Merge pull request #5091 from galaxyproject/cofest

Cofest

_layouts/topic-maintainer.html

@@ -4,6 +4,7 @@
 
 {% assign topic = site.data[page.topic_name] | default: page.topic %}
 {% assign topic_material = site | list_materials_structured:topic.name %}
+{% assign topic_material_flat = site | list_materials_flat:topic.name %}
 
 <h1>{{ topic.title }} Editorial Board Home</h1>
 
@@ -60,6 +61,34 @@ <h2>Action Items</h2>
 	</tbody>
 </table>
 
+<h2>Topic Workflows</h2>
+<table  class="table table-striped">
+	<thead>
+		<tr>
+			<th>Material</th>
+			<th>Workflow</th>
+
+			<th>Tests</th>
+			<th>Reports</th>
+			<th>Comments</th>
+		</tr>
+	</thead>
+	<tbody>
+{% for material in topic_material_flat %}
+	{% for workflow in material['workflows'] %}
+		<tr>
+			<td><a href="{{ site.baseurl }}{{ material.url }}">{{ material.title }}</a></td>
+			<td><a href="{{ workflow.url_html }}">{{ workflow.name }}</a></td>
+			<td>{% if workflow.tests %} ✅ {% else %} ❌ {% endif %}</td>
+			<td>{% if workflow.features.report %} ✅ {% else %} ❌ {% endif %}</td>
+			<td>{% if workflow.features.comments %} ✅ {% else %} ❌ {% endif %}</td>
+		</tr>
+	{% endfor %}
+{% endfor %}
+	</tbody>
+</table>
+
+
 <h2>Your topic's Workflow Testing Results</h2>
 
 Coming Soon™

_plugins/jekyll-topic-filter.rb

@@ -672,6 +672,7 @@ def self.resolve_material(site, material)
           'workflow' => wf,
           'tests' => Dir.glob("#{folder}/workflows/" + wf.gsub(/.ga/, '-test*')).length.positive?,
           'url' => "#{domain}/#{folder}/workflows/#{wf}",
+          'url_html' => "#{domain}/#{folder}/workflows/#{wf.gsub(/.ga$/, '.html')}",
           'path' => wf_path,
           'wfid' => wfid,
           'wfname' => wfname,
@@ -1126,6 +1127,13 @@ def list_materials_structured(site, topic_name)
       TopicFilter.list_materials_structured(site, topic_name)
     end
 
+    def list_materials_flat(site, topic_name)
+      TopicFilter
+        .list_materials_structured(site, topic_name)
+        .map { |k, v| v['materials'] }
+        .flatten
+    end
+
     def list_all_tags(site)
       TopicFilter.list_all_tags(site)
     end

bin/lint.rb

@@ -394,6 +394,22 @@ def self.bad_tool_links(contents)
       end
   end
 
+  def self.bad_zenodo_links(contents)
+    find_matching_texts(contents, /https:\/\/zenodo.org\/api\//)
+      .reject { |_idx, _text, selected| _text =~ /files-archive/ }
+      .map do |idx, _text, selected|
+        ReviewDogEmitter.error(
+          path: @path,
+          idx: idx,
+          match_start: selected.begin(0),
+          match_end: selected.end(0) + 1,
+          replacement: nil,
+          message: 'Please do not use zenodo.org/api/ links, instead it should look like zenodo.org/records/id/files/<filename>',
+          code: 'GTN:040'
+        )
+      end
+  end
+
   def self.snippets_too_close_together(contents)
     prev_line = -2
     res = []
@@ -822,6 +838,7 @@ def self.fix_md(contents)
       *check_bad_heading_order(contents),
       *check_bolded_heading(contents),
       *snippets_too_close_together(contents),
+      *bad_zenodo_links(contents),
       *zenodo_api(contents),
       *empty_alt_text(contents),
       *check_bad_trs_link(contents),

faqs/gtn/gtn_faq_create.md

@@ -5,6 +5,7 @@ area: contributors
 layout: faq
 box_type: tip
 contributors: [hexylena]
+description: "If you have a snippet of knowledge that is reusable, we recommend you to share with the GTN community, and we encourage you to create an FAQ for it!"
 ---
 
 If you have a snippet of knowledge that is reusable, we recommend you to share with the GTN community, and we encourage you to create an FAQ for it!

faqs/gtn/translations.md

@@ -0,0 +1,16 @@
+---
+title: Translations within the GTN
+area: other
+layout: faq
+box_type: tip
+contributors: [hexylena]
+---
+
+The GTN currently supports two forms of translation:
+
+- Manual (`tutorial_ES.md` and `slides_ES.html` for example)
+- Automated (via linking through to Google Translate)
+
+We accept manual translations if and only if there is a team that is able to commit to their maintenance. We need to ensure the trainings are kept up to date and high quality, but that requires native speakers of that language to maintain those translations.
+
+Please contact us if you have any questions regarding translations.

faqs/random.html

@@ -0,0 +1,28 @@
+---
+layout: base
+title: Random FAQ
+---
+
+<style>
+div.main-content > blockquote {
+	display: none;
+}
+</style>
+
+{% snippet faqs/galaxy/analysis_troubleshooting.md box_type="comment" %}
+
+{% snippet faqs/galaxy/why_not_excel.md box_type="comment" %}
+
+{% snippet faqs/galaxy/tutorial_mode.md box_type="comment" %}
+
+{% snippet faqs/gtn/fair_training.md box_type="comment" %}
+
+{% snippet faqs/gtn/why-the-gtn.md box_type="comment" %}
+
+<script>
+let faqs = document.querySelectorAll("div.main-content > blockquote")
+let random_faq = Math.floor(Math.random() * faqs.length);
+faqs[random_faq].style.display = 'block';
+</script>
+
+{% bibliography --cited %}

topics/assembly/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: assembly
+---
+

topics/climate/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: climate
+---
+

topics/computational-chemistry/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: computational-chemistry
+---
+

topics/contributing/tutorials/running-jekyll/tutorial.md

@@ -86,7 +86,7 @@ Once Jekyll and its modules are installed in our conda environment, we can check
 With `make serve-quick`, a local Jekyll server will run in background. It will check the changes and regenerate the website accordingly. You may need to reload the page to see the changes (and sometimes to wait 1-2 minutes).
 
 
-> <tip-title>Tips</tip-title>
+> <tip-title></tip-title>
 >
 > 1. Use `make serve` instead of `make serve-quick` to get all plugins, but also configure the post, host and pass additional flags. This however can be quite slow.
 >

topics/ecology/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: ecology
+---
+

topics/epigenetics/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: epigenetics
+---
+

topics/evolution/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: evolution
+---
+

topics/galaxy-interface/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: galaxy-interface
+---
+

topics/genome-annotation/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: genome-annotation
+---
+

topics/imaging/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: imaging
+---
+

topics/introduction/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: introduction
+---
+

topics/materials-science/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: materials-science
+---
+

topics/metabolomics/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: metabolomics
+---
+

topics/microbiome/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: microbiome
+---
+

topics/proteomics/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: proteomics
+---
+

topics/sequence-analysis/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: sequence-analysis
+---
+

topics/statistics/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: statistics
+---
+

topics/synthetic-biology/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: synthetic-biology
+---
+

topics/transcriptomics/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: transcriptomics
+---
+

topics/variant-analysis/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: variant-analysis
+---
+

topics/visualisation/maintainer.md

@@ -0,0 +1,5 @@
+---
+layout: topic-maintainer
+topic_name: visualisation
+---
+

user/privacy.md

@@ -3,6 +3,8 @@ layout: page
 title: Data Privacy
 ---
 
+Tip: [Looking for language settings?]({% link faqs/gtn/translations.md %})
+
 The GTN is invested in preserving your privacy. We attempt to balance your
 rights and needs to private access of the GTN resources, with our needs to
 continue receiving funding and provide a good experience for you, the user.

user/theme.md

@@ -5,6 +5,8 @@ redirect_from:
 - /preferences
 ---
 
+Tip: [Looking for language settings?]({% link faqs/gtn/translations.md %}) or [Data Privacy Settings]({% link user/privacy.md %})
+
 ## Colour Scheme
 
 We have attempted to decompose our themes into several axes depending on your accessibility needs:
@@ -114,4 +116,3 @@ document.getElementById("font").value = gtnLocalGet("fontMain");
 document.getElementById("font-code").value = gtnLocalGet("fontCode");
 </script>
 
-Are you looking for Data Privacy settings? [They have moved to their own page]({% link user/privacy.md %})