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<li class="toctree-l1"><a class="reference internal" href="src.html">HDF5 Data Operations</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#utils.g5505_utils.augment_with_filenumber"><code class="docutils literal notranslate"><span class="pre">augment_with_filenumber()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#utils.g5505_utils.augment_with_filetype"><code class="docutils literal notranslate"><span class="pre">augment_with_filetype()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#utils.g5505_utils.convert_attrdict_to_np_structured_array"><code class="docutils literal notranslate"><span class="pre">convert_attrdict_to_np_structured_array()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#utils.g5505_utils.convert_dataframe_to_np_structured_array"><code class="docutils literal notranslate"><span class="pre">convert_dataframe_to_np_structured_array()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#utils.g5505_utils.convert_string_to_bytes"><code class="docutils literal notranslate"><span class="pre">convert_string_to_bytes()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#utils.g5505_utils.copy_directory_with_contraints"><code class="docutils literal notranslate"><span class="pre">copy_directory_with_contraints()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#utils.g5505_utils.is_callable_list"><code class="docutils literal notranslate"><span class="pre">is_callable_list()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#utils.g5505_utils.is_str_list"><code class="docutils literal notranslate"><span class="pre">is_str_list()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#utils.g5505_utils.is_structured_array"><code class="docutils literal notranslate"><span class="pre">is_structured_array()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#utils.g5505_utils.make_file_copy"><code class="docutils literal notranslate"><span class="pre">make_file_copy()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#utils.g5505_utils.progressBar"><code class="docutils literal notranslate"><span class="pre">progressBar()</span></code></a></li>
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<li class="toctree-l2"><a class="reference internal" href="#utils.g5505_utils.sanitize_dataframe"><code class="docutils literal notranslate"><span class="pre">sanitize_dataframe()</span></code></a></li>
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<section id="module-utils.g5505_utils">
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<span id="data-structure-conversion"></span><h1>Data Structure Conversion<a class="headerlink" href="#module-utils.g5505_utils" title="Link to this heading"></a></h1>
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<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.augment_with_filenumber">
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<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">augment_with_filenumber</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#augment_with_filenumber"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.augment_with_filenumber" title="Link to this definition"></a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py function">
|
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<dt class="sig sig-object py" id="utils.g5505_utils.augment_with_filetype">
|
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<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">augment_with_filetype</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#augment_with_filetype"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.augment_with_filetype" title="Link to this definition"></a></dt>
|
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<dd></dd></dl>
|
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|
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<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.convert_attrdict_to_np_structured_array">
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<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">convert_attrdict_to_np_structured_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attr_value</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#convert_attrdict_to_np_structured_array"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.convert_attrdict_to_np_structured_array" title="Link to this definition"></a></dt>
|
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<dd><p>Converts a dictionary of attributes into a numpy structured array for HDF5
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compound type compatibility.</p>
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<p>Each dictionary key is mapped to a field in the structured array, with the
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data type (S) determined by the longest string representation of the values.
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If the dictionary is empty, the function returns ‘missing’.</p>
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<section id="parameters">
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||
<h2>Parameters<a class="headerlink" href="#parameters" title="Link to this heading"></a></h2>
|
||
<dl>
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||
<dt>attr_value<span class="classifier">dict</span></dt><dd><p>Dictionary containing the attributes to be converted. Example:
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||
attr_value = {</p>
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||
<blockquote>
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||
<div><p>‘name’: ‘Temperature’,
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||
‘unit’: ‘Celsius’,
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‘value’: 23.5,
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‘timestamp’: ‘2023-09-26 10:00’</p>
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||
</div></blockquote>
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<p>}</p>
|
||
</dd>
|
||
</dl>
|
||
</section>
|
||
<section id="returns">
|
||
<h2>Returns<a class="headerlink" href="#returns" title="Link to this heading"></a></h2>
|
||
<dl class="simple">
|
||
<dt>new_attr_value<span class="classifier">ndarray or str</span></dt><dd><p>Numpy structured array with UTF-8 encoded fields. Returns ‘missing’ if
|
||
the input dictionary is empty.</p>
|
||
</dd>
|
||
</dl>
|
||
</section>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.convert_dataframe_to_np_structured_array">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">convert_dataframe_to_np_structured_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#convert_dataframe_to_np_structured_array"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.convert_dataframe_to_np_structured_array" title="Link to this definition"></a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.convert_string_to_bytes">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">convert_string_to_bytes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_list</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#convert_string_to_bytes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.convert_string_to_bytes" title="Link to this definition"></a></dt>
|
||
<dd><p>Convert a list of strings into a numpy array with utf8-type entries.</p>
|
||
<section id="id1">
|
||
<h2>Parameters<a class="headerlink" href="#id1" title="Link to this heading"></a></h2>
|
||
<p>input_list (list) : list of string objects</p>
|
||
</section>
|
||
<section id="id2">
|
||
<h2>Returns<a class="headerlink" href="#id2" title="Link to this heading"></a></h2>
|
||
<p>input_array_bytes (ndarray): array of ut8-type entries.</p>
|
||
</section>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.copy_directory_with_contraints">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">copy_directory_with_contraints</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_dir_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dir_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">select_dir_keywords</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">select_file_keywords</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allowed_file_extensions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dry_run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#copy_directory_with_contraints"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.copy_directory_with_contraints" title="Link to this definition"></a></dt>
|
||
<dd><p>Copies files from input_dir_path to output_dir_path based on specified constraints.</p>
|
||
<section id="id3">
|
||
<h2>Parameters<a class="headerlink" href="#id3" title="Link to this heading"></a></h2>
|
||
<blockquote>
|
||
<div><p>input_dir_path (str): Path to the input directory.
|
||
output_dir_path (str): Path to the output directory.
|
||
select_dir_keywords (list): optional, List of keywords for selecting directories.
|
||
select_file_keywords (list): optional, List of keywords for selecting files.
|
||
allowed_file_extensions (list): optional, List of allowed file extensions.</p>
|
||
</div></blockquote>
|
||
</section>
|
||
<section id="id4">
|
||
<h2>Returns<a class="headerlink" href="#id4" title="Link to this heading"></a></h2>
|
||
<blockquote>
|
||
<div><p>path_to_files_dict (dict): dictionary mapping directory paths to lists of copied file names satisfying the constraints.</p>
|
||
</div></blockquote>
|
||
</section>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.created_at">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">created_at</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">datetime_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'%Y-%m-%d</span> <span class="pre">%H:%M:%S'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#created_at"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.created_at" title="Link to this definition"></a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.group_by_df_column">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">group_by_df_column</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">column_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#group_by_df_column"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.group_by_df_column" title="Link to this definition"></a></dt>
|
||
<dd><p>df (pandas.DataFrame):
|
||
column_name (str): column_name of df by which grouping operation will take place.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.infer_units">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">infer_units</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">column_name</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#infer_units"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.infer_units" title="Link to this definition"></a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.is_callable_list">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">is_callable_list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#is_callable_list"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.is_callable_list" title="Link to this definition"></a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.is_str_list">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">is_str_list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#is_str_list"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.is_str_list" title="Link to this definition"></a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.is_structured_array">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">is_structured_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attr_val</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#is_structured_array"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.is_structured_array" title="Link to this definition"></a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.make_file_copy">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">make_file_copy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source_file_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_folder_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'tmp_files'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#make_file_copy"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.make_file_copy" title="Link to this definition"></a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.progressBar">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">progressBar</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">count_value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">total</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">suffix</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#progressBar"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.progressBar" title="Link to this definition"></a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.sanitize_dataframe">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">sanitize_dataframe</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="reference internal" href="../_modules/utils/g5505_utils.html#sanitize_dataframe"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.sanitize_dataframe" title="Link to this definition"></a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.setup_logging">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">setup_logging</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">log_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log_filename</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#setup_logging"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.setup_logging" title="Link to this definition"></a></dt>
|
||
<dd><p>Sets up logging to a specified directory and file.</p>
|
||
<dl class="simple">
|
||
<dt>Parameters:</dt><dd><p>log_dir (str): Directory to save the log file.
|
||
log_filename (str): Name of the log file.</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.split_sample_col_into_sample_and_data_quality_cols">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">split_sample_col_into_sample_and_data_quality_cols</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#split_sample_col_into_sample_and_data_quality_cols"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.split_sample_col_into_sample_and_data_quality_cols" title="Link to this definition"></a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="utils.g5505_utils.to_serializable_dtype">
|
||
<span class="sig-prename descclassname"><span class="pre">utils.g5505_utils.</span></span><span class="sig-name descname"><span class="pre">to_serializable_dtype</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/utils/g5505_utils.html#to_serializable_dtype"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#utils.g5505_utils.to_serializable_dtype" title="Link to this definition"></a></dt>
|
||
<dd><p>Transform value’s dtype into YAML/JSON compatible dtype</p>
|
||
<section id="id5">
|
||
<h2>Parameters<a class="headerlink" href="#id5" title="Link to this heading"></a></h2>
|
||
<dl class="simple">
|
||
<dt>value<span class="classifier">_type_</span></dt><dd><p>_description_</p>
|
||
</dd>
|
||
</dl>
|
||
</section>
|
||
<section id="id6">
|
||
<h2>Returns<a class="headerlink" href="#id6" title="Link to this heading"></a></h2>
|
||
<dl class="simple">
|
||
<dt>_type_</dt><dd><p>_description_</p>
|
||
</dd>
|
||
</dl>
|
||
</section>
|
||
</dd></dl>
|
||
|
||
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