code documentation

.github/workflows/ci.yml

@@ -48,8 +48,8 @@ jobs:
       - name: Validate all links, enforce alt text
         run: |
           bundle exec htmlproofer \
-            --ignore-urls "/.*localhost.*/","/.*vimeo\.com.*/","/.*gitter\.im.*/","/.*drmaa\.org.*/","/.*slides.html#.*/,/#embedded_jbrowse/","/.*videos.*.mp4.png/","/krona_(all|multisample).html/","/workflows\/trs_import/" \
-            --ignore-files "/.*krona.*\.html/","/.*\/files\/.*/","/.*\/node_modules\/.*/","/\/tutorials\/.*\/docker\//","/.*content.html/","/.*recentrifuge.*\.html/" \
+            --ignore-urls "/.*localhost.*/","/.*vimeo\.com.*/","/.*gitter\.im.*/","/.*drmaa\.org.*/","/.*slides.html#.*/,/#embedded_jbrowse/","/.*videos.*.mp4.png/","/krona_(all|multisample).html/","/workflows\/trs_import/","/api/","/by-tool/" \
+            --ignore-files "/.*krona.*\.html/","/.*\/files\/.*/","/.*\/node_modules\/.*/","/\/tutorials\/.*\/docker\//","/.*content.html/","/.*recentrifuge.*\.html/","/short/" \
             --swap-urls "github.com/galaxyproject/training-material/tree/main:github.com/${GITHUB_REPOSITORY}/tree/${GITHUB_HEAD_REF}" \
             --disable-external=true \
             --enforce-https=false \

.github/workflows/deploy.yml

@@ -73,7 +73,7 @@ jobs:
           curl -L https://edamontology.org/EDAM.csv > metadata/EDAM.csv
           make rebuild-search-index ACTIVATE_ENV=pwd
           cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json
-          rdoc bin _plugins/ --output gtn_rdoc
+          rdoc bin _plugins/ --output gtn_rdoc --template rorvswild
 
       - name: Build Site
         run: |

Gemfile

@@ -27,3 +27,5 @@ gem 'commander'
 
 # RO-Crates
 gem 'rubyzip', '~> 2.3.0'
+
+gem 'rorvswild_theme_rdoc'

Gemfile.lock

@@ -96,6 +96,7 @@ GEM
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rexml (3.3.9)
+    rorvswild_theme_rdoc (0.2)
     rouge (4.1.3)
     rubyzip (2.3.2)
     safe_yaml (1.0.5)
@@ -131,6 +132,7 @@ DEPENDENCIES
   kwalify
   nokogiri (>= 1.10.4)
   pkg-config
+  rorvswild_theme_rdoc
   rubyzip (~> 2.3.0)
   webrick
 

_includes/quiz.html

@@ -5,11 +5,94 @@
 {% endif %}
 {% endfor %}
 
-<div markdown="1">
-> <div class="box-title" aria-label="quiz box: {{ quiz.title | replace: '"', '&quot;' }}"><i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden"></span> Quiz: {{ quiz.title }}</div>
-> Check your knowledge with a quiz!
->
->  - [Self Study Mode]({% link quiz/quiz.html %}?mode=self&quiz={{ site.baseurl }}/{{ quiz.path }}) - do the quiz at your own pace, to check your understanding.
->  - [Classroom Mode]({% link quiz/quiz.html %}?mode=teacher&quiz={{ site.baseurl }}/{{ quiz.path }}) - do the quiz synchronously with a classroom of students.
-{: .question}
+<blockquote class="comment" id="{{ quiz.id | slugify }}">
+	<div class="box-title comment-title">
+		<i class="far fa-comment-dots" aria-hidden="true"></i>
+		Quiz: {{ quiz.title }}
+	</div>
+
+
+{% for question in quiz.questions %}
+	{% assign qnum = forloop.index %}
+	<form class="quiz-{{ quiz.id | slugify }} question-{{ qnum }}">
+	<b class="question-title"><span class="result"></span> Question {{ qnum }}: {{ question.title }}</b>
+
+	{% if question.image %}
+		<img src="{{ question.image }}" alt="Image for question {{ forloop.index }}" />
+	{% endif %}
+
+		{% unless question.type == "poll" %}
+		<ul>
+		{% for answer in question.answers %}
+
+		{%- capture is_correct -%}
+			{%- if question.type == "choose-1" -%}
+				 {%- if answer == question.correct -%}correct{%- endif -%}
+			{%- elsif question.type == "choose-many" -%}
+				{%- for a in question.correct -%}{%- if answer == a -%}correct{%- endif -%}{%- endfor -%}
+			{%- endif -%}
+		{%- endcapture -%}
+
+		<li class="answer {{is_correct}}">
+			<span class="result"></span>
+			{% if question.type == "choose-1" %}
+			<input type="radio" id="a-{{ qnum }}-{{ forloop.index }}" name="answer" value="{{ answer }}" class="answer-input {{is_correct}}"/>
+			{% elsif question.type == "choose-many" %}
+			<input type="checkbox" id="a-{{ qnum }}-{{ forloop.index }}" name="answer" value="{{ answer }}" class="answer-input  {{is_correct}}" />
+			{% elsif question.type == "free-text" %}
+			<input type="text" id="a-{{ qnum }}-{{ forloop.index }}" name="answer" value="{{ answer }}" class="answer-input {{is_correct}}"/>
+			{% endif %}
+
+			<label for="a-{{ qnum }}-{{ forloop.index }}">{{ answer }}</label>
+		</li>
+		{% endfor %}
+		</ul>
+		{% endunless %}
+	</form>
+{% endfor %}
+
+<div class="quiz-results" aria-live="polite" role="status">
 </div>
+
+<button type="submit" class="btn btn-primary" id="check-answers"  onclick="checkQuiz('{{ quiz.id | slugify}}')">Check Answers</button>
+</blockquote>
+
+<script>
+function checkQuiz(id){
+	var quiz = document.getElementById(id);
+	var correct = 0;
+	var total = document.querySelectorAll(`#${id} form`).length;
+	var questions = document.querySelectorAll(`#${id} form`);
+	for (var i = 0; i < questions.length; i++) {
+		var question = questions[i];
+		var answer = question.querySelectorAll("li.answer");
+		// Only grade completed questions.
+
+		var any_wrong = false;
+		var any_selected = [...answer].map(e => e.querySelector("input").checked).includes(true);
+		// Loop over the inputs for this question
+		if (any_selected) {
+			question.querySelectorAll("input").forEach((input) => {
+				if (input.checked != input.classList.contains('correct')) {
+					any_wrong = true;
+				}
+			});
+
+			answer.forEach((li) => {
+				li.querySelector('.result').innerHTML = li.classList.contains('correct') ? "✅" : "❌";
+			});
+
+			if (any_wrong) {
+				question.querySelector(".result").innerHTML = "❌";
+			} else {
+				question.querySelector(".result").innerHTML = "✅";
+				correct++;
+			}
+		} else {
+			question.querySelector(".result").innerHTML = "❓";
+		}
+	}
+	var result = correct / total * 100;
+	quiz.querySelector('.quiz-results').innerHTML = `<p>You got ${correct} out of ${total} correct (${parseInt(result)}%)</p>`;
+}
+</script>

_layouts/tutorial_hands_on.html

@@ -322,6 +322,7 @@ <h1>{{ locale['faqs'] | default: "Frequently Asked Questions" }}</h1>
                 If not, please ask your question on the <a href="{{site.gitter_url}}">GTN Gitter Channel</a> or the
                 <a href="https://help.galaxyproject.org">Galaxy Help Forum</a>
 
+		<!--
                 {% if own_material.quiz %}
                 <h1 data-toc-skip>Quizzes</h1>
                 <p>Check your understanding with these quizzes</p>
@@ -338,6 +339,7 @@ <h2>{{ q.title }}</h2>
                     </ul>
                     {% endfor %}
                 {% endif %}
+		-->
 
                 {% if topic.references %}
                 <h1 data-toc-skip>Useful literature</h1>

_plugins/abbr.rb

@@ -3,61 +3,63 @@
 require 'jekyll'
 
 module Jekyll
-  ##
-  # This class modifies the page contents to replace {abbr} with the associated
-  # abbreviation in a proper <abbr> tag. It's done as a generator because it's
-  # easier to operate once per page and be able to easily see if we've generated
-  # the abbreviation before.
-  #
-  # This could in theory operate as a simple tag, but I'm not sure how to keep
-  # track of "# of times seen per page" there.
-  class Abbreviate < Jekyll::Generator
-    safe true
-
-    def initialize(config) # :nodoc:
-      super
-      @config = config['abbreviate'] ||= {}
-    end
+  module Generators
+    ##
+    # This class modifies the page contents to replace {abbr} with the associated
+    # abbreviation in a proper <abbr> tag. It's done as a generator because it's
+    # easier to operate once per page and be able to easily see if we've generated
+    # the abbreviation before.
+    #
+    # This could in theory operate as a simple tag, but I'm not sure how to keep
+    # track of "# of times seen per page" there.
+    class Abbreviate < Jekyll::Generator
+      safe true
 
-    def generate(site) # :nodoc:
-      site.pages
-          .reject { |page| skip_layout?(page.data['layout']) }
-          .each { |page| abbreviate page }
-      site.posts.docs
-          .reject { |post| skip_layout?(post.data['layout']) }
-          .each { |post| abbreviate post }
-    end
+      def initialize(config) # :nodoc:
+        super
+        @config = config['abbreviate'] ||= {}
+      end
+
+      def generate(site) # :nodoc:
+        site.pages
+            .reject { |page| skip_layout?(page.data['layout']) }
+            .each { |page| abbreviate page }
+        site.posts.docs
+            .reject { |post| skip_layout?(post.data['layout']) }
+            .each { |post| abbreviate post }
+      end
 
-    private
+      private
 
-    def abbreviate(page) # :nodoc:
-      return unless page.data.key?('abbreviations')
+      def abbreviate(page) # :nodoc:
+        return unless page.data.key?('abbreviations')
 
-      seen = {}
-      page.data['abbreviations'].each do |abbr, definition|
-        page.content = page.content.gsub(/\{(#{abbr})\}/) do
-          if seen.key?(abbr)
-            firstdef = false
-          else
-            firstdef = true
-            seen[abbr] = true
-          end
+        seen = {}
+        page.data['abbreviations'].each do |abbr, definition|
+          page.content = page.content.gsub(/\{(#{abbr})\}/) do
+            if seen.key?(abbr)
+              firstdef = false
+            else
+              firstdef = true
+              seen[abbr] = true
+            end
 
-          if firstdef
-            "#{definition} (#{abbr})"
-          else
-            "<abbr title=\"#{definition}\">#{abbr}</abbr>"
+            if firstdef
+              "#{definition} (#{abbr})"
+            else
+              "<abbr title=\"#{definition}\">#{abbr}</abbr>"
+            end
           end
         end
       end
-    end
 
-    def skip_layout?(layout)
-      to_skip = @config['skip_layouts'] || []
+      def skip_layout?(layout)
+        to_skip = @config['skip_layouts'] || []
 
-      true if to_skip.empty?
+        true if to_skip.empty?
 
-      to_skip.include?(layout)
+        to_skip.include?(layout)
+      end
     end
   end
 end