Merge pull request #5513 from galaxyproject/java-mixolydian

misc framework

.github/workflows/monthly-release.yml

@@ -53,7 +53,7 @@ jobs:
             ${{ runner.os }}-gems-
       - name: Install dependencies
         run: |
-          sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config # for node
+          sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config pandoc # for node, release notes
           gem install bundler
           pip install pyyaml
           bundle config path vendor/bundle
@@ -103,4 +103,9 @@ jobs:
           RELEASE_TAG: ${{ env.release_tag }}
           RELEASE_TITLE: ${{ env.release_title }}
         run: |
-          gh release create "$RELEASE_TAG" --title "Release $RELEASE_TITLE" --notes "Monthly release of the GTN materials is now [available on the archive](https://training.galaxyproject.org/archive/$RELEASE_TAG/)." --target main --latest
+          # Compile release notes
+          echo "Monthly release of the GTN materials is now [available on the archive](https://training.galaxyproject.org/archive/$RELEASE_TAG/)." > /tmp/last-month-on.md
+          echo >> /tmp/last-month-on.md
+          bundle exec ruby bin/last-month-on.rb | pandoc --wrap none -t markdown -f html >> /tmp/last-month-on.md
+          # Create the release
+          gh release create "$RELEASE_TAG" --title "Release $RELEASE_TITLE" --notes-file /tmp/last-month-on.md  --target main --latest

_layouts/recordings.html

@@ -17,7 +17,7 @@ <h1 data-toc-skip>Recordings - {{ material.title }} </h1>
 
   <p><b>Want to add your own recording?</b> We would love to have it to our library!</p>
 
-  <a href="{% link faqs/gtn/recordings_add.md %}" class="btn btn-info">Add your recordings!</a>
+  <a class="btn btn-info" href="{% link faqs/gtn/recordings_add.md %}">Add your Recording!</a>
 
   </div>
 

_plugins/feeds.rb

@@ -16,15 +16,27 @@ def to_euro_lunch
 PRIO = [
   'news',
   'events',
+  'learning-pathways',
   'tutorials',
   'slides',
+  'recordings',
   'faqs',
   'workflows',
   'contributors',
   'grants',
   'organisations'
 ].map.with_index { |x, i| [x, i] }.to_h
 
+def track(url)
+  if url =~ /utm_source/
+    url
+  elsif url.include? '#'
+    url.gsub(/#/, TRACKING + '#')
+  else
+    url + TRACKING
+  end
+end
+
 def objectify(attrs, url, path)
   obj = attrs.clone
   obj['__path'] = path
@@ -96,6 +108,8 @@ def markdownify(site, text)
   'news' => '📰',
   'faqs' => '❓',
   'workflows' => '🛠️',
+  'learning-pathways' => '🛤️',
+  'recordings' => '🎥',
 }
 
 def generate_opml(site, groups)
@@ -146,7 +160,7 @@ def generate_topic_feeds(site, topic, bucket)
 
       mats.each do |time, group, page, tags|
         xml.entry do
-          xml.title(ICON_FOR[group] + " " +page.data['title'])
+          xml.title(ICON_FOR[group] + " " + page.data['title'])
           link = "#{site.config['url']}#{site.baseurl}#{page.url}"
           xml.link(href: link)
           # Our links are (mostly) stable
@@ -206,6 +220,7 @@ def all_date_sorted_materials(site)
   materials = TopicFilter.list_all_materials(site).reject { |k, _v| k['draft'] }
   news = site.posts.select { |x| x['layout'] == 'news' }
   faqs = site.pages.select { |x| x['layout'] == 'faq' }
+  pathways = site.pages.select { |x| x['layout'] == 'learning-pathway' }
   workflows = Dir.glob('topics/**/*.ga')
 
   bucket = events.map do |e|
@@ -214,12 +229,35 @@ def all_date_sorted_materials(site)
 
   materials.each do |m|
     tags = [m['topic_name']] + (m['tags'] || [])
-    bucket += m.fetch('ref_tutorials', []).map do |t|
-      [Gtn::PublicationTimes.obtain_time(t.path).to_datetime, 'tutorials', t, tags]
+    m.fetch('ref_tutorials', []).map do |t|
+      bucket << [Gtn::PublicationTimes.obtain_time(t.path).to_datetime, 'tutorials', t, tags]
+
+      (t['recordings'] || []).map do |r|
+        url = '/' + t.path.gsub(/tutorial(_[A_Z_]*)?.(html|md)$/, 'recordings/')
+        url += "#tutorial-recording-#{Date.parse(r['date']).strftime('%-d-%B-%Y').downcase}"
+        attr = {'title' => "Recording of " + t['title'], 
+                'contributors' => r['speakers'] + (r['captions'] || []),
+                'content' => "A #{r['length']} long recording is now available."}
+
+        obj = objectify(attr, url, t.path)
+        bucket << [DateTime.parse(r['date'].to_s), 'recordings', obj, tags]
+      end
     end
 
-    bucket += m.fetch('ref_slides', []).reject { |s| s.url =~ /-plain.html/ }.map do |s|
-      [Gtn::PublicationTimes.obtain_time(s.path).to_datetime, 'slides', s, tags]
+
+
+    m.fetch('ref_slides', []).reject { |s| s.url =~ /-plain.html/ }.map do |s|
+      bucket << [Gtn::PublicationTimes.obtain_time(s.path).to_datetime, 'slides', s, tags]
+
+      (s['recordings'] || []).map do |r|
+        url = '/' + s.path.gsub(/slides(_[A_Z_]*)?.(html|md)$/, 'recordings/')
+        url += "#tutorial-recording-#{Date.parse(r['date']).strftime('%-d-%B-%Y').downcase}"
+        attr = {'title' => "Recording of " + s['title'], 
+                'contributors' => r['speakers'] + (r['captions'] || []),
+                'content' => "A #{r['length']} long recording is now available."}
+        obj = objectify(attr, url, s.path)
+        bucket << [DateTime.parse(r['date'].to_s), 'recordings', obj, tags]
+      end
     end
   end
 
@@ -232,6 +270,11 @@ def all_date_sorted_materials(site)
     [Gtn::PublicationTimes.obtain_time(n.path).to_datetime, 'faqs', n, ['faqs', tag]]
   end
 
+  bucket += pathways.map do |n|
+    tags = ['learning-pathway'] + (n['tags'] || [])
+    [Gtn::PublicationTimes.obtain_time(n.path).to_datetime, 'learning-pathways', n, tags]
+  end
+
   bucket += workflows.map do |n|
     tag = Gtn::PublicationTimes.clean_path(n).split('/')[1]
     wf_data = JSON.parse(File.read(n))
@@ -241,7 +284,6 @@ def all_date_sorted_materials(site)
       'description' => wf_data['annotation'],
       'tags' => wf_data['tags'],
       'contributors' => wf_data.fetch('creator', []).map do |c|
-        p ">> #{c}"
         matched = site.data['contributors'].select{|k, v| 
           v.fetch('orcid', "does-not-exist") == c.fetch('identifier', "").gsub('https://orcid.org/', '')
         }.first
@@ -297,6 +339,7 @@ def all_date_sorted_materials(site)
 
   bucket
     .reject{|x| x[0] > DateTime.now } # Remove future-dated materials
+    .reject{|x| x[2]['draft'] == true } # Remove drafts
     .sort_by {|x| x[0] } # Date-sorted, not strictly necessary since will be grouped.
     .reverse
 end
@@ -407,7 +450,7 @@ def generate_matrix_feed_itemized(site, mats, group_by: 'day', filter_by: nil)
                 href = "#{site.config['url']}#{site.config['baseurl']}#{page.url}"
 
                 xml.id(href)
-                xml.link(href: href + TRACKING)
+                xml.link(href: track(href))
 
                 tags.uniq.each do |tag|
                   xml.category(term: tag)
@@ -423,7 +466,7 @@ def generate_matrix_feed_itemized(site, mats, group_by: 'day', filter_by: nil)
                   xml.summary(text)
                 end
 
-                prefix = type.gsub(/s$/, '').capitalize.gsub(/Faq/, 'FAQ').gsub(/New$/, 'Post')
+                prefix = type.gsub(/s$/, '').gsub(/-/, ' ').capitalize.gsub(/Faq/, 'FAQ').gsub(/New$/, 'Post')
                 title = "#{ICON_FOR[type]} New #{prefix}: #{page.data['title']}"
 
                 xml.title(title)
@@ -527,7 +570,7 @@ def generate_matrix_feed(site, mats, group_by: 'day', filter_by: nil)
       xml.id("#{site.config['url']}#{site.baseurl}/#{path}")
       title_parts = [filter_title, "#{lookup[group_by]} Updates"].compact
       xml.title(title_parts.join(' — '))
-      xml.subtitle('The latest events, tutorials, slides, blog posts, FAQs, workflows, and contributors in the GTN.')
+      xml.subtitle('The latest events, tutorials, slides, blog posts, FAQs, workflows, learning paths, recordings, and contributors in the GTN.')
       xml.logo("#{site.config['url']}#{site.baseurl}/assets/images/GTN-60px.png")
 
       bucket.each do |date, parts|
@@ -554,17 +597,17 @@ def generate_matrix_feed(site, mats, group_by: 'day', filter_by: nil)
               # xml.h4 title
 
               parts.group_by { |x| x[1] }.sort_by { |x| PRIO[x[0]] }.each do |type, items|
-                xml.h4 "#{ICON_FOR[type]} #{type.capitalize}"
+                xml.h4 "#{ICON_FOR[type]} #{type.gsub(/-/, ' ').capitalize}"
                 if items.length.positive?
                   xml.ul do
                     items.each do |date, _type, page, _tags|
                       xml.li do
                         if page.is_a?(String)
-                          href = "#{site.config['url']}#{site.config['baseurl']}/hall-of-fame/#{page}/#{TRACKING}"
+                          href = track("#{site.config['url']}#{site.config['baseurl']}/hall-of-fame/#{page}/")
                           text = "@#{page}"
                         else
                           text = page.data['title']
-                          href = "#{site.config['url']}#{site.config['baseurl']}#{page.url}#{TRACKING}"
+                          href = track("#{site.config['url']}#{site.config['baseurl']}#{page.url}")
                         end
                         if group_by != 'day'
                           text += " (#{date.strftime('%B %d, %Y')})"

_plugins/jekyll-jsonld.rb

@@ -691,11 +691,18 @@ def generate_material_jsonld(material, topic, site)
         # "award":,
         # "author" described below
         # "character":,
-        citation: {
-          '@type': 'CreativeWork',
-          name: 'Community-Driven Data Analysis Training for Biology',
-          url: 'https://doi.org/10.1016/j.cels.2018.05.012'
-        },
+        citation: [
+          {
+            '@type': 'CreativeWork',
+            name: 'Galaxy Training: A Powerful Framework for Teaching!',
+            url: 'https://doi.org/10.1371/journal.pcbi.1010752'
+          },
+          {
+            '@type': 'CreativeWork',
+            name: 'Community-Driven Data Analysis Training for Biology',
+            url: 'https://doi.org/10.1016/j.cels.2018.05.012'
+          }
+        ],
         # "comment":,
         # "commentCount":,
         # "contentLocation":,

_plugins/sitemap.rb

@@ -33,7 +33,12 @@ def _build(site)
                 'http://www.sitemaps.org/schemas/sitemap/0.9/sitemap.xsd" ' \
                 'xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">'
 
-      site.pages.reject { |t| t.path =~ /ipynb$/ || t.path =~ /api\/ga4gh\/trs\/v2/}.each do |t|
+      subset_pages = site.pages
+        .reject { |t| t.path =~ /ipynb$/ || t.path =~ /api\/ga4gh\/trs\/v2/}
+        .reject { |t| t.data.fetch('layout', 'page') =~ /external/}
+        .reject { |t| t.data.fetch('hands_on', '') == 'external'}
+
+      subset_pages.each do |t|
         begin
           d = Gtn::ModificationTimes.obtain_time(t.path)
           d.format = '%FT%T%:z'

_plugins_dev/sitemap-fake.rb

@@ -1,6 +1,6 @@
 module Jekyll
   # Fake sitemap generator.
-  class SitemapGenerator < Generator
+  class SitemapGenerator2 < Generator
     safe true
 
     def generate(site)
@@ -11,7 +11,13 @@ def generate(site)
                 'http://www.sitemaps.org/schemas/sitemap/0.9/sitemap.xsd" ' \
                 'xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">'
 
-      site.pages.each do |t|
+
+      subset_pages = site.pages
+        .reject { |t| t.path =~ /ipynb$/ || t.path =~ /api\/ga4gh\/trs\/v2/}
+        .reject { |t| t.data.fetch('layout', 'page') =~ /external/}
+        .reject { |t| t.data.fetch('hands_on', '') == 'external'}
+
+      subset_pages.each do |t|
         result += "<url><loc>#{site.config['url'] + site.config['baseurl'] + t.url}</loc>" \
                   '<lastmod>2016-06-30T18:00:00-07:00</lastmod></url>'
       end

bin/last-month-on.rb

@@ -0,0 +1,7 @@
+require 'nokogiri'
+
+data = File.read('_site/training-material/feeds/matrix-month.xml')
+doc = Nokogiri::XML(data)
+res = doc.css('entry content')[0].children[1].children.to_s
+res.gsub!(/utm_source=matrix.*utm_campaign=matrix-news/, 'utm_source=github&utm_medium=release&utm_campaign=release-notes')
+puts res

faqs/gtn/recordings_add.md

@@ -8,7 +8,7 @@ contributors: [shiltemann]
 
 **We welcome anybody to submit their recordings!** Your videos can be used in (online) training events, or for self-study by learners on the GTN.
 
-For some tips and tricks about recording the video itself, please see
+For some tips and tricks about recording the video itself, please ensure your recording conforms to our recommendations:
 
 [Recording Tips & Tricks]({% link faqs/gtn/recordings_create.md %}){: .btn.btn-info}
 [Submit a Recording](https://forms.gle/qNG8FkTN1yRZPNZY6){: .btn.btn-info}

learning-pathways/beyond_single_cell.md

@@ -1,6 +1,6 @@
 ---
 layout: learning-pathway
-tags: [intermediate]
+tags: [intermediate, single-cell]
 cover-image: assets/images/wab-annotatedcells-2.png
 cover-image-alt: "Image of cells in different coloured clusters"
 type: use

learning-pathways/intro_single_cell.md

@@ -1,6 +1,6 @@
 ---
 layout: learning-pathway
-tags: [beginner]
+tags: [beginner, single-cell]
 cover-image: assets/images/wab-annotatedcells-2.png
 cover-image-alt: "Image of cells in different coloured clusters"
 type: use