Merge pull request #4273 from galaxyproject/editorial-board

Rename maintainers as editorial board
galaxyproject · Jul 19, 2023 · 6c8602b · 6c8602b
2 parents 83794dd + 8ca81ec
commit 6c8602b
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diff --git a/_layouts/contributor_index.html b/_layouts/contributor_index.html
@@ -175,6 +175,21 @@ <h3> GitHub Activity</h4>
                 {% endunless %}
 		{% endunless %}
                 </p>
+				{% if page.editor_count > 0 %}
+				<h3>Editorial Roles</h3>
+				<p>This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.</p>
+				<ul>
+				{% for res in page.editors %}
+					<li>
+						{% if res.layout == 'learning-pathway' %}
+						<a href="{{ site.baseurl }}{{ res.url }}">{{ res.title }}</a>
+						{% else %}
+						<a href="{{ site.baseurl }}/topics/{{ res.name }}">{{ res.title }}</a>
+						{% endif %}
+					</li>
+				{% endfor %}
+				</ul>
+				{% endif %}
 
 				{% if page.tutorials_count > 0 %}
 				<h3>Tutorials</h3>

diff --git a/_layouts/learning-pathway.html b/_layouts/learning-pathway.html
@@ -54,10 +54,10 @@ <h3 id="st-{{ section.section | slugify }}">{{ section.section }}</h3>
 <hr style="margin-top: 6em"/>
 <section>
 	<!-- Maintained by -->
-	<h2 id="maintainers">Maintained by</h2>
-	<p>This material is maintained by:</p>
-	{% assign maintainers = pathway.maintainers | sorted %}
-	{% include _includes/contributor-list.html contributors=maintainers badge=true %}
+	<h2 id="editorial-board">Editorial Board</h2>
+	<p>This material is reviewed by our Editorial Board:</p>
+	{% assign editorial_board = pathway.maintainers %}
+	{% include _includes/contributor-list.html contributors=editorial_board badge=true %}
 
 	<h2 id="funders">Funders</h2>
 	<p>This material was funded by:</p>

diff --git a/_layouts/topic.html b/_layouts/topic.html
@@ -61,10 +61,10 @@ <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 %}
 
-    <h2 id="maintainers">Maintainers</h2>
-    <p>This material is maintained by:</p>
-    {% assign maintainers = topic.maintainers | sorted %}
-    {% include _includes/contributor-list.html contributors=maintainers badge=true %}
+    <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 %}
 
     <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>

diff --git a/_plugins/api.rb b/_plugins/api.rb
@@ -221,7 +221,7 @@ def generate(site)
 
           q
         end
-        out['maintainers'] = out['maintainers'].map { |c| mapContributor(site, c) }
+        out['editorial_board'] = out['editorial_board'].map { |c| mapContributor(site, c) }
 
         page2 = PageWithoutAFile.new(site, '', 'api/topics/', "#{topic}.json")
         page2.content = JSON.pretty_generate(out)
@@ -233,14 +233,14 @@ def generate(site)
       puts '[GTN/API] Topics'
       # Individual Topic Indexes
       site.data.each_pair do |k, v|
-        if v.is_a?(Hash) && v.key?('type') && v.key?('maintainers')
+        if v.is_a?(Hash) && v.key?('type') && v.key?('editorial_board')
 
           topics[k] = {
             'name' => v['name'],
             'title' => v['title'],
             'summary' => v['summary'],
             'url' => site.config['url'] + site.config['baseurl'] + "/api/topics/#{k}.json",
-            'maintainers' => v['maintainers'].map { |c| mapContributor(site, c) }
+            'editorial_board' => v['editorial_board'].map { |c| mapContributor(site, c) }
           }
         end
       end

diff --git a/_plugins/author-page.rb b/_plugins/author-page.rb
@@ -103,6 +103,15 @@ def generate(site)
         page2.data['news_count'] = news_by_author[contributor].length
         page2.data['learning_pathways_count'] = learning_pathways_by_author[contributor].length
 
+        page2.data['editors'] = TopicFilter.enumerate_topics(site).select do |t|
+          t.fetch('editorial_board', []).include?(contributor)
+        end
+        # Also their learning pathways
+        page2.data['editors'] += site.pages.select do |t|
+          t['layout'] == 'learning-pathway' && t.data.fetch('editorial_board', []).include?(contributor)
+        end
+        page2.data['editor_count'] = page2.data['editors'].length
+
         page2.data['has_philosophy'] = has_philosophy[contributor]
 
         site.pages << page2

diff --git a/_plugins/jekyll-duration.rb b/_plugins/jekyll-duration.rb
@@ -29,7 +29,7 @@ def duration_to_human(duration)
       hour = 'hour'
       hours = 'hours'
       minutes = 'minutes'
-      if @context.registers[:page]&.key?('lang') and @context.registers[:page]['lang'] != 'en'
+      if @context.registers[:page]&.key?('lang') && (@context.registers[:page]['lang'] != 'en')
         lang = @context.registers[:page]['lang']
         hour = @context.registers[:site].data['lang'][lang]['hour']
         hours = @context.registers[:site].data['lang'][lang]['hours']

diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb
@@ -13,7 +13,17 @@ module TopicFilter
   # Returns:
   # +Array+:: The list of topics
   def self.list_topics(site)
-    site.data.select { |_k, v| v.is_a?(Hash) && v.key?('maintainers') }.map { |k, _v| k }
+    site.data.select { |_k, v| v.is_a?(Hash) && v.key?('editorial_board') }.map { |k, _v| k }
+  end
+
+  ##
+  # This function returns a list of all the topics that are available.
+  # Params:
+  # +site+:: The +Jekyll::Site+ object
+  # Returns:
+  # +Array+:: The topic objects themselves
+  def self.enumerate_topics(site)
+    site.data.select { |_k, v| v.is_a?(Hash) && v.key?('editorial_board') }.map { |_k, v| v }
   end
 
   ##

diff --git a/bin/lint.rb b/bin/lint.rb
@@ -108,7 +108,7 @@ def self.message(path: '', idx: 0, match_start: 0, match_end: 1, replacement: ni
 # Linting functions for the GTN
 module GtnLinter
   @BAD_TOOL_LINK = /{% tool (\[[^\]]*\])\(https?.*tool_id=([^)]*)\)\s*%}/i
-  @BAD_TOOL_LINK2 = /{% tool (\[[^\]]*\])\(https:\/\/toolshed.g2([^)]*)\)\s*%}/i
+  @BAD_TOOL_LINK2 = %r{{% tool (\[[^\]]*\])\(https://toolshed.g2([^)]*)\)\s*%}}i
 
   def self.find_matching_texts(contents, query)
     contents.map.with_index do |text, idx|
@@ -350,18 +350,19 @@ def self.non_existent_snippet(contents)
   end
 
   def self.bad_tool_links(contents)
-    find_matching_texts(contents, @BAD_TOOL_LINK) + find_matching_texts(contents, @BAD_TOOL_LINK2)
+    find_matching_texts(contents, @BAD_TOOL_LINK) + \
+      find_matching_texts(contents, @BAD_TOOL_LINK2)
       .map do |idx, _text, selected|
-      ReviewDogEmitter.error(
-        path: @path,
-        idx: idx,
-        match_start: selected.begin(0),
-        match_end: selected.end(0) + 1,
-        replacement: "{% tool #{selected[1]}(#{selected[2]}) %}",
-        message: 'You have used the full tool URL to a specific server, here we only need the tool ID portion.',
-        code: 'GTN:009'
-      )
-    end
+        ReviewDogEmitter.error(
+          path: @path,
+          idx: idx,
+          match_start: selected.begin(0),
+          match_end: selected.end(0) + 1,
+          replacement: "{% tool #{selected[1]}(#{selected[2]}) %}",
+          message: 'You have used the full tool URL to a specific server, here we only need the tool ID portion.',
+          code: 'GTN:009'
+        )
+      end
   end
 
   def self.snippets_too_close_together(contents)

diff --git a/bin/schema-learning-pathway.yaml b/bin/schema-learning-pathway.yaml
@@ -32,6 +32,23 @@ mapping:
         type: int
         description: priority within learning path list
 
+    editorial_board:
+        type: seq
+        required: true
+        sequence:
+            - type: str
+              required: true
+              description: A contributor's ID in the CONTRIBUTORS.yaml file.
+                #enum:
+                #- CONTRIBUTORS
+
+    funding:
+        type: seq
+        description: These entities provided funding support for the development of this resource
+        sequence:
+        - type: str
+          #enum:
+          #- CONTRIBUTORS
     tags:
         type: seq
         sequence:

diff --git a/bin/schema-topic.yaml b/bin/schema-topic.yaml
@@ -97,7 +97,7 @@ mapping:
                       description: |
                         `false` to hide your topic from the production GTN. This is useful if you need a topic for a workshop, but have not finished making it up to GTN standards.
 
-    maintainers:
+    editorial_board:
         type: seq
         required: true
         sequence:

diff --git a/bin/validate-frontmatter.rb b/bin/validate-frontmatter.rb
@@ -227,7 +227,7 @@ def self.run
                 .grep_v(/schema-*/)
                 .select do |x|
       d = YAML.load_file(x)
-      d.key? 'maintainers' or d.key? 'summary' or d.key? 'type'
+      d.key? 'editorial_board' or d.key? 'summary' or d.key? 'type'
     end
 
     errors += materials.map { |x| [x, lint_topic(x)] }

diff --git a/learning-pathways/admin-training.md b/learning-pathways/admin-training.md
@@ -9,6 +9,10 @@ description: |
 
 cover-image: assets/images/gat.png
 cover-image-alt: GTN Logo on a spiral galaxy background with text galaxy admin training
+editorial_board:
+- hexylena
+- natefoo
+- slugger70
 
 tags: [Galaxy administrators, 5-day course]
 

diff --git a/learning-pathways/genome-annotation-eukaryote.md b/learning-pathways/genome-annotation-eukaryote.md
@@ -8,7 +8,7 @@ tags: [genome annotation, eukaryote]
 
 cover-image: assets/images/gga.png
 cover-image-alt: "Galaxy Genome Annotation logo"
-maintainers:
+editorial_board:
 - abretaud
 funding:
 - erasmusplus

diff --git a/learning-pathways/genome-annotation-prokaryote.md b/learning-pathways/genome-annotation-prokaryote.md
@@ -8,7 +8,7 @@ tags: [genome annotation, prokaryote]
 
 cover-image: assets/images/gga.png
 cover-image-alt: "Galaxy Genome Annotation logo"
-maintainers:
+editorial_board:
 - abretaud
 funding:
 - erasmusplus

diff --git a/learning-pathways/intro-to-galaxy-and-ecology.md b/learning-pathways/intro-to-galaxy-and-ecology.md
@@ -13,7 +13,7 @@ tags: [beginner]
 cover-image: assets/images/galaxy-e-logo.png
 cover-image-alt: "Drawing of an Ecological System"
 
-maintainers:
+editorial_board:
 - yvanlebras
 funding:
 - erasmusplus

diff --git a/learning-pathways/intro-to-galaxy-and-genomics.md b/learning-pathways/intro-to-galaxy-and-genomics.md
@@ -3,7 +3,7 @@ layout: learning-pathway
 tags: [beginner]
 type: use
 
-maintainers:
+editorial_board:
 - shiltemann
 funding:
 - erasmusplus

diff --git a/learning-pathways/intro-to-r-and-ml.md b/learning-pathways/intro-to-r-and-ml.md
@@ -3,7 +3,7 @@ layout: learning-pathway
 tags: [beginner]
 type: use
 
-maintainers:
+editorial_board:
 - fpsom
 funding:
 - erasmusplus

diff --git a/learning-pathways/metagenomics.md b/learning-pathways/metagenomics.md
@@ -4,7 +4,7 @@ type: use
 cover-image: assets/images/microgalaxy-logo.png
 cover-image-alt: "microgalaxy logo"
 
-maintainers:
+editorial_board:
 - bebatut
 funding:
 - erasmusplus

diff --git a/learning-pathways/pathway-example.md b/learning-pathways/pathway-example.md
@@ -9,6 +9,8 @@ description: |
 
 type: use  # 'use' for science topics, or admin-dev or instructors
 tags: [some, keywords, here ]
+editorial_board:
+- shiltemann
 
 cover-image: assets/images/gat.png # optional, define your own cover image for the pathway index page, default is the GTN logo
 cover-image-alt: alt text for this image

diff --git a/learning-pathways/train-the-trainers.md b/learning-pathways/train-the-trainers.md
@@ -7,7 +7,7 @@ description: |
   This pathway introduces trainers to learning principles, training techniques, lesson, session, course, and material design as well as assessment and feedback. This is has been developed for by trainers in the bioinformatics but is suitable for all trainers and educators in higher education.
 tags: [training, trainers]
 
-maintainers:
+editorial_board:
 - bebatut
 - fpsom
 funding:

diff --git a/metadata/covid19.yaml b/metadata/covid19.yaml
@@ -5,7 +5,7 @@ title: "SARS-CoV-2"
 summary: "Tutorials covering analysis of SARS-CoV-2 (COVID 19)"
 tag_based: true
 
-maintainers:
+editorial_board:
   - wm75
 
 gitter: galaxyproject/sars-cov-2
diff --git a/metadata/one-health.yaml b/metadata/one-health.yaml
@@ -7,7 +7,7 @@ summary: |
 
 tag_based: true
 
-maintainers:
+editorial_board:
   - wm75
   - pvanheus
   - TKlingstrom

diff --git a/metadata/swagger.yaml b/metadata/swagger.yaml
@@ -344,7 +344,7 @@ components:
         summary:
           type: string
           description: A human readable description of the topic's contents.
-        maintainers:
+        editorial_board:
           $ref: '#/components/schemas/ArrayOfUsers'
     TopicDetail:
       type: object
@@ -383,7 +383,7 @@ components:
               description:
                 type: string
                 description: A helpful subtopic description.
-        maintainers:
+        editorial_board:
           $ref: '#/components/schemas/ArrayOfUsers'
         materials:
           type: array

diff --git a/topics/admin/metadata.yaml b/topics/admin/metadata.yaml
@@ -32,7 +32,7 @@ subtopics:
     title: "Deprecated Tutorials"
     description: "Please do not run these. They are outdated and for historical, archival purposes only."
 
-maintainers:
+editorial_board:
   - hexylena
   - natefoo
   - slugger70

diff --git a/topics/ai4life/metadata.yaml b/topics/ai4life/metadata.yaml
@@ -12,7 +12,7 @@ summary: |
 logo: /training-material/topics/ai4life/images/AI4Life-logo_neg_giraffe-solid.png
 logo_alt: "Giraffe icon. AI 4 life"
 
-maintainers:
+editorial_board:
 - beatrizserrano
 edam_ontology: ["topic_3382"]
 

diff --git a/topics/assembly/metadata.yaml b/topics/assembly/metadata.yaml
@@ -16,7 +16,7 @@ requirements:
     tutorials:
       - quality-control
 
-maintainers:
+editorial_board:
   - slugger70
   - nekrut
   - delphine-l

diff --git a/topics/climate/metadata.yaml b/topics/climate/metadata.yaml
@@ -7,5 +7,5 @@ requirements:
 - type: internal
   topic_name: introduction
 docker_image: ''
-maintainers:
+editorial_board:
 - annefou
diff --git a/topics/computational-chemistry/metadata.yaml b/topics/computational-chemistry/metadata.yaml
@@ -11,7 +11,7 @@ requirements:
     type: "internal"
     topic_name: introduction
 
-maintainers:
+editorial_board:
   - chrisbarnettster
   - tsenapathi
   - simonbray

diff --git a/topics/contributing/metadata.yaml b/topics/contributing/metadata.yaml
@@ -24,6 +24,6 @@ subtopics:
     title: "Contributing through GitHub"
     description: "How to collaborate with the GTN"
 
-maintainers:
+editorial_board:
   - bebatut
   - bgruening
diff --git a/topics/contributing/tutorials/create-new-topic/tutorial.md b/topics/contributing/tutorials/create-new-topic/tutorial.md
@@ -206,7 +206,7 @@ For tag based topics, first ensure that all of the relevant tutorials share a si
 
 ## Defining the topic
 
-Compare with other topic level metadata files in the `metadata/` directory of the training material. Then create a file of your own naming the topic and providing maintainers and so on. We will use the Covid-19 synthetic topic as an example:
+Compare with other topic level metadata files in the `metadata/` directory of the training material. Then create a file of your own naming the topic and providing editorial board members and so on. We will use the Covid-19 synthetic topic as an example:
 
 ```
 ---
@@ -216,7 +216,7 @@ title: "SARS-CoV-2"
 summary: "Tutorials covering analysis of SARS-CoV-2 (COVID 19)"
 tag_based: true
 
-maintainers:
+editorial_board:
   - wm75
 
 gitter: galaxyproject/sars-cov-2