jekyll-pubmed 0.1.1
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- checksums.yaml +7 -0
- data/.gitignore +10 -0
- data/.rspec +2 -0
- data/.travis.yml +19 -0
- data/Gemfile +4 -0
- data/README.md +32 -0
- data/Rakefile +2 -0
- data/jekyll-pubmed.gemspec +27 -0
- data/lib/jekyll-pubmed.rb +98 -0
- data/lib/jekyll-pubmed/version.rb +3 -0
- data/scripts/bootstrap +3 -0
- data/scripts/cibuild +4 -0
- data/spec/dest/assets/header.png +0 -0
- data/spec/dest/assets/main.css +106 -0
- data/spec/dest/publications/index.html +427 -0
- data/spec/fixtures/_includes/footer.html +9 -0
- data/spec/fixtures/_includes/head.html +12 -0
- data/spec/fixtures/_includes/header.html +40 -0
- data/spec/fixtures/_layouts/default.html +21 -0
- data/spec/fixtures/_layouts/home.html +7 -0
- data/spec/fixtures/_layouts/page.html +7 -0
- data/spec/fixtures/_layouts/post.html +5 -0
- data/spec/fixtures/_layouts/project.html +3 -0
- data/spec/fixtures/_layouts/projects.html +49 -0
- data/spec/fixtures/_layouts/publications.html +87 -0
- data/spec/fixtures/assets/header.png +0 -0
- data/spec/fixtures/assets/main.css +106 -0
- data/spec/fixtures/publications.md +7 -0
- data/spec/jekyll-pubmed_spec.rb +35 -0
- data/spec/spec_helper.rb +45 -0
- metadata +157 -0
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<head>
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<link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
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<link rel="stylesheet" href="https://code.getmdl.io/1.3.0/material.blue_grey-indigo.min.css" />
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<script defer src="https://code.getmdl.io/1.3.0/material.min.js"></script>
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<link rel="stylesheet" href="{{ "/assets/main.css" | relative_url }}">
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<title>{% if page.title %}{{ page.title | escape }}{% else %}{{ site.title | escape }}{% endif %}</title>
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<meta name="description" content="{{ page.excerpt | default: site.description | strip_html | normalize_whitespace | truncate: 160 | escape }}">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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</head>
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<div class="banner">
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<div class="header-img">
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<span class="main-title">Bioinformatics (Mis)adventures</span>
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<br/>
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<span class="sub-title">Regular Mishaps with Bioinformatics</span>
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</div>
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</div>
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<div id="header" class="mdl-layout mdl-js-layout mdl-layout--fixed-header">
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<header class="mdl-layout__header ">
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<div class="mdl-layout__header-row">
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<nav class="mdl-navigation mdl-layout--large-screen-only mdl-js-ripple-effect">
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<a class="mdl-navigation__link" href="/">Home</a>
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<a class="mdl-navigation__link" href="/education/">Education</a>
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<a class="mdl-navigation__link" href="/projects/">Projects</a>
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<a class="mdl-navigation__link" href="/research/">Research</a>
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<a class="mdl-navigation__link" href="">Tools</a>
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<a class="mdl-navigation__link" href="">Posts</a>
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<a class="mdl-navigation__link" href="/publications/">Publications</a>
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<a class="mdl-navigation__link" href="">Contact</a>
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</nav>
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<div class="mdl-layout-spacer"></div>
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</div>
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</header>
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<div class="mdl-layout__drawer">
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<nav class="mdl-navigation">
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<a class="mdl-navigation__link" href="/">Home</a>
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<a class="mdl-navigation__link" href="/education">Education</a>
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<a class="mdl-navigation__link" href="/projects/">Projects</a>
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<a class="mdl-navigation__link" href="/research/">Research</a>
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<a class="mdl-navigation__link" href="">Tools</a>
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<a class="mdl-navigation__link" href="">Posts</a>
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<a class="mdl-navigation__link" href="/publications/">Publications</a>
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<a class="mdl-navigation__link" href="">Contact</a>
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</nav>
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</div>
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<!DOCTYPE html>
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<html lang="{{ page.lang | default: site.lang | default: "en" }}">
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{% include head.html %}
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<body>
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{% include header.html %}
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<main class="mdl-layout__content">
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<div class="page-content">
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{{ content }}
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</div>
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</main>
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{% include footer.html %}
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</div>
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</div>
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</body>
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</html>
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---
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layout: default
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---
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<h1>Projects</h1>
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<div class="mdl-grid">
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{% for project in site.categories.projects %}
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<div class="mdl-cell mdl-cell--4-col mdl-cell--4-col-phone mdl-card mdl-shadow--4dp">
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<div class="mdl-card__title">
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<h1 class="mdl-card__title-text">{{ project.title}}</h1>
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<img src="{{ project.logo }}" />
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</div>
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<div class="mdl-card__media">
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<img src="{{project.img}}"/>
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</div>
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<div class="mdl-card__supporting-text mdl-card--expand">
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{{ project.content }}
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</div>
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<div class="mdl-card__actions mdl-card--border">
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{% if project.publication == "" %}
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<a id="pinemap_pub" class="right-button mdl-button mdl-js-button mdl-js-ripple-effect mdl-button--fab mdl-button--colored" disabled>
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<i class="material-icons">description</i>
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</a>
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{% else %}{{child.MedlineCitation.PMID}}_link
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<a id="{{ project.title}}_pub" class="right-button mdl-button mdl-js-button mdl-js-ripple-effect mdl-button--fab mdl-button--colored" href="{{ project.publication }}" target="_blank">
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<i class="material-icons">description</i>
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</a>
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{% endif %}
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<div class="mdl-tooltip mdl-tooltip--large" for="{{ project.title}}_pub"> Publication</div>
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{% if project.link == "" %}
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<button id="{{ project.title}}_link" class="right-btn mdl-button mdl-js-button mdl-js-ripple-effect mdl-button--fab mdl-button--colored" disabled >
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<i class="material-icons">launch</i>
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</button>
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{% else %}
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<a id="{{ project.title}}_link" class="right-btn mdl-button mdl-js-button mdl-js-ripple-effect mdl-button--fab mdl-button--colored" target="_blank" href="{{project.link}}">
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<i class="material-icons">launch</i>
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</a>
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{% endif %}
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<div class="mdl-tooltip mdl-tooltip--large" for="{{ project.title}}_link"> Website </div>
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</div>
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</div>
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{% endfor %}
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</div>
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---
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layout: default
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---
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<h1>Publications</h1>
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<section class="mdl-grid pub_table">
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{% for year in site.data.abstracts.years %}
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<div class="mdl-cell mdl-cell--12-col-desktop mdl-cell--4-col-phone mdl-cell--middle pub_year mdl-cell--stretch">
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<h4>{{ year }}</h4>
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</div>
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{% for pub_date in site.data.abstracts.pmids %}
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{% assign pub_year = pub_date[0] | date: "%Y" %}
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{% if pub_year == year %}
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{% for article in site.data.abstracts.articles %}
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{% if article[0] == pub_date[1] %}
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<div class="mdl-cell mdl-cell--10-col mdl-cell--4-col-phone pub_details">
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<div class="pub_title">
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<a tooltip="{{article[1].title}}" class = 'dialog-link-{{pub_date[1]}}'>{{article[1].title}}</a>
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</div>
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<div class="authors">
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{% for pub_author in article[1].authors %}
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{% if pub_author contains "Wimalanathan" %}
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<span class="bold_author">{{pub_author}}, </span>
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{% elsif forloop.first %}
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{{pub_author}}*,
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{% elsif forloop.last %}
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{{pub_author}}.
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{% else %}
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{{pub_author}},
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{% endif %}
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{% endfor %}
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</div>
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</div>
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<div class="mdl-cell mdl-cell--1-col-desktop mdl-cell--4-col mdl-cell--middle pub_link mdl-cell--stretch">
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<a id="{{pub_date[1]}}_link" class="right-button mdl-button mdl-js-button mdl-js-ripple-effect mdl-button--fab mdl-button--colored"
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href="http://www.ncbi.nlm.nih.gov/pubmed?term={{pub_date[1]}}" target="_blank">
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<i class="material-icons">description</i>
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</a>
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<div class="mdl-tooltip mdl-tooltip--large" for="{{pub_date[1]}}_link"> Go to Pubmed </div>
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</div>
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<dialog id="dialog-{{pub_date[1]}}" class="mdl-dialog abstract-dialog">
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<h3 class="mdl-dialog__title">{{article[1].title}}</h3>
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<div class="mdl-dialog__content">
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<p>
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{{article[1].abstract}}
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</p>
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</div>
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<div class="mdl-dialog__actions">
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<button type="button" class="mdl-button">Close</button>
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</div>
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</dialog>
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<script>
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(function() {
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'use strict';
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var dialogButton = document.querySelector('.dialog-link-{{pub_date[1]}}');
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var dialog = document.querySelector('#dialog-{{pub_date[1]}}');
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if (! dialog.showModal) {
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dialogPolyfill.registerDialog(dialog);
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}
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dialogButton.addEventListener('click', function() {
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dialog.showModal();
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});
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dialog.querySelector('button:not([disabled])')
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.addEventListener('click', function() {
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dialog.close();
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});
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}());
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</script>
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{% endif %}
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{% endfor %}
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{% endif %}
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{% endfor %}
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{% endfor %}
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</section>
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<!-- <span>
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({{ child.MedlineCitation.Article.Journal.JournalIssue.PubDate.Year }}.)
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{{ child.MedlineCitation.Article.Journal.ISOAbbreviation }}.
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{{ child.MedlineCitation.Article.Journal.JournalIssue.Volume }}
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{% if child.MedlineCitation.Article.Journal.JournalIssue.Issue %}
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,({{ child.MedlineCitation.Article.Journal.JournalIssue.Issue }})
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{% endif %}
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:{{child.MedlineCitation.Article.Pagination.MedlinePgn}}
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</span> -->
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Binary file
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.banner{
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/*background-image: url("/assets/header.png");*/
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background: rgb(96,125,139);
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color:white;
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height:80px;
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width:100%;
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}
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.main-title{
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top:20;
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margin:20px 20px;
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font-size:32pt;
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font-weight: bolder;
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line-height: normal;
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}
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.sub-title{
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font-size:24px;
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padding-left: 75px;
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font-style: italic;
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}
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/*@media (max-width: 512px) and (min-resolution: 1.5dppx),
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(max-width: 1024px) and (max-resolution: 1.5dppx) {
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.main-title{
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font-size: 24pt;
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}
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.sub-title{
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font-style: italic;
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font-size: 12pt;
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}
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.banner{
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height:60px;
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width:100%;
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}
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}
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.demo-layout-transparent .mdl-layout__header{
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background: url('/assets/header.png') center / cover;
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background: url('/assets/header.png') center / cover;
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background: url('/assets/header.png') center / cover;
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background: url('/assets/header.png') center / cover;
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}
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} color:white;
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padding-left:20px;
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}*/
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div.mdl-card__media > img{
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max-width:100%;
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max-height:100%;
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}
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.mdl-card__title{
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width:100%;
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}
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div.mdl-card__title > img{
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position: absolute;
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right: 5px;
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height:50px;
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}
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.subheader{8
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color: white;
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background: rgb(96,125,139);
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margin: 0px 20px ;
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padding: 0px 20px ;
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}
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.right-btn{
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position:absolute;
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right:10px;
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}
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.bold_author{
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font-weight: bold;
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font-style: italic;
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}
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.pub-list{
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margin:20px 20px;
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80
|
+
}
|
|
81
|
+
|
|
82
|
+
.pub_title{
|
|
83
|
+
font-size: 14pt;
|
|
84
|
+
font-weight: bold;
|
|
85
|
+
}
|
|
86
|
+
|
|
87
|
+
.pub_year{
|
|
88
|
+
color:white;
|
|
89
|
+
font-weight: bolder;
|
|
90
|
+
text-align: center;
|
|
91
|
+
background: rgb(96,125,139);
|
|
92
|
+
}
|
|
93
|
+
.pub_link{
|
|
94
|
+
text-align: center;
|
|
95
|
+
}
|
|
96
|
+
.authors{
|
|
97
|
+
font-size:12pt;
|
|
98
|
+
}
|
|
99
|
+
|
|
100
|
+
.abstract-dialog{
|
|
101
|
+
width:90%;
|
|
102
|
+
}
|
|
103
|
+
|
|
104
|
+
.pub_details{
|
|
105
|
+
margin:20px;
|
|
106
|
+
}
|
|
@@ -0,0 +1,35 @@
|
|
|
1
|
+
require "spec_helper"
|
|
2
|
+
|
|
3
|
+
describe Jekyll:Jekyll_Pubmed do
|
|
4
|
+
let(:overrides) { Hash.new }
|
|
5
|
+
let(:config) do
|
|
6
|
+
Jekyll.configuration(Jekyll::Utils.deep_merge_hashes({
|
|
7
|
+
"full_rebuild" => true,
|
|
8
|
+
"source" => source_dir,
|
|
9
|
+
"destination" => dest_dir,
|
|
10
|
+
"url" => "http://example.org",
|
|
11
|
+
"name" => "My awesome site",
|
|
12
|
+
"author" => {
|
|
13
|
+
"name" => "Dr. Jekyll"
|
|
14
|
+
},
|
|
15
|
+
"collections" => {
|
|
16
|
+
"my_collection" => { "output" => true },
|
|
17
|
+
"other_things" => { "output" => false }
|
|
18
|
+
},
|
|
19
|
+
"jekyll_pubmed" => {
|
|
20
|
+
"data" => "publications",
|
|
21
|
+
"term" => "Wimalanathan K"
|
|
22
|
+
}
|
|
23
|
+
}, overrides))
|
|
24
|
+
end
|
|
25
|
+
let(:site) { Jekyll::Site.new(config) }
|
|
26
|
+
let(:context) { make_context(site: site) }
|
|
27
|
+
before(:each) do
|
|
28
|
+
site.process
|
|
29
|
+
end
|
|
30
|
+
it "creates publications" do
|
|
31
|
+
expect(Pathname.new(dest_dir("publications/index.html"))).to exist
|
|
32
|
+
end
|
|
33
|
+
|
|
34
|
+
|
|
35
|
+
end
|
data/spec/spec_helper.rb
ADDED
|
@@ -0,0 +1,45 @@
|
|
|
1
|
+
# spec_helper.rb
|
|
2
|
+
$LOAD_PATH.unshift File.expand_path("../../jekyll-pubmed", __FILE__)
|
|
3
|
+
require "jekyll"
|
|
4
|
+
require "jekyll-pubmed"
|
|
5
|
+
|
|
6
|
+
Jekyll.logger.log_level = :error
|
|
7
|
+
|
|
8
|
+
RSpec.configure do |config|
|
|
9
|
+
config.run_all_when_everything_filtered = true
|
|
10
|
+
config.filter_run :focus
|
|
11
|
+
config.order = "random"
|
|
12
|
+
|
|
13
|
+
SOURCE_DIR = File.expand_path("../fixtures", __FILE__)
|
|
14
|
+
DEST_DIR = File.expand_path("../dest", __FILE__)
|
|
15
|
+
|
|
16
|
+
def source_dir(*files)
|
|
17
|
+
File.join(SOURCE_DIR, *files)
|
|
18
|
+
end
|
|
19
|
+
|
|
20
|
+
def dest_dir(*files)
|
|
21
|
+
File.join(DEST_DIR, *files)
|
|
22
|
+
end
|
|
23
|
+
|
|
24
|
+
# def make_context(registers = {}, environments = {})
|
|
25
|
+
# Liquid::Context.new(environments, {},
|
|
26
|
+
# { :site => site, :page => page }.merge(registers))
|
|
27
|
+
# end
|
|
28
|
+
end
|
|
29
|
+
|
|
30
|
+
# CONFIG_DEFAULTS = {
|
|
31
|
+
# "source" => source_dir,
|
|
32
|
+
# "destination" => dest_dir,
|
|
33
|
+
# "gems" => ["jekyll-pubmed"]
|
|
34
|
+
# }.freeze
|
|
35
|
+
#
|
|
36
|
+
# def make_page(options = {})
|
|
37
|
+
# page = Jekyll::Page.new(site, CONFIG_DEFAULTS["source"], "", "page.md")
|
|
38
|
+
# page.data = options
|
|
39
|
+
# page
|
|
40
|
+
# end
|
|
41
|
+
#
|
|
42
|
+
# def make_site(options = {})
|
|
43
|
+
# site_config = Jekyll.configuration(CONFIG_DEFAULTS.merge(options))
|
|
44
|
+
# Jekyll::Site.new(site_config)
|
|
45
|
+
# end
|