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@pkalita-lbl
pkalita-lbl committed Feb 9, 2024
1 parent 76b8092 commit f9ed81f
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Showing 17 changed files with 171 additions and 470 deletions.
4 changes: 0 additions & 4 deletions _static/basic.css
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Original file line number Diff line number Diff line change
Expand Up @@ -237,10 +237,6 @@ a.headerlink {
visibility: hidden;
}

a:visited {
color: #551A8B;
}

h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
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3 changes: 2 additions & 1 deletion _static/documentation_options.js
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
const DOCUMENTATION_OPTIONS = {
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '0.0.0',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
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26 changes: 9 additions & 17 deletions _static/searchtools.js
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Original file line number Diff line number Diff line change
Expand Up @@ -57,12 +57,12 @@ const _removeChildren = (element) => {
const _escapeRegExp = (string) =>
string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string

const _displayItem = (item, searchTerms, highlightTerms) => {
const _displayItem = (item, searchTerms) => {
const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
const contentRoot = document.documentElement.dataset.content_root;

const [docName, title, anchor, descr, score, _filename] = item;

Expand All @@ -75,24 +75,20 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
if (dirname.match(/\/index\/$/))
dirname = dirname.substring(0, dirname.length - 6);
else if (dirname === "index/") dirname = "";
requestUrl = contentRoot + dirname;
requestUrl = docUrlRoot + dirname;
linkUrl = requestUrl;
} else {
// normal html builders
requestUrl = contentRoot + docName + docFileSuffix;
requestUrl = docUrlRoot + docName + docFileSuffix;
linkUrl = docName + docLinkSuffix;
}
let linkEl = listItem.appendChild(document.createElement("a"));
linkEl.href = linkUrl + anchor;
linkEl.dataset.score = score;
linkEl.innerHTML = title;
if (descr) {
if (descr)
listItem.appendChild(document.createElement("span")).innerHTML =
" (" + descr + ")";
// highlight search terms in the description
if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js
highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
}
else if (showSearchSummary)
fetch(requestUrl)
.then((responseData) => responseData.text())
Expand All @@ -101,9 +97,6 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
listItem.appendChild(
Search.makeSearchSummary(data, searchTerms)
);
// highlight search terms in the summary
if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js
highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
});
Search.output.appendChild(listItem);
};
Expand All @@ -122,15 +115,14 @@ const _finishSearch = (resultCount) => {
const _displayNextItem = (
results,
resultCount,
searchTerms,
highlightTerms,
searchTerms
) => {
// results left, load the summary and display it
// this is intended to be dynamic (don't sub resultsCount)
if (results.length) {
_displayItem(results.pop(), searchTerms, highlightTerms);
_displayItem(results.pop(), searchTerms);
setTimeout(
() => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
() => _displayNextItem(results, resultCount, searchTerms),
5
);
}
Expand Down Expand Up @@ -368,7 +360,7 @@ const Search = {
// console.info("search results:", Search.lastresults);

// print the results
_displayNextItem(results, results.length, searchTerms, highlightTerms);
_displayNextItem(results, results.length, searchTerms);
},

/**
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16 changes: 3 additions & 13 deletions _static/sphinx_highlight.js
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Original file line number Diff line number Diff line change
Expand Up @@ -29,19 +29,14 @@ const _highlight = (node, addItems, text, className) => {
}

span.appendChild(document.createTextNode(val.substr(pos, text.length)));
const rest = document.createTextNode(val.substr(pos + text.length));
parent.insertBefore(
span,
parent.insertBefore(
rest,
document.createTextNode(val.substr(pos + text.length)),
node.nextSibling
)
);
node.nodeValue = val.substr(0, pos);
/* There may be more occurrences of search term in this node. So call this
* function recursively on the remaining fragment.
*/
_highlight(rest, addItems, text, className);

if (isInSVG) {
const rect = document.createElementNS(
Expand Down Expand Up @@ -145,10 +140,5 @@ const SphinxHighlight = {
},
};

_ready(() => {
/* Do not call highlightSearchWords() when we are on the search page.
* It will highlight words from the *previous* search query.
*/
if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
SphinxHighlight.initEscapeListener();
});
_ready(SphinxHighlight.highlightSearchWords);
_ready(SphinxHighlight.initEscapeListener);
72 changes: 8 additions & 64 deletions genindex.html
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,9 @@

<script src="_static/jquery.js?v=5d32c60e"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script src="_static/documentation_options.js?v=7026087e"></script>
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=525cde36"></script>
<script src="_static/doctools.js?v=888ff710"></script>
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="_static/sphinx_highlight.js?v=4825356b"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
Expand Down Expand Up @@ -81,7 +81,6 @@ <h1 id="index">Index</h1>
| <a href="#M"><strong>M</strong></a>
| <a href="#N"><strong>N</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#R"><strong>R</strong></a>
| <a href="#S"><strong>S</strong></a>
| <a href="#U"><strong>U</strong></a>
| <a href="#V"><strong>V</strong></a>
Expand Down Expand Up @@ -146,8 +145,6 @@ <h2 id="C">C</h2>
<li><a href="prefixmaps.datamodel.html#prefixmaps.datamodel.context.Context.combine">(prefixmaps.datamodel.context.Context method)</a>
</li>
</ul></li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.etl_runner.COMBINED">COMBINED (in module prefixmaps.ingest.etl_runner)</a>
</li>
<li><a href="prefixmaps.html#prefixmaps.Context.comments">comments (prefixmaps.Context attribute)</a>

<ul>
Expand All @@ -171,8 +168,6 @@ <h2 id="C">C</h2>
<li><a href="prefixmaps.data.html#prefixmaps.data.context_paths">context_paths (in module prefixmaps.data)</a>
</li>
<li><a href="prefixmaps.io.html#prefixmaps.io.writer.context_to_file">context_to_file() (in module prefixmaps.io.writer)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.etl_runner.CONTEXTS">CONTEXTS (in module prefixmaps.ingest.etl_runner)</a>
</li>
</ul></td>
</tr></table>
Expand Down Expand Up @@ -216,35 +211,23 @@ <h2 id="F">F</h2>
<li><a href="prefixmaps.datamodel.html#prefixmaps.datamodel.context.Context.format">(prefixmaps.datamodel.context.Context attribute)</a>
</li>
</ul></li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_bioregistry.from_bioregistry">from_bioregistry() (in module prefixmaps.ingest.ingest_bioregistry)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_bioregistry.from_bioregistry_upper">from_bioregistry_upper() (in module prefixmaps.ingest.ingest_bioregistry)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_jsonld.from_jsonld_context">from_jsonld_context() (in module prefixmaps.ingest.ingest_jsonld)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_jsonld.from_jsonld_context_file">from_jsonld_context_file() (in module prefixmaps.ingest.ingest_jsonld)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_jsonld.from_jsonld_context_url">from_jsonld_context_url() (in module prefixmaps.ingest.ingest_jsonld)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_jsonld.from_jsonld_context_url">from_jsonld_context_url() (in module prefixmaps.ingest.ingest_jsonld)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_linkml.from_linkml">from_linkml() (in module prefixmaps.ingest.ingest_linkml)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_linkml.from_linkml_file">from_linkml_file() (in module prefixmaps.ingest.ingest_linkml)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_linkml.from_linkml_url">from_linkml_url() (in module prefixmaps.ingest.ingest_linkml)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_shacl.from_obo">from_obo() (in module prefixmaps.ingest.ingest_shacl)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_jsonld.from_prefixcc">from_prefixcc() (in module prefixmaps.ingest.ingest_jsonld)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_linkml.from_semweb_curated">from_semweb_curated() (in module prefixmaps.ingest.ingest_linkml)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_shacl.from_shacl_file">from_shacl_file() (in module prefixmaps.ingest.ingest_shacl)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_shacl.from_shacl_graph">from_shacl_graph() (in module prefixmaps.ingest.ingest_shacl)</a>
</li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_shacl.from_shacl_url">from_shacl_url() (in module prefixmaps.ingest.ingest_shacl)</a>
</li>
</ul></td>
</tr></table>
Expand All @@ -258,22 +241,20 @@ <h2 id="L">L</h2>
<li><a href="prefixmaps.io.html#prefixmaps.io.parser.load_context">(in module prefixmaps.io.parser)</a>
</li>
</ul></li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.etl_runner.load_context_from_source">load_context_from_source() (in module prefixmaps.ingest.etl_runner)</a>
</li>
<li><a href="prefixmaps.html#prefixmaps.load_converter">load_converter() (in module prefixmaps)</a>

<ul>
<li><a href="prefixmaps.io.html#prefixmaps.io.parser.load_converter">(in module prefixmaps.io.parser)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="prefixmaps.html#prefixmaps.load_multi_context">load_multi_context() (in module prefixmaps)</a>

<ul>
<li><a href="prefixmaps.io.html#prefixmaps.io.parser.load_multi_context">(in module prefixmaps.io.parser)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="prefixmaps.html#prefixmaps.Context.location">location (prefixmaps.Context attribute)</a>

<ul>
Expand Down Expand Up @@ -311,18 +292,12 @@ <h2 id="M">M</h2>
<li><a href="prefixmaps.datamodel.html#module-prefixmaps.datamodel.context">prefixmaps.datamodel.context</a>
</li>
<li><a href="prefixmaps.ingest.html#module-prefixmaps.ingest">prefixmaps.ingest</a>
</li>
<li><a href="prefixmaps.ingest.html#module-prefixmaps.ingest.etl_runner">prefixmaps.ingest.etl_runner</a>
</li>
<li><a href="prefixmaps.ingest.html#module-prefixmaps.ingest.ingest_bioregistry">prefixmaps.ingest.ingest_bioregistry</a>
</li>
<li><a href="prefixmaps.ingest.html#module-prefixmaps.ingest.ingest_go">prefixmaps.ingest.ingest_go</a>
</li>
<li><a href="prefixmaps.ingest.html#module-prefixmaps.ingest.ingest_jsonld">prefixmaps.ingest.ingest_jsonld</a>
</li>
<li><a href="prefixmaps.ingest.html#module-prefixmaps.ingest.ingest_linkml">prefixmaps.ingest.ingest_linkml</a>
</li>
<li><a href="prefixmaps.ingest.html#module-prefixmaps.ingest.ingest_shacl">prefixmaps.ingest.ingest_shacl</a>
</li>
<li><a href="prefixmaps.io.html#module-prefixmaps.io">prefixmaps.io</a>
</li>
Expand Down Expand Up @@ -432,34 +407,20 @@ <h2 id="P">P</h2>
<li><a href="prefixmaps.datamodel.html#module-prefixmaps.datamodel">module</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
prefixmaps.datamodel.context

<ul>
<li><a href="prefixmaps.datamodel.html#module-prefixmaps.datamodel.context">module</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
prefixmaps.ingest

<ul>
<li><a href="prefixmaps.ingest.html#module-prefixmaps.ingest">module</a>
</li>
</ul></li>
<li>
prefixmaps.ingest.etl_runner

<ul>
<li><a href="prefixmaps.ingest.html#module-prefixmaps.ingest.etl_runner">module</a>
</li>
</ul></li>
<li>
prefixmaps.ingest.ingest_bioregistry

<ul>
<li><a href="prefixmaps.ingest.html#module-prefixmaps.ingest.ingest_bioregistry">module</a>
</li>
</ul></li>
<li>
Expand All @@ -481,13 +442,6 @@ <h2 id="P">P</h2>

<ul>
<li><a href="prefixmaps.ingest.html#module-prefixmaps.ingest.ingest_linkml">module</a>
</li>
</ul></li>
<li>
prefixmaps.ingest.ingest_shacl

<ul>
<li><a href="prefixmaps.ingest.html#module-prefixmaps.ingest.ingest_shacl">module</a>
</li>
</ul></li>
<li>
Expand All @@ -511,16 +465,6 @@ <h2 id="P">P</h2>
<li><a href="prefixmaps.io.html#module-prefixmaps.io.writer">module</a>
</li>
</ul></li>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.ingest_bioregistry.PROBLEMATIC_CURIE_PREFIX_SYNONYMS_RECORDS">PROBLEMATIC_CURIE_PREFIX_SYNONYMS_RECORDS (in module prefixmaps.ingest.ingest_bioregistry)</a>
</li>
</ul></td>
</tr></table>

<h2 id="R">R</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="prefixmaps.ingest.html#prefixmaps.ingest.etl_runner.run_etl">run_etl() (in module prefixmaps.ingest.etl_runner)</a>
</li>
</ul></td>
</tr></table>

Expand Down
8 changes: 4 additions & 4 deletions index.html
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Original file line number Diff line number Diff line change
Expand Up @@ -13,9 +13,9 @@

<script src="_static/jquery.js?v=5d32c60e"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script src="_static/documentation_options.js?v=7026087e"></script>
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=525cde36"></script>
<script src="_static/doctools.js?v=888ff710"></script>
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="_static/sphinx_highlight.js?v=4825356b"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
Expand Down Expand Up @@ -72,7 +72,7 @@
<div itemprop="articleBody">

<section id="welcome-to-prefixmaps-s-documentation">
<h1>Welcome to prefixmaps’s documentation!<a class="headerlink" href="#welcome-to-prefixmaps-s-documentation" title="Link to this heading"></a></h1>
<h1>Welcome to prefixmaps’s documentation!<a class="headerlink" href="#welcome-to-prefixmaps-s-documentation" title="Permalink to this heading"></a></h1>
<div class="toctree-wrapper compound">
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
Expand All @@ -92,7 +92,7 @@ <h1>Welcome to prefixmaps’s documentation!<a class="headerlink" href="#welcome
</div>
</section>
<section id="indices-and-tables">
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Link to this heading"></a></h1>
<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this heading"></a></h1>
<ul class="simple">
<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
Expand Down
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