Merge branch 'galaxyproject:main' into main

galaxyproject · Sep 27, 2024 · 180f483 · 180f483
2 parents d033608 + d14fd5e
commit 180f483
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diff --git a/.github/workflows/ci-main.yml b/.github/workflows/ci-main.yml
@@ -66,8 +66,8 @@ jobs:
 
       - name: Check Tutorial Formatting
         run: |
-          find topics/ -name tutorial.md | xargs -n 1 python bin/check-broken-boxes.py | reviewdog -efm="%f:%l: %m" -filter-mode=file -reporter=github-pr-review
-          bundle exec ruby bin/lint.rb --format rdjson | reviewdog -filter-mode=file -reporter=github-pr-review -f=rdjsonl -fail-on-error
+          find topics/ -name tutorial.md | xargs -n 1 python bin/check-broken-boxes.py | reviewdog -efm="%f:%l: %m" -filter-mode=file -reporter=github-pr-review -fail-level=any
+          bundle exec ruby bin/lint.rb --format rdjson | reviewdog -filter-mode=file -reporter=github-pr-review -f=rdjsonl -fail-level=any
         env:
             REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -110,7 +110,7 @@ GEM
     typhoeus (1.4.0)
       ethon (>= 0.9.0)
     unicode-display_width (2.5.0)
-    webrick (1.8.1)
+    webrick (1.8.2)
     yell (2.2.2)
     zeitwerk (2.6.12)
 

diff --git a/_config.yml b/_config.yml
@@ -166,6 +166,7 @@ icon-tag:
   galaxy-toggle: fas fa-toggle-on
   galaxy-upload: fas fa-upload
   galaxy-download: fas fa-download
+  galaxy-wf-best-practices: fas fa-wand-magic-sparkles
   galaxy-wf-connection: fas fa-arrows-alt-h
   galaxy-wf-edit: fa fa-edit
   galaxy-wf-new: fas fa-plus

diff --git a/_layouts/event-track.html b/_layouts/event-track.html
@@ -6,11 +6,18 @@
 
 <section class="event-track">
   <h1>{{track.title}}</h1>
-  <p>{{track.description}}</p>
+  <p>{{track.description | markdownify }}</p>
   {% if page.contributions %}
     {% include _includes/contributor-list2.html contributors=page.contributions badge=true %}
   {% endif %}
 
+  {% if track.slack_channel %}
+  <div>
+    <h4> Need help with these tutorials?</h4>
+    Open Slack support channel for this track: <a href="https://gtnsmrgsbord.slack.com/channels/{{track.slack_channel}}" class="btn btn-success"> {% icon comment %} &nbsp; #{{track.slack_channel}}</a>
+  </div>
+  {% endif %}
+
   <div>
   {% for section in track.program %}
     {% if section.subsection %}

diff --git a/_layouts/event.html b/_layouts/event.html
@@ -502,14 +502,15 @@ <h3>Promote the Event</h3>
 
         // on load of the page: switch to the currently selected tab
         var hash = window.location.hash;
-
-        var potential_tab = $('#myTab button[data-target="' + hash + '"]')
-        if (potential_tab.length != 0) {
-            potential_tab.tab('show');
-        } else {
-            var target_tab = '#' + $(`${hash}`).closest(".tab-pane").attr("id")
-            $('#myTab button[data-target="' + target_tab + '"]').tab('show');
-            $(hash).get(0).scrollIntoView();
+        if (hash){
+        	var potential_tab = $('#myTab button[data-target="' + hash + '"]')
+        	if (potential_tab.length != 0) {
+            	potential_tab.tab('show');
+        	} else {
+            	var target_tab = '#' + $(`${hash}`).closest(".tab-pane").attr("id")
+            	$('#myTab button[data-target="' + target_tab + '"]').tab('show');
+            	$(hash).get(0).scrollIntoView();
+        	}
         }
     });
 })(window, document);

diff --git a/_plugins/jekyll-jsonld.rb b/_plugins/jekyll-jsonld.rb
@@ -3,6 +3,7 @@
 require 'json'
 require './_plugins/gtn'
 require './_plugins/gtn/git'
+require './_plugins/util'
 
 module Jekyll
   # Generate JSON-LD metadata for the GTN.
@@ -794,12 +795,35 @@ def generate_material_jsonld(material, topic, site)
 
       data['isPartOf'] = topic_desc
 
+      data['abstract'] = material
+        .fetch('content', '')
+        .strip
+        .split("\n")
+        .first
+
+      if ! data['abstract'].nil?
+        data['abstract'] = data['abstract']
+          .gsub(/\{\{\s*site.baseurl\s*\}\}/, url_prefix(site))
+          .gsub(/\[{{\s*site.url\s*}}/, '[' + url_prefix(site))
+          .gsub(/{% link (topics[^%]*).md %}/, url_prefix(site) + '\1.html')
+          .gsub(/{% link (topics[^%]*).html %}/, url_prefix(site) + '\1.html')
+          .gsub(/\s*\(?{%\s*cite [^}]+\s*%}\)?/, '')
+          .gsub('{{ site.github_repository }}', safe_site_config(site, 'github_repository', 'https://example.com'))
+          .gsub(/{% snippet ([^%]*) %}/, '')
+          .gsub(/{% include ([^%]*) %}/, '')
+      end
+
+      description.push("## Abstract\n\n#{data['abstract']}\n\n")
+
       if (material['name'] == 'tutorial.md') || (material['name'] == 'slides.html')
-        data['learningResourceType'] = if material['name'] == 'tutorial.md'
-                                         'hands-on tutorial'
-                                       else
-                                         'slides'
-                                       end
+
+        if material['name'] == 'tutorial.md'
+          data['learningResourceType'] = 'e-learning'
+          description.push("## About This Material\n\nThis is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.\n\n")
+        else
+          data['learningResourceType'] = 'slides'
+        end
+
         data['name'] = material['title']
         data['url'] = "#{site['url']}#{site['baseurl']}#{material['url']}"
 
@@ -817,8 +841,8 @@ def generate_material_jsonld(material, topic, site)
           description.push("## Questions this #{material['type']} will address\n\n - #{questions}\n\n")
         end
         if material.key?('objectives') && !material['objectives'].nil? && material['objectives'].length.positive?
-          objectives = material['objectives'].join("\n - ")
-          description.push("## Learning Objectives\n\n - #{objectives}\n\n")
+          objectives = material['objectives'].map{|x| "- #{x}"}.join("\n")
+          description.push("## Learning Objectives\n\n#{objectives}\n\n")
           data['teaches'] = objectives
         end
         if material.key?('keypoints') && !material['keypoints'].nil? && material['keypoints'].length.positive?
@@ -844,12 +868,41 @@ def generate_material_jsonld(material, topic, site)
                         name: "Associated Workflows"
                       })
       end
-      if actual_material.key?('zenodo_link')
-        mentions.push({
-                        '@type': 'Thing',
-                        url: (actual_material['zenodo_link']).to_s,
-                        name: "Associated Training Datasets"
-                      })
+
+      # Notebooks
+      if actual_material.key?('notebook')
+        if actual_material['notebook']['language'] != 'r'
+          # Python, Bash, SQL (all via jupyter)
+          url = "#{site['url']}#{site['baseurl']}#{material['dir']}#{material['topic_name']}-#{material['tutorial_name']}.ipynb"
+          mentions.push({
+                          '@type': 'Thing',
+                          url: url,
+                          name: "Jupyter Notebook (with Solutions)"
+                        })
+          mentions.push({
+                          '@type': 'Thing',
+                          url: url.gsub(/\.ipynb$/, '-course.ipynb'),
+                          name: "Jupyter Notebook (without Solutions)"
+                        })
+        elsif actual_material['notebook']['language'] == 'r' # Actual R
+          url = "#{site['url']}#{site['baseurl']}#{material['dir']}#{material['topic_name']}-#{material['tutorial_name']}.Rmd"
+          mentions.push({
+                          '@type': 'Thing',
+                          url: url,
+                          name: "Quarto/RMarkdown Notebook"
+                        })
+        end
+      end
+
+      # Zenodo link out
+      if actual_material.key?('zenodo_link') && ! actual_material['zenodo_link'].nil?
+        if actual_material['zenodo_link'].length.positive?
+          mentions.push({
+                          '@type': 'Thing',
+                          url: (actual_material['zenodo_link']).to_s,
+                          name: "Associated Training Datasets"
+                        })
+        end
       end
 
       if description.empty?
@@ -905,7 +958,7 @@ def generate_material_jsonld(material, topic, site)
                             '@context': 'http://schema.org',
                             '@type': 'LearningResource',
                             url: (page['hands_on_url']).to_s,
-                            learningResourceType: 'hands-on tutorial',
+                            learningResourceType: 'e-learning',
                             interactivityType: 'expositive',
                           }
                         )
@@ -921,7 +974,7 @@ def generate_material_jsonld(material, topic, site)
                                "/#{tuto}/tutorial.html",
                           name: (page['title']).to_s,
                           description: "Hands-on for '#{page['title']}' tutorial",
-                          learningResourceType: 'hands-on tutorial',
+                          learningResourceType: 'e-learning',
                           interactivityType: 'expositive',
                           provider: GTN
                         }
@@ -991,7 +1044,6 @@ def generate_material_jsonld(material, topic, site)
 
       data['educationalLevel'] = material.key?('level') ? eduLevel[material['level']] : 'Beginner'
       data['mentions'] = mentions
-      data['abstract'] = material.fetch('content', '').strip.split("\n").first
 
       data
     end

diff --git a/_plugins/util.rb b/_plugins/util.rb
@@ -27,3 +27,26 @@ def collapse_event_date_pretty(event)
     "#{s.strftime('%B')} #{s.day}, #{s.year}#{dash}#{e.strftime('%B')} #{e.day}, #{e.year}"
   end
 end
+
+def safe_site_config(site, key, default)
+  if !site.config.nil? && site.config.key?(key)
+    site.config[key]
+  else
+    default
+  end
+end
+
+
+def url_prefix(site)
+  if !site.config.nil? && site.config.key?('url')
+    "#{site.config['url']}#{site.config['baseurl']}"
+  else
+    'http://localhost:4000/training-material/'
+  end
+end
+
+def markdownify(site, text)
+  site.find_converter_instance(
+    Jekyll::Converters::Markdown
+  ).convert(text.to_s)
+end
diff --git a/bin/lint.rb b/bin/lint.rb
@@ -875,10 +875,12 @@ def self.bib_missing_mandatory_fields(bib)
 
   def self.fix_ga_wf(contents)
     results = []
-    if !contents.key?('tags')
-      topic = @path.split('/')[1]
+    if !contents.key?('tags') or contents['tags'].empty?
+      path_parts = @path.split('/')
+      topic = path_parts[path_parts.index('topics') + 1]
+
       results.push(ReviewDogEmitter.file_error(
-                     path: @path, message: "This workflow is missing tags. Please add `\"tags\": [\"#{topic}\"]`",
+                     path: @path, message: "This workflow is missing required tags. Please add `\"tags\": [\"#{topic}\"]`",
                      code: 'GTN:015'
                    ))
     end
@@ -988,7 +990,7 @@ def self.enable_auto_fix
   def self.format_reviewdog_output(message)
     return if !@LIMIT_EMITTED_CODES.nil? && !@LIMIT_EMITTED_CODES.include?(message['code']['value'])
 
-    if !message.nil? && (message != [])
+    if !message.nil? && (message != []) && message.is_a?(Hash)
       if @PLAIN_OUTPUT # $stdout.tty? or
         parts = [
           message['location']['path'],
@@ -1051,7 +1053,7 @@ def self.filter_results(results, ignores)
       # Remove any empty lists
       results = results.select { |x| !x.nil? && x.length.positive? }.flatten
       # Before ignoring anything matching GTN:IGNORE:###
-      return results if ignores.nil?
+      return results if ignores.nil? or ignores.empty?
 
       results = results.select { |x| ignores.index(x['code']['value']).nil? } if results.length.positive?
       return results

diff --git a/bin/news.rb b/bin/news.rb
@@ -292,11 +292,11 @@ def send_news(output, options, channel: 'default')
   end
 end
 
-output, newsworthy = build_news(data)
-if newsworthy
-  channel = options[:useTestRoom] ? 'test' : 'default'
-  send_news(output, options, channel: channel)
-end
+#output, newsworthy = build_news(data)
+#if newsworthy
+#  channel = options[:useTestRoom] ? 'test' : 'default'
+#  send_news(output, options, channel: channel)
+#end
 
 # Single Cell
 output, newsworthy = build_news(data, filter: 'single-cell', updates: false)

diff --git a/events/galaxy-academy-2024.md b/events/galaxy-academy-2024.md
@@ -1,7 +1,7 @@
 ---
 layout: event
 
-title: Galaxy Academy 2024
+title: Galaxy Training Academy 2024
 description: |
   The Galaxy Academy is a online training event for Beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we will have a different topic and focus every day.
 
@@ -107,7 +107,8 @@ infrastructure:
 program:
   - section: "Monday: Galaxy introduction"
     description: |
-      Kick off the week with a hands-on introduction to Galaxy, covering everything from basic navigation and data manipulation to reproducing published analyses, quality control, and mapping sequences to a reference genome. Whether you're new to Galaxy or looking to strengthen your skills, today's sessions will equip you with the foundational knowledge needed for more advanced topics.
+      Kick off the week with a hands-on introduction to Galaxy, covering everything from basic navigation and data manipulation to reproducing published analyses, quality control, and mapping sequences to a reference genome. Whether you're new to Galaxy or looking to strengthen your skills, today's sessions will equip you with the foundational knowledge needed for more advanced topics. 
+      In the morning you can take part in the Icebreaker by joining us in the [Slack introduction channel](https://gtnsmrgsbord.slack.com/archives/C07NKAJ8THA). Or you can directly start with the tutorials. If you need support contact us via the [Slack introduction channel](https://gtnsmrgsbord.slack.com/archives/C07NKAJ8THA).
   - section: Start to get to know Galaxy
     subsection: true
     tutorials:
@@ -160,6 +161,7 @@ program:
   - section: "Friday: Grab bag"
     description: |
       Can't get enough? Then please pick one of our FAIR tutorials or any of the tutorials of the GTN. Please be aware that only trainings that are part of the introduction day or a learning track have been tested on all instances for the event. The trainers present on Slack will do their best to help you if you have a problem and answer questions, but they may not be expert in the topic you selected.
+      You can directly start with you prefered tutorial. If you need support contact us via the Slack Channel [#gta_friday-grab-bag](https://gtnsmrgsbord.slack.com/archives/C07N2A4HQ15).
   - section: Fair training
     subsection: true
     tutorials:

diff --git a/events/tracks/gta2024-assembly.md b/events/tracks/gta2024-assembly.md
@@ -2,21 +2,23 @@
 layout: event-track
 
 title: Assembly
-description: Learn all about Genome assembly. 
+description: Learn all about Genome assembly. Start with the tutorial at your own pace. If you need support contact us via the Slack Channel [gta_assembly](https://gtnsmrgsbord.slack.com/archives/C07NGNT0DB5).
+
+slack_channel: gta_assembly
 
 contributions:
     organisers:
         - delphine-l
     instructors:
-        - delphine-l
-        - SaimMomin12
+        - annasyme
         - bgruening
         - clsiguret
-        - mschatz
+        - delphine-l
         - GarethPrice-Aus
-        - annasyme
-        - trungN
         - igormakunin
+        - mschatz
+        - SaimMomin12
+        - trungN
 
 
 program:

diff --git a/events/tracks/gta2024-bacterial-genomics.md b/events/tracks/gta2024-bacterial-genomics.md
@@ -4,19 +4,25 @@ redirect_from:
 - /events/tracks/gta2024-bacterial-genomeics
 
 title: Bacterial genomics and AMR detection
-description: This track explains the basic steps to (1) process, assemble, annotate a bacterial genome and (2) detect Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy.
+description: This track explains the basic steps to (1) process, assemble, annotate a bacterial genome and (2) detect Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy. Start with the tutorial at your own pace. If you need support contact us via the Slack Channel [#gta_bacterial_genomics](https://gtnsmrgsbord.slack.com/archives/C07NE0FHM6H).
+
+slack_channel: gta_bacterial_genomics
 
 contributions:
     organisers:
         - bebatut
         - clsiguret
     instructors:
+        - annasyme
         - bebatut
         - clsiguret
-        - SaimMomin12
         - EngyNasr
+        - GarethPrice-Aus
+        - igormakunin
         - meltemktn
         - paulzierep
+        - SaimMomin12
+
 
 
 program: