> <span class="pre">required=False,</span> <span class="pre">default='openai:'),</span> <span class="pre">'executed_on':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'extractor':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default='BasicExtractor'),</span> <span class="pre">'fields_to_mask':</span> <span class="pre">FieldInfo(annotation=Union[List[str],</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'fields_to_predict':</span> <span class="pre">FieldInfo(annotation=Union[List[str],</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'generate_background':</span> <span class="pre">FieldInfo(annotation=bool,</span> <span 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class="pre">default=None)}</span></em><a class="headerlink" href="#curate_gpt.evaluation.evaluation_datamodel.Task.model_fields" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">model_fields</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">ClassVar[dict[str,</span> <span class="pre">FieldInfo]]</span></em><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'additional_collections':</span> <span class="pre">FieldInfo(annotation=Union[List[str],</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'agent':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default='dae'),</span> <span class="pre">'embedding_model_name':</span> <span class="pre">FieldInfo(annotation=str,</span> <span class="pre">required=False,</span> <span class="pre">default='openai:'),</span> <span class="pre">'executed_on':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'extractor':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default='BasicExtractor'),</span> <span class="pre">'fields_to_mask':</span> <span class="pre">FieldInfo(annotation=Union[List[str],</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'fields_to_predict':</span> <span class="pre">FieldInfo(annotation=Union[List[str],</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'generate_background':</span> <span class="pre">FieldInfo(annotation=bool,</span> <span 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class="pre">'report_path':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'results':</span> <span class="pre">FieldInfo(annotation=Union[ClassificationMetrics,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'source_collection':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'source_db_path':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'stratified_collection':</span> <span class="pre">FieldInfo(annotation=Union[StratifiedCollection,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'target_db_path':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'task_finished':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'task_started':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None),</span> <span class="pre">'working_directory':</span> <span class="pre">FieldInfo(annotation=Union[str,</span> <span class="pre">Path,</span> <span class="pre">NoneType],</span> <span class="pre">required=False,</span> <span class="pre">default=None)}</span></em><a class="headerlink" href="#curate_gpt.evaluation.evaluation_datamodel.Task.model_fields" title="Link to this definition"></a></dt>
 <dd><p>Metadata about the fields defined on the model,
 mapping of field names to [<cite>FieldInfo</cite>][pydantic.fields.FieldInfo].</p>
 <p>This replaces <cite>Model.__fields__</cite> from Pydantic V1.</p>
@@ -592,7 +592,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
 <dl class="py attribute">
 <dt class="sig sig-object py" id="curate_gpt.evaluation.evaluation_datamodel.Task.working_directory">
-<span class="sig-name descname"><span class="pre">working_directory</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code><span class="pre">[</span><code class="xref py py-class docutils literal notranslate"><span class="pre">Path</span></code><span class="pre">,</span> <code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code><span class="pre">,</span> <code class="xref py py-obj docutils literal notranslate"><span class="pre">None</span></code><span class="pre">]</span></em><a class="headerlink" href="#curate_gpt.evaluation.evaluation_datamodel.Task.working_directory" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">working_directory</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code><span class="pre">[</span><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code><span class="pre">,</span> <code class="xref py py-class docutils literal notranslate"><span class="pre">Path</span></code><span class="pre">,</span> <code class="xref py py-obj docutils literal notranslate"><span class="pre">None</span></code><span class="pre">]</span></em><a class="headerlink" href="#curate_gpt.evaluation.evaluation_datamodel.Task.working_directory" title="Link to this definition"></a></dt>
 <dd></dd></dl>
 
 </dd></dl>

curate_gpt.html

@@ -1107,7 +1107,9 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l4"><a class="reference internal" href="curate_gpt.wrappers.bio.html#module-curate_gpt.wrappers.bio.bacdive_wrapper">curate_gpt.wrappers.bio.bacdive_wrapper module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="curate_gpt.wrappers.bio.html#module-curate_gpt.wrappers.bio.gocam_wrapper">curate_gpt.wrappers.bio.gocam_wrapper module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="curate_gpt.wrappers.bio.html#module-curate_gpt.wrappers.bio.mediadive_wrapper">curate_gpt.wrappers.bio.mediadive_wrapper module</a></li>
+<li class="toctree-l4"><a class="reference internal" href="curate_gpt.wrappers.bio.html#module-curate_gpt.wrappers.bio.omicsdi_wrapper">curate_gpt.wrappers.bio.omicsdi_wrapper module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="curate_gpt.wrappers.bio.html#module-curate_gpt.wrappers.bio.reactome_wrapper">curate_gpt.wrappers.bio.reactome_wrapper module</a></li>
+<li class="toctree-l4"><a class="reference internal" href="curate_gpt.wrappers.bio.html#module-curate_gpt.wrappers.bio.uniprot_wrapper">curate_gpt.wrappers.bio.uniprot_wrapper module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="curate_gpt.wrappers.bio.html#module-curate_gpt.wrappers.bio">Module contents</a></li>
 </ul>
 </li>
@@ -1132,10 +1134,6 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l4"><a class="reference internal" href="curate_gpt.wrappers.general.html#module-curate_gpt.wrappers.general">Module contents</a></li>
 </ul>
 </li>
-<li class="toctree-l3"><a class="reference internal" href="curate_gpt.wrappers.genes.html">curate_gpt.wrappers.genes package</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="curate_gpt.wrappers.genes.html#module-curate_gpt.wrappers.genes">Module contents</a></li>
-</ul>
-</li>
 <li class="toctree-l3"><a class="reference internal" href="curate_gpt.wrappers.investigation.html">curate_gpt.wrappers.investigation package</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="curate_gpt.wrappers.investigation.html#submodules">Submodules</a></li>
 <li class="toctree-l4"><a class="reference internal" href="curate_gpt.wrappers.investigation.html#module-curate_gpt.wrappers.investigation.ess_deepdive_wrapper">curate_gpt.wrappers.investigation.ess_deepdive_wrapper module</a></li>

curate_gpt.store.html

@@ -1302,7 +1302,7 @@ <h3>Returns<a class="headerlink" href="#returns" title="Link to this heading">
 <dd><p>Dump the collection to a file
 :type collection: <span class="sphinx_autodoc_typehints-type"><code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>]</span>
 :param collection:
-:type to_file: <span class="sphinx_autodoc_typehints-type"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">Path</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>, <code class="xref py py-obj docutils literal notranslate"><span class="pre">None</span></code>]</span>
+:type to_file: <span class="sphinx_autodoc_typehints-type"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">Path</span></code>, <code class="xref py py-obj docutils literal notranslate"><span class="pre">None</span></code>]</span>
 :param to_file:
 :type format: <span class="sphinx_autodoc_typehints-type"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></span>
 :param format:
@@ -3116,7 +3116,7 @@ <h3>Returns<a class="headerlink" href="#id2" title="Link to this heading"></a
 <dd><p>Dump the collection to a file
 :type collection: <span class="sphinx_autodoc_typehints-type"><code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>]</span>
 :param collection:
-:type to_file: <span class="sphinx_autodoc_typehints-type"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">Path</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>, <code class="xref py py-obj docutils literal notranslate"><span class="pre">None</span></code>]</span>
+:type to_file: <span class="sphinx_autodoc_typehints-type"><code class="xref py py-data docutils literal notranslate"><span class="pre">Union</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">Path</span></code>, <code class="xref py py-obj docutils literal notranslate"><span class="pre">None</span></code>]</span>
 :param to_file:
 :type format: <span class="sphinx_autodoc_typehints-type"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></span>
 :param format: