Merge branch 'main' into create-pull-request/patch-1728378303

_layouts/contributor_index.html

@@ -23,9 +23,9 @@
 					<h1>
 						{{ entity.name | default: page.contributor }}
 					</h1>
-				{% if entity.funder_name %}
-					<p>Funded by {{ entity.funder_name }}</p>
-				{% endif %}
+					{% if entity.funder%}
+					<p>The activities listed below were partially funded by this project.</p>
+					{% endif %}
 				</hgroup>
 
 				{% if entity.bio %}
@@ -34,9 +34,6 @@ <h1>
 				</p>
 				{% endif %}
 
-				{% if entity.funder %}
-				<div class="label label-default label-large" style="{{ 'GTN Funder' | colour_tag }}">GTN Funder</div>
-				{% endif %}
 				{% if entity.in_memoriam %}
 				<div class="alert alert-dark" role="alert">
 					<h2 class="alert-heading">In Memoriam</h2>

_layouts/tutorial_hands_on.html

@@ -289,11 +289,14 @@ <h3>You've Finished the Tutorial</h3>
                         <p style="display: none" id="tutorial-finish-text">Please also consider filling out the <a href="#gtn-feedback">Feedback Form</a> as well!</p>
                         <script>
                         function tutorial_finish() {
-                          if(plausible !== undefined){
-                            plausible('TutorialComplete', {callback: tutorial_finish_finish, props: {path: document.location.pathname}})
-                          } else {
-                            tutorial_finish_finish();
+                          if(typeof plausible !== 'undefined'){
+                            // Plausible may be undefined (script blocked)
+                            // or it may be defined, but opted-out (select box/DNT), 
+                            // which means `plausible()` will work but not send data, *nor* execute the callback.
+                            plausible('TutorialComplete', {props: {path: document.location.pathname}})
                           }
+                          // since the callback is completely cosmetic, we'll just issue it optimistically.
+                          tutorial_finish_finish();
                         }
                         function tutorial_finish_finish() {
                           document.getElementById("tutorial-finish-button").innerText = 'Congrats! Thanks for letting us know! 🎉'

_plugins/gtn/contributors.rb

@@ -91,9 +91,26 @@ def self.get_non_authors(material)
     # +data+:: +Hash+ of the YAML frontmatter from a material
     # Returns:
     # +Array+ of contributor IDs
-    def self.get_funders(data)
+    def self.get_funders(site, data)
       if data.key?('contributions') && data['contributions'].key?('funding')
-        data['contributions']['funding']
+        # The ones specifically in the Grants table
+        data['contributions']['funding'].reject{ |f| site.data['funders'].key?(f) }
+      else
+        []
+      end
+    end
+
+    ##
+    # Get the funders of a material.
+    # Params:
+    # +site+:: +Jekyll::Site+ object
+    # +data+:: +Hash+ of the YAML frontmatter from a material
+    # Returns:
+    # +Array+ of grant IDs
+    def self.get_grants(site, data)
+      if data.key?('contributions') && data['contributions'].key?('funding')
+        # The ones specifically in the Grants table
+        data['contributions']['funding'].select{ |f| site.data['funders'].key?(f) }
       else
         []
       end

_plugins/jekyll-jsonld.rb

@@ -184,7 +184,7 @@ def generate_funding_jsonld(id, contributor, site)
         '@context': 'https://schema.org',
         '@type': 'Grant',
         identifier: contributor['funding_id'],
-        url: contributor['url'] || Gtn::Contributors.fetch_funding_url(contributor),
+        url: Gtn::Contributors.fetch_funding_url(contributor) || contributor['url'],
         funder: generate_funder_jsonld(id, contributor, site)
       }
 
@@ -274,10 +274,10 @@ def generate_event_jsonld(page, site)
       instructors = Gtn::Contributors.get_instructors(page.to_h).map do |x|
         to_pfo_jsonld(x, site, json: false)
       end
-      funders = Gtn::Contributors.get_funders(page.to_h).map do |x|
+      funders = Gtn::Contributors.get_funders(site, page.to_h).map do |x|
         to_pfo_jsonld(x, site, json: false)
       end
-      funding = Gtn::Contributors.get_funders(page.to_h).map do |x|
+      funding = Gtn::Contributors.get_grants(site, page.to_h).map do |x|
         generate_funding_jsonld(x, Gtn::Contributors.fetch_contributor(site, x), site)
       end
 
@@ -511,6 +511,18 @@ def generate_learning_pathway_jsonld(page, site)
         material.fetch('objectives', [])
       end.flatten.compact
 
+      funders = materials.map do |material|
+        Gtn::Contributors.get_funders(site, material).map do |x|
+          to_pfo_jsonld(x, site, json: false)
+        end
+      end.flatten.uniq.compact
+
+      funding = materials.map do |material|
+        Gtn::Contributors.get_grants(site, material).map do |x|
+          generate_funding_jsonld(x, Gtn::Contributors.fetch_contributor(site, x), site)
+        end
+      end.flatten.uniq.compact
+
       # TODO: add topic edam terms too? Not sure.
       parts = []
       materials.each do |material|
@@ -558,8 +570,8 @@ def generate_learning_pathway_jsonld(page, site)
         # learningResourceType
         # teaches
 
-        # funder: funders, # Org or person
-        # funding: funding, # Grant
+        funder: funders, # Org or person
+        funding: funding, # Grant
         publisher: GTN,
         provider: GTN,
         syllabusSections: syllab,
@@ -690,7 +702,8 @@ def generate_material_jsonld(material, topic, site)
         # "contentRating":,
         # "contentReferenceTime":,
         # "contributor" described below
-        copyrightHolder: GTN,
+        # copyrightHolder: GTN,
+        # copyrightNotice: m
         # "copyrightYear":,
         # "correction":,
         # "creator":,
@@ -704,7 +717,7 @@ def generate_material_jsonld(material, topic, site)
         # "encodingFormat":,
         # "exampleOfWork":,
         # "expires":,
-        # "funder":,
+        # "funder": funding,
         # "genre":,
         # "hasPart" described below
         headline: (material['title']).to_s,
@@ -780,6 +793,24 @@ def generate_material_jsonld(material, topic, site)
         end
       end
 
+      if material.key?('copyright')
+        # copyrightHolder: GTN,
+        data['copyrightNotice'] = material['copyright']
+      else
+        # I'm not sure this is accurate.
+        data['copyrightHolder'] = GTN
+      end
+
+      funders = Gtn::Contributors.get_funders(site, material).map do |x|
+        to_pfo_jsonld(x, site, json: false)
+      end
+      funding = Gtn::Contributors.get_grants(site, material).map do |x|
+        generate_funding_jsonld(x, Gtn::Contributors.fetch_contributor(site, x), site)
+      end
+
+      data['funder'] = funders
+      data['funding'] = funding
+
       data['identifier'] = "https://gxy.io/GTN:#{material['short_id']}" if material.key?('short_id')
 
       data.update(A11Y)

assets/css/main.scss

@@ -1289,6 +1289,9 @@ div.highlight .btn{
 	transition: none;
   }
 }
+.btn {
+	cursor: pointer;
+}
 
 
 div.highlight:hover .btn,div.highlight .btn:focus{

bin/schema-tutorial.yaml

@@ -535,7 +535,7 @@ mapping:
               pattern: /^(?:([0-9]*)[Hh])*(?:([0-9]*)[Mm])*(?:([0-9.]*)[Ss])*$/
             youtube_id:
               type: str
-              pattern: /[A-Za-z0-9_-]{9,13}/
+              pattern: /[A-Za-z0-9_-]{11}/
             type:
               type: str
             archive-id:

topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md

@@ -1,31 +1,46 @@
 ---
 layout: tutorial_hands_on
-
 title: ERGA post-assembly QC
 questions:
 - "What combination of tools can assess the quality of a genome assembly?"
 - "What metrics can help to analyse the quality of an assembly?"
 - "How do we evaluate the outputs?"
 objectives:
-- "Apply the post-assembly-QC-workflow using the necessary tools"
-- "Analyse and evaluate the results of the workflow"
+- Apply the post-assembly-QC-workflow using the necessary tools
+- Analyse and evaluate the results of the workflow
 time_estimation: 3H
 key_points:
-- "The ERGA post-assembly pipeline allows users to assess and improve the quality of genome assemblies"
-- "The ERGA post-assembly pipeline consists of three main steps: Genome assembly decontamination and overview with BlobToolKit, providing analysis information and statistics, and Hi-C scaffolding."
+- The ERGA post-assembly pipeline allows users to assess and improve the quality of
+  genome assemblies
+- 'The ERGA post-assembly pipeline consists of three main steps: Genome assembly decontamination
+  and overview with BlobToolKit, providing analysis information and statistics, and
+  Hi-C scaffolding.'
 contributors:
 - GitFab93
 - gallardoalba
 - tbrown91
 - delphine-l
 tags:
-  - plants
-  - animals
-  - genome
-  - assembly
-  - QC
+- plants
+- animals
+- genome
+- assembly
+- QC
+recordings:
+- youtube_id: n4PNTTa2d6U
+  length: 44M
+  galaxy_version: 24.1.3.dev0
+  date: '2024-10-06'
+  speakers:
+  - delphine-l
+  captioners:
+  - delphine-l
+  bot-timestamp: 1728229662
+
+
 ---
 
+
 ![ERGA logo, 4 colorful letters on white background, with the European star circle](../../images/post-assembly-QC/ERGA.logo.jpg){: width="20px"}
 
 The European Reference Genome Atlas ([ERGA](https://www.erga-biodiversity.eu/), {% cite Mazzoni2023 %}) is a large-scale network of researchers aiming to generate high-quality reference genomes for all eukaryotic life in Europe and build capacity to allow researchers anywhere to generate reference genomes and use them to answer questions regarding species conservation and biodiversity. ERGA uses state-of-the-art sequencing technologies and advanced bioinformatics tools to produce high-quality genome assemblies.

topics/assembly/tutorials/vgp_workflow_training/tutorial.md

@@ -49,7 +49,7 @@ abbreviations:
   VGP: Vertebrate Genome Project
   G10K: Genome 10K
 recordings:
-- youtube_id: LO-migvwcM
+- youtube_id: _LO-migvwcM
   length: 1H56M
   galaxy_version: 24.1.2.dev0
   date: '2024-09-12'

topics/dev/tutorials/tool-from-scratch/tutorial.md

@@ -433,8 +433,7 @@ anyone wrapping a tool, a more complete list is available in [the Galaxy tool do
 
 Planemo is an important tool within the Galaxy development workflow. Although it will be covered in greater detail in the
 next section of this tutorial, one of its functions is necessary for the tool wrapper development. `planemo` is available
-via the python package manager `pip`. To that end, before beginning this section, please install `planemo` locally by running
-`planemo`. To that end, before beginning this section, please install planemo locally by running
+via the python package manager `pip`. To that end, before beginning this section, please install planemo locally by running
 
 > <hands-on-title>Installing `planemo` via pip</hands-on-title>
 >