Merge branch 'main' into coydog-powan

_layouts/base.html

@@ -46,7 +46,7 @@
         {%- elsif page.tags contains "gat" %}{% assign coverimage = "assets/images/gat.png" %}
         {%- else %}{% assign coverimage = "assets/images/GTNLogo1000.png" %}{% endif %}
         {% assign og_image = page.og_image | default: page['cover-image'] | default: topic.og_image | default: coverimage | default: "assets/images/GTNLogo1000.png" %}
-	<meta property="og:image" content="{% if og_image contains 'https://' %}{{ og_image }}{% else %}{{ site.baseurl }}/{{ og_image }}{% endif %}">
+	<meta property="og:image" content="{% if og_image contains 'https://' %}{{ og_image }}{% else %}{{ site.url }}{{ site.baseurl }}/{{ og_image }}{% endif %}">
 
         {%- if page.layout == "tutorial_hands_on" -%}
         <script type="application/ld+json">

_plugins/api.rb

@@ -156,6 +156,12 @@ def generate(site)
       page2.data['layout'] = nil
       site.pages << page2
 
+      # Feedback Data
+      page2 = PageWithoutAFile.new(site, '', 'api/', 'feedback2.json')
+      page2.content = JSON.generate(site.data['feedback2'])
+      page2.data['layout'] = nil
+      site.pages << page2
+
       # Contributors
       Jekyll.logger.debug '[GTN/API] Contributors, Funders, Organisations'
       %w[contributors funders organisations].each do |type|
@@ -375,6 +381,8 @@ def generate(site)
         path = File.join(site.dest, 'api', directory, 'slides.json')
         p = material.dup
         p.delete('ref')
+        p.delete('ref_tutorials')
+        p.delete('ref_slides')
         p['contributors'] = Gtn::Contributors.get_contributors(p).dup.map { |c| mapContributor(site, c) }
 
         # Here we un-do the tutorial metadata priority, and overwrite with
@@ -392,6 +400,8 @@ def generate(site)
         path = File.join(site.dest, 'api', directory, 'tutorial.json')
         p = material.dup
         p.delete('ref')
+        p.delete('ref_tutorials')
+        p.delete('ref_slides')
         p['contributors'] = Gtn::Contributors.get_contributors(p).dup.map { |c| mapContributor(site, c) }
         if !Dir.exist?(File.dirname(path))
           FileUtils.mkdir_p(File.dirname(path))

_plugins/feeds.rb

@@ -72,6 +72,33 @@ def markdownify(site, text)
   'workflows' => '🛠️',
 }
 
+def generate_opml(site, groups)
+  builder = Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
+    # Set stylesheet
+    xml.opml(version: '2.0') do
+      xml.head do
+        xml.title('Galaxy Training Network')
+        xml.dateCreated(DateTime.now.rfc3339)
+        xml.dateModified(DateTime.now.rfc3339)
+        xml.ownerEmail('[email protected]')
+      end
+      xml.body do
+        groups.each do |group, items|
+          xml.outline(text: group) do
+            items.each do |item|
+              xml.outline(text: item[:title], type: 'rss', version: 'RSS', xmlUrl: item[:url], htmlUrl: item[:url])
+            end
+          end
+        end
+      end
+    end
+  end
+
+  opml_path = File.join(site.dest, 'feeds', 'gtn.opml')
+  finalised = Nokogiri::XML builder.to_xml
+  File.write(opml_path, finalised.to_xml)
+end
+
 def generate_topic_feeds(site, topic, bucket)
   mats = bucket.select { |x| x[3].include?(topic) }
   feed_path = File.join(site.dest, 'topics', topic, 'feed.xml')
@@ -476,18 +503,37 @@ def generate_event_feeds(site)
 # Basically like `PageWithoutAFile`
 Jekyll::Hooks.register :site, :post_write do |site|
   if Jekyll.env == 'production'
+    opml = {}
     generate_event_feeds(site)
+    opml['GTN Events'] = [
+      {title: 'Events', url: "#{site.config['url']}#{site.baseurl}/events/feed.xml"}
+    ]
 
     bucket = all_date_sorted_materials(site)
     bucket.freeze
 
+    opml['GTN Topics'] = []
+    opml['GTN Topics - Digests'] = []
     TopicFilter.list_topics(site).each do |topic|
       generate_topic_feeds(site, topic, bucket)
+      opml['GTN Topics'] <<
+        {title: "#{topic} all changes", url: "#{site.config['url']}#{site.baseurl}/topic/feed.xml"}
+
       generate_matrix_feed(site, bucket, group_by: 'month', filter_by: topic)
+      opml['GTN Topics - Digests'] <<
+        {title: "#{topic} monthly changes", url: "#{site.config['url']}#{site.baseurl}/feeds/#{topic}-month.xml"}
     end
 
     generate_matrix_feed(site, bucket, group_by: 'day')
     generate_matrix_feed(site, bucket, group_by: 'week')
     generate_matrix_feed(site, bucket, group_by: 'month')
+
+    opml['GTN Digests'] = [
+      {title: "GTN daily changes", url: "#{site.config['url']}#{site.baseurl}/feeds/matrix-daily.xml"},
+      {title: "GTN weekly changes", url: "#{site.config['url']}#{site.baseurl}/feeds/matrix-weekly.xml"},
+      {title: "GTN monthly changes", url: "#{site.config['url']}#{site.baseurl}/feeds/matrix-monthly.xml"}
+    ]
+
+    generate_opml(site, opml)
   end
 end

_plugins/gtn/supported.rb

@@ -121,8 +121,61 @@ def test_exact
       end
     end
   else
+    server = ARGV[0]
+    workflow = ARGV[1]
+
+    def short_id(tool_id)
+      if tool_id.count('/') > 4
+        tool_id.split('/')[0..-2].join('/')
+      else
+        tool_id
+      end
+    end
+
     require 'json'
-    pp ARGV
-    pp Gtn::Supported.calculate(JSON.parse(File.open('metadata/public-server-tools.json')), ARGV)
+    tool_list = JSON.parse(`curl -s #{server}/api/tools?in_panel=False`).map{|x| x['id']}
+    puts "Found #{tool_list.length} tools in #{server}"
+
+    version_smash = tool_list.map{|x|
+      if x.count('/') > 4
+        [x.split('/')[0..-2].join('/'), x.split('/')[-1]]
+      else
+        [x, []]
+      end
+    }
+    version_smash = version_smash.group_by{|x, y| x}.to_a.map{|k, v| [k, v.map{|x, y| y}]}.to_h
+
+    workflow_tools = JSON.parse(File.open(workflow).read)['steps'].map{|_, x| x['tool_id']}
+    workflow_tools.select!{|x| x && x.length.positive?}
+    puts "Found #{workflow_tools.length} tools in the #{workflow}"
+
+    workflow_tools.each do |tool|
+      if tool_list.include?(tool)
+        puts "✅ #{tool} is supported"
+      else
+        if version_smash.key?(short_id(tool))
+          puts "❔ #{tool} is not supported, but #{version_smash[short_id(tool)]} are"
+        else
+          puts "❌ #{tool} is not supported"
+        end
+      end
+    end
+
+    metadata = {
+      "servers" => [{"url" => server, "name" => "CLI Tested Server"}],
+      "tools" => {}
+    }
+    version_smash.each do |k, v|
+      if k.count('/') > 3
+        metadata["tools"][k] = v.map{|x| [x, [0]]}.to_h
+      else
+        metadata["tools"][k] = {
+          "_" => [0]
+        }
+      end
+    end
+
+    puts "GTN Rendering:"
+    pp Gtn::Supported.calculate(metadata, workflow_tools)
   end
 end

_plugins/jekyll-topic-filter.rb

@@ -661,6 +661,7 @@ def self.resolve_material(site, material)
           'modified' => File.mtime(wf_path),
           'mermaid' => mermaid(wf_json),
           'graph_dot' => graph_dot(wf_json),
+          'workflow_tools' => extract_workflow_tool_list(wf_json).uniq,
         }
       end
     end
@@ -678,8 +679,7 @@ def self.resolve_material(site, material)
     page_obj['workflows']&.each do |wf|
       wf_path = "#{folder}/workflows/#{wf['workflow']}"
 
-      wf_data = JSON.parse(File.read(wf_path))
-      page_obj['tools'] += extract_workflow_tool_list(wf_data)
+      page_obj['tools'] += wf['workflow_tools']
     end
     page_obj['tools'] = page_obj['tools'].flatten.sort.uniq
 

_plugins/sitemap.rb

@@ -33,7 +33,7 @@ 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$/ }.each do |t|
+      site.pages.reject { |t| t.path =~ /ipynb$/ || t.path =~ /api\/ga4gh\/trs\/v2/}.each do |t|
         begin
           d = Gtn::ModificationTimes.obtain_time(t.path)
           d.format = '%FT%T%:z'