Merge pull request #4600 from galaxyproject/aardwolf-pyruvate

More OpenGraph fixes

404.md

@@ -1,12 +1,10 @@
 ---
 layout: "base"
 permalink: /404.html
+title: "404 Page Not Found"
 ---
 
-
-# Oops!
-
-## We can't seem to find the page you're looking for.
+## Oops! We can't seem to find the page you're looking for.
 
 Perhaps you are here due to a mis-typed URL
 

_includes/help.html

@@ -16,15 +16,19 @@
         </a>
         {% if topic %}
         {% unless topic.tag_based %}
+        {% if topic.title %}
         <a class="dropdown-item" href="{{ site.baseurl }}/topics/{{topic.name}}/faqs/" title="Check our FAQs for the {{topic.title}} topic">
            {% icon question %} Topic FAQs
         </a>
+        {% endif %}
         {% endunless %}
         {% elsif page.layout == 'topic' %}
         {% unless page.tag_based %}
+        {% if page.topic_title %}
         <a class="dropdown-item" href="{{ site.baseurl }}/topics/{{page.topic_name}}/faqs/" title="Check our FAQs for the {{page.topic_title}} topic">
            {% icon question %} Topic FAQs
         </a>
+        {% endif %}
         {% endunless %}
         {% endif %}
         <a class="dropdown-item" href="{{ site.help_url }}" title="Discuss on Galaxy Help">

_layouts/base.html

@@ -4,7 +4,13 @@
         <meta charset="utf-8">
         <meta http-equiv="x-ua-compatible" content="ie=edge">
         <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-        <title>{{ page.title | default: site.title }}</title>
+
+	{%- assign topic_id = page | get_topic -%}
+	{%- assign topic = site.data[topic_id] -%}
+	{%- assign og_title = site | get_og_title:page,false -%}
+	{%- assign og_title_rev = site | get_og_title:page,true-%}
+
+        <title>{{ og_title_rev | default: site.title }}</title>
         {% if jekyll.environment == 'production' %}
             {% include _includes/analytics.html %}
         {% endif %}
@@ -25,17 +31,12 @@
         <meta name="theme-color" content="#2c3143"/>
 
         {{ page | generate_dublin_core: site }}
+	{%- assign og_desc = page.description | default: page.excerpt | default:topic.summary | default: page.content | default: "Collection of tutorials developed and maintained by the worldwide Galaxy community" -%}
 
-        {% assign topic = site.data[page.topic_name] %}
-        {% assign og_title = topic.title %}
-        {% if page.title %}
-            {% assign og_title = page.title %}
-        {% endif %}
-        {% assign og_desc = page.description | default:topic.summary | default: "Collection of tutorials developed and maintained by the worldwide Galaxy community" %}
-        <meta name="description" content="{{ og_desc | strip_html}}">
+        <meta name="description" content="{{ og_desc | strip_html | regex_replace:'[\n\r\s]',' ' | truncate: 1000 }}">
         <meta property="og:site_name" content="Galaxy Training Network">
-	<meta property="og:title" content="[{% if topic.title %}{{ topic.title }}{% endif %}]{% if page.layout == "faq" %}FAQS {% elsif page.layout == "topic" %}Topic: {% endif %}{{ og_title }} {% if page.layout == "workflow-list" %}Workflows{% endif %}">
-        <meta property="og:description" content="{{ og_desc | strip_html}}">
+	<meta property="og:title" content="{{ og_title | default: page.title }}">
+        <meta property="og:description" content="{{ og_desc | strip_html | regex_replace:'[\n\r\s]',' ' | truncate: 1000 }}">
 
         {%- if page.cover %}{% assign coverimage = page.cover %}
         {%- elsif page.tags contains "cofest" %}{% assign coverimage = "/assets/images/cofest.png" %}
@@ -45,11 +46,11 @@
         {% assign og_image = page.og_image | default: coverimage | default: topic.og_image | default: "/assets/images/GTNLogo1000.png" %}
         <meta property="og:image" content="{{ og_image | prepend: site.baseurl }}">
 
-        {% if page.layout == "tutorial_hands_on" %}
+        {%- if page.layout == "tutorial_hands_on" -%}
         <script type="application/ld+json">
-            {% include _includes/material.jsonld material=page topic=topic site=site %}
+            {%- include _includes/material.jsonld material=page topic=topic site=site -%}
         </script>
-        {% endif %}
+        {%- endif -%}
     </head>
     <body data-spy="scroll" data-target="#toc" data-brightness="auto" data-contrast="auto">
         {{ 'theme' | load_bundle }}

_layouts/hall-of-fame.html

@@ -1,6 +1,7 @@
 ---
 layout: base
 lang: en
+title: Hall of Fame
 ---
 
 {% assign contributors = site.data['contributors'] %}

_plugins/api.rb

@@ -102,7 +102,7 @@ def generateVersion(site)
     # Returns:
     # nil
     def generateLibrary(site)
-      puts '[GTN/API] Data Library'
+      Jekyll.logger.info '[GTN/API] Data Library'
       page2 = PageWithoutAFile.new(site, '', 'api/', 'data-library.yaml')
       data_libraries = Dir.glob('topics/**/data-library.yaml')
       data_libraries.map! { |x| YAML.load_file(x) }
@@ -123,9 +123,10 @@ def generate(site)
       # TODO:
       # generateLibrary(site)
 
+      Jekyll.logger.info '[GTN/API] Generating API'
       # Full Bibliography
       Gtn::Scholar.load_bib(site)
-      puts '[GTN/API] Bibliography'
+      Jekyll.logger.debug '[GTN/API] Bibliography'
       page3 = PageWithoutAFile.new(site, '', 'api/', 'gtn.bib')
       page3.content = site.config['cached_global_bib'].to_s
       page3.data['layout'] = nil
@@ -156,7 +157,7 @@ def generate(site)
       site.pages << page2
 
       # Contributors
-      puts '[GTN/API] Contributors, Funders, Organisations'
+      Jekyll.logger.debug '[GTN/API] Contributors, Funders, Organisations'
       %w[contributors funders organisations].each do |type|
         page2 = PageWithoutAFile.new(site, '', 'api/', "#{type}.json")
         page2.content = JSON.pretty_generate(site.data[type].map { |c, _| mapContributor(site, c) })
@@ -196,7 +197,7 @@ def generate(site)
       site.pages << page2
 
       # Trigger the topic cache to generate if it hasn't already
-      puts '[GTN/API] Tutorials'
+      Jekyll.logger.debug '[GTN/API] Tutorials'
       TopicFilter.topic_filter(site, 'does-not-matter')
       TopicFilter.list_topics(site).map do |topic|
         out = site.data[topic].dup
@@ -238,7 +239,7 @@ def generate(site)
       end
 
       topics = {}
-      puts '[GTN/API] Topics'
+      Jekyll.logger.debug '[GTN/API] Topics'
       # Individual Topic Indexes
       site.data.each_pair do |k, v|
         if v.is_a?(Hash) && v.key?('type') && v.key?('editorial_board')
@@ -277,7 +278,7 @@ def generate(site)
       page2.data['layout'] = nil
       site.pages << page2
 
-      puts '[GTN/API] Tutorial and Slide pages'
+      Jekyll.logger.debug '[GTN/API] Tutorial and Slide pages'
 
       TopicFilter.list_all_materials(site).each do |material|
         directory = material['dir']
@@ -316,7 +317,7 @@ def generate(site)
       site.pages << page2
 
       # Top Tools
-      puts '[GTN/API] Top Tools'
+      Jekyll.logger.debug '[GTN/API] Top Tools'
       page2 = PageWithoutAFile.new(site, '', 'api/', 'top-tools.json')
       page2.content = JSON.pretty_generate(TopicFilter.list_materials_by_tool(site))
       page2.data['layout'] = nil

_plugins/by-tag-pages.rb

@@ -22,7 +22,7 @@ def generate(site)
           'hidden' => true,
         }
 
-        topic_index = PageWithoutAFile.new(site, '', "tags/#{tag}", 'index.md')
+        topic_index = PageWithoutAFile.new(site, '', "tags/#{Jekyll::Utils.slugify(tag)}", 'index.md')
         topic_index.content = ''
         topic_index.data['layout'] = 'topic'
         topic_index.data['topic_name'] = "by_tag_#{tag}"
@@ -33,7 +33,7 @@ def generate(site)
 
       Jekyll.logger.info '[GTN/SyntheticTopics] Generating By-Tag Embeds'
       TopicFilter.list_all_tags(site).map do |tag|
-        topic_index = PageWithoutAFile.new(site, '', "tags/#{tag}", 'embed.html')
+        topic_index = PageWithoutAFile.new(site, '', "tags/#{Jekyll::Utils.slugify(tag)}", 'embed.html')
         topic_index.content = ''
         topic_index.data['layout'] = 'topic-embed'
         topic_index.data['topic_name'] = "by_tag_#{tag}"

_plugins/gtn.rb

@@ -397,6 +397,63 @@ def get_topic(page)
       page['path'].split('/')[1]
     end
 
+    def get_og_desc(site, page); end
+
+    def get_og_title(site, page, reverse)
+      og_title = []
+      topic_id = page['path'].gsub(%r{^\./}, '').split('/')[1]
+
+      if site.data.key?(topic_id)
+        if site.data[topic_id].is_a?(Hash) && site.data[topic_id].key?('title')
+          og_title = [site.data[topic_id]['title']]
+        else
+          Jekyll.logger.warn "Missing title for #{topic_id}"
+        end
+      end
+
+      if page['layout'] == 'topic'
+        og_title.push 'Tutorial List'
+        return og_title.join(' / ')
+      end
+
+      material_id = page['path'].gsub(%r{^\./}, '').split('/')[3]
+      material = nil
+      material = fetch_tutorial_material(site, topic_id, material_id) if site.data.key? topic_id
+
+      og_title.push material['title'] if !material.nil?
+
+      case page['layout']
+      when 'workflow-list'
+        og_title.push 'Workflows'
+      when 'faq-page', 'faqs'
+        if page['path'] =~ %r{faqs/gtn}
+          og_title.push 'GTN FAQs'
+        elsif page['path'] =~ %r{faqs/galaxy}
+          og_title.push 'Galaxy FAQs'
+        else
+          og_title.push 'FAQs'
+        end
+      when 'faq'
+        og_title.push "FAQ: #{page['title']}"
+      when 'learning-pathway'
+        og_title.push "Learning Pathway: #{page['title']}"
+      when 'tutorial_hands_on'
+        og_title[-1]&.prepend 'Hands-on: '
+      when /slides/
+        og_title[-1]&.prepend 'Slide Deck: '
+      else
+        og_title.push page['title']
+      end
+
+      Jekyll.logger.debug "Material #{page['layout']} :: #{page['path']} => #{topic_id}/#{material_id} => #{og_title}"
+
+      if reverse.to_s == 'true'
+        og_title.compact.reverse.join(' / ')
+      else
+        og_title.compact.join(' / ')
+      end
+    end
+
     ##
     # Gets the 'default' link for a material, hands on if it exists, otherwise slides.
     # Params:

_plugins/gtn/boxify.rb

@@ -167,7 +167,7 @@ def self.generate_static_title(box_type, title, lang = 'en', key, noprefix: fals
       box_id = get_id(box_type, title, key)
       box_title = format_box_title(title, box_type, lang, noprefix: noprefix)
 
-      puts "Static | typ=#{box_type} | t=#{title} | l=#{lang} | k=#{key}" if title.nil?
+      Jekyll.logger.debug "Static | typ=#{box_type} | t=#{title} | l=#{lang} | k=#{key}" if title.nil?
 
       [box_id, %(
         <div class="box-title #{box_type}-title" id="#{box_id}">

_plugins/gtn/mod.rb

@@ -13,7 +13,7 @@ def self.init_cache
 
       @@TIME_CACHE = {}
       @@COMMIT_COUNT_CACHE = Hash.new(0)
-      puts '[GTN/Time/Mod] Filling Time Cache'
+      Jekyll.logger.info '[GTN/Time/Mod] Filling Time Cache'
       `git log --name-only --pretty='GTN_GTN:%ct'`
         .split('GTN_GTN:')
         .map { |x| x.split("\n\n") }
@@ -79,7 +79,7 @@ def self.init_cache
       @@TIME_CACHE = {}
       renames = {}
 
-      puts '[GTN/Time/Pub] Filling Publication Time Cache'
+      Jekyll.logger.info '[GTN/Time/Pub] Filling Publication Time Cache'
       `git log --first-parent --name-status --diff-filter=AR --pretty='GTN_GTN:%ct' main`
         .split('GTN_GTN:')
         .map { |x| x.split("\n\n") }
@@ -125,9 +125,10 @@ def self.obtain_time(f)
   # Gtn::ModificationTimes.init_cache
   # pp Gtn::ModificationTimes.commit_count_cache
 
-  Gtn::PublicationTimes.init_cache
-  Gtn::PublicationTimes.time_cache.select do |_, v|
-    # Things in last 6 months
-    v > Time.now - (6 * 30 * 24 * 60 * 60)
-  end.map { |k, v| puts "#{v} #{k}" }
+  puts ' Moved tobin/list-recently-modified.rb'
+  # Gtn::PublicationTimes.init_cache
+  # Gtn::PublicationTimes.time_cache.select do |_, v|
+  #   # Things in last 6 months
+  #   v > Time.now - (6 * 30 * 24 * 60 * 60)
+  # end.map { |k, v| puts "#{v} #{k}" }
 end

_plugins/gtn/scholar.rb

@@ -30,7 +30,7 @@ def self.render_citation(key)
     end
 
     def self.discover_bib
-      puts '[GTN/scholar] Creating global bib cache'
+      Jekyll.logger.info '[GTN/scholar] Creating global bib cache'
       global_bib = BibTeX::Bibliography.new
       bib_paths = [Find.find('./topics'), Find.find('./faqs'), Find.find('./news')].lazy.flat_map(&:lazy).grep(/bib$/)
       bib_paths.each do |path|
@@ -39,7 +39,7 @@ def self.discover_bib
           global_bib << x
         end
       end
-      puts "[GTN/scholar] Done: #{global_bib.length}"
+      Jekyll.logger.info "[GTN/scholar] Done: #{global_bib.length}"
       style = CSL::Style.load('_layouts/g3.csl')
       cp = CiteProc::Processor.new style: style,
                                    format: 'html', locale: 'en'

_plugins/jekyll-boxify.rb

@@ -12,7 +12,7 @@ def initialize(config) # :nodoc:
     end
 
     def generate(site) # :nodoc:
-      puts '[GTN/Boxify]'
+      Jekyll.logger.info '[GTN/Boxify]'
       site.pages.each { |page| boxify page, site }
       site.posts.docs.each { |post| boxify post, site }
     end

_plugins/jekyll-scholar.rb

@@ -56,7 +56,7 @@ def render(context)
           res = %(<span class="citation"><a href="##{@text}">#{citation_text}</a></span>)
         end
       rescue StandardError => e
-        puts "[GTN/scholar] Could not render #{@text} from #{source_page} (#{e})"
+        Jekyll.logger.warn "[GTN/scholar] Could not render #{@text} from #{source_page} (#{e})"
         res = %(<span>ERROR INVALID CITATION #{@text}</span>)
       end
 
@@ -108,7 +108,7 @@ def render(context)
         end
         res = url
       rescue StandardError => e
-        puts "[GTN/scholar] Could not render #{@text} from #{source_page} (#{e})"
+        Jekyll.logger.warn "[GTN/scholar] Could not render #{@text} from #{source_page} (#{e})"
         res = %(<span>https://example.com/ERROR+INVALID+CITATION+#{@text}</span>)
       end
       res

_plugins/jekyll-topic-filter.rb

@@ -39,14 +39,14 @@ def self.enumerate_topics(site)
   def self.fill_cache(site)
     return if site.data.key?('cache_topic_filter')
 
-    puts '[GTN/TopicFilter] Begin Cache Prefill'
+    Jekyll.logger.debug '[GTN/TopicFilter] Begin Cache Prefill'
     site.data['cache_topic_filter'] = {}
 
     # For each topic
     list_topics(site).each do |topic|
       site.data['cache_topic_filter'][topic] = filter_by_topic(site, topic)
     end
-    puts '[GTN/TopicFilter] End Cache Prefill'
+    Jekyll.logger.debug '[GTN/TopicFilter] End Cache Prefill'
   end
 
   ##
@@ -183,7 +183,8 @@ def self.list_materials_structured(site, topic_name)
   def self.fetch_tutorial_material(site, topic_name, tutorial_name)
     fill_cache(site)
     if site.data['cache_topic_filter'][topic_name].nil?
-      Jekyll.logger.warn "Topic cache not filled, cannot fetch tutorial material for #{topic_name}"
+      Jekyll.logger.warn "Cannot fetch tutorial material for #{topic_name}"
+      nil
     else
       site.data['cache_topic_filter'][topic_name].select { |p| p['tutorial_name'] == tutorial_name }[0]
     end
@@ -582,7 +583,7 @@ def self.process_pages(site, pages)
     return site.data['cache_processed_pages'] if site.data.key?('cache_processed_pages')
 
     materials = collate_materials(site, pages).map { |_k, v| resolve_material(site, v) }
-    puts '[GTN/TopicFilter] Filling Materials Cache'
+    Jekyll.logger.info '[GTN/TopicFilter] Filling Materials Cache'
     site.data['cache_processed_pages'] = materials
 
     # Prepare short URLs
@@ -874,7 +875,6 @@ def recently_published_tutorials(site)
         Gtn::PublicationTimes.obtain_time(y.path) <=> Gtn::PublicationTimes.obtain_time(x.path)
       end
 
-      latest.each { |x| puts [x.path, Gtn::PublicationTimes.obtain_time(x.path)] }
       latest.slice(0, 10)
     end
 

_plugins/jekyll-webfinger.rb

@@ -4,7 +4,7 @@
 
 Jekyll::Hooks.register :site, :post_write do |site|
   # Make the directory
-  Jekyll.logger.info 'Generating webfinger files'
+  Jekyll.logger.info '[GTN/Webfinger] Generating webfinger files'
   FileUtils.mkdir_p "#{site.dest}/api/fedi"
 
   Gtn::Contributors.list(site)