deploy: 15f35b0

cli.html

@@ -96,7 +96,7 @@ <h3>populate<a class="headerlink" href="#populate" title="Permalink to this head
              <span class="p">[</span><span class="o">-</span><span class="n">c</span> <span class="n">COLUMNS</span> <span class="p">[</span><span class="n">COLUMNS</span> <span class="o">...</span><span class="p">]]</span> <span class="p">[</span><span class="o">-</span><span class="n">R</span> <span class="n">ROW_SELECTION_FILE</span><span class="p">]</span>
              <span class="p">[</span><span class="o">-</span><span class="n">r</span> <span class="n">ROW_SELECTION</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">s</span> <span class="n">SAMPLE</span><span class="p">]</span>
              <span class="n">database</span>
-             <span class="p">{</span><span class="n">journal</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">funder</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">pubmed</span><span class="p">,</span><span class="n">uspto</span><span class="p">,</span><span class="n">asjcs</span><span class="p">,</span><span class="n">doaj</span><span class="p">,</span><span class="n">ror</span><span class="p">,</span><span class="n">issn</span><span class="o">-</span><span class="n">subject</span><span class="o">-</span><span class="n">codes</span><span class="p">,</span><span class="n">datacite</span><span class="p">,</span><span class="n">orcid</span><span class="p">,</span><span class="n">crossref</span><span class="p">}</span>
+             <span class="p">{</span><span class="n">funder</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">journal</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">orcid</span><span class="p">,</span><span class="n">doaj</span><span class="p">,</span><span class="n">issn</span><span class="o">-</span><span class="n">subject</span><span class="o">-</span><span class="n">codes</span><span class="p">,</span><span class="n">asjcs</span><span class="p">,</span><span class="n">datacite</span><span class="p">,</span><span class="n">pubmed</span><span class="p">,</span><span class="n">crossref</span><span class="p">,</span><span class="n">uspto</span><span class="p">,</span><span class="n">ror</span><span class="p">}</span>
              <span class="p">[</span><span class="n">data_location</span><span class="p">]</span>
 </pre></div>
 </div>
@@ -107,7 +107,7 @@ <h4>Positional Arguments<a class="headerlink" href="#positional-arguments_repeat
 <dd><p>File path of the database to populate</p>
 </dd>
 <dt><kbd>data_name</kbd></dt>
-<dd><p>Possible choices: journal-names, funder-names, pubmed, uspto, asjcs, doaj, ror, issn-subject-codes, datacite, orcid, crossref</p>
+<dd><p>Possible choices: funder-names, journal-names, orcid, doaj, issn-subject-codes, asjcs, datacite, pubmed, crossref, uspto, ror</p>
 <p>Name of the data source to use</p>
 </dd>
 <dt><kbd>data_location</kbd></dt>
@@ -142,7 +142,7 @@ <h3>process<a class="headerlink" href="#process" title="Permalink to this headli
 <p>Run a processing step on the specified database.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">a3k</span> <span class="n">process</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span>
             <span class="n">database</span>
-            <span class="p">{</span><span class="n">link</span><span class="o">-</span><span class="n">aa</span><span class="o">-</span><span class="n">top</span><span class="o">-</span><span class="n">ror</span><span class="p">,</span><span class="n">link</span><span class="o">-</span><span class="n">works</span><span class="o">-</span><span class="n">asjcs</span><span class="p">,</span><span class="n">link</span><span class="o">-</span><span class="n">uspto</span><span class="o">-</span><span class="n">doi</span><span class="p">,</span><span class="n">link</span><span class="o">-</span><span class="n">aa</span><span class="o">-</span><span class="n">base</span><span class="o">-</span><span class="n">ror</span><span class="p">}</span>
+            <span class="p">{</span><span class="n">link</span><span class="o">-</span><span class="n">works</span><span class="o">-</span><span class="n">asjcs</span><span class="p">,</span><span class="n">link</span><span class="o">-</span><span class="n">uspto</span><span class="o">-</span><span class="n">doi</span><span class="p">,</span><span class="n">link</span><span class="o">-</span><span class="n">aa</span><span class="o">-</span><span class="n">base</span><span class="o">-</span><span class="n">ror</span><span class="p">,</span><span class="n">link</span><span class="o">-</span><span class="n">aa</span><span class="o">-</span><span class="n">top</span><span class="o">-</span><span class="n">ror</span><span class="p">}</span>
 </pre></div>
 </div>
 <div class="section" id="positional-arguments_repeat2">
@@ -152,7 +152,7 @@ <h4>Positional Arguments<a class="headerlink" href="#positional-arguments_repeat
 <dd><p>file path of the database to run the process on</p>
 </dd>
 <dt><kbd>process</kbd></dt>
-<dd><p>Possible choices: link-aa-top-ror, link-works-asjcs, link-uspto-doi, link-aa-base-ror</p>
+<dd><p>Possible choices: link-works-asjcs, link-uspto-doi, link-aa-base-ror, link-aa-top-ror</p>
 <p>Name of the process to perform;see the data processing operations in the Alexandria3k Python user API documentation for more details</p>
 </dd>
 </dl>
@@ -164,15 +164,15 @@ <h3>query<a class="headerlink" href="#query" title="Permalink to this headline">
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">a3k</span> <span class="n">query</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">a</span> <span class="n">ATTACH_DATABASES</span> <span class="p">[</span><span class="n">ATTACH_DATABASES</span> <span class="o">...</span><span class="p">]]</span>
           <span class="p">[</span><span class="o">-</span><span class="n">E</span> <span class="n">OUTPUT_ENCODING</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">F</span> <span class="n">FIELD_SEPARATOR</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">H</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">o</span> <span class="n">OUTPUT</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">P</span><span class="p">]</span>
           <span class="p">(</span><span class="o">-</span><span class="n">Q</span> <span class="n">QUERY_FILE</span> <span class="o">|</span> <span class="o">-</span><span class="n">q</span> <span class="n">QUERY</span><span class="p">)</span> <span class="p">[</span><span class="o">-</span><span class="n">s</span> <span class="n">SAMPLE</span><span class="p">]</span>
-          <span class="p">{</span><span class="n">journal</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">funder</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">pubmed</span><span class="p">,</span><span class="n">uspto</span><span class="p">,</span><span class="n">asjcs</span><span class="p">,</span><span class="n">doaj</span><span class="p">,</span><span class="n">ror</span><span class="p">,</span><span class="n">issn</span><span class="o">-</span><span class="n">subject</span><span class="o">-</span><span class="n">codes</span><span class="p">,</span><span class="n">datacite</span><span class="p">,</span><span class="n">orcid</span><span class="p">,</span><span class="n">crossref</span><span class="p">}</span>
+          <span class="p">{</span><span class="n">funder</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">journal</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">orcid</span><span class="p">,</span><span class="n">doaj</span><span class="p">,</span><span class="n">issn</span><span class="o">-</span><span class="n">subject</span><span class="o">-</span><span class="n">codes</span><span class="p">,</span><span class="n">asjcs</span><span class="p">,</span><span class="n">datacite</span><span class="p">,</span><span class="n">pubmed</span><span class="p">,</span><span class="n">crossref</span><span class="p">,</span><span class="n">uspto</span><span class="p">,</span><span class="n">ror</span><span class="p">}</span>
           <span class="p">[</span><span class="n">data_location</span><span class="p">]</span>
 </pre></div>
 </div>
 <div class="section" id="positional-arguments_repeat3">
 <h4>Positional Arguments<a class="headerlink" href="#positional-arguments_repeat3" title="Permalink to this headline">¶</a></h4>
 <dl class="option-list">
 <dt><kbd>data_name</kbd></dt>
-<dd><p>Possible choices: journal-names, funder-names, pubmed, uspto, asjcs, doaj, ror, issn-subject-codes, datacite, orcid, crossref</p>
+<dd><p>Possible choices: funder-names, journal-names, orcid, doaj, issn-subject-codes, asjcs, datacite, pubmed, crossref, uspto, ror</p>
 <p>Name of the data source to use</p>
 </dd>
 <dt><kbd>data_location</kbd></dt>
@@ -236,14 +236,14 @@ <h3>list-complete-schema<a class="headerlink" href="#list-complete-schema" title
 <h3>list-source-schema<a class="headerlink" href="#list-source-schema" title="Permalink to this headline">¶</a></h3>
 <p>List all data source schemas (default) or the specified one.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">a3k</span> <span class="nb">list</span><span class="o">-</span><span class="n">source</span><span class="o">-</span><span class="n">schema</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span>
-                       <span class="p">[{</span><span class="n">journal</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">funder</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">pubmed</span><span class="p">,</span><span class="n">uspto</span><span class="p">,</span><span class="n">asjcs</span><span class="p">,</span><span class="n">doaj</span><span class="p">,</span><span class="n">ror</span><span class="p">,</span><span class="n">issn</span><span class="o">-</span><span class="n">subject</span><span class="o">-</span><span class="n">codes</span><span class="p">,</span><span class="n">datacite</span><span class="p">,</span><span class="n">orcid</span><span class="p">,</span><span class="n">crossref</span><span class="p">}]</span>
+                       <span class="p">[{</span><span class="n">funder</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">journal</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">orcid</span><span class="p">,</span><span class="n">doaj</span><span class="p">,</span><span class="n">issn</span><span class="o">-</span><span class="n">subject</span><span class="o">-</span><span class="n">codes</span><span class="p">,</span><span class="n">asjcs</span><span class="p">,</span><span class="n">datacite</span><span class="p">,</span><span class="n">pubmed</span><span class="p">,</span><span class="n">crossref</span><span class="p">,</span><span class="n">uspto</span><span class="p">,</span><span class="n">ror</span><span class="p">}]</span>
 </pre></div>
 </div>
 <div class="section" id="positional-arguments_repeat4">
 <h4>Positional Arguments<a class="headerlink" href="#positional-arguments_repeat4" title="Permalink to this headline">¶</a></h4>
 <dl class="option-list">
 <dt><kbd>facility</kbd></dt>
-<dd><p>Possible choices: journal-names, funder-names, pubmed, uspto, asjcs, doaj, ror, issn-subject-codes, datacite, orcid, crossref</p>
+<dd><p>Possible choices: funder-names, journal-names, orcid, doaj, issn-subject-codes, asjcs, datacite, pubmed, crossref, uspto, ror</p>
 </dd>
 </dl>
 </div>
@@ -252,14 +252,14 @@ <h4>Positional Arguments<a class="headerlink" href="#positional-arguments_repeat
 <h3>list-process-schema<a class="headerlink" href="#list-process-schema" title="Permalink to this headline">¶</a></h3>
 <p>List the schema of all processes (default) or of the specified one.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">a3k</span> <span class="nb">list</span><span class="o">-</span><span class="n">process</span><span class="o">-</span><span class="n">schema</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span>
-                        <span class="p">[{</span><span class="n">link</span><span class="o">-</span><span class="n">aa</span><span class="o">-</span><span class="n">top</span><span class="o">-</span><span class="n">ror</span><span class="p">,</span><span class="n">link</span><span class="o">-</span><span class="n">works</span><span class="o">-</span><span class="n">asjcs</span><span class="p">,</span><span class="n">link</span><span class="o">-</span><span class="n">uspto</span><span class="o">-</span><span class="n">doi</span><span class="p">,</span><span class="n">link</span><span class="o">-</span><span class="n">aa</span><span class="o">-</span><span class="n">base</span><span class="o">-</span><span class="n">ror</span><span class="p">}]</span>
+                        <span class="p">[{</span><span class="n">link</span><span class="o">-</span><span class="n">works</span><span class="o">-</span><span class="n">asjcs</span><span class="p">,</span><span class="n">link</span><span class="o">-</span><span class="n">uspto</span><span class="o">-</span><span class="n">doi</span><span class="p">,</span><span class="n">link</span><span class="o">-</span><span class="n">aa</span><span class="o">-</span><span class="n">base</span><span class="o">-</span><span class="n">ror</span><span class="p">,</span><span class="n">link</span><span class="o">-</span><span class="n">aa</span><span class="o">-</span><span class="n">top</span><span class="o">-</span><span class="n">ror</span><span class="p">}]</span>
 </pre></div>
 </div>
 <div class="section" id="positional-arguments_repeat5">
 <h4>Positional Arguments<a class="headerlink" href="#positional-arguments_repeat5" title="Permalink to this headline">¶</a></h4>
 <dl class="option-list">
 <dt><kbd>facility</kbd></dt>
-<dd><p>Possible choices: link-aa-top-ror, link-works-asjcs, link-uspto-doi, link-aa-base-ror</p>
+<dd><p>Possible choices: link-works-asjcs, link-uspto-doi, link-aa-base-ror, link-aa-top-ror</p>
 </dd>
 </dl>
 </div>
@@ -284,15 +284,15 @@ <h3>download<a class="headerlink" href="#download" title="Permalink to this head
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">a3k</span> <span class="n">download</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">d</span> <span class="p">[</span><span class="n">DATABASE</span><span class="p">]]</span> <span class="p">[</span><span class="o">--</span><span class="n">sql</span><span class="o">-</span><span class="n">query</span> <span class="n">SQL_QUERY</span><span class="p">]</span>
              <span class="p">[</span><span class="o">--</span><span class="n">extra_args</span> <span class="p">[</span><span class="n">EXTRA_ARGS</span> <span class="p">[</span><span class="n">EXTRA_ARGS</span> <span class="o">...</span><span class="p">]]]</span> <span class="p">[</span><span class="o">-</span><span class="n">s</span> <span class="n">SAMPLE</span><span class="p">]</span>
              <span class="p">[</span><span class="o">-</span><span class="n">a</span> <span class="n">ATTACH_DATABASES</span> <span class="p">[</span><span class="n">ATTACH_DATABASES</span> <span class="o">...</span><span class="p">]]</span>
-             <span class="p">{</span><span class="n">journal</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">funder</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">pubmed</span><span class="p">,</span><span class="n">uspto</span><span class="p">,</span><span class="n">asjcs</span><span class="p">,</span><span class="n">doaj</span><span class="p">,</span><span class="n">ror</span><span class="p">,</span><span class="n">issn</span><span class="o">-</span><span class="n">subject</span><span class="o">-</span><span class="n">codes</span><span class="p">,</span><span class="n">datacite</span><span class="p">,</span><span class="n">orcid</span><span class="p">,</span><span class="n">crossref</span><span class="p">}</span>
+             <span class="p">{</span><span class="n">funder</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">journal</span><span class="o">-</span><span class="n">names</span><span class="p">,</span><span class="n">orcid</span><span class="p">,</span><span class="n">doaj</span><span class="p">,</span><span class="n">issn</span><span class="o">-</span><span class="n">subject</span><span class="o">-</span><span class="n">codes</span><span class="p">,</span><span class="n">asjcs</span><span class="p">,</span><span class="n">datacite</span><span class="p">,</span><span class="n">pubmed</span><span class="p">,</span><span class="n">crossref</span><span class="p">,</span><span class="n">uspto</span><span class="p">,</span><span class="n">ror</span><span class="p">}</span>
              <span class="n">data_location</span>
 </pre></div>
 </div>
 <div class="section" id="positional-arguments_repeat6">
 <h4>Positional Arguments<a class="headerlink" href="#positional-arguments_repeat6" title="Permalink to this headline">¶</a></h4>
 <dl class="option-list">
 <dt><kbd>data_name</kbd></dt>
-<dd><p>Possible choices: journal-names, funder-names, pubmed, uspto, asjcs, doaj, ror, issn-subject-codes, datacite, orcid, crossref</p>
+<dd><p>Possible choices: funder-names, journal-names, orcid, doaj, issn-subject-codes, asjcs, datacite, pubmed, crossref, uspto, ror</p>
 <p>Name of the data source to use</p>
 </dd>
 <dt><kbd>data_location</kbd></dt>