Merge branch 'galaxyproject:main' into DASH-1211

galaxyproject · Oct 23, 2023 · a3fa713 · a3fa713
2 parents f58fb4e + 0d38876
commit a3fa713
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diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml
@@ -882,6 +882,7 @@ khanteymoori:
 Khaled196:
     name: Khaled Jum'ah
     email: [email protected]
+    orcid: 0000-0001-5481-8893
     joined: 2022-09
 
 kinow:
@@ -1753,18 +1754,20 @@ carpentries:
     name: The Carpentries
     joined: 2021-09
 
-erasmusplus:
-    name: Erasmus+ Programme
+gallantries:
+    name: Gallantries Project
     joined: 2020-09
-    avatar: "https://www.erasmusplus.nl/assets/images/logo.png"
+    avatar: "https://gallantries.github.io/assets/images/gallantries-logo.png"
     github: false
     funder: true
     url: "https://www.erasmusplus.nl"
+    funder_name: Erasmus+ Programme
     funding_id: 2020-1-NL01-KA203-064717
     funding_system: erasmusplus
     funding_statement: |
         This project ([`2020-1-NL01-KA203-064717`](https://ec.europa.eu/programmes/erasmus-plus/projects/eplus-project-details/#project/2020-1-NL01-KA203-064717)) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
         ![eu flag with the text: with the support of the erasmus programme of the european union](https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg)
+        ![erasmus plus logo](https://www.erasmusplus.nl/assets/images/logo.png)
 
 avans-atgm:
     name: Avans Hogeschool

diff --git a/_layouts/contributor_index.html b/_layouts/contributor_index.html
@@ -137,9 +137,14 @@ <h4>Favourite Formats</h4>
 			</div>
 
 			<div class="col-md-9">
-				<h1>
-					{{ contributors[page.contributor].name | default: page.contributor }}
-				</h1>
+				<hgroup>
+					<h1>
+						{{ contributors[page.contributor].name | default: page.contributor }}
+					</h1>
+				{% if contributors[page.contributor].funder_name %}
+					<p>Funded by {{ contributors[page.contributor].funder_name }}</p>
+				{% endif %}
+				</hgroup>
 				{% if contributors[page.contributor].funder %}
 				<div class="label label-default label-large" style="{{ 'GTN Funder' | colour_tag }}">GTN Funder</div>
 				{% endif %}

diff --git a/_layouts/learning-pathway.html b/_layouts/learning-pathway.html
@@ -12,21 +12,14 @@
 {% endif %}
 
 
-<section>
-<h3> GTN Learning Pathway </h3>
-<div>
-  <div style="display:inline-block;vertical-align:top;width:10%">
-   <img src="{{site.baseurl}}/assets/images/learning-pathway.png" alt="A graphic depicting a winding path from a start symbol to a trophy, with tutorials along the way" />
-   </div>
-   <div  style="display:inline-block; margin-left: 2em; width:70%">
-      We recommend you follow the tutorials in the order presented on this page. They have been selected to fit together and build up your knowledge step by step. If a lesson has both slides and a tutorial, we recommend you start with the slides, then proceed with the tutorial.
-   </div>
-</div>
-</section>
+<section class="tutorials-list {{ page.topic_name }} topic-type-{{ topic.type }}">
+    <hgroup>
+      <h1>{{ pathway.title }}</h1>
+      {% icon purl %}<abbr title="Persistent URL">PURL</abbr>:</strong> <a href="https://gxy.io/GTN:{{ page.short_id }}">https://gxy.io/GTN:{{ page.short_id }}</a>
+    </hgroup>
 
+    {% snippet faqs/gtn/what-is-a-learning-pathway.md %}
 
-<section class="tutorials-list {{ page.topic_name }} topic-type-{{ topic.type }}">
-    <h1>{{ pathway.title }}</h1>
     <p>{{ pathway.description | markdownify }}</p>
     <p>{{ content | markdownify }}</p>
 

diff --git a/_plugins/gtn/shortlinks.rb b/_plugins/gtn/shortlinks.rb
@@ -3,6 +3,12 @@
 module Gtn
   # This module is responsible for generating shortlinks for tutorials and FAQs
   module Shortlinks
+    CATEGORY_TUTORIAL = 'T'
+    CATEGORY_SLIDES = 'S'
+    CATEGORY_FAQ = 'F'
+    CATEGORY_NEWS = 'N'
+    CATEGORY_PATHWAYS = 'P'
+
     def self.mapped?(tutorial, current_mapping)
       current_mapping['id'].values.include? tutorial
     end
@@ -18,8 +24,8 @@ def self.update(current_mapping)
         # If it's not already mapped by a key, add it.
         if !mapped?(html_path, current_mapping)
           # Generate a short code
-          short_code_number = current_mapping['id'].select { |x| x[0] == 'T' }.length.to_s.rjust(5, '0')
-          short_code = "T#{short_code_number}"
+          short_code_number = current_mapping['id'].select { |x| x[0] == CATEGORY_TUTORIAL }.length.to_s.rjust(5, '0')
+          short_code = CATEGORY_TUTORIAL + short_code_number
           puts "Discovered tutorial #{short_code}"
           # If the target of this flavour of short code isn't already in here, then add it
           current_mapping['id'][short_code] = html_path
@@ -37,8 +43,8 @@ def self.update(current_mapping)
         # If it's not already mapped by a key, add it.
         if !mapped?(html_path, current_mapping)
           # Generate a short code
-          short_code_number = current_mapping['id'].select { |x| x[0] == 'S' }.length.to_s.rjust(5, '0')
-          short_code = "S#{short_code_number}"
+          short_code_number = current_mapping['id'].select { |x| x[0] == CATEGORY_SLIDES }.length.to_s.rjust(5, '0')
+          short_code = CATEGORY_SLIDES + short_code_number
           puts "Discovered slides #{short_code}"
           # If the target of this flavour of short code isn't already in here, then add it
           current_mapping['id'][short_code] = html_path
@@ -64,8 +70,8 @@ def self.update(current_mapping)
         # If it's not already mapped by a key, add it.
         if !mapped?(html_path, current_mapping)
           # Generate a short code
-          short_code_number = current_mapping['id'].select { |x| x[0] == 'F' }.length.to_s.rjust(5, '0')
-          short_code = "F#{short_code_number}"
+          short_code_number = current_mapping['id'].select { |x| x[0] == CATEGORY_FAQ }.length.to_s.rjust(5, '0')
+          short_code = CATEGORY_FAQ + short_code_number
           puts "Discovered FAQ #{short_code}"
           # If the target of this flavour of short code isn't already in here, then add it
           current_mapping['id'][short_code] = html_path
@@ -79,14 +85,32 @@ def self.update(current_mapping)
         # If it's not already mapped by a key, add it.
         if !mapped?(html_path, current_mapping)
           # Generate a short code
-          short_code_number = current_mapping['id'].select { |x| x[0] == 'N' }.length.to_s.rjust(5, '0')
-          short_code = "N#{short_code_number}"
+          short_code_number = current_mapping['id'].select { |x| x[0] == CATEGORY_NEWS }.length.to_s.rjust(5, '0')
+          short_code = CATEGORY_NEWS + short_code_number
           puts "Discovered news #{short_code}"
           # If the target of this flavour of short code isn't already in here, then add it
           current_mapping['id'][short_code] = html_path
         end
       end
 
+      # Discover learning pathways
+      lps = Dir.glob('learning-pathways/*.md')
+      lps.reject! { |t| t =~ /index.md/ }
+      lps.reject! { |t| t =~ /pathway-example.md/ }
+
+      lps.each do |tutorial|
+        html_path = "/#{tutorial.gsub(/md$/, 'html')}"
+        # If it's not already mapped by a key, add it.
+        if !mapped?(html_path, current_mapping)
+          # Generate a short code
+          short_code_number = current_mapping['id'].select { |x| x[0] == CATEGORY_PATHWAYS }.length.to_s.rjust(5, '0')
+          short_code = CATEGORY_PATHWAYS + short_code_number
+          puts "Discovered slides #{short_code}"
+          # If the target of this flavour of short code isn't already in here, then add it
+          current_mapping['id'][short_code] = html_path
+        end
+      end
+
       current_mapping
     end
   end

diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb
@@ -610,7 +610,7 @@ def self.list_videos(site)
   #
   def self.list_all_tags(site)
     materials = process_pages(site, site.pages)
-    (materials.map { |x| x['tags'] || [] }.flatten + self.list_topics(site)).sort.uniq
+    (materials.map { |x| x['tags'] || [] }.flatten + list_topics(site)).sort.uniq
   end
 
   def self.filter_by_topic(site, topic_name)

diff --git a/assets/css/main.scss b/assets/css/main.scss
@@ -275,7 +275,7 @@ body {
 // boxes visible, no matter what their collapse state.
 @media screen {
 	.box-collapsed {
-		display: none;
+		display: none !important; // important Overrides specifically one case of a learning pathway FAQ where we use some custom display already to get objects floating correctly in the snippet.
 	}
 }
 

diff --git a/bin/news.rb b/bin/news.rb
@@ -74,8 +74,8 @@ def linkify(text, path)
 
 def printableMaterial(path)
   d = YAML.load_file(path)
-  {md: linkify(d['title'], path.gsub(/.md/, '.html')),
-  path: path}
+  { md: linkify(d['title'], path.gsub(/.md/, '.html')),
+    path: path }
 end
 
 def fixNews(n)
@@ -110,34 +110,30 @@ def fixNews(n)
 }
 
 def titleize(t)
-  t.gsub(/-/, ' ').gsub(/\w+/) do |word|
-    word.capitalize
-  end
+  t.gsub('-', ' ').gsub(/\w+/, &:capitalize)
 end
 
 def format_news(news)
-  output = ""
+  output = ''
   if news.length.positive?
     output += "\n\n## Big News!\n\n"
     output += news.join("\n").gsub(/^/, '- ')
   end
   output
 end
 
-def format_tutorials(added, modified, kind: "tutorials")
-  output =""
-  if added.length.positive? or modified.length.positive?
-    output += "\n\n## #{added.length + modified.length} #{kind}!"
-  end
+def format_tutorials(added, modified, kind: 'tutorials')
+  output = ''
+  output += "\n\n## #{added.length + modified.length} #{kind}!" if added.length.positive? || modified.length.positive?
 
   if added.length.positive?
     output += "\n\nNew #{kind}:\n\n"
-    output += added.map{|n| n[:md]}.join("\n").gsub(/^/, '- ')
+    output += added.map { |n| n[:md] }.join("\n").gsub(/^/, '- ')
   end
 
   if modified.length.positive?
     output += "\n\nUpdated #{kind}:\n\n"
-    output += modified.map{|n| n[:md]}.join("\n").gsub(/^/, '- ')
+    output += modified.map { |n| n[:md] }.join("\n").gsub(/^/, '- ')
   end
   output
 end
@@ -148,33 +144,33 @@ def build_news(data, filter: nil)
   newsworthy = false
 
   if filter.nil?
-  output += format_news(data[:added][:news])
-  newsworthy = newsworthy | format_news(data[:added][:news]).length.positive?
+    output += format_news(data[:added][:news])
+    newsworthy |= format_news(data[:added][:news]).length.positive?
   end
 
   o = format_tutorials(
-    data[:added][:tutorials].select{|n| filter.nil? || n[:path] =~ /topics\/#{filter}/ },
-    data[:modified][:tutorials].select{|n| filter.nil? || n[:path] =~ /topics\/#{filter}/ }
+    data[:added][:tutorials].select { |n| filter.nil? || n[:path] =~ %r{topics/#{filter}} },
+    data[:modified][:tutorials].select { |n| filter.nil? || n[:path] =~ %r{topics/#{filter}} }
   )
 
   output += o
-  newsworthy = newsworthy | o.length.positive?
+  newsworthy |= o.length.positive?
 
   o = format_tutorials(
-    data[:added][:slides].select{|n| filter.nil? || n[:path] =~ /topics\/#{filter}/ },
-    data[:modified][:slides].select{|n| filter.nil? || n[:path] =~ /topics\/#{filter}/ },
-    kind: "slides"
+    data[:added][:slides].select { |n| filter.nil? || n[:path] =~ %r{topics/#{filter}} },
+    data[:modified][:slides].select { |n| filter.nil? || n[:path] =~ %r{topics/#{filter}} },
+    kind: 'slides'
   )
   output += o
-  newsworthy = newsworthy | o.length.positive?
+  newsworthy |= o.length.positive?
 
   if filter.nil? && data[:contributors].length.positive?
     newsworthy = true
     output += "\n\n## #{data[:contributors].length} new contributors!\n\n"
     output += data[:contributors].map { |c| linkify("@#{c}", "hall-of-fame/#{c}") }.join("\n").gsub(/^/, '- ')
   end
 
-  return output, newsworthy
+  [output, newsworthy]
 end
 
 def send_news(output, options, channel: 'default')
@@ -200,23 +196,21 @@ def send_news(output, options, channel: 'default')
     resp = JSON.parse(req.body)
     puts resp
 
-    if resp['errcode'] == 'M_FORBIDDEN'
-      if resp['error'] =~ /not in room/
-        puts "Not in room, attempting to join"
-        # Join room
-        #  POST /_matrix/client/v3/join/{roomIdOrAlias}
-        uri_join = URI("#{homeserver[:server]}/_matrix/client/v3/join/#{homeserver[:room]}")
-        req = Net::HTTP.post(uri_join, JSON.generate({}), headers)
+    if resp['errcode'] == 'M_FORBIDDEN' && (resp['error'] =~ /not in room/)
+      puts 'Not in room, attempting to join'
+      # Join room
+      #  POST /_matrix/client/v3/join/{roomIdOrAlias}
+      uri_join = URI("#{homeserver[:server]}/_matrix/client/v3/join/#{homeserver[:room]}")
+      req = Net::HTTP.post(uri_join, JSON.generate({}), headers)
+      # Parse response
+      resp = JSON.parse(req.body)
+
+      # Now we're safe to re-try
+      if resp.key?('room_id')
+        req = Net::HTTP.post(uri_send_message, JSON.generate(data), headers)
         # Parse response
         resp = JSON.parse(req.body)
-
-        # Now we're safe to re-try
-        if resp.key?('room_id')
-          req = Net::HTTP.post(uri_send_message, JSON.generate(data), headers)
-          # Parse response
-          resp = JSON.parse(req.body)
-          puts resp
-        end
+        puts resp
       end
     end
   else
@@ -231,6 +225,4 @@ def send_news(output, options, channel: 'default')
 end
 
 output, newsworthy = build_news(data, filter: 'single-cell')
-if newsworthy
-  send_news(output, options, channel: 'single-cell')
-end
+send_news(output, options, channel: 'single-cell') if newsworthy
diff --git a/bin/schema-contributors.yaml b/bin/schema-contributors.yaml
@@ -118,6 +118,9 @@ mapping:
             funder:
                 type: bool
                 description: Set this to true if this entity is a funding agency.
+            funder_name:
+                type: str
+                description: A human-readable name which will be the biggest name on their contributor page.
             funding_id:
                 type: str
                 description: The short identifier for your grant.

diff --git a/bin/schema-news.yaml b/bin/schema-news.yaml
@@ -59,7 +59,7 @@ mapping:
                 translation:
                     - shiltemann
                 funding:
-                    - erasmusplus
+                    - gallantries
         type: map
         mapping:
             authorship:

diff --git a/bin/schema-slides.yaml b/bin/schema-slides.yaml
@@ -108,7 +108,7 @@ mapping:
                 translation:
                     - shiltemann
                 funding:
-                    - erasmusplus
+                    - gallantries
         type: map
         mapping:
             authorship:

diff --git a/bin/schema-tutorial.yaml b/bin/schema-tutorial.yaml
@@ -108,7 +108,7 @@ mapping:
                 translation:
                     - shiltemann
                 funding:
-                    - erasmusplus
+                    - gallantries
         type: map
         mapping:
             authorship:

diff --git a/faqs/gtn/what-is-a-learning-pathway.md b/faqs/gtn/what-is-a-learning-pathway.md
@@ -0,0 +1,14 @@
+---
+title: What is a Learning Pathway?
+area: introduction
+layout: faq
+box_type: comment
+contributors: [shiltemann]
+---
+
+<div style="display:inline-block;vertical-align:top;width:10%">
+<img src="{{site.baseurl}}/assets/images/learning-pathway.png" alt="A graphic depicting a winding path from a start symbol to a trophy, with tutorials along the way" />
+</div>
+<div  style="display:inline-block; margin-left: 2em; width:70%">
+We recommend you follow the tutorials in the order presented on this page. They have been selected to fit together and build up your knowledge step by step. If a lesson has both slides and a tutorial, we recommend you start with the slides, then proceed with the tutorial.
+</div>
diff --git a/learning-pathways/genome-annotation-eukaryote.md b/learning-pathways/genome-annotation-eukaryote.md
@@ -11,7 +11,7 @@ cover-image-alt: "Galaxy Genome Annotation logo"
 editorial_board:
 - abretaud
 funding:
-- erasmusplus
+- gallantries
 
 
 

diff --git a/learning-pathways/genome-annotation-prokaryote.md b/learning-pathways/genome-annotation-prokaryote.md
@@ -11,7 +11,7 @@ cover-image-alt: "Galaxy Genome Annotation logo"
 editorial_board:
 - abretaud
 funding:
-- erasmusplus
+- gallantries
 
 pathway:
   - section: "Module 1: Introduction"

diff --git a/learning-pathways/intro-to-galaxy-and-ecology.md b/learning-pathways/intro-to-galaxy-and-ecology.md
@@ -16,7 +16,7 @@ cover-image-alt: "Drawing of an Ecological System"
 editorial_board:
 - yvanlebras
 funding:
-- erasmusplus
+- gallantries
 
 
 pathway: