DOI Metadata Template

.gitignore

@@ -2,7 +2,8 @@
 .idea
 node_modules
 .vscode/*
+/.vscode/*
+.directory
 # scripts
-scripts/metaBuilder/metaJSON/old
-scripts/metaBuilder/toMD/old/
-scripts/metaBuilder/__pycache__/
+scripts/*
+docs/metaTemplate/.gitignore

docs/404.html

@@ -35,7 +35,7 @@
       <div class="c-header__main"><a class="c-header__logo navbar-brand" href="/"><img src="/logo192.png" alt="HuBMAP Documentation"></a>
         <button class="navbar-toggler" aria-label="Toggle navigation" aria-expanded="false" aria-controls="js-header__menu" data-target="#js-header__menu" data-toggle="collapse" type="button"><span class="navbar-toggler-icon"></span></button>
         <div class="c-header__menu collapse navbar-collapse" id="js-header__menu">
-          <ul class="navbar-nav mr-auto">{% include {{ include.content_to_render }} %}</ul>
+          <!-- <ul class="navbar-nav mr-auto"></ul> -->
           <div class="c-header__search js-app--search">
             <form>
               <input class="is-hidden" id="js-searchInput" type="search" placeholder="Search" aria-label="Search">

docs/_includes/doi-template/box-list.html

@@ -0,0 +1,19 @@
+<div class="{{ include.class | default: 'box' }}">
+  <h3>{{ include.title }}</h3>
+  <p class="hint">{{ include.hint }}</p>
+  <div class="scroll">
+    {% if include.intro and include.intro | strip != "" %}
+      <div class="intro">{{ include.intro | strip | markdownify }}</div>
+    {% endif %}
+
+    {% if include.markdown_items %}
+      <div class="markdown-content">{{ include.items | strip | markdownify }}</div>
+    {% else %}
+      <ul>
+        {% for item in include.items %}
+          <li>{{ item }}</li>
+        {% endfor %}
+      </ul>
+    {% endif %}
+  </div>
+</div>

docs/_includes/doi-template/button-row.html

@@ -0,0 +1,4 @@
+<div class="button-row">
+  <a class="secondary-btn" href="{{ page.schema_doc_href | default: '#' }}">CEDAR OpenView Documentation</a>
+  <a class="secondary-btn" href="{{ page.validator_href | default: '#' }}">CEDAR Validator</a>
+</div>

docs/_includes/doi-template/content-section.html

@@ -0,0 +1,7 @@
+<section>
+  <h2>{{ include.title }}</h2>
+  <p>{{ include.body }}</p>
+  {% if include.button_label and include.button_href %}
+    <a class="secondary-btn" href="{{ include.button_href }}">{{ include.button_label }}</a>
+  {% endif %}
+</section>

docs/_includes/doi-template/contributors.html

@@ -0,0 +1,25 @@
+<section>
+  <h2>Contributors</h2>
+  <p>{{ page.contributors_intro }}</p>
+  <p>{{ page.contributors_note }}</p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Affiliation</th>
+        <th>Contact</th>
+        <th>ORCID</th>
+      </tr>
+    </thead>
+    <tbody>
+      {% for contributor in page.contributors %}
+        <tr>
+          <td>{{ contributor.name }}</td>
+          <td>{{ contributor.affiliation }}</td>
+          <td><a href="mailto:{{ contributor.contact }}">{{ contributor.contact }}</a></td>
+          <td><a href="{{ contributor.orcid }}">{{ contributor.orcid }}</a></td>
+        </tr>
+      {% endfor %}
+    </tbody>
+  </table>
+</section>

docs/_includes/doi-template/definitions.html

@@ -0,0 +1,21 @@
+<div class="box">
+  <h3>Definitions</h3>
+  <table>
+    <thead>
+      <tr>
+        <th>Field</th>
+        <th>Description</th>
+        <th>Regexp / Rules</th>
+      </tr>
+    </thead>
+    <tbody>
+      {% for row in page.definitions %}
+        <tr>
+          <td><code>{{ row.field }}</code></td>
+          <td>{{ row.description }}</td>
+          <td>{{ row.rules }}</td>
+        </tr>
+      {% endfor %}
+    </tbody>
+  </table>
+</div>

docs/_includes/doi-template/example-tree.html

@@ -0,0 +1,4 @@
+<div class="box">
+  <h3>Example</h3>
+  <pre>{{ page.example_tree }}</pre>
+</div>

docs/_includes/doi-template/hero.html

@@ -0,0 +1,32 @@
+<h1>Metadata Reporting Standards</h1>
+<p class="spec-name">{{ page.spec_name }}</p>
+
+<div class="hero">
+  <div>
+    <p>{{ page.summary }}</p>
+    <p class="doi">
+      DOI: <a href="https://doi.org/{{ page.doi }}">https://doi.org/{{ page.doi }}</a>
+    </p>
+    <p class="hint" style="margin-top: 8px; margin-bottom: 0;">
+      Published: {{ page.published }}<br />
+      Subjects: {{ page.subjects }}
+    </p>
+  </div>
+
+  <div class="actions">
+    <div class="icon-row">
+      {% if page.help_href %}
+        <a class="icon-btn help" href="{{ page.help_href | relative_url }}" title="Help" aria-label="Help">?</a>
+      {% else %}
+        <button class="icon-btn help" type="button" title="Help" aria-label="Help">?</button>
+      {% endif %}
+      <button class="icon-btn share" type="button" title="Share" aria-label="Share">
+        <svg viewBox="0 0 24 24" aria-hidden="true" focusable="false">
+          <path fill="currentColor" d="M18 15.2c-1.04 0-1.98.42-2.66 1.1l-5.9-3.32a3.25 3.25 0 0 0 0-1.96l5.9-3.33A3.77 3.77 0 1 0 14.6 6L8.7 9.34a3.8 3.8 0 1 0 0 5.32l5.9 3.33a3.77 3.77 0 1 0 3.4-2.8Z"/>
+        </svg>
+      </button>
+    </div>
+    <a class="primary-btn download" href="{{ page.download_href | default: '#' }}">Download (ZIP)</a>
+    <p class="checksum">MD5 hash: {{ page.md5_hash | default: '7531483d85468575da1e0d2437695b46' }}</p>
+  </div>
+</div>

docs/_includes/doi-template/page.html

@@ -0,0 +1,6 @@
+{% include doi-template/hero.html %}
+{% include doi-template/tabs.html %}
+{% include doi-template/content-section.html title="HuBMAP Datasets" body=page.datasets_text button_label="View HuBMAP Datasets" button_href=page.datasets_href %}
+{% include doi-template/content-section.html title="Citation" body=page.citation_text %}
+{% include doi-template/content-section.html title="Reuse" body=page.reuse_text %}
+{% include doi-template/contributors.html %}

docs/_includes/doi-template/tabs.html

@@ -0,0 +1,32 @@
+<div class="tab-wrap" role="tablist" aria-label="Specification sections">
+  <button class="tab active" role="tab" aria-selected="true" aria-controls="panel-meta" id="tab-meta" type="button">Descriptive Metadata</button>
+  <button class="tab" role="tab" aria-selected="false" aria-controls="panel-files" id="tab-files" type="button">File Organization</button>
+</div>
+
+<section class="panel" id="panel-meta" role="tabpanel" aria-labelledby="tab-meta">
+  {% assign deprecated_items = page.deprecated_items | strip %}
+  <section class="schema-section">
+    <h3>Schema</h3>
+    <div class="schema-wrap">
+      <div class="scroll">
+        <div class="markdown-content">{{ page.schema_items | strip | markdownify }}</div>
+      </div>
+    </div>
+  </section>
+  {% if deprecated_items != "" %}
+  <section class="deprecated-section">
+    <h3>Deprecated</h3>
+    <div class="deprecated-wrap">
+      <div class="scroll">
+        <div class="markdown-content">{{ page.deprecated_items | strip | markdownify }}</div>
+      </div>
+    </div>
+  </section>
+  {% endif %}
+  {% include doi-template/button-row.html %}
+</section>
+
+<section class="panel" id="panel-files" role="tabpanel" aria-labelledby="tab-files" hidden>
+  {% include doi-template/definitions.html %}
+  {% include doi-template/example-tree.html %}
+</section>

docs/_includes/pageAlt.html

@@ -32,6 +32,7 @@
     <script src="/js/popper.min.js" crossorigin="anonymous"></script>
     <script src="/js/bootstrap.min.js" crossorigin="anonymous"></script>
     <script src="/js/alt-collapse.js"></script>
+    <script src="/js/assay-title.js"></script>
     {% seo %}
   </head>
   <body data-js-gtm class="altStyle">
@@ -58,4 +59,4 @@
       </div>
     </footer>
   </body>
-</html>
+</html>

docs/_layouts/doi-help-page.html

@@ -0,0 +1,29 @@
+<!doctype html>
+<html lang="{{ site.lang | default: 'en-US' }}">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <title>{{ page.title | default: 'Metadata Reporting Standards - Documents Provided' }}</title>
+
+    <link rel="preconnect" href="https://fonts.googleapis.com" />
+    <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin />
+    <link href="https://fonts.googleapis.com/css2?family=Inter:opsz,wght@14..32,100..900&display=swap" rel="stylesheet" />
+    <link rel="stylesheet" href="{{ '/css/doi-hm-code.css' | relative_url }}" />
+    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/7.0.1/css/all.min.css" integrity="sha512-2SwdPD6INVrV/lHTZbO2nodKhrnDdJK9/kg2XD1r9uGqPo1cUbujc+IYdlYdEErWNu69gVcYgdxlmVmzTWnetw==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+    <link rel="stylesheet" href="{{ '/css/doi-template.css' | relative_url }}" />
+    {% seo %}
+  </head>
+  <body class="doiStyle">
+    <div class="topbar">
+      <div class="topbar-inner">
+        <a class="brand" href="https://hubmapconsortium.org" aria-label="HuBMAP Home">
+          <img class="brand-logo" src="/logo192.png" alt="HuBMAP" />
+        </a>
+      </div>
+    </div>
+
+    <main class="page doi-template help-layout">
+      {{ content }}
+    </main>
+  </body>
+</html>

docs/_layouts/doi-landing-page.html

@@ -0,0 +1,36 @@
+<!doctype html>
+<html lang="{{ site.lang | default: 'en-US' }}">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <title>{{ page.title | default: 'Metadata Reporting Standards' }}</title>
+
+    {% if page.doi %}
+      <meta name="citation_doi" content="{{ page.doi }}" />
+      <meta name="dc.identifier" content="https://doi.org/{{ page.doi }}" />
+      <meta name="dc.identifier.doi" content="{{ page.doi }}" />
+    {% endif %}
+
+    <link rel="preconnect" href="https://fonts.googleapis.com" />
+    <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin />
+    <link href="https://fonts.googleapis.com/css2?family=Inter:opsz,wght@14..32,100..900&display=swap" rel="stylesheet" />
+    <link rel="stylesheet" href="{{ '/css/doi-hm-code.css' | relative_url }}" />
+    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/7.0.1/css/all.min.css" integrity="sha512-2SwdPD6INVrV/lHTZbO2nodKhrnDdJK9/kg2XD1r9uGqPo1cUbujc+IYdlYdEErWNu69gVcYgdxlmVmzTWnetw==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+    <link rel="stylesheet" href="{{ '/css/doi-template.css' | relative_url }}" />
+    <script src="{{ '/js/av-popover.js' | relative_url }}" defer></script>
+    {% seo %}
+  </head>
+  <body class="doiStyle">
+    <div class="topbar">
+      <div class="topbar-inner">
+        <a class="brand" href="https://hubmapconsortium.org" aria-label="HuBMAP Home">
+          <img class="brand-logo" src="/logo192.png" alt="HuBMAP" />
+        </a>
+      </div>
+    </div>
+
+    <main class="page doi-template">
+      {{ content }}
+    </main>
+  </body>
+</html>