Add GO REFs page

.gitignore

@@ -30,6 +30,10 @@ tramp
 .org-id-locations
 *_archive
 
+## Other IDEs
+.vscode
+.idea
+
 ###
 ### From upstream jekyll theme.
 ###
@@ -42,3 +46,6 @@ _site
 vendor/bundle
 
 _algolia_api_key
+
+## Transient data
+_data/gorefs.yaml

Gemfile

@@ -14,7 +14,10 @@ group :jekyll_plugins do
    gem "jekyll-redirect-from"
    gem "jekyll-seo-tag"
    gem 'jekyll-algolia', '~> 1.0'
+   gem 'jekyll-datapage-generator'
 end
 
 # Windows does not include zoneinfo files, so bundle the tzinfo-data gem
 gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]
+
+gem "rinku", "~> 2.0"

Gemfile.lock

@@ -34,6 +34,7 @@ GEM
       nokogiri (~> 1.6)
       progressbar (~> 1.9)
       verbal_expressions (~> 0.1.5)
+    jekyll-datapage-generator (1.4.0)
     jekyll-feed (0.11.0)
       jekyll (~> 3.3)
     jekyll-redirect-from (0.16.0)
@@ -65,6 +66,7 @@ GEM
     rb-fsevent (0.11.0)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
+    rinku (2.0.6)
     rouge (1.11.1)
     safe_yaml (1.0.5)
     sass (3.7.4)
@@ -81,10 +83,12 @@ PLATFORMS
 DEPENDENCIES
   jekyll (= 3.4.3)
   jekyll-algolia (~> 1.0)
+  jekyll-datapage-generator
   jekyll-feed
   jekyll-redirect-from
   jekyll-seo-tag
   jekyll-sitemap
+  rinku (~> 2.0)
   tzinfo-data
   webrick
 

Makefile

@@ -0,0 +1,4 @@
+.PHONY: _data/gorefs.yaml
+
+_data/gorefs.yaml:
+	wget -O $@ https://raw.githubusercontent.com/geneontology/go-site/master/metadata/gorefs.yaml

_config.yml

@@ -23,6 +23,7 @@ gems:
   - jekyll-redirect-from
   - jekyll-seo-tag
   - jekyll-sitemap
+  - jekyll-datapage-generator
 
 exclude:
   - Gemfile
@@ -60,9 +61,6 @@ collections:
     permalink: /blog/:year/:month/:day/:title/
     output: true
 
-plugins_dir:
-- jekyll-redirect-from
-
 sass:
   sass_dir: _sass
 
@@ -81,3 +79,8 @@ algolia:
     - covid-19.html
 #   nodes_to_index: 'article' # elements to be indexed 
   nodes_to_index: 'p,blockquote,li,div,paragraph,td,span,h1,h2,h3'
+
+page_gen:
+  - data: gorefs
+    template: goref
+    name: id

_includes/goref.html

@@ -0,0 +1,42 @@
+<div>
+    <span class="label label-primary">{{ include.goref.id }}</span>
+    {% if include.goref.is_obsolete %}
+    <span class="label label-danger text-uppercase">obsolete</span>
+    {% endif %}
+</div>
+<h2>{{ include.goref.title }}</h2>
+<p>{{ include.goref.authors }}; {{ include.goref.year }}</p>
+<p>{{ include.goref.description | markdownify | autolinkify }}</p>
+
+{% if include.goref.comments %}
+<h3>Comments</h3>
+<ul>
+{% for comment in include.goref.comments %}
+    <li>{{ comment | markdownify | autolinkify  }}</li>
+{% endfor %}
+</ul>
+{% endif %}
+
+{% if include.goref.citation %}
+<div class="row">
+    <div class="col-sm-2"><b>Citation</b></div>
+    <div class="col-sm-10">
+        <a href="http://www.ncbi.nlm.nih.gov/pubmed/{{ include.goref.citation | remove_first: 'PMID:' }}" target="_blank">
+            {{ include.goref.citation }}
+        </a>
+    </div>
+</div>
+{% endif %}
+
+{% if include.goref.external_accession %}
+<div class="row">
+    <div class="col-sm-2"><b>External xrefs</b></div>
+    <div class="col-sm-10">
+        <ul class="list-unstyled">
+        {% for xref in include.goref.external_accession %}
+            <li>{{ xref }}</li>
+        {% endfor %}
+        </ul>
+    </div>
+</div>
+{% endif %}

_includes/goref_toc_list_item.html

@@ -0,0 +1,5 @@
+<li>
+    <a class="u-margin-bottom-xsmall" href="{{ include.goref.id | datapage_url: 'gorefs' }}">
+        [{{ include.goref.id }}] {{ include.goref.title }}
+    </a>
+</li>

_layouts/goref.html

@@ -0,0 +1,13 @@
+---
+layout: default
+---
+
+<div class="container">
+    <div class="u-margin-bottom-medium">
+        <a href="{{ '/gorefs.html' | relative_url }}">
+            <i class="fa fa-chevron-left" aria-hidden="true"></i>
+            All GO REFs
+        </a>
+    </div>
+    {% include goref.html goref=page %}
+</div>

_plugins/autolinkify.rb

@@ -0,0 +1,11 @@
+require 'rinku'
+
+module Jekyll
+    module AutolinkifyFilter
+        def autolinkify(input)
+            Rinku.auto_link(input, :all, 'target="_blank"')
+        end
+    end
+end
+
+Liquid::Template.register_filter(Jekyll::AutolinkifyFilter)

_sass/custom/_typography.scss

@@ -37,29 +37,59 @@ a {
     text-decoration: none;
 }
 
-a:not(.btn):not(.yasr_btn):not(.list-group-item):not(.dropdown-menu__item__link):not(.go-link):not(.basic-link) {
-    color: $color-primary;
-    text-decoration: none !important;
-    display: inline-block;
+.permalink {
+    font-family: inherit;
     position: relative;
+
+    &:hover::before {
+        content: '#';
+        position: absolute;
+        left: -0.8em;
+        top: 0.2em;
+        font-size: 0.8em;
+        opacity: 0.7;
+    }
 }
 
-a:not(.btn):not(.yasr_btn):not(.list-group-item):not(.dropdown-menu__item__link):not(.go-link):not(.basic-link):after {
-    background: none repeat scroll 0 0 transparent;
-    bottom: 0;
-    content: "";
+.permalink-anchor {
+    // Account for the fixed header
     display: block;
-    height: 2px;
-    left: 50%;
-    position: absolute;
-    background: $color-primary;
-    transition: width 0.3s ease 0s, left 0.3s ease 0s;
-    width: 0;
+    position: relative;
+    top: -65px;
+    visibility: hidden;
 }
 
-a:not(.btn):not(.list-group-item):not(.dropdown-menu__item__link):not(.go-link):not(.basic-link):hover:after {
-    width: 100%;
-    left: 0;
+a:not(.btn):not(.yasr_btn):not(.list-group-item):not(.dropdown-menu__item__link):not(.go-link):not(.basic-link):not(.permalink) {
+    color: $color-primary;
+    text-decoration: none !important;
+    display: inline-block;
+    position: relative;
+
+    &::after {
+        background: none repeat scroll 0 0 transparent;
+        bottom: 0;
+        content: "";
+        display: block;
+        height: 2px;
+        left: 50%;
+        position: absolute;
+        background: $color-primary;
+        transition: width 0.3s ease 0s, left 0.3s ease 0s;
+        width: 0;
+    }
+
+    &:hover::after {
+        width: 100%;
+        left: 0;
+    }
+
+    // Because these links are inline-block elements, in a <li> element the ::marker next to one
+    // would be aligned to the bottom by default if it wraps across multiple lines. This looks
+    // weird. So if the link is a direct child of a list item, set the vertical-align to top.
+    // Re funky syntax: https://github.com/sass/sass/issues/1425
+    @at-root li > #{&} {
+        vertical-align: top;
+    }
 }
 
 .btn {
@@ -107,10 +137,10 @@ a:not(.btn):not(.list-group-item):not(.dropdown-menu__item__link):not(.go-link):
         padding: 8px 6px;
         text-decoration: none;
         font-weight: 400 !important;
-        width: 100%; 
+        width: 100%;
         transition: padding 0.2s;
         // transition:  0.15s text-align ease;
-        
+
         &:hover {
             text-decoration: none;
             font-weight: 400 !important;
@@ -207,7 +237,7 @@ a:not(.btn):not(.list-group-item):not(.dropdown-menu__item__link):not(.go-link):
 }
 
 .fa {
-    text-shadow: rgba(0, 0, 0, 0.25) 1.5px 1.5px 5px;    
+    text-shadow: rgba(0, 0, 0, 0.25) 1.5px 1.5px 5px;
 }
 
 .input_hint {

gorefs.html

@@ -0,0 +1,39 @@
+---
+# Note that when developing locally, this page must be reached by visiting /gorefs.html. Without
+# the .html extension (/gorefs), an index page for the gorefs directory generated by the
+# jekyll-datapage-generator plugin will be displayed instead. This is a quirk of the Jekyll
+# development web server. When deployed on GitHub pages, this page will be available at /gorefs
+# without the .html extension.
+
+layout: default
+---
+
+<div class="container">
+    <h1>GO REFs</h1>
+    <p>This is a collection of references used by the GO Consortium</p>
+
+    {% if jekyll.environment == "development" %}
+        {% unless site.data.gorefs %}
+            <div class="alert alert-warning">
+                <strong>Warning!</strong> No GO_REFs found. Did you run <code>make _data/gorefs.yml</code>?
+            </div>
+        {% endunless %}
+    {% endif %}
+
+    <ul>
+        {% for goref in site.data.gorefs %}
+        {% unless goref.is_obsolete %}
+            {% include goref_toc_list_item.html goref=goref %}
+        {% endunless %}
+        {% endfor %}
+    </ul>
+
+    <h2>Obsolete GO REFs</h2>
+    <ul>
+        {% for goref in site.data.gorefs %}
+        {% if goref.is_obsolete %}
+            {% include goref_toc_list_item.html goref=goref %}
+        {% endif %}
+        {% endfor %}
+    </ul>
+</div>