Merge pull request #4379 from galaxyproject/lion-uaru

Topic embeds, topics by tag

.github/labeler.yml

@@ -11,6 +11,8 @@ template-and-tools:
 # topic labels
 admin:
  - topics/admin/**/*
+ai4life:
+ - topics/ai4life/**/*
 assembly:
   - topics/assembly/**/*
 climate:
@@ -29,6 +31,8 @@ epigenetics:
   - topics/epigenetics/**/*
 evolution:
   - topics/evolution/**/*
+fair:
+  - topics/fair/**/*
 galaxy-interface:
   - topics/galaxy-interface/**/*
 genome-annotation:
@@ -61,4 +65,3 @@ variant-analysis:
   - topics/variant-analysis/**/*
 visualisation:
   - topics/visualisation/**/*
-

Makefile

@@ -234,6 +234,7 @@ annotate: ## annotate the tutorials with usable Galaxy instances
 	${ACTIVATE_ENV} && \
 	wget https://github.com/hexylena/toolshed-version-database/raw/main/guid-rev.json -O metadata/toolshed-revisions.json && \
 	python bin/supported-fetch.py
+	bin/workflows-fetch.rb
 .PHONY: annotate
 
 rebuild-search-index: ## Rebuild search index

_layouts/home.html

@@ -4,16 +4,7 @@
 
 {% assign contributors = site.data['contributors'] %}
 
-{% assign sorted_topics = "" | split: "," %}
-{% assign sorted_topics_pre = site.data | sort | order: "title" %}
-
-{% for topic in sorted_topics_pre %}
-    {% if topic[0] == "introduction" %}
-        {% assign sorted_topics = sorted_topics | unshift: topic %}
-    {% else %}
-        {% assign sorted_topics = sorted_topics | push: topic %}
-    {% endif %}
-{% endfor %}
+{% assign sorted_topics = site | list_topics_ids %}
 
 <section>
     <h1>Welcome to {{ site.title }}</h1>
@@ -49,12 +40,13 @@ <h2>Galaxy for Scientists</h2>
                     </tr>
                 </thead>
                 <tbody>
-                {% for topic in sorted_topics %}
-                    {% if topic[1].type == "use" %}
-                    {% if topic[1].draft != true or jekyll.environment != "production" %}
+                {% for topic_name in sorted_topics %}
+                    {% assign topic = site.data[topic_name] %}
+                    {% if topic.type == "use" %}
+                    {% if topic.draft != true or jekyll.environment != "production" %}
                     <tr>
-                        {% assign tutorial_number = site | topic_filter:topic[1].name | topic_count %}
-                        <td><a href="{{ site.baseurl }}/topics/{{ topic[1].name }}/">{{ topic[1].title }}</a>{% if topic[1].draft %} <div class="label label-default tutorial_tag" style="{{ 'work-in-progress' | colour_tag }}">work-in-progress</div>{% endif %}</td>
+                        {% assign tutorial_number = site | topic_filter_tutorial_count:topic.name %}
+                        <td><a href="{{ site.baseurl }}/topics/{{ topic.name }}/">{{ topic.title }}</a>{% if topic.draft %} <div class="label label-default tutorial_tag" style="{{ 'work-in-progress' | colour_tag }}">work-in-progress</div>{% endif %}</td>
                         <td>{{ tutorial_number }}</td>
                     </tr>
                     {% endif %}
@@ -72,12 +64,13 @@ <h2>Galaxy Tips & Tricks</h2>
                     </tr>
                 </thead>
                 <tbody>
-                {% for topic in sorted_topics %}
-                    {% if topic[1].type == "basics" %}
-                    {% if topic[1].draft != true or jekyll.environment != "production" %}
+                {% for topic_name in sorted_topics %}
+                    {% assign topic = site.data[topic_name] %}
+                    {% if topic.type == "basics" %}
+                    {% if topic.draft != true or jekyll.environment != "production" %}
                     <tr>
-                        {% assign tutorial_number = site | topic_filter:topic[1].name | topic_count %}
-                        <td><a href="{{ site.baseurl }}/topics/{{ topic[1].name }}/">{{ topic[1].title }}</a>{% if topic[1].draft %} <div class="label label-default tutorial_tag" style="{{ 'work-in-progress' | colour_tag }}">work-in-progress</div>{% endif %}</td>
+                        {% assign tutorial_number = site | topic_filter:topic.name | topic_count %}
+                        <td><a href="{{ site.baseurl }}/topics/{{ topic.name }}/">{{ topic.title }}</a>{% if topic.draft %} <div class="label label-default tutorial_tag" style="{{ 'work-in-progress' | colour_tag }}">work-in-progress</div>{% endif %}</td>
                         <td>{{ tutorial_number }}</td>
                     </tr>
                     {% endif %}
@@ -95,12 +88,13 @@ <h2>Data Science Survival Kit</h2>
                     </tr>
                 </thead>
                 <tbody>
-                {% for topic in sorted_topics %}
-                    {% if topic[1].type == "data-science" %}
-                    {% if topic[1].draft != true or jekyll.environment != "production" %}
+                {% for topic_name in sorted_topics %}
+                    {% assign topic = site.data[topic_name] %}
+                    {% if topic.type == "data-science" %}
+                    {% if topic.draft != true or jekyll.environment != "production" %}
                     <tr>
-                        {% assign tutorial_number = site | topic_filter:topic[1].name | topic_count %}
-                        <td><a href="{{ site.baseurl }}/topics/{{ topic[1].name }}/">{{ topic[1].title }}</a>{% if topic[1].draft %} <div class="label label-default tutorial_tag" style="{{ 'work-in-progress' | colour_tag }}">work-in-progress</div>{% endif %}</td>
+                        {% assign tutorial_number = site | topic_filter:topic.name | topic_count %}
+                        <td><a href="{{ site.baseurl }}/topics/{{ topic.name }}/">{{ topic.title }}</a>{% if topic.draft %} <div class="label label-default tutorial_tag" style="{{ 'work-in-progress' | colour_tag }}">work-in-progress</div>{% endif %}</td>
                         <td>{{ tutorial_number }}</td>
                     </tr>
                     {% endif %}
@@ -118,12 +112,13 @@ <h2>Galaxy for Developers and Admins</h2>
                     </tr>
                 </thead>
                 <tbody>
-                {% for topic in sorted_topics %}
-                    {% if topic[1].type == "admin-dev" %}
-                    {% if topic[1].draft != true or jekyll.environment != "production" %}
+                {% for topic_name in sorted_topics %}
+                    {% assign topic = site.data[topic_name] %}
+                    {% if topic.type == "admin-dev" %}
+                    {% if topic.draft != true or jekyll.environment != "production" %}
                     <tr>
-                        {% assign tutorial_number = site | topic_filter:topic[1].name | topic_count %}
-                        <td><a href="{{ site.baseurl }}/topics/{{ topic[1].name }}/">{{ topic[1].title }}</a>{% if topic[1].draft %} <div class="label label-default tutorial_tag" style="{{ 'work-in-progress' | colour_tag }}">work-in-progress</div>{% endif %}</td>
+                        {% assign tutorial_number = site | topic_filter:topic.name | topic_count %}
+                        <td><a href="{{ site.baseurl }}/topics/{{ topic.name }}/">{{ topic.title }}</a>{% if topic.draft %} <div class="label label-default tutorial_tag" style="{{ 'work-in-progress' | colour_tag }}">work-in-progress</div>{% endif %}</td>
                         <td>{{ tutorial_number }}</td>
                     </tr>
                     {% endif %}
@@ -149,12 +144,13 @@ <h2>Galaxy for Contributors and Instructors</h2>
                     </tr>
                 </thead>
                 <tbody>
-                {% for topic in sorted_topics %}
-                    {% if topic[1].type == "instructors" %}
-                    {% if topic[1].draft != true or jekyll.environment != "production" %}
+                {% for topic_name in sorted_topics %}
+                    {% assign topic = site.data[topic_name] %}
+                    {% if topic.type == "instructors" %}
+                    {% if topic.draft != true or jekyll.environment != "production" %}
                     <tr>
-                        {% assign tutorial_number = site | topic_filter:topic[1].name | topic_count %}
-                        <td><a href="{{ site.baseurl }}/topics/{{ topic[1].name }}/">{{ topic[1].title }}</a>{% if topic[1].draft %} <div class="label label-default tutorial_tag" style="{{ 'work-in-progress' | colour_tag }}">work-in-progress</div>{% endif %}</td>
+                        {% assign tutorial_number = site | topic_filter:topic.name | topic_count %}
+                        <td><a href="{{ site.baseurl }}/topics/{{ topic.name }}/">{{ topic.title }}</a>{% if topic.draft %} <div class="label label-default tutorial_tag" style="{{ 'work-in-progress' | colour_tag }}">work-in-progress</div>{% endif %}</td>
                         <td>{{ tutorial_number }}</td>
                     </tr>
                     {% endif %}

_layouts/topic-embed.html

@@ -0,0 +1,20 @@
+---
+layout: embed
+---
+
+<section class="tutorials-list {{ page.topic_name }} topic-type-{{ topic.type }}">
+
+{% assign topic = site.data[page.topic_name] | default: page.topic %}
+{% assign topic_material = site | list_materials_structured:page.topic_name %}
+
+{% for subtopic in topic_material %}
+{% if subtopic[0] != "__FLAT__" %}
+<h3 id="st-{{ subtopic[0] | slugify }}">{{ subtopic[1].subtopic.title }}</h3>
+<p>{{ subtopic[1].subtopic.description }}</p>
+{% endif %}
+
+{% include _includes/tutorial_list.html sub=subtopic %}
+{% endfor %}
+
+{{ content }}
+</section>

_layouts/topic.html

@@ -2,11 +2,8 @@
 layout: base
 ---
 
-{% assign topic = site.data[page.topic_name] %}
-{% assign contributors = site.data['contributors'] %}
-{% assign instances = site.data['instances'] %}
-{% assign language = site.other_languages %}
-{% assign topic_material = site | list_materials_structured:page.topic_name %}
+{% assign topic = site.data[page.topic_name] | default: page.topic %}
+{% assign topic_material = site | list_materials_structured:topic.name %}
 
 <!-- Gitter -->
 {% if topic.gitter %}
@@ -15,7 +12,7 @@
   {% assign gitter = site.gitter_url %}
 {% endif %}
 
-<section class="tutorials-list {{ page.topic_name }} topic-type-{{ topic.type }}">
+<section class="tutorials-list {{ topic.name }} topic-type-{{ topic.type }}">
     <h1>{{ topic.title }}</h1>
     <p>{{ topic.summary | markdownify }}</p>
     <i>You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides ({% icon slides %}) and tutorial ({% icon tutorial %}) buttons below. </i>
@@ -61,10 +58,12 @@ <h2 id="topic-faq">Frequently Asked Questions</h2>
     Common questions regarding this topic have been collected on a <a href="faqs/">dedicated FAQ page </a>. Common questions related to specific tutorials can be accessed from the tutorials themselves.
     {% endunless %}
 
+    {% if topic.editorial_board %}
     <h2 id="editorial-board">Editorial Board</h2>
     <p>This material is reviewed by our Editorial Board:</p>
     {% assign editorial_board = topic.editorial_board | sorted %}
     {% include _includes/contributor-list.html contributors=editorial_board badge=true %}
+    {% endif %}
 
     <p>
         <em>For any question related to this topic and the content, you can contact them or visit our <a href="https://gitter.im/Galaxy-Training-Network/Lobby">Gitter channel</a>.</em>

_plugins/api.rb

@@ -199,7 +199,9 @@ def generate(site)
         out = site.data[topic].dup
         out['materials'] = TopicFilter.topic_filter(site, topic).map do |x|
           q = x.dup
-          q['contributors'] = get_contributors(q).dup.map { |c| mapContributor(site, c) }
+          q['contributors'] = get_contributors(q).dup.map do |c|
+            mapContributor(site, c)
+          end
 
           q['urls'] = {}
 
@@ -221,9 +223,12 @@ def generate(site)
 
           q
         end
-        out['editorial_board'] = out['editorial_board'].map { |c| mapContributor(site, c) }
+        out['editorial_board'] = out['editorial_board'].map do |c|
+          mapContributor(site, c)
+        end
 
-        page2 = PageWithoutAFile.new(site, '', 'api/topics/', "#{topic}.json")
+        page2 = PageWithoutAFile.new(site, '', 'api/topics/',
+                                     "#{topic}.json")
         page2.content = JSON.pretty_generate(out)
         page2.data['layout'] = nil
         site.pages << page2

_plugins/by-tag-pages.rb

@@ -0,0 +1,46 @@
+require './_plugins/jekyll-topic-filter'
+
+module Jekyll
+  ##
+  # This class generates the GTN's author pags
+  class TagPageGenerator < Generator
+    safe true
+
+    ##
+    # This generates the author pages
+    # Params
+    # +site+:: The site object
+    def generate(site)
+      Jekyll.logger.info '[GTN/SyntheticTopics] Generating By-Tag Indexes'
+      TopicFilter.list_all_tags(site).map do |tag|
+        site.data["by_tag_#{tag}"] = {
+          'name' => "by_tag_#{tag}",
+          'type' => 'use',
+          'title' => tag,
+          'summary' => "Tutorials covering #{tag}",
+          'tag_based' => true,
+          'hidden' => true,
+        }
+
+        topic_index = PageWithoutAFile.new(site, '', "tags/#{tag}", 'index.md')
+        topic_index.content = ''
+        topic_index.data['layout'] = 'topic'
+        topic_index.data['topic_name'] = "by_tag_#{tag}"
+        topic_index.data['topic'] = site.data["by_tag_#{tag}"]
+
+        site.pages << topic_index
+      end
+
+      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.content = ''
+        topic_index.data['layout'] = 'topic-embed'
+        topic_index.data['topic_name'] = "by_tag_#{tag}"
+        topic_index.data['topic'] = site.data["by_tag_#{tag}"]
+
+        site.pages << topic_index
+      end
+    end
+  end
+end

_plugins/gtn.rb

@@ -274,9 +274,7 @@ def regex_replace_once(str, regex_search, value_replace)
 
     def convert_to_material_list(site, materials)
       # [{"name"=>"introduction", "topic"=>"admin"}]
-      if materials.nil?
-        return []
-      end
+      return [] if materials.nil?
 
       materials.map do |m|
         if m.key?('name') && m.key?('topic')

_plugins/gtn/synthetic.rb

@@ -7,10 +7,10 @@ module Jekyll
   class SyntheticTopicGenerator < Generator
     def generate(site)
       # Full Bibliography
-      puts '[GTN/SyntheticTopics] Generating Indexes'
+      Jekyll.logger.info '[GTN/SyntheticTopics] Generating Indexes'
 
       TopicFilter.list_topics(site).select { |t| site.data[t]['tag_based'] }.each do |topic|
-        puts "[GTN/SyntheticTopics] Creating #{topic} topic"
+        Jekyll.logger.debug "[GTN/SyntheticTopics] Creating #{topic} topic"
 
         topic_index = PageWithoutAFile.new(site, '', "topics/#{topic}", 'index.md')
         topic_index.content = ''