Skip to content

Commit

Permalink
Deploying to gh-pages from @ 321dbfa 🚀
Browse files Browse the repository at this point in the history
  • Loading branch information
frehburg committed Sep 25, 2024
1 parent eaf7b0a commit 66a5cc9
Show file tree
Hide file tree
Showing 9 changed files with 69 additions and 6 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -546,6 +546,9 @@ <h1>Source code for phenopacket_mapper.data_standards.data_model</h1><div class=
<span class="sd"> :param fields: Data fields to be preprocessed, will be passed onto `mapping`</span>
<span class="sd"> :param mapping: A dictionary or method to use for preprocessing</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">fields</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
<span class="n">fields</span> <span class="o">=</span> <span class="p">[</span><span class="n">fields</span><span class="p">]</span>

<span class="n">field_ids</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">fields</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">field</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
Expand Down
22 changes: 21 additions & 1 deletion latest/_modules/phenopacket_mapper/data_standards/date.html
Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,9 @@
<div itemprop="articleBody">

<h1>Source code for phenopacket_mapper.data_standards.date</h1><div class="highlight"><pre>
<span></span><span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span><span class="p">,</span> <span class="n">field</span>
<span></span><span class="kn">from</span> <span class="nn">google.protobuf.timestamp_pb2</span> <span class="kn">import</span> <span class="n">Timestamp</span>

<span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">dataclass</span><span class="p">,</span> <span class="n">field</span>
<span class="kn">from</span> <span class="nn">datetime</span> <span class="kn">import</span> <span class="n">datetime</span>
<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">Union</span><span class="p">,</span> <span class="n">Literal</span>

Expand Down Expand Up @@ -163,6 +165,24 @@ <h1>Source code for phenopacket_mapper.data_standards.date</h1><div class="highl
<span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">hour_str</span> <span class="o">+</span> <span class="s2">&quot;:&quot;</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">minute_str</span> <span class="o">+</span> <span class="s2">&quot;:&quot;</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">second_str</span> <span class="o">+</span> <span class="s2">&quot;Z&quot;</span><span class="p">)</span></div>


<div class="viewcode-block" id="Date.protobuf_timestamp">
<a class="viewcode-back" href="../../../apidocs/phenopacket_mapper.data_standards.date.html#phenopacket_mapper.data_standards.Date.protobuf_timestamp">[docs]</a>
<span class="k">def</span> <span class="nf">protobuf_timestamp</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Timestamp</span><span class="p">:</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the date in a Google Protobuf Timestamp object</span>

<span class="sd"> :return: the date in a Google Protobuf Timestamp object</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="n">Timestamp</span><span class="p">()</span><span class="o">.</span><span class="n">fromDatetime</span><span class="p">(</span><span class="n">datetime</span><span class="p">(</span>
<span class="n">year</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">year</span><span class="p">,</span>
<span class="n">month</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">month</span><span class="p">,</span>
<span class="n">day</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">day</span><span class="p">,</span>
<span class="n">hour</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">hour</span><span class="p">,</span>
<span class="n">minute</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">minute</span><span class="p">,</span>
<span class="n">second</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">second</span>
<span class="p">))</span></div>


<div class="viewcode-block" id="Date.formatted_string">
<a class="viewcode-back" href="../../../apidocs/phenopacket_mapper.data_standards.date.html#phenopacket_mapper.data_standards.Date.formatted_string">[docs]</a>
<span class="k">def</span> <span class="nf">formatted_string</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fmt</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
Expand Down
7 changes: 6 additions & 1 deletion latest/_modules/phenopacket_mapper/mapping/mapper.html
Original file line number Diff line number Diff line change
Expand Up @@ -145,7 +145,12 @@ <h1>Source code for phenopacket_mapper.mapping.mapper</h1><div class="highlight"
<span class="n">data_field</span> <span class="o">=</span> <span class="n">e</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">value</span><span class="p">:</span> <span class="n">DataFieldValue</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">instance</span><span class="p">,</span> <span class="n">data_field</span><span class="o">.</span><span class="n">id</span><span class="p">)</span><span class="o">.</span><span class="n">value</span>
<span class="n">kwargs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
<span class="kn">from</span> <span class="nn">phenopacket_mapper.data_standards</span> <span class="kn">import</span> <span class="n">Date</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">Date</span><span class="p">):</span>
<span class="n">date</span> <span class="o">=</span> <span class="n">value</span>
<span class="n">kwargs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">date</span><span class="o">.</span><span class="n">protobuf_timestamp</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">kwargs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">continue</span>
<span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="n">PhenopacketElement</span><span class="p">):</span>
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,12 @@ <h1>Source code for phenopacket_mapper.mapping.phenopacket_element</h1><div clas
<span class="n">df</span> <span class="o">=</span> <span class="n">e</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">value</span><span class="p">:</span> <span class="n">DataFieldValue</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">instance</span><span class="p">,</span> <span class="n">df</span><span class="o">.</span><span class="n">id</span><span class="p">)</span><span class="o">.</span><span class="n">value</span>
<span class="n">kwargs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
<span class="kn">from</span> <span class="nn">phenopacket_mapper.data_standards</span> <span class="kn">import</span> <span class="n">Date</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">Date</span><span class="p">):</span>
<span class="n">date</span> <span class="o">=</span> <span class="n">value</span>
<span class="n">kwargs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">date</span><span class="o">.</span><span class="n">protobuf_timestamp</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">kwargs</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
<span class="k">except</span> <span class="ne">AttributeError</span><span class="p">:</span>
<span class="k">continue</span>
<span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="n">PhenopacketElement</span><span class="p">):</span>
Expand Down
12 changes: 12 additions & 0 deletions latest/apidocs/phenopacket_mapper.data_standards.date.html
Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,7 @@
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.date.Date.minute_str"><code class="docutils literal notranslate"><span class="pre">Date.minute_str</span></code></a></li>
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.date.Date.second_str"><code class="docutils literal notranslate"><span class="pre">Date.second_str</span></code></a></li>
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.date.Date.iso_8601_datestring"><code class="docutils literal notranslate"><span class="pre">Date.iso_8601_datestring()</span></code></a></li>
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.date.Date.protobuf_timestamp"><code class="docutils literal notranslate"><span class="pre">Date.protobuf_timestamp()</span></code></a></li>
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.date.Date.formatted_string"><code class="docutils literal notranslate"><span class="pre">Date.formatted_string()</span></code></a></li>
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.date.Date.from_datetime"><code class="docutils literal notranslate"><span class="pre">Date.from_datetime()</span></code></a></li>
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.date.Date.from_iso_8601"><code class="docutils literal notranslate"><span class="pre">Date.from_iso_8601()</span></code></a></li>
Expand Down Expand Up @@ -191,6 +192,17 @@
</div></blockquote>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="phenopacket_mapper.data_standards.date.Date.protobuf_timestamp">
<span class="sig-name descname"><span class="pre">protobuf_timestamp</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Timestamp</span></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/date.html#Date.protobuf_timestamp"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.date.Date.protobuf_timestamp" title="Link to this definition"></a></dt>
<dd><p>Returns the date in a Google Protobuf Timestamp object</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>the date in a Google Protobuf Timestamp object</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="phenopacket_mapper.data_standards.date.Date.formatted_string">
<span class="sig-name descname"><span class="pre">formatted_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fmt</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/date.html#Date.formatted_string"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.date.Date.formatted_string" title="Link to this definition"></a></dt>
Expand Down
12 changes: 12 additions & 0 deletions latest/apidocs/phenopacket_mapper.data_standards.html
Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,7 @@
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.Date.minute_str"><code class="docutils literal notranslate"><span class="pre">Date.minute_str</span></code></a></li>
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.Date.second_str"><code class="docutils literal notranslate"><span class="pre">Date.second_str</span></code></a></li>
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.Date.iso_8601_datestring"><code class="docutils literal notranslate"><span class="pre">Date.iso_8601_datestring()</span></code></a></li>
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.Date.protobuf_timestamp"><code class="docutils literal notranslate"><span class="pre">Date.protobuf_timestamp()</span></code></a></li>
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.Date.formatted_string"><code class="docutils literal notranslate"><span class="pre">Date.formatted_string()</span></code></a></li>
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.Date.from_datetime"><code class="docutils literal notranslate"><span class="pre">Date.from_datetime()</span></code></a></li>
<li><a class="reference internal" href="#phenopacket_mapper.data_standards.Date.from_iso_8601"><code class="docutils literal notranslate"><span class="pre">Date.from_iso_8601()</span></code></a></li>
Expand Down Expand Up @@ -728,6 +729,17 @@
</div></blockquote>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="phenopacket_mapper.data_standards.Date.protobuf_timestamp">
<span class="sig-name descname"><span class="pre">protobuf_timestamp</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Timestamp</span></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/date.html#Date.protobuf_timestamp"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.Date.protobuf_timestamp" title="Link to this definition"></a></dt>
<dd><p>Returns the date in a Google Protobuf Timestamp object</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>the date in a Google Protobuf Timestamp object</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="phenopacket_mapper.data_standards.Date.formatted_string">
<span class="sig-name descname"><span class="pre">formatted_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fmt</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/date.html#Date.formatted_string"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.Date.formatted_string" title="Link to this definition"></a></dt>
Expand Down
10 changes: 8 additions & 2 deletions latest/genindex.html
Original file line number Diff line number Diff line change
Expand Up @@ -828,15 +828,15 @@ <h2 id="P">P</h2>
<li><a href="apidocs/phenopacket_mapper.mapping.html#module-phenopacket_mapper.mapping">module</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
phenopacket_mapper.mapping.map_field

<ul>
<li><a href="apidocs/phenopacket_mapper.mapping.map_field.html#module-phenopacket_mapper.mapping.map_field">module</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
phenopacket_mapper.mapping.mapper

Expand Down Expand Up @@ -1039,6 +1039,12 @@ <h2 id="P">P</h2>

<ul>
<li><a href="apidocs/phenopacket_mapper.preprocessing.preprocess_method.html#phenopacket_mapper.preprocessing.preprocess_method.preprocess_method">(in module phenopacket_mapper.preprocessing.preprocess_method)</a>
</li>
</ul></li>
<li><a href="apidocs/phenopacket_mapper.data_standards.html#phenopacket_mapper.data_standards.Date.protobuf_timestamp">protobuf_timestamp() (phenopacket_mapper.data_standards.Date method)</a>

<ul>
<li><a href="apidocs/phenopacket_mapper.data_standards.date.html#phenopacket_mapper.data_standards.date.Date.protobuf_timestamp">(phenopacket_mapper.data_standards.date.Date method)</a>
</li>
</ul></li>
</ul></td>
Expand Down
Binary file modified latest/objects.inv
Binary file not shown.
2 changes: 1 addition & 1 deletion latest/searchindex.js

Large diffs are not rendered by default.

0 comments on commit 66a5cc9

Please sign in to comment.