adding flies

.circleci/_config.yml

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+# Welcome to Jekyll!
+#
+# This config file is meant for settings that affect your whole blog, values
+# which you are expected to set up once and rarely need to edit after that.
+# For technical reasons, this file is *NOT* reloaded automatically when you use
+# 'jekyll serve'. If you change this file, please restart the server process.
+
+# Site settings
+title: OpenSchemas
+email: [email protected]
+description: > # this means to ignore newlines until "baseurl:"
+  OpenSchemas relies and extends from schema.org to generate specifications for open science.
+logo: https://openschemas.github.io/assets/images/logos/openschemas/logo_hexagon.png
+
+# Alias
+github_username:  openschemas
+repo: https://github.com/openschemas/spec-virtualization
+name: OpenSchemas
+
+# Build settings
+markdown: kramdown
+
+plugins:
+ - jekyll-sitemap
+
+# Collections
+collections:
+  specifications:
+    output: true
+    permalink: /:collection/:path/
+  archive:
+    output: true
+    permalink: /:collection/:path/

.circleci/_includes/collections_footer.html

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+<div class="inner footer_buttons">
+
+    <div class="inner footer_links">
+
+        <a href="#top" id="top_link"><div>Top &#9650;</div></a>
+
+    </div>
+
+    <div class="inner footer_links">
+        <a href="/{{page.collection}}/" id="back_groups"><div>&#9668; {{ page.collection | capitalize }}</div></a>
+    </div>
+
+</div>
+
+<div id="footer_wrap" class="outer">
+    <footer class="inner">
+        <img class="img_bottom rotation" src="https://openschemas.github.io/assets/images/logos/openschemas/logo_hexagon.png" alt="OpenSchemas">
+        <p class="p_bottom">Hugs &amp; bugs: <a href="https://www.github.com/openschemas/openschemas.github.io/issues">OpenSchemas Issue Board</a></p>
+        <p class="p_bottom">&copy; 2016</p>
+
+
+    </footer>
+</div>
+<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
+<script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.0/umd/popper.min.js" integrity="sha384-cs/chFZiN24E4KMATLdqdvsezGxaGsi4hLGOzlXwp5UZB1LY//20VyM2taTB4QvJ" crossorigin="anonymous"></script>
+<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.0/js/bootstrap.min.js" integrity="sha384-uefMccjFJAIv6A+rW+L4AHf99KvxDjWSu1z9VI8SKNVmz4sk7buKt/6v9KI65qnm" crossorigin="anonymous"></script>
+<script src="https://openschemas.github.io/assets/js/clipboard.min.js"></script>
+<script src="https://openschemas.github.io/assets/js/scripts.js"></script>

.circleci/_includes/favicon.html

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+<link rel="apple-touch-icon" sizes="57x57" href="https://openschemas.github.io/assets/images/favicon/apple-icon-57x57.png">
+<link rel="apple-touch-icon" sizes="60x60" href="https://openschemas.github.io/assets/images/favicon/apple-icon-60x60.png">
+<link rel="apple-touch-icon" sizes="72x72" href="https://openschemas.github.io/assets/images/favicon/apple-icon-72x72.png">
+<link rel="apple-touch-icon" sizes="76x76" href="https://openschemas.github.io/assets/images/favicon/apple-icon-76x76.png">
+<link rel="apple-touch-icon" sizes="114x114" href="https://openschemas.github.io/assets/images/favicon/apple-icon-114x114.png">
+<link rel="apple-touch-icon" sizes="120x120" href="https://openschemas.github.io/assets/images/favicon/apple-icon-120x120.png">
+<link rel="apple-touch-icon" sizes="144x144" href="https://openschemas.github.io/assets/images/favicon/apple-icon-144x144.png">
+<link rel="apple-touch-icon" sizes="152x152" href="https://openschemas.github.io/assets/images/favicon/apple-icon-152x152.png">
+<link rel="apple-touch-icon" sizes="180x180" href="https://openschemas.github.io/assets/images/favicon/apple-icon-180x180.png">
+<link rel="icon" type="image/png" sizes="192x192"  href="https://openschemas.github.io/assets/images/favicon/android-icon-192x192.png">
+<link rel="icon" type="image/png" sizes="32x32" href="https://openschemas.github.io/assets/images/favicon/favicon-32x32.png">
+<link rel="icon" type="image/png" sizes="96x96" href="https://openschemas.github.io/assets/images/favicon/favicon-96x96.png">
+<link rel="icon" type="image/png" sizes="16x16" href="https://openschemas.github.io/assets/images/favicon/favicon-16x16.png">
+<link rel="manifest" href="https://openschemas.github.io/assets/images/favicon/manifest.json">
+<meta name="msapplication-TileColor" content="#ffffff">
+<meta name="msapplication-TileImage" content="https://openschemas.github.io/assets/images/favicon/ms-icon-144x144.png">
+<meta name="theme-color" content="#ffffff">

.circleci/_includes/footer.html

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+
+<div class="inner">
+    <p><a href="#top" id="top_link">Top &#9650;</a></p>
+</div>
+<div id="footer_wrap" class="outer">
+    <footer class="inner">
+        <div class="acknowledge">
+             <img class="img_bottom rotation" src="https://openschemas.github.io/assets/images/logos/openschemas/logo_hexagon.png" alt="OpenSchemas">
+        </div>
+    </footer>
+</div>
+<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
+<script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.0/umd/popper.min.js" integrity="sha384-cs/chFZiN24E4KMATLdqdvsezGxaGsi4hLGOzlXwp5UZB1LY//20VyM2taTB4QvJ" crossorigin="anonymous"></script>
+<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.0/js/bootstrap.min.js" integrity="sha384-uefMccjFJAIv6A+rW+L4AHf99KvxDjWSu1z9VI8SKNVmz4sk7buKt/6v9KI65qnm" crossorigin="anonymous"></script>
+<script src="https://openschemas.github.io/assets/js/clipboard.min.js"></script>
+<script src="https://openschemas.github.io/assets/js/scripts.js"></script>

.circleci/_includes/head.html

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+<head>
+  <link href='https://fonts.googleapis.com/css?family=Noto+Sans' rel='stylesheet' type='text/css'>
+  <meta charset="utf-8">
+  <meta http-equiv="X-UA-Compatible" content="chrome=1">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+
+  <title>{% if page.title %}{{ page.title | prepend: site.name | escape }}{% else %}{{ site.title | escape }}{% endif %}</title>
+  <meta name="description" content="{% if page.excerpt %}{{ page.excerpt | strip_html | strip_newlines | truncate: 160 }}{% else %}{{ site.description }}{% endif %}">
+
+  {% include favicon.html %}
+  <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
+  <link rel="stylesheet" href="https://openschemas.github.io/assets/css/main.css"> 
+  <link rel="stylesheet" href="https://openschemas.github.io/assets/css/stylesheet.css"">
+  <link rel="alternate" type="application/rss+xml" title="Open Schema Specification" href="https://openschemas.github.io/feed.xml"">
+
+  <!-- Font Awesome -->
+  <script defer src="https://openschemas.github.io/assets/js/fontawesome-all.js"></script>
+</head>

.circleci/_includes/header.html

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+<a name="top"></a>
+
+<div id="header_wrap" class="outer">
+    <header class="inner">
+
+        <a id="forkme_banner" href="{{ site.repo }}"></a>
+        <a id="twitter_banner" href="https://www.twitter.com/{{ site.twitter }}"></a>
+
+        <div class="biohex-logo">
+            <a href="{{ site.github.url }}">
+                <img class="hexagon" src="https://openschemas.github.io/assets/images/logos/openschemas/logo_hexagon.png" alt="OpenSchemas">
+            </a><span style="font-size:60px; padding:30px; position: absolute">OpenSchemas</span>
+        </div>
+    </header>
+</div>

.circleci/_includes/mobile_navbar.html

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+<div id="mobile_cont">
+
+    <div class="mobile_nav">
+        <div class="navbar-toggle">
+            <span class="sr-only">Toggle navigation</span>
+            <span class="icon-bar"></span>
+            <span class="icon-bar"></span>
+            <span class="icon-bar"></span>
+        </div>
+    </div>
+
+    <div id="mobile_links">
+        <p><a href="https://openschemas.github.io" class="link-navbar"><div class="mobile_buttons">Home</div></a></p>
+        <p><a href="https://openschemas.github.io/join/" class="link-navbar"><div class="mobile_buttons">Join</div></a></p>
+        <p><a href="https://openschemas.github.io/specifications/" class="link-navbar"><div class="mobile_buttons">Specifications</div></a></p>
+        <p><a href="https://openschemas.github.io/software/" class="link-navbar"><div class="mobile_buttons">Software</div></a></p>
+    </div>
+
+</div>

.circleci/_includes/navbar.html

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+<!-- If you edit this file, remember to edit the mobile_navbar.html file as well -->
+<div class="trigger">
+    <div class="trigger_links">
+        <a href="https://openschemas.github.io" role="button" class="btn btn-primary"><i class="fas fa-home"></i> Home</a>
+        <a href="https://openschemas.github.io/join/" role="button" class="btn btn-primary">Join</a>
+        <div class="btn-group" role="group">
+                <button class="btn btn-primary dropdown-toggle" type="button" id="btnCommunity" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
+                Specifications
+                </button>
+                <div class="dropdown-menu" aria-labelledby="btnCommunity">
+                    <a class="dropdown-item" href="https://openschemas.github.io/specifications/">Current</a>
+                </div>
+            </div>
+        <a href="https://openschemas.github.io/software/" role="button" class="btn btn-primary">Software</a>
+    </div>
+
+    {% include mobile_navbar.html %}
+
+</div>

.circleci/_includes/profile_start.html

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+{% assign current_name = page.spec_info.title %}
+{% assign current_version = page.spec_info.version %}
+{% assign current_subtitle = page.spec_info.subtitle %}
+
+{% if page.status == 'release' %}
+<h1>{{ current_name }} Specification v. {{ current_version }}</h1>
+{% else %}
+<h1>{{ current_name }} <u>DRAFT</u> Specification v. {{ current_version }}</h1>
+{% endif %}
+<h2>{{ current_subtitle }}</h2>
+<br />
+<input id="tab1" type="radio" name="tabs" checked>
+<label for="tab1">Description</label>
+<input id="tab2" type="radio" name="tabs">
+<label for="tab2">Contributors</label>
+<input id="tab3" type="radio" name="tabs">
+<label for="tab3">Links</label>
+<section id="description" class="tabs">
+   <!-- Bioschemas <a href="/specifications/">specifications and types list.</a> -->
+   <h3>Description</h3>
+   <p>{{ page.spec_info.description }}</p>
+   <br />
+   <h3>Schema.org hierarchy</h3>
+   This is a new {{ page.spec_type }} that fits into the schema.org hierarchy as follows:
+   <br />
+   <br />
+   {% for branch_name in page.hierarchy %}
+   <a href="http://schema.org/{{ branch_name }}">{{ branch_name }}</a>
+   {%if forloop.index < page.hierarchy.size%}
+   &gt;
+   {%endif%}
+   {%endfor%}
+   {%if page.spec_type == 'Type'%}
+   &gt;
+   <a href="#">{{ page.name }}</a>
+   {%endif%}
+</section>
+<section id="links" class="tabs">
+   <table class="bioschemas_spec_list" style="width: 100%; margin-left: auto; margin-right: auto;">
+      <thead>
+         <tr>
+            <th>Group</th>
+            <th>Use Cases</th>
+            <th>Task &amp; Issues</th>
+            <th>Examples</th>
+         </tr>
+      </thead>
+      <tbody>
+         <tr>
+            <td>
+               {% for g in group %}
+               <a href="{{ g.url }}">{{ g.name }}</a>
+               {% endfor %}
+            </td>
+            <td class="spec_links">
+               {% if page.use_cases_url == '' %}
+               <a>
+               <img src="https://openschemas.github.io/assets/images/use_case_spec.png" alt="View BioSchemas {{  page.name  }} Use Cases"  style="filter: grayscale(100%);">
+               </a>
+               {%else%}
+               <a href="{{ page.use_cases_url }}">
+               <img src="https://openschemas.github.io/assets/images/use_case_spec.png" alt="View BioSchemas {{  page.name  }} Use Cases">
+               </a>
+               {%endif%}
+            </td>
+            <td class="spec_links">
+               {% if page.gh_tasks == '' %}
+               <a>
+               <img src="https://openschemas.github.io/assets/images/specs_tasks.png" alt="BioSchemas {{  page.name  }} Github Tasks or Issues" style="filter: grayscale(100%);">
+               </a>
+               {% else %}
+               <a href="{{ page.gh_tasks }}" target="_blank">
+               <img src="https://openschemas.github.io/assets/images/specs_tasks.png" alt="BioSchemas {{  page.name  }} Github Tasks or Issues">
+               </a>
+               {% endif %}
+            </td>
+            <td class="spec_links" target="_blank">
+               {% if page.spec_info.full_example == '' %}
+               <a>
+               <img src="https://openschemas.github.io/assets/images/spec_examples.png" alt="View BioSchemas {{  page.name  }} Examples" style="filter: grayscale(100%);">
+               </a>
+               {% else %}
+               <a href="{{ page.spec_info.full_example }}" target="_blank">
+               <img src="https://openschemas.github.io/assets/images/spec_examples.png" alt="View BioSchemas {{  page.name  }} Examples">
+               </a>
+               {% endif %}
+            </td>
+         </tr>
+      </tbody>
+   </table>
+   <br />
+   {% if page.name != 'Organization' and page.name != 'Person' and page.name != 'Chemical' and page.name != 'ChemicalStructure' and page.name != 'Course' and page.name != 'Standard' %}
+   <p>You can read the <a href="https://openschemas.github.io/specifications/{{ page.name }}">release version of this specification here</a>.</p>
+   {% endif %}
+</section>
+<br />
+<hr />
+<br />
+<h5>Key to specification table</h5>
+<br />
+<p>Schema.org properties where the Expected Types have been changed, or new (i.e., Bioschemas created) properties/types are <em style="color: #0B794B;"><strong>green</strong></em>.</p>
+<p>Schema.org properties/types are <em style="color: #990000;"><strong>red</strong></em>.</p>
+<p>Pending Schema.org properties/types are <em style="color: #0000CC;"><strong>blue</strong></em>.</p>
+<p>External (i.e., from 3rd party ontology) properties/types are <em style="color: #454547;"><strong>black</strong></em>.</p>
+<br />
+<p>CD = Cardinality</p>
+<br />
+<!-- change number columns based on device -->
+<script type="application/x-javascript">
+   if(navigator.userAgent.match(/android/i)) {
+       document.getElementById('peopleTable').style.columnCount = 1;
+       document.getElementById('leadTable').style.columnCount = 1;
+   } else if(navigator.userAgent.match(/phone/i)) {
+       document.getElementById('peopleTable').style.columnCount = 1;
+       document.getElementById('leadTable').style.columnCount = 1;
+   } else if(navigator.userAgent.match(/tablet/i)) {
+       document.getElementById('peopleTable').style.columnCount = 1;
+       document.getElementById('leadTable').style.columnCount = 1;
+   } else if(navigator.userAgent.match(/ipad/i)) {
+       document.getElementById('peopleTable').style.columnCount = 1;
+       document.getElementById('leadTable').style.columnCount = 1;
+   } else {
+       document.getElementById('peopleTable').style.columnCount = 4;
+       document.getElementById('leadTable').style.columnCount = 4;
+   }
+</script>