From cd02f08ffd5a54d210e411a8dfb9f645b2034391 Mon Sep 17 00:00:00 2001 From: frehburg <43171336+frehburg@users.noreply.github.com> Date: Tue, 8 Oct 2024 10:52:58 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20BIH-CEI/?= =?UTF-8?q?phenopacket=5Fmapper@8b934fe2572239cd3e26050c75cf5c0de91c31b0?= =?UTF-8?q?=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../data_standards/data_model.html | 47 +++++++++++------- .../phenopacket_mapper/pipeline/input.html | 12 ++--- ...cket_mapper.data_standards.data_model.html | 24 ++++----- .../phenopacket_mapper.data_standards.html | 24 ++++----- .../apidocs/phenopacket_mapper.pipeline.html | 2 +- .../phenopacket_mapper.pipeline.input.html | 2 +- latest/genindex.html | 10 +--- latest/objects.inv | Bin 3361 -> 3353 bytes latest/searchindex.js | 2 +- 9 files changed, 57 insertions(+), 66 deletions(-) diff --git a/latest/_modules/phenopacket_mapper/data_standards/data_model.html b/latest/_modules/phenopacket_mapper/data_standards/data_model.html index c9bd884..25f0c45 100644 --- a/latest/_modules/phenopacket_mapper/data_standards/data_model.html +++ b/latest/_modules/phenopacket_mapper/data_standards/data_model.html @@ -124,25 +124,23 @@ <h1>Source code for phenopacket_mapper.data_standards.data_model</h1><div class= <span class="sd"> If the `value_set` is a single type, it can be passed directly as the `value_set` parameter.</span> <span class="sd"> e.g.:</span> -<span class="sd"> >>> DataField(name="Field 1", value_set=int)</span> -<span class="sd"> DataField(name='Field 1', value_set=ValueSet(elements=[<class 'int'>], name='', description=''), id='field_1', description='', section='', required=True, specification='', ordinal='')</span> +<span class="sd"> >>> DataField(name="Field 1", specification=int)</span> +<span class="sd"> DataField(name='Field 1', specification=ValueSet(elements=[<class 'int'>], name='', description=''), id='field_1', description='', section='', required=True, ordinal='')</span> <span class="sd"> :ivar name: Name of the field</span> -<span class="sd"> :ivar value_set: Value set of the field, if the value set is only one type, can also pass that type directly</span> +<span class="sd"> :ivar specification: Value set of the field, if the value set is only one type, can also pass that type directly</span> <span class="sd"> :ivar id: The identifier of the field, adhering to the naming rules stated above</span> <span class="sd"> :ivar description: Description of the field</span> <span class="sd"> :ivar section: Section of the field (Only applicable if the data model is divided into sections)</span> <span class="sd"> :ivar required: Required flag of the field</span> -<span class="sd"> :ivar specification: Text specification of the field (a description of the value set and field)</span> <span class="sd"> :ivar ordinal: Ordinal of the field (E.g. 1.1, 1.2, 2.1, etc.)</span> <span class="sd"> """</span> <span class="n">name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">field</span><span class="p">()</span> - <span class="n">value_set</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">ValueSet</span><span class="p">,</span> <span class="nb">type</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">()</span> + <span class="n">specification</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="n">ValueSet</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">List</span><span class="p">[</span><span class="nb">type</span><span class="p">]]</span> <span class="o">=</span> <span class="n">field</span><span class="p">()</span> <span class="nb">id</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span> <span class="n">description</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default</span><span class="o">=</span><span class="s1">''</span><span class="p">)</span> <span class="n">section</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default</span><span class="o">=</span><span class="s1">''</span><span class="p">)</span> <span class="n">required</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> - <span class="n">specification</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default</span><span class="o">=</span><span class="s1">''</span><span class="p">)</span> <span class="n">ordinal</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default</span><span class="o">=</span><span class="s1">''</span><span class="p">)</span> <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> @@ -150,18 +148,28 @@ <h1>Source code for phenopacket_mapper.data_standards.data_model</h1><div class= <span class="kn">from</span> <span class="nn">phenopacket_mapper.utils</span> <span class="kn">import</span> <span class="n">str_to_valid_id</span> <span class="nb">object</span><span class="o">.</span><span class="fm">__setattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'id'</span><span class="p">,</span> <span class="n">str_to_valid_id</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">))</span> - <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">value_set</span><span class="p">,</span> <span class="nb">type</span><span class="p">):</span> - <span class="nb">object</span><span class="o">.</span><span class="fm">__setattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'value_set'</span><span class="p">,</span> <span class="n">ValueSet</span><span class="p">(</span><span class="n">elements</span><span class="o">=</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">value_set</span><span class="p">]))</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">specification</span><span class="p">,</span> <span class="nb">type</span><span class="p">):</span> + <span class="nb">object</span><span class="o">.</span><span class="fm">__setattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'specification'</span><span class="p">,</span> <span class="n">ValueSet</span><span class="p">(</span><span class="n">elements</span><span class="o">=</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">specification</span><span class="p">]))</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">specification</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span> + <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="nb">type</span><span class="p">)</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">specification</span><span class="p">):</span> + <span class="nb">object</span><span class="o">.</span><span class="fm">__setattr__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'specification'</span><span class="p">,</span> <span class="n">ValueSet</span><span class="p">(</span><span class="n">elements</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">specification</span><span class="p">))</span> <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> <span class="n">ret</span> <span class="o">=</span> <span class="s2">"DataField(</span><span class="se">\n</span><span class="s2">"</span> <span class="n">ret</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"</span><span class="se">\t\t</span><span class="s2">id: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">id</span><span class="si">}</span><span class="s2">,</span><span class="se">\n</span><span class="s2">"</span> <span class="n">ret</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"</span><span class="se">\t\t</span><span class="s2">section: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">section</span><span class="si">}</span><span class="s2">,</span><span class="se">\n</span><span class="s2">"</span> <span class="n">ret</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"</span><span class="se">\t\t</span><span class="s2">ordinal, name: (</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">ordinal</span><span class="si">}</span><span class="s2">, </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">),</span><span class="se">\n</span><span class="s2">"</span> - <span class="n">ret</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"</span><span class="se">\t\t</span><span class="s2">value_set: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">value_set</span><span class="si">}</span><span class="s2">, required: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">required</span><span class="si">}</span><span class="s2">,</span><span class="se">\n</span><span class="s2">"</span> + <span class="n">ret</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"</span><span class="se">\t\t</span><span class="s2">value_set: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">specification</span><span class="si">}</span><span class="s2">, required: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">required</span><span class="si">}</span><span class="s2">,</span><span class="se">\n</span><span class="s2">"</span> <span class="n">ret</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"</span><span class="se">\t\t</span><span class="s2">specification: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">specification</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span> <span class="n">ret</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\t</span><span class="s2">)"</span> - <span class="k">return</span> <span class="n">ret</span></div> + <span class="k">return</span> <span class="n">ret</span> + + + <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span> + <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">DataField</span><span class="p">):</span> + <span class="k">return</span> <span class="kc">False</span> + <span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">id</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">id</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">specification</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">specification</span> + <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">required</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">required</span><span class="p">)</span></div> @@ -194,13 +202,13 @@ <h1>Source code for phenopacket_mapper.data_standards.data_model</h1><div class= <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">field</span><span class="o">.</span><span class="n">required</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">value</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span> <span class="c1"># no value</span> <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Field </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">field</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2"> is required but has no value"</span><span class="p">)</span> <span class="k">return</span> <span class="kc">False</span> - <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">value</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">field</span><span class="o">.</span><span class="n">value_set</span><span class="p">:</span> - <span class="k">if</span> <span class="n">Any</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">field</span><span class="o">.</span><span class="n">value_set</span><span class="p">:</span> <span class="c1"># value set allows any</span> + <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">value</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">field</span><span class="o">.</span><span class="n">specification</span><span class="p">:</span> + <span class="k">if</span> <span class="n">Any</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">field</span><span class="o">.</span><span class="n">specification</span><span class="p">:</span> <span class="c1"># value set allows any</span> <span class="k">return</span> <span class="kc">True</span> - <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">value</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">field</span><span class="o">.</span><span class="n">value_set</span><span class="p">:</span> <span class="c1"># raw value (likely a primitive) is in the value set</span> + <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">value</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">field</span><span class="o">.</span><span class="n">specification</span><span class="p">:</span> <span class="c1"># raw value (likely a primitive) is in the value set</span> <span class="k">return</span> <span class="kc">True</span> <span class="k">else</span><span class="p">:</span> <span class="c1"># check if the value matches one of the types in the value set</span> - <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">field</span><span class="o">.</span><span class="n">value_set</span><span class="p">:</span> + <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">field</span><span class="o">.</span><span class="n">specification</span><span class="p">:</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="nb">type</span><span class="p">):</span> <span class="n">cur_type</span> <span class="o">=</span> <span class="n">e</span> <span class="k">if</span> <span class="n">cur_type</span> <span class="ow">is</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">value</span><span class="p">):</span> @@ -231,9 +239,9 @@ <h1>Source code for phenopacket_mapper.data_standards.data_model</h1><div class= <span class="sd"> be accessed using the `id` as an attribute of the `DataModel` object. E.g.: `data_model.date_of_birth`. This is</span> <span class="sd"> useful in the data reading and mapping processes.</span> -<span class="sd"> >>> data_model = DataModel("Test data model", (DataField(name="Field 1", value_set=ValueSet()),))</span> +<span class="sd"> >>> data_model = DataModel("Test data model", (DataField(name="Field 1", specification=ValueSet()),))</span> <span class="sd"> >>> data_model.field_1</span> -<span class="sd"> DataField(name='Field 1', value_set=ValueSet(elements=[], name='', description=''), id='field_1', description='', section='', required=True, specification='', ordinal='')</span> +<span class="sd"> DataField(name='Field 1', specification=ValueSet(elements=[], name='', description=''), id='field_1', description='', section='', required=True, ordinal='')</span> <span class="sd"> :ivar data_model_name: Name of the data model</span> <span class="sd"> :ivar fields: List of `DataField` objects</span> @@ -345,7 +353,7 @@ <h1>Source code for phenopacket_mapper.data_standards.data_model</h1><div class= <span class="n">DataField</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'data_field_name'</span><span class="p">,</span> <span class="n">DataField</span><span class="o">.</span><span class="n">section</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'data_model_section'</span><span class="p">,</span> <span class="n">DataField</span><span class="o">.</span><span class="n">description</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'description'</span><span class="p">,</span> - <span class="n">DataField</span><span class="o">.</span><span class="n">value_set</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'value_set'</span><span class="p">,</span> + <span class="n">DataField</span><span class="o">.</span><span class="n">specification</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'value_set'</span><span class="p">,</span> <span class="n">DataField</span><span class="o">.</span><span class="n">required</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'required'</span><span class="p">,</span> <span class="n">DataField</span><span class="o">.</span><span class="n">specification</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'specification'</span><span class="p">,</span> <span class="n">DataField</span><span class="o">.</span><span class="n">ordinal</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'ordinal'</span> @@ -594,6 +602,11 @@ <h1>Source code for phenopacket_mapper.data_standards.data_model</h1><div class= <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">"No data frame object available for this dataset"</span><span class="p">)</span></div> </div> + + +<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span> + <span class="n">df</span> <span class="o">=</span> <span class="n">DataField</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">"Field 1"</span><span class="p">,</span> <span class="n">specification</span><span class="o">=</span><span class="nb">int</span><span class="p">)</span> + <span class="nb">print</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">specification</span> <span class="o">==</span> <span class="n">ValueSet</span><span class="p">([</span><span class="nb">int</span><span class="p">]))</span> </pre></div> </div> diff --git a/latest/_modules/phenopacket_mapper/pipeline/input.html b/latest/_modules/phenopacket_mapper/pipeline/input.html index 86a9026..cab7e22 100644 --- a/latest/_modules/phenopacket_mapper/pipeline/input.html +++ b/latest/_modules/phenopacket_mapper/pipeline/input.html @@ -104,9 +104,8 @@ <h1>Source code for phenopacket_mapper.pipeline.input</h1><div class="highlight" <span class="n">DataField</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'data_field_name'</span><span class="p">,</span> <span class="n">DataField</span><span class="o">.</span><span class="n">section</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'data_model_section'</span><span class="p">,</span> <span class="n">DataField</span><span class="o">.</span><span class="n">description</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'description'</span><span class="p">,</span> - <span class="n">DataField</span><span class="o">.</span><span class="n">value_set</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'value_set'</span><span class="p">,</span> + <span class="n">DataField</span><span class="o">.</span><span class="n">specification</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'value_set'</span><span class="p">,</span> <span class="n">DataField</span><span class="o">.</span><span class="n">required</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'required'</span><span class="p">,</span> - <span class="n">DataField</span><span class="o">.</span><span class="n">specification</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'specification'</span><span class="p">,</span> <span class="n">DataField</span><span class="o">.</span><span class="n">ordinal</span><span class="o">.</span><span class="vm">__name__</span><span class="p">:</span> <span class="s1">'ordinal'</span> <span class="p">}),</span> <span class="n">parse_value_sets</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> @@ -178,23 +177,21 @@ <h1>Source code for phenopacket_mapper.pipeline.input</h1><div class="highlight" <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">)):</span> <span class="n">data_field_name</span> <span class="o">=</span> <span class="n">loc_default</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">row_index</span><span class="o">=</span><span class="n">i</span><span class="p">,</span> <span class="n">column_name</span><span class="o">=</span><span class="n">column_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">DataField</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">''</span><span class="p">))</span> <span class="n">section</span> <span class="o">=</span> <span class="n">loc_default</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">row_index</span><span class="o">=</span><span class="n">i</span><span class="p">,</span> <span class="n">column_name</span><span class="o">=</span><span class="n">column_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">DataField</span><span class="o">.</span><span class="n">section</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">''</span><span class="p">))</span> - <span class="n">value_set</span> <span class="o">=</span> <span class="n">loc_default</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">row_index</span><span class="o">=</span><span class="n">i</span><span class="p">,</span> <span class="n">column_name</span><span class="o">=</span><span class="n">column_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">DataField</span><span class="o">.</span><span class="n">value_set</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">''</span><span class="p">))</span> + <span class="n">value_set</span> <span class="o">=</span> <span class="n">loc_default</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">row_index</span><span class="o">=</span><span class="n">i</span><span class="p">,</span> <span class="n">column_name</span><span class="o">=</span><span class="n">column_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">DataField</span><span class="o">.</span><span class="n">specification</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">''</span><span class="p">))</span> <span class="n">description</span> <span class="o">=</span> <span class="n">loc_default</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">row_index</span><span class="o">=</span><span class="n">i</span><span class="p">,</span> <span class="n">column_name</span><span class="o">=</span><span class="n">column_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">DataField</span><span class="o">.</span><span class="n">description</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">''</span><span class="p">))</span> <span class="n">required</span> <span class="o">=</span> <span class="nb">bool</span><span class="p">(</span><span class="n">loc_default</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">row_index</span><span class="o">=</span><span class="n">i</span><span class="p">,</span> <span class="n">column_name</span><span class="o">=</span><span class="n">column_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">DataField</span><span class="o">.</span><span class="n">required</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">''</span><span class="p">)))</span> - <span class="n">specification</span> <span class="o">=</span> <span class="n">loc_default</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">row_index</span><span class="o">=</span><span class="n">i</span><span class="p">,</span> <span class="n">column_name</span><span class="o">=</span><span class="n">column_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">DataField</span><span class="o">.</span><span class="n">specification</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">''</span><span class="p">))</span> <span class="n">ordinal</span> <span class="o">=</span> <span class="n">loc_default</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">row_index</span><span class="o">=</span><span class="n">i</span><span class="p">,</span> <span class="n">column_name</span><span class="o">=</span><span class="n">column_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">DataField</span><span class="o">.</span><span class="n">ordinal</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">''</span><span class="p">))</span> <span class="k">if</span> <span class="n">remove_line_breaks</span><span class="p">:</span> <span class="n">data_field_name</span> <span class="o">=</span> <span class="n">remove_line_breaks_if_not_none</span><span class="p">(</span><span class="n">data_field_name</span><span class="p">)</span> <span class="n">section</span> <span class="o">=</span> <span class="n">remove_line_breaks_if_not_none</span><span class="p">(</span><span class="n">section</span><span class="p">)</span> <span class="n">description</span> <span class="o">=</span> <span class="n">remove_line_breaks_if_not_none</span><span class="p">(</span><span class="n">description</span><span class="p">)</span> - <span class="n">specification</span> <span class="o">=</span> <span class="n">remove_line_breaks_if_not_none</span><span class="p">(</span><span class="n">specification</span><span class="p">)</span> <span class="k">if</span> <span class="n">parse_ordinals</span><span class="p">:</span> <span class="n">ordinal</span><span class="p">,</span> <span class="n">data_field_name</span> <span class="o">=</span> <span class="n">parse_ordinal</span><span class="p">(</span><span class="n">data_field_name</span><span class="p">)</span> <span class="k">if</span> <span class="n">parse_value_sets</span><span class="p">:</span> - <span class="k">if</span> <span class="ow">not</span> <span class="n">column_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">DataField</span><span class="o">.</span><span class="n">value_set</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">''</span><span class="p">):</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">column_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">DataField</span><span class="o">.</span><span class="n">specification</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">''</span><span class="p">):</span> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Value set column name must be provided to parse value sets."</span><span class="p">)</span> <span class="n">value_set</span> <span class="o">=</span> <span class="n">parsing</span><span class="o">.</span><span class="n">parse_value_set</span><span class="p">(</span> @@ -207,10 +204,9 @@ <h1>Source code for phenopacket_mapper.pipeline.input</h1><div class="highlight" <span class="n">DataField</span><span class="p">(</span> <span class="n">name</span><span class="o">=</span><span class="n">data_field_name</span><span class="p">,</span> <span class="n">section</span><span class="o">=</span><span class="n">section</span><span class="p">,</span> - <span class="n">value_set</span><span class="o">=</span><span class="n">value_set</span><span class="p">,</span> + <span class="n">specification</span><span class="o">=</span><span class="n">value_set</span><span class="p">,</span> <span class="n">description</span><span class="o">=</span><span class="n">description</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="n">required</span><span class="p">,</span> - <span class="n">specification</span><span class="o">=</span><span class="n">specification</span><span class="p">,</span> <span class="n">ordinal</span><span class="o">=</span><span class="n">ordinal</span> <span class="p">),</span> <span class="p">)</span> diff --git a/latest/apidocs/phenopacket_mapper.data_standards.data_model.html b/latest/apidocs/phenopacket_mapper.data_standards.data_model.html index ab0cdcd..9345c2f 100644 --- a/latest/apidocs/phenopacket_mapper.data_standards.data_model.html +++ b/latest/apidocs/phenopacket_mapper.data_standards.data_model.html @@ -104,7 +104,7 @@ <cite>DataModelInstance</cite> class is used to define an instance of a <cite>DataModel</cite>, i.e. a record in a dataset.</p> <dl class="py class"> <dt class="sig sig-object py" id="phenopacket_mapper.data_standards.data_model.DataField"> -<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.data_standards.data_model.</span></span><span class="sig-name descname"><span class="pre">DataField</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</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 v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">value_set</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="phenopacket_mapper.data_standards.value_set.html#phenopacket_mapper.data_standards.value_set.ValueSet" title="phenopacket_mapper.data_standards.value_set.ValueSet"><span class="pre">ValueSet</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><span class="pre">type</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">id</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">section</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">required</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">specification</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ordinal</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/data_model.html#DataField"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.data_model.DataField" title="Link to this definition"></a></dt> +<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.data_standards.data_model.</span></span><span class="sig-name descname"><span class="pre">DataField</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</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 v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">specification</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="phenopacket_mapper.data_standards.value_set.html#phenopacket_mapper.data_standards.value_set.ValueSet" title="phenopacket_mapper.data_standards.value_set.ValueSet"><span class="pre">ValueSet</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><span class="pre">type</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><span class="pre">type</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">section</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">required</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ordinal</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/data_model.html#DataField"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.data_model.DataField" title="Link to this definition"></a></dt> <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p> <p>This class defines fields used in the definition of a <cite>DataModel</cite></p> <p>A dataa field is the equivalent of a column in a table. It has a name, a value set, a description, a section, a @@ -121,18 +121,17 @@ - The <cite>id</cite> field must be unique within a <cite>DataModel</cite></p> <p>If the <cite>value_set</cite> is a single type, it can be passed directly as the <cite>value_set</cite> parameter.</p> <p>e.g.: ->>> DataField(name=”Field 1”, value_set=int) -DataField(name=’Field 1’, value_set=ValueSet(elements=[<class ‘int’>], name=’’, description=’’), id=’field_1’, description=’’, section=’’, required=True, specification=’’, ordinal=’’)</p> +>>> DataField(name=”Field 1”, specification=int) +DataField(name=’Field 1’, specification=ValueSet(elements=[<class ‘int’>], name=’’, description=’’), id=’field_1’, description=’’, section=’’, required=True, ordinal=’’)</p> <dl class="field-list simple"> <dt class="field-odd">Variables<span class="colon">:</span></dt> <dd class="field-odd"><ul class="simple"> <li><p><strong>name</strong> – Name of the field</p></li> -<li><p><strong>value_set</strong> – Value set of the field, if the value set is only one type, can also pass that type directly</p></li> +<li><p><strong>specification</strong> – Value set of the field, if the value set is only one type, can also pass that type directly</p></li> <li><p><strong>id</strong> – The identifier of the field, adhering to the naming rules stated above</p></li> <li><p><strong>description</strong> – Description of the field</p></li> <li><p><strong>section</strong> – Section of the field (Only applicable if the data model is divided into sections)</p></li> <li><p><strong>required</strong> – Required flag of the field</p></li> -<li><p><strong>specification</strong> – Text specification of the field (a description of the value set and field)</p></li> <li><p><strong>ordinal</strong> – Ordinal of the field (E.g. 1.1, 1.2, 2.1, etc.)</p></li> </ul> </dd> @@ -143,8 +142,8 @@ <dd></dd></dl> <dl class="py attribute"> -<dt class="sig sig-object py" id="phenopacket_mapper.data_standards.data_model.DataField.value_set"> -<span class="sig-name descname"><span class="pre">value_set</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="phenopacket_mapper.data_standards.value_set.html#phenopacket_mapper.data_standards.value_set.ValueSet" title="phenopacket_mapper.data_standards.value_set.ValueSet"><span class="pre">ValueSet</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><span class="pre">type</span></a></em><a class="headerlink" href="#phenopacket_mapper.data_standards.data_model.DataField.value_set" title="Link to this definition"></a></dt> +<dt class="sig sig-object py" id="phenopacket_mapper.data_standards.data_model.DataField.specification"> +<span class="sig-name descname"><span class="pre">specification</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="phenopacket_mapper.data_standards.value_set.html#phenopacket_mapper.data_standards.value_set.ValueSet" title="phenopacket_mapper.data_standards.value_set.ValueSet"><span class="pre">ValueSet</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><span class="pre">type</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><span class="pre">type</span></a><span class="p"><span class="pre">]</span></span></em><a class="headerlink" href="#phenopacket_mapper.data_standards.data_model.DataField.specification" title="Link to this definition"></a></dt> <dd></dd></dl> <dl class="py attribute"> @@ -167,11 +166,6 @@ <span class="sig-name descname"><span class="pre">required</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></em><a class="headerlink" href="#phenopacket_mapper.data_standards.data_model.DataField.required" title="Link to this definition"></a></dt> <dd></dd></dl> -<dl class="py attribute"> -<dt class="sig sig-object py" id="phenopacket_mapper.data_standards.data_model.DataField.specification"> -<span class="sig-name descname"><span class="pre">specification</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></em><a class="headerlink" href="#phenopacket_mapper.data_standards.data_model.DataField.specification" title="Link to this definition"></a></dt> -<dd></dd></dl> - <dl class="py attribute"> <dt class="sig sig-object py" id="phenopacket_mapper.data_standards.data_model.DataField.ordinal"> <span class="sig-name descname"><span class="pre">ordinal</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></em><a class="headerlink" href="#phenopacket_mapper.data_standards.data_model.DataField.ordinal" title="Link to this definition"></a></dt> @@ -234,9 +228,9 @@ E.g.: <cite>DataField(name=’Date of Birth’, …)</cite> will have an <cite>id</cite> of <cite>‘date_of_birth’</cite>. The <cite>DataField</cite> objects can be accessed using the <cite>id</cite> as an attribute of the <cite>DataModel</cite> object. E.g.: <cite>data_model.date_of_birth</cite>. This is useful in the data reading and mapping processes.</p> -<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">data_model</span> <span class="o">=</span> <span class="n">DataModel</span><span class="p">(</span><span class="s2">"Test data model"</span><span class="p">,</span> <span class="p">(</span><span class="n">DataField</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">"Field 1"</span><span class="p">,</span> <span class="n">value_set</span><span class="o">=</span><span class="n">ValueSet</span><span class="p">()),))</span> +<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">data_model</span> <span class="o">=</span> <span class="n">DataModel</span><span class="p">(</span><span class="s2">"Test data model"</span><span class="p">,</span> <span class="p">(</span><span class="n">DataField</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">"Field 1"</span><span class="p">,</span> <span class="n">specification</span><span class="o">=</span><span class="n">ValueSet</span><span class="p">()),))</span> <span class="gp">>>> </span><span class="n">data_model</span><span class="o">.</span><span class="n">field_1</span> -<span class="go">DataField(name='Field 1', value_set=ValueSet(elements=[], name='', description=''), id='field_1', description='', section='', required=True, specification='', ordinal='')</span> +<span class="go">DataField(name='Field 1', specification=ValueSet(elements=[], name='', description=''), id='field_1', description='', section='', required=True, ordinal='')</span> </pre></div> </div> <dl class="field-list simple"> @@ -315,7 +309,7 @@ <dl class="py method"> <dt class="sig sig-object py" id="phenopacket_mapper.data_standards.data_model.DataModel.from_file"> -<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_model_name</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 v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</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/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="phenopacket_mapper.data_standards.code_system.html#phenopacket_mapper.data_standards.code_system.CodeSystem" title="phenopacket_mapper.data_standards.code_system.CodeSystem"><span class="pre">CodeSystem</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</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 v3.13)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.13)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_type</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/typing.html#typing.Literal" title="(in Python v3.13)"><span class="pre">Literal</span></a><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'csv'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'excel'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'unknown'</span></span><span class="p"><span class="pre">]</span></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">'unknown'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">column_names</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/typing.html#typing.Dict" title="(in Python v3.13)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></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">mappingproxy({'name':</span> <span class="pre">'data_field_name',</span> <span class="pre">'section':</span> <span class="pre">'data_model_section',</span> <span class="pre">'description':</span> <span class="pre">'description',</span> <span class="pre">'value_set':</span> <span class="pre">'value_set',</span> <span class="pre">'required':</span> <span class="pre">'required',</span> <span class="pre">'specification':</span> <span class="pre">'specification',</span> <span class="pre">'ordinal':</span> <span class="pre">'ordinal'})</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_value_sets</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_line_breaks</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_ordinals</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#phenopacket_mapper.data_standards.data_model.DataModel" title="phenopacket_mapper.data_standards.data_model.DataModel"><span class="pre">DataModel</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/data_model.html#DataModel.from_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.data_model.DataModel.from_file" title="Link to this definition"></a></dt> +<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_model_name</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 v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</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/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="phenopacket_mapper.data_standards.code_system.html#phenopacket_mapper.data_standards.code_system.CodeSystem" title="phenopacket_mapper.data_standards.code_system.CodeSystem"><span class="pre">CodeSystem</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</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 v3.13)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.13)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_type</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/typing.html#typing.Literal" title="(in Python v3.13)"><span class="pre">Literal</span></a><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'csv'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'excel'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'unknown'</span></span><span class="p"><span class="pre">]</span></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">'unknown'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">column_names</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/typing.html#typing.Dict" title="(in Python v3.13)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></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">mappingproxy({'name':</span> <span class="pre">'data_field_name',</span> <span class="pre">'section':</span> <span class="pre">'data_model_section',</span> <span class="pre">'description':</span> <span class="pre">'description',</span> <span class="pre">'specification':</span> <span class="pre">'specification',</span> <span class="pre">'required':</span> <span class="pre">'required',</span> <span class="pre">'ordinal':</span> <span class="pre">'ordinal'})</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_value_sets</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_line_breaks</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_ordinals</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#phenopacket_mapper.data_standards.data_model.DataModel" title="phenopacket_mapper.data_standards.data_model.DataModel"><span class="pre">DataModel</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/data_model.html#DataModel.from_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.data_model.DataModel.from_file" title="Link to this definition"></a></dt> <dd><p>Reads a Data Model from a file</p> <dl class="field-list simple"> <dt class="field-odd">Parameters<span class="colon">:</span></dt> diff --git a/latest/apidocs/phenopacket_mapper.data_standards.html b/latest/apidocs/phenopacket_mapper.data_standards.html index 13f9fa8..32b124f 100644 --- a/latest/apidocs/phenopacket_mapper.data_standards.html +++ b/latest/apidocs/phenopacket_mapper.data_standards.html @@ -203,9 +203,9 @@ E.g.: <cite>DataField(name=’Date of Birth’, …)</cite> will have an <cite>id</cite> of <cite>‘date_of_birth’</cite>. The <cite>DataField</cite> objects can be accessed using the <cite>id</cite> as an attribute of the <cite>DataModel</cite> object. E.g.: <cite>data_model.date_of_birth</cite>. This is useful in the data reading and mapping processes.</p> -<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">data_model</span> <span class="o">=</span> <span class="n">DataModel</span><span class="p">(</span><span class="s2">"Test data model"</span><span class="p">,</span> <span class="p">(</span><span class="n">DataField</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">"Field 1"</span><span class="p">,</span> <span class="n">value_set</span><span class="o">=</span><span class="n">ValueSet</span><span class="p">()),))</span> +<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">data_model</span> <span class="o">=</span> <span class="n">DataModel</span><span class="p">(</span><span class="s2">"Test data model"</span><span class="p">,</span> <span class="p">(</span><span class="n">DataField</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">"Field 1"</span><span class="p">,</span> <span class="n">specification</span><span class="o">=</span><span class="n">ValueSet</span><span class="p">()),))</span> <span class="gp">>>> </span><span class="n">data_model</span><span class="o">.</span><span class="n">field_1</span> -<span class="go">DataField(name='Field 1', value_set=ValueSet(elements=[], name='', description=''), id='field_1', description='', section='', required=True, specification='', ordinal='')</span> +<span class="go">DataField(name='Field 1', specification=ValueSet(elements=[], name='', description=''), id='field_1', description='', section='', required=True, ordinal='')</span> </pre></div> </div> <dl class="field-list simple"> @@ -284,7 +284,7 @@ <dl class="py method"> <dt class="sig sig-object py" id="phenopacket_mapper.data_standards.DataModel.from_file"> -<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_model_name</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 v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</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/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="phenopacket_mapper.data_standards.code_system.html#phenopacket_mapper.data_standards.code_system.CodeSystem" title="phenopacket_mapper.data_standards.code_system.CodeSystem"><span class="pre">CodeSystem</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</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 v3.13)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.13)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_type</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/typing.html#typing.Literal" title="(in Python v3.13)"><span class="pre">Literal</span></a><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'csv'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'excel'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'unknown'</span></span><span class="p"><span class="pre">]</span></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">'unknown'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">column_names</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/typing.html#typing.Dict" title="(in Python v3.13)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></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">mappingproxy({'name':</span> <span class="pre">'data_field_name',</span> <span class="pre">'section':</span> <span class="pre">'data_model_section',</span> <span class="pre">'description':</span> <span class="pre">'description',</span> <span class="pre">'value_set':</span> <span class="pre">'value_set',</span> <span class="pre">'required':</span> <span class="pre">'required',</span> <span class="pre">'specification':</span> <span class="pre">'specification',</span> <span class="pre">'ordinal':</span> <span class="pre">'ordinal'})</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_value_sets</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_line_breaks</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_ordinals</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.DataModel" title="phenopacket_mapper.data_standards.data_model.DataModel"><span class="pre">DataModel</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/data_model.html#DataModel.from_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.DataModel.from_file" title="Link to this definition"></a></dt> +<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_model_name</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 v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</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/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="phenopacket_mapper.data_standards.code_system.html#phenopacket_mapper.data_standards.code_system.CodeSystem" title="phenopacket_mapper.data_standards.code_system.CodeSystem"><span class="pre">CodeSystem</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</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 v3.13)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.13)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_type</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/typing.html#typing.Literal" title="(in Python v3.13)"><span class="pre">Literal</span></a><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'csv'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'excel'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'unknown'</span></span><span class="p"><span class="pre">]</span></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">'unknown'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">column_names</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/typing.html#typing.Dict" title="(in Python v3.13)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></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">mappingproxy({'name':</span> <span class="pre">'data_field_name',</span> <span class="pre">'section':</span> <span class="pre">'data_model_section',</span> <span class="pre">'description':</span> <span class="pre">'description',</span> <span class="pre">'specification':</span> <span class="pre">'specification',</span> <span class="pre">'required':</span> <span class="pre">'required',</span> <span class="pre">'ordinal':</span> <span class="pre">'ordinal'})</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_value_sets</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_line_breaks</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_ordinals</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.DataModel" title="phenopacket_mapper.data_standards.data_model.DataModel"><span class="pre">DataModel</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/data_model.html#DataModel.from_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.DataModel.from_file" title="Link to this definition"></a></dt> <dd><p>Reads a Data Model from a file</p> <dl class="field-list simple"> <dt class="field-odd">Parameters<span class="colon">:</span></dt> @@ -330,7 +330,7 @@ <dl class="py class"> <dt class="sig sig-object py" id="phenopacket_mapper.data_standards.DataField"> -<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.data_standards.</span></span><span class="sig-name descname"><span class="pre">DataField</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</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 v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">value_set</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="phenopacket_mapper.data_standards.value_set.html#phenopacket_mapper.data_standards.value_set.ValueSet" title="phenopacket_mapper.data_standards.value_set.ValueSet"><span class="pre">ValueSet</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><span class="pre">type</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">id</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">section</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">required</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">specification</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ordinal</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/data_model.html#DataField"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.DataField" title="Link to this definition"></a></dt> +<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.data_standards.</span></span><span class="sig-name descname"><span class="pre">DataField</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</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 v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">specification</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="phenopacket_mapper.data_standards.value_set.html#phenopacket_mapper.data_standards.value_set.ValueSet" title="phenopacket_mapper.data_standards.value_set.ValueSet"><span class="pre">ValueSet</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><span class="pre">type</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><span class="pre">type</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">section</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">required</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ordinal</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 v3.13)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/phenopacket_mapper/data_standards/data_model.html#DataField"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.data_standards.DataField" title="Link to this definition"></a></dt> <dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.13)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p> <p>This class defines fields used in the definition of a <cite>DataModel</cite></p> <p>A dataa field is the equivalent of a column in a table. It has a name, a value set, a description, a section, a @@ -347,18 +347,17 @@ - The <cite>id</cite> field must be unique within a <cite>DataModel</cite></p> <p>If the <cite>value_set</cite> is a single type, it can be passed directly as the <cite>value_set</cite> parameter.</p> <p>e.g.: ->>> DataField(name=”Field 1”, value_set=int) -DataField(name=’Field 1’, value_set=ValueSet(elements=[<class ‘int’>], name=’’, description=’’), id=’field_1’, description=’’, section=’’, required=True, specification=’’, ordinal=’’)</p> +>>> DataField(name=”Field 1”, specification=int) +DataField(name=’Field 1’, specification=ValueSet(elements=[<class ‘int’>], name=’’, description=’’), id=’field_1’, description=’’, section=’’, required=True, ordinal=’’)</p> <dl class="field-list simple"> <dt class="field-odd">Variables<span class="colon">:</span></dt> <dd class="field-odd"><ul class="simple"> <li><p><strong>name</strong> – Name of the field</p></li> -<li><p><strong>value_set</strong> – Value set of the field, if the value set is only one type, can also pass that type directly</p></li> +<li><p><strong>specification</strong> – Value set of the field, if the value set is only one type, can also pass that type directly</p></li> <li><p><strong>id</strong> – The identifier of the field, adhering to the naming rules stated above</p></li> <li><p><strong>description</strong> – Description of the field</p></li> <li><p><strong>section</strong> – Section of the field (Only applicable if the data model is divided into sections)</p></li> <li><p><strong>required</strong> – Required flag of the field</p></li> -<li><p><strong>specification</strong> – Text specification of the field (a description of the value set and field)</p></li> <li><p><strong>ordinal</strong> – Ordinal of the field (E.g. 1.1, 1.2, 2.1, etc.)</p></li> </ul> </dd> @@ -369,8 +368,8 @@ <dd></dd></dl> <dl class="py attribute"> -<dt class="sig sig-object py" id="phenopacket_mapper.data_standards.DataField.value_set"> -<span class="sig-name descname"><span class="pre">value_set</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="phenopacket_mapper.data_standards.value_set.html#phenopacket_mapper.data_standards.value_set.ValueSet" title="phenopacket_mapper.data_standards.value_set.ValueSet"><span class="pre">ValueSet</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><span class="pre">type</span></a></em><a class="headerlink" href="#phenopacket_mapper.data_standards.DataField.value_set" title="Link to this definition"></a></dt> +<dt class="sig sig-object py" id="phenopacket_mapper.data_standards.DataField.specification"> +<span class="sig-name descname"><span class="pre">specification</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="phenopacket_mapper.data_standards.value_set.html#phenopacket_mapper.data_standards.value_set.ValueSet" title="phenopacket_mapper.data_standards.value_set.ValueSet"><span class="pre">ValueSet</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><span class="pre">type</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.13)"><span class="pre">type</span></a><span class="p"><span class="pre">]</span></span></em><a class="headerlink" href="#phenopacket_mapper.data_standards.DataField.specification" title="Link to this definition"></a></dt> <dd></dd></dl> <dl class="py attribute"> @@ -393,11 +392,6 @@ <span class="sig-name descname"><span class="pre">required</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></em><a class="headerlink" href="#phenopacket_mapper.data_standards.DataField.required" title="Link to this definition"></a></dt> <dd></dd></dl> -<dl class="py attribute"> -<dt class="sig sig-object py" id="phenopacket_mapper.data_standards.DataField.specification"> -<span class="sig-name descname"><span class="pre">specification</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></em><a class="headerlink" href="#phenopacket_mapper.data_standards.DataField.specification" title="Link to this definition"></a></dt> -<dd></dd></dl> - <dl class="py attribute"> <dt class="sig sig-object py" id="phenopacket_mapper.data_standards.DataField.ordinal"> <span class="sig-name descname"><span class="pre">ordinal</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a></em><a class="headerlink" href="#phenopacket_mapper.data_standards.DataField.ordinal" title="Link to this definition"></a></dt> diff --git a/latest/apidocs/phenopacket_mapper.pipeline.html b/latest/apidocs/phenopacket_mapper.pipeline.html index 7bceb37..f294c47 100644 --- a/latest/apidocs/phenopacket_mapper.pipeline.html +++ b/latest/apidocs/phenopacket_mapper.pipeline.html @@ -98,7 +98,7 @@ <p>This module includes the pipeline for mapping data to phenopackets.</p> <dl class="py function"> <dt class="sig sig-object py" id="phenopacket_mapper.pipeline.read_data_model"> -<span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.pipeline.</span></span><span class="sig-name descname"><span class="pre">read_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_model_name</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 v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</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/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="phenopacket_mapper.data_standards.code_system.html#phenopacket_mapper.data_standards.code_system.CodeSystem" title="phenopacket_mapper.data_standards.code_system.CodeSystem"><span class="pre">CodeSystem</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</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 v3.13)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.13)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_type</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/typing.html#typing.Literal" title="(in Python v3.13)"><span class="pre">Literal</span></a><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'csv'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'excel'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'unknown'</span></span><span class="p"><span class="pre">]</span></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">'unknown'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">column_names</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/typing.html#typing.Dict" title="(in Python v3.13)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></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">mappingproxy({'name':</span> <span class="pre">'data_field_name',</span> <span class="pre">'section':</span> <span class="pre">'data_model_section',</span> <span class="pre">'description':</span> <span class="pre">'description',</span> <span class="pre">'value_set':</span> <span class="pre">'value_set',</span> <span class="pre">'required':</span> <span class="pre">'required',</span> <span class="pre">'specification':</span> <span class="pre">'specification',</span> <span class="pre">'ordinal':</span> <span class="pre">'ordinal'})</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_value_sets</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_line_breaks</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_ordinals</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.DataModel" title="phenopacket_mapper.data_standards.data_model.DataModel"><span class="pre">DataModel</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/pipeline/input.html#read_data_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.pipeline.read_data_model" title="Link to this definition"></a></dt> +<span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.pipeline.</span></span><span class="sig-name descname"><span class="pre">read_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_model_name</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 v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</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/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="phenopacket_mapper.data_standards.code_system.html#phenopacket_mapper.data_standards.code_system.CodeSystem" title="phenopacket_mapper.data_standards.code_system.CodeSystem"><span class="pre">CodeSystem</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</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 v3.13)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.13)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_type</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/typing.html#typing.Literal" title="(in Python v3.13)"><span class="pre">Literal</span></a><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'csv'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'excel'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'unknown'</span></span><span class="p"><span class="pre">]</span></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">'unknown'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">column_names</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/typing.html#typing.Dict" title="(in Python v3.13)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></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">mappingproxy({'name':</span> <span class="pre">'data_field_name',</span> <span class="pre">'section':</span> <span class="pre">'data_model_section',</span> <span class="pre">'description':</span> <span class="pre">'description',</span> <span class="pre">'specification':</span> <span class="pre">'value_set',</span> <span class="pre">'required':</span> <span class="pre">'required',</span> <span class="pre">'ordinal':</span> <span class="pre">'ordinal'})</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_value_sets</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_line_breaks</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_ordinals</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.DataModel" title="phenopacket_mapper.data_standards.data_model.DataModel"><span class="pre">DataModel</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/pipeline/input.html#read_data_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.pipeline.read_data_model" title="Link to this definition"></a></dt> <dd><p>Reads a Data Model from a file</p> <dl class="field-list simple"> <dt class="field-odd">Parameters<span class="colon">:</span></dt> diff --git a/latest/apidocs/phenopacket_mapper.pipeline.input.html b/latest/apidocs/phenopacket_mapper.pipeline.input.html index c1aedac..d7af9ee 100644 --- a/latest/apidocs/phenopacket_mapper.pipeline.input.html +++ b/latest/apidocs/phenopacket_mapper.pipeline.input.html @@ -98,7 +98,7 @@ <span id="phenopacket-mapper-pipeline-input-module"></span><h1>phenopacket_mapper.pipeline.input module<a class="headerlink" href="#module-phenopacket_mapper.pipeline.input" title="Link to this heading"></a></h1> <dl class="py function"> <dt class="sig sig-object py" id="phenopacket_mapper.pipeline.input.read_data_model"> -<span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.pipeline.input.</span></span><span class="sig-name descname"><span class="pre">read_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_model_name</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 v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</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/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="phenopacket_mapper.data_standards.code_system.html#phenopacket_mapper.data_standards.code_system.CodeSystem" title="phenopacket_mapper.data_standards.code_system.CodeSystem"><span class="pre">CodeSystem</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</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 v3.13)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.13)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_type</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/typing.html#typing.Literal" title="(in Python v3.13)"><span class="pre">Literal</span></a><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'csv'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'excel'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'unknown'</span></span><span class="p"><span class="pre">]</span></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">'unknown'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">column_names</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/typing.html#typing.Dict" title="(in Python v3.13)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></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">mappingproxy({'name':</span> <span class="pre">'data_field_name',</span> <span class="pre">'section':</span> <span class="pre">'data_model_section',</span> <span class="pre">'description':</span> <span class="pre">'description',</span> <span class="pre">'value_set':</span> <span class="pre">'value_set',</span> <span class="pre">'required':</span> <span class="pre">'required',</span> <span class="pre">'specification':</span> <span class="pre">'specification',</span> <span class="pre">'ordinal':</span> <span class="pre">'ordinal'})</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_value_sets</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_line_breaks</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_ordinals</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.DataModel" title="phenopacket_mapper.data_standards.data_model.DataModel"><span class="pre">DataModel</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/pipeline/input.html#read_data_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.pipeline.input.read_data_model" title="Link to this definition"></a></dt> +<span class="sig-prename descclassname"><span class="pre">phenopacket_mapper.pipeline.input.</span></span><span class="sig-name descname"><span class="pre">read_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_model_name</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 v3.13)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</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/typing.html#typing.List" title="(in Python v3.13)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference internal" href="phenopacket_mapper.data_standards.code_system.html#phenopacket_mapper.data_standards.code_system.CodeSystem" title="phenopacket_mapper.data_standards.code_system.CodeSystem"><span class="pre">CodeSystem</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</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 v3.13)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.13)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_type</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/typing.html#typing.Literal" title="(in Python v3.13)"><span class="pre">Literal</span></a><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'csv'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'excel'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'unknown'</span></span><span class="p"><span class="pre">]</span></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">'unknown'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">column_names</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/typing.html#typing.Dict" title="(in Python v3.13)"><span class="pre">Dict</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.13)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></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">mappingproxy({'name':</span> <span class="pre">'data_field_name',</span> <span class="pre">'section':</span> <span class="pre">'data_model_section',</span> <span class="pre">'description':</span> <span class="pre">'description',</span> <span class="pre">'specification':</span> <span class="pre">'value_set',</span> <span class="pre">'required':</span> <span class="pre">'required',</span> <span class="pre">'ordinal':</span> <span class="pre">'ordinal'})</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_value_sets</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_line_breaks</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parse_ordinals</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/functions.html#bool" title="(in Python v3.13)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.DataModel" title="phenopacket_mapper.data_standards.data_model.DataModel"><span class="pre">DataModel</span></a></span></span><a class="reference internal" href="../_modules/phenopacket_mapper/pipeline/input.html#read_data_model"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#phenopacket_mapper.pipeline.input.read_data_model" title="Link to this definition"></a></dt> <dd><p>Reads a Data Model from a file</p> <dl class="field-list simple"> <dt class="field-odd">Parameters<span class="colon">:</span></dt> diff --git a/latest/genindex.html b/latest/genindex.html index 0002f9d..3a0f874 100644 --- a/latest/genindex.html +++ b/latest/genindex.html @@ -1326,18 +1326,12 @@ <h2 id="V">V</h2> </ul></li> <li><a href="apidocs/phenopacket_mapper.pipeline.validate.html#phenopacket_mapper.pipeline.validate.Validator">Validator (class in phenopacket_mapper.pipeline.validate)</a> </li> - <li><a href="apidocs/phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.DataFieldValue.value">value (phenopacket_mapper.data_standards.data_model.DataFieldValue attribute)</a> - - <ul> - <li><a href="apidocs/phenopacket_mapper.data_standards.html#phenopacket_mapper.data_standards.DataFieldValue.value">(phenopacket_mapper.data_standards.DataFieldValue attribute)</a> -</li> - </ul></li> </ul></td> <td style="width: 33%; vertical-align: top;"><ul> - <li><a href="apidocs/phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.DataField.value_set">value_set (phenopacket_mapper.data_standards.data_model.DataField attribute)</a> + <li><a href="apidocs/phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.DataFieldValue.value">value (phenopacket_mapper.data_standards.data_model.DataFieldValue attribute)</a> <ul> - <li><a href="apidocs/phenopacket_mapper.data_standards.html#phenopacket_mapper.data_standards.DataField.value_set">(phenopacket_mapper.data_standards.DataField attribute)</a> + <li><a href="apidocs/phenopacket_mapper.data_standards.html#phenopacket_mapper.data_standards.DataFieldValue.value">(phenopacket_mapper.data_standards.DataFieldValue attribute)</a> </li> </ul></li> <li><a href="apidocs/phenopacket_mapper.data_standards.data_model.html#phenopacket_mapper.data_standards.data_model.DataModelInstance.values">values 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module", "phenopacket_mapper.data_standards.data_model module", "phenopacket_mapper.data_standards.data_models package", "phenopacket_mapper.data_standards.data_models.erdri_cds module", "phenopacket_mapper.data_standards.data_models.rarelink_datamodel module", "phenopacket_mapper.data_standards.date module", "phenopacket_mapper.data_standards.value_set module", "phenopacket_mapper.mapping package", "phenopacket_mapper.mapping.map_field module", "phenopacket_mapper.mapping.mapper module", "phenopacket_mapper.mapping.phenopacket_building_block module", "phenopacket_mapper.pipeline package", "phenopacket_mapper.pipeline.input module", "phenopacket_mapper.pipeline.mapper module", "phenopacket_mapper.pipeline.output module", "phenopacket_mapper.pipeline.validate module", "phenopacket_mapper.preprocessing package", "phenopacket_mapper.preprocessing.preprocess module", "phenopacket_mapper.preprocessing.preprocess_dict module", "phenopacket_mapper.preprocessing.preprocess_method module", "phenopacket_mapper.utils package", "phenopacket_mapper.utils.create_ipynb_in_code module", "phenopacket_mapper.utils.get_field_name module", "phenopacket_mapper.utils.pandas_utils module", "phenopacket_mapper.utils.parsing package", "phenopacket_mapper.utils.parsing.get_codesystem_by_namespace_prefix module", "phenopacket_mapper.utils.parsing.parse_coding module", "phenopacket_mapper.utils.parsing.parse_data_type module", "phenopacket_mapper.utils.parsing.parse_date module", "phenopacket_mapper.utils.parsing.parse_ordinal module", "phenopacket_mapper.utils.parsing.parse_primitive_data_value module", "phenopacket_mapper.utils.parsing.parse_value module", "phenopacket_mapper.utils.parsing.parse_value_set module", "phenopacket_mapper.utils.str_to_valid_id module", "Welcome to Phenopacket Mapper\u2019s documentation!", "Installation", "Introduction", "Quickstart", "User Guides", "Create a Data Model in Code", "Read a Data Model from a File"], "titleterms": {"": 49, "about": 49, 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