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titipata · Aug 19, 2024 · b6d6898 · b6d6898
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 18bab0713659a3e0a8054d4799da3b04
+config: 4403808061e5ec20fbfa783a07f2c982
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_modules/index.html b/_modules/index.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en">
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
@@ -14,9 +14,9 @@
 
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=4e78f113"></script>
-        <script src="../_static/doctools.js?v=888ff710"></script>
-        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
+        <script src="../_static/documentation_options.js?v=6c02275b"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 

diff --git a/_modules/pubmed_parser/medline_parser.html b/_modules/pubmed_parser/medline_parser.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en">
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
@@ -14,9 +14,9 @@
 
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=4e78f113"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
-        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
+        <script src="../../_static/documentation_options.js?v=6c02275b"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -412,7 +412,9 @@ <h1>Source code for pubmed_parser.medline_parser</h1><div class="highlight"><pre
     <span class="k">return</span> <span class="n">dict_info</span>
 
 
-<div class="viewcode-block" id="parse_grant_id"><a class="viewcode-back" href="../../api.html#pubmed_parser.parse_grant_id">[docs]</a><span class="k">def</span> <span class="nf">parse_grant_id</span><span class="p">(</span><span class="n">pubmed_article</span><span class="p">):</span>
+<div class="viewcode-block" id="parse_grant_id">
+<a class="viewcode-back" href="../../api.html#pubmed_parser.parse_grant_id">[docs]</a>
+<span class="k">def</span> <span class="nf">parse_grant_id</span><span class="p">(</span><span class="n">pubmed_article</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Parse Grant ID and related information from a given MEDLINE tree</span>
 
 <span class="sd">    Parameters</span>
@@ -465,6 +467,7 @@ <h1>Source code for pubmed_parser.medline_parser</h1><div class="highlight"><pre
     <span class="k">return</span> <span class="n">grant_list</span></div>
 
 
+
 <span class="k">def</span> <span class="nf">parse_author_affiliation</span><span class="p">(</span><span class="n">medline</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Parse MEDLINE authors and their corresponding affiliations</span>
 
@@ -769,7 +772,9 @@ <h1>Source code for pubmed_parser.medline_parser</h1><div class="highlight"><pre
     <span class="k">return</span> <span class="n">dict_out</span>
 
 
-<div class="viewcode-block" id="parse_medline_xml"><a class="viewcode-back" href="../../api.html#pubmed_parser.parse_medline_xml">[docs]</a><span class="k">def</span> <span class="nf">parse_medline_xml</span><span class="p">(</span>
+<div class="viewcode-block" id="parse_medline_xml">
+<a class="viewcode-back" href="../../api.html#pubmed_parser.parse_medline_xml">[docs]</a>
+<span class="k">def</span> <span class="nf">parse_medline_xml</span><span class="p">(</span>
     <span class="n">path</span><span class="p">,</span>
     <span class="n">year_info_only</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
     <span class="n">nlm_category</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
@@ -839,6 +844,7 @@ <h1>Source code for pubmed_parser.medline_parser</h1><div class="highlight"><pre
                 <span class="n">res</span><span class="p">[</span><span class="s1">&#39;grant_ids&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">parse_grant_id</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
                 <span class="n">element</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span>
                 <span class="k">yield</span> <span class="n">res</span></div>
+
 </pre></div>
 
            </div>

diff --git a/_modules/pubmed_parser/pubmed_oa_parser.html b/_modules/pubmed_parser/pubmed_oa_parser.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en">
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
@@ -14,9 +14,9 @@
 
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=4e78f113"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
-        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
+        <script src="../../_static/documentation_options.js?v=6c02275b"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -209,7 +209,9 @@ <h1>Source code for pubmed_parser.pubmed_oa_parser</h1><div class="highlight"><p
             <span class="k">yield</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">el</span><span class="o">.</span><span class="n">itertext</span><span class="p">())</span>
 
 
-<div class="viewcode-block" id="parse_pubmed_xml"><a class="viewcode-back" href="../../api.html#pubmed_parser.parse_pubmed_xml">[docs]</a><span class="k">def</span> <span class="nf">parse_pubmed_xml</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">include_path</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">nxml</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<div class="viewcode-block" id="parse_pubmed_xml">
+<a class="viewcode-back" href="../../api.html#pubmed_parser.parse_pubmed_xml">[docs]</a>
+<span class="k">def</span> <span class="nf">parse_pubmed_xml</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">include_path</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">nxml</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Given an input XML path to PubMed XML file, extract information and metadata</span>
 <span class="sd">    from a given XML file and return parsed XML file in dictionary format.</span>
@@ -347,6 +349,7 @@ <h1>Source code for pubmed_parser.pubmed_oa_parser</h1><div class="highlight"><p
     <span class="k">return</span> <span class="n">dict_out</span></div>
 
 
+
 <span class="k">def</span> <span class="nf">get_reference</span><span class="p">(</span><span class="n">reference</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Get reference from one of the three possible positions.&quot;&quot;&quot;</span>
     <span class="k">for</span> <span class="n">tag</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;mixed-citation&quot;</span><span class="p">,</span> <span class="s2">&quot;element-citation&quot;</span><span class="p">,</span> <span class="s2">&quot;citation&quot;</span><span class="p">]:</span>
@@ -356,7 +359,9 @@ <h1>Source code for pubmed_parser.pubmed_oa_parser</h1><div class="highlight"><p
     <span class="k">return</span> <span class="kc">None</span>
 
 
-<div class="viewcode-block" id="parse_pubmed_references"><a class="viewcode-back" href="../../api.html#pubmed_parser.parse_pubmed_references">[docs]</a><span class="k">def</span> <span class="nf">parse_pubmed_references</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
+<div class="viewcode-block" id="parse_pubmed_references">
+<a class="viewcode-back" href="../../api.html#pubmed_parser.parse_pubmed_references">[docs]</a>
+<span class="k">def</span> <span class="nf">parse_pubmed_references</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Given path to xml file, parse references articles</span>
 <span class="sd">    to list of dictionary</span>
@@ -445,7 +450,10 @@ <h1>Source code for pubmed_parser.pubmed_oa_parser</h1><div class="highlight"><p
     <span class="k">return</span> <span class="n">dict_refs</span></div>
 
 
-<div class="viewcode-block" id="parse_pubmed_paragraph"><a class="viewcode-back" href="../../api.html#pubmed_parser.parse_pubmed_paragraph">[docs]</a><span class="k">def</span> <span class="nf">parse_pubmed_paragraph</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">all_paragraph</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+
+<div class="viewcode-block" id="parse_pubmed_paragraph">
+<a class="viewcode-back" href="../../api.html#pubmed_parser.parse_pubmed_paragraph">[docs]</a>
+<span class="k">def</span> <span class="nf">parse_pubmed_paragraph</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">all_paragraph</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Give path to a given PubMed OA file, parse and return</span>
 <span class="sd">    a dictionary of all paragraphs, section that it belongs to,</span>
@@ -505,7 +513,10 @@ <h1>Source code for pubmed_parser.pubmed_oa_parser</h1><div class="highlight"><p
     <span class="k">return</span> <span class="n">dict_pars</span></div>
 
 
-<div class="viewcode-block" id="parse_pubmed_caption"><a class="viewcode-back" href="../../api.html#pubmed_parser.parse_pubmed_caption">[docs]</a><span class="k">def</span> <span class="nf">parse_pubmed_caption</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
+
+<div class="viewcode-block" id="parse_pubmed_caption">
+<a class="viewcode-back" href="../../api.html#pubmed_parser.parse_pubmed_caption">[docs]</a>
+<span class="k">def</span> <span class="nf">parse_pubmed_caption</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Given single xml path, extract figure caption and</span>
 <span class="sd">    reference id back to that figure</span>
@@ -581,6 +592,7 @@ <h1>Source code for pubmed_parser.pubmed_oa_parser</h1><div class="highlight"><p
     <span class="k">return</span> <span class="n">dict_captions</span></div>
 
 
+
 <span class="k">def</span> <span class="nf">table_to_df</span><span class="p">(</span><span class="n">table_text</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    This is a function to transform an input table XML text to list of row values and columns.</span>
@@ -620,7 +632,9 @@ <h1>Source code for pubmed_parser.pubmed_oa_parser</h1><div class="highlight"><p
         <span class="k">return</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span>
 
 
-<div class="viewcode-block" id="parse_pubmed_table"><a class="viewcode-back" href="../../api.html#pubmed_parser.parse_pubmed_table">[docs]</a><span class="k">def</span> <span class="nf">parse_pubmed_table</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">return_xml</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+<div class="viewcode-block" id="parse_pubmed_table">
+<a class="viewcode-back" href="../../api.html#pubmed_parser.parse_pubmed_table">[docs]</a>
+<span class="k">def</span> <span class="nf">parse_pubmed_table</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">return_xml</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Parse table from given Pubmed Open-Access XML file</span>
 
@@ -692,6 +706,7 @@ <h1>Source code for pubmed_parser.pubmed_oa_parser</h1><div class="highlight"><p
         <span class="k">return</span> <span class="n">table_dicts</span>
     <span class="k">else</span><span class="p">:</span>
         <span class="k">return</span> <span class="kc">None</span></div>
+
 </pre></div>
 
            </div>

diff --git a/_modules/pubmed_parser/pubmed_web_parser.html b/_modules/pubmed_parser/pubmed_web_parser.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en">
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
@@ -14,9 +14,9 @@
 
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=4e78f113"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
-        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
+        <script src="../../_static/documentation_options.js?v=6c02275b"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -243,7 +243,9 @@ <h1>Source code for pubmed_parser.pubmed_web_parser</h1><div class="highlight"><
     <span class="k">return</span> <span class="n">dict_out</span>
 
 
-<div class="viewcode-block" id="parse_xml_web"><a class="viewcode-back" href="../../api.html#pubmed_parser.parse_xml_web">[docs]</a><span class="k">def</span> <span class="nf">parse_xml_web</span><span class="p">(</span><span class="n">pmid</span><span class="p">,</span> <span class="n">sleep</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">save_xml</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<div class="viewcode-block" id="parse_xml_web">
+<a class="viewcode-back" href="../../api.html#pubmed_parser.parse_xml_web">[docs]</a>
+<span class="k">def</span> <span class="nf">parse_xml_web</span><span class="p">(</span><span class="n">pmid</span><span class="p">,</span> <span class="n">sleep</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">save_xml</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Give an input PMID, load and parse XML using PubMed eutils</span>
 
@@ -288,6 +290,7 @@ <h1>Source code for pubmed_parser.pubmed_web_parser</h1><div class="highlight"><
     <span class="k">return</span> <span class="n">dict_out</span></div>
 
 
+
 <span class="k">def</span> <span class="nf">extract_citations</span><span class="p">(</span><span class="n">tree</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Extract number of citations from a given eutils XML tree.</span>
@@ -384,7 +387,9 @@ <h1>Source code for pubmed_parser.pubmed_web_parser</h1><div class="highlight"><
     <span class="k">return</span> <span class="p">{</span><span class="s2">&quot;pmc&quot;</span><span class="p">:</span> <span class="n">pmc</span><span class="p">,</span> <span class="s2">&quot;pmid&quot;</span><span class="p">:</span> <span class="n">pmid</span><span class="p">,</span> <span class="s2">&quot;doi&quot;</span><span class="p">:</span> <span class="n">doi</span><span class="p">}</span>
 
 
-<div class="viewcode-block" id="parse_citation_web"><a class="viewcode-back" href="../../api.html#pubmed_parser.parse_citation_web">[docs]</a><span class="k">def</span> <span class="nf">parse_citation_web</span><span class="p">(</span><span class="n">doc_id</span><span class="p">,</span> <span class="n">id_type</span><span class="o">=</span><span class="s2">&quot;PMC&quot;</span><span class="p">):</span>
+<div class="viewcode-block" id="parse_citation_web">
+<a class="viewcode-back" href="../../api.html#pubmed_parser.parse_citation_web">[docs]</a>
+<span class="k">def</span> <span class="nf">parse_citation_web</span><span class="p">(</span><span class="n">doc_id</span><span class="p">,</span> <span class="n">id_type</span><span class="o">=</span><span class="s2">&quot;PMC&quot;</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Parse citations from given document id</span>
 
@@ -451,7 +456,10 @@ <h1>Source code for pubmed_parser.pubmed_web_parser</h1><div class="highlight"><
     <span class="k">return</span> <span class="n">dict_out</span></div>
 
 
-<div class="viewcode-block" id="parse_outgoing_citation_web"><a class="viewcode-back" href="../../api.html#pubmed_parser.parse_outgoing_citation_web">[docs]</a><span class="k">def</span> <span class="nf">parse_outgoing_citation_web</span><span class="p">(</span><span class="n">doc_id</span><span class="p">,</span> <span class="n">id_type</span><span class="o">=</span><span class="s2">&quot;PMC&quot;</span><span class="p">):</span>
+
+<div class="viewcode-block" id="parse_outgoing_citation_web">
+<a class="viewcode-back" href="../../api.html#pubmed_parser.parse_outgoing_citation_web">[docs]</a>
+<span class="k">def</span> <span class="nf">parse_outgoing_citation_web</span><span class="p">(</span><span class="n">doc_id</span><span class="p">,</span> <span class="n">id_type</span><span class="o">=</span><span class="s2">&quot;PMC&quot;</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    A function to load citations from NCBI eutils API for a given document</span>
 
@@ -507,6 +515,7 @@ <h1>Source code for pubmed_parser.pubmed_web_parser</h1><div class="highlight"><
         <span class="s2">&quot;pmid_cited&quot;</span><span class="p">:</span> <span class="n">pmid_cited_all</span><span class="p">,</span>
     <span class="p">}</span>
     <span class="k">return</span> <span class="n">dict_out</span></div>
+
 </pre></div>
 
            </div>