Merge branch 'master' into development

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: f49cd49aee437c98221521f7763ecb8386855e17
+  revision: 169afb7c1002f9db2b3276af36d552575cc80ba2
   branch: development
   specs:
     ontologies_api_client (2.2.0)
@@ -109,7 +109,7 @@ GEM
       sassc-rails (>= 2.0.0)
     brakeman (5.4.1)
     builder (3.2.4)
-    capistrano (3.17.3)
+    capistrano (3.18.0)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
@@ -143,7 +143,7 @@ GEM
       addressable
     cube-ruby (0.0.3)
     daemons (1.4.1)
-    dalli (3.2.5)
+    dalli (3.2.6)
     date (3.3.3)
     debug (1.8.0)
       irb (>= 1.5.0)
@@ -175,7 +175,8 @@ GEM
     flamegraph (0.9.5)
     globalid (1.2.1)
       activesupport (>= 6.1)
-    graphql (2.1.0)
+    graphql (2.1.3)
+      racc (~> 1.4)
     graphql-client (0.18.0)
       activesupport (>= 3.0)
       graphql
@@ -215,7 +216,7 @@ GEM
       activesupport (>= 3.0)
       nokogiri (>= 1.6)
     io-console (0.6.0)
-    irb (1.8.1)
+    irb (1.8.3)
       rdoc
       reline (>= 0.3.8)
     iso-639 (0.3.6)
@@ -239,7 +240,7 @@ GEM
     listen (3.8.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    loofah (2.21.3)
+    loofah (2.21.4)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     lookbook (1.5.5)
@@ -266,7 +267,7 @@ GEM
     method_source (1.0.0)
     mime-types (3.5.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.0808)
+    mime-types-data (3.2023.1003)
     mini_mime (1.1.5)
     minitest (5.20.0)
     msgpack (1.7.2)
@@ -279,7 +280,7 @@ GEM
       time
     net-http (0.3.2)
       uri
-    net-imap (0.3.7)
+    net-imap (0.4.1)
       date
       net-protocol
     net-pop (0.1.2)
@@ -333,7 +334,7 @@ GEM
       omniauth (~> 2.0)
     open_uri_redirections (0.2.1)
     parallel (1.23.0)
-    parser (3.2.2.3)
+    parser (3.2.2.4)
       ast (~> 2.4.1)
       racc
     popper_js (1.16.1)
@@ -430,7 +431,7 @@ GEM
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
-      parser (>= 3.2.2.3)
+      parser (>= 3.2.2.4)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
@@ -477,7 +478,7 @@ GEM
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     stackprof (0.2.25)
-    stimulus-rails (1.2.2)
+    stimulus-rails (1.3.0)
       railties (>= 6.0.0)
     temple (0.10.2)
     terminal-table (3.0.2)
@@ -493,7 +494,7 @@ GEM
     time (0.2.2)
       date
     timeout (0.4.0)
-    turbo-rails (1.4.0)
+    turbo-rails (1.5.0)
       actionpack (>= 6.0.0)
       activejob (>= 6.0.0)
       railties (>= 6.0.0)
@@ -507,7 +508,7 @@ GEM
     unf (0.1.4)
       unf_ext
     unf_ext (0.0.8.2)
-    unicode-display_width (2.4.2)
+    unicode-display_width (2.5.0)
     uri (0.12.2)
     version_gem (1.1.3)
     view_component (2.82.0)

app/controllers/concepts_controller.rb

@@ -44,7 +44,7 @@ def show
       display = params[:callback].eql?('load') ? {full: true} : {display: "prefLabel"}
       @concept = @ontology.explore.single_class(display, params[:id])
       concept_not_found(params[:id]) if @concept.nil?
-      @schemes = params[:concept_schemes].split(',')
+      @schemes = params[:concept_schemes]&.split(',')
       show_ajax_request # process an ajax call
     else
       # Get the latest 'ready' submission, or fallback to any latest submission

app/controllers/home_controller.rb

@@ -73,7 +73,7 @@ def feedback
     unless params[:question].nil? || params[:question].empty?
       @tags << "Question"
     end
-    unless params[:ontology_submissions_request].nil? || params[:bug].empty?
+    unless params[:ontology_submissions_request].nil? || params[:ontology_submissions_request].empty?
       @tags << "Ontology submissions request"
     end
 

app/helpers/application_helper.rb

@@ -185,14 +185,14 @@ def draw_note_tree_leaves(notes,level,output,key)
     end
   end
 
-  def draw_tree(root, id = nil, concept_schemes = [])
+  def draw_tree(root, acronym, id = nil, concept_schemes = nil)
     id = root.children.first.id if id.nil?
 
     # TODO: handle tree view for obsolete classes, e.g. 'http://purl.obolibrary.org/obo/GO_0030400'
-    raw build_tree(root, '', id, concept_schemes: concept_schemes)
+    raw build_tree(root, '', id, acronym, concept_schemes: concept_schemes)
   end
 
-  def build_tree(node, string, id, concept_schemes: [])
+  def build_tree(node, string, id, acronym, concept_schemes: nil)
 
     return string if node.children.nil? || node.children.empty?
 
@@ -203,16 +203,16 @@ def build_tree(node, string, id, concept_schemes: [])
       # This fake root will be present at the root of "flat" ontologies, we need to keep the id intact
 
       if child.id.eql?('bp_fake_root')
-        string << tree_link_to_concept(child: child, ontology_acronym: '',
-                                       active_style: active_style, node: node)
+        string << tree_link_to_concept(child: child, ontology_acronym: acronym,
+                                       active_style: active_style, node: node, skos: !concept_schemes.nil?)
       else
-        string << tree_link_to_concept(child: child, ontology_acronym: child.explore.ontology.acronym,
-                                       active_style: active_style, node: node)
+        string << tree_link_to_concept(child: child, ontology_acronym: acronym,
+                                       active_style: active_style, node: node, skos: !concept_schemes.nil?)
         if child.hasChildren && !child.expanded?
-          string << tree_link_to_children(child: child, concept_schemes: concept_schemes)
+          string << tree_link_to_children(child: child, acronym: acronym, concept_schemes: concept_schemes)
         elsif child.expanded?
           string << '<ul>'
-          build_tree(child, string, id, concept_schemes: concept_schemes)
+          build_tree(child, string, id, acronym, concept_schemes: concept_schemes)
           string << '</ul>'
         end
         string << '</li>'
@@ -221,45 +221,35 @@ def build_tree(node, string, id, concept_schemes: [])
     string
   end
 
-  def tree_link_to_concept(child:, ontology_acronym:, active_style:, node: nil)
+  def tree_link_to_concept(child:, ontology_acronym:, active_style:, node: nil, skos: false)
     language = request_lang
     li_id = child.id.eql?('bp_fake_root') ? 'bp_fake_root' : short_uuid
     open = child.expanded? ? "class='open'" : ''
     icons = child.relation_icon(node)
-    muted_style = child.isInActiveScheme&.empty? ? 'text-muted' : ''
+    muted_style = skos && Array(child.isInActiveScheme).empty? ? 'text-muted' : nil
+    muted_title = muted_style  && !child.obsolete? ? "title='is not in a scheme'" : nil
     href = ontology_acronym.blank? ? '#' : "/ontologies/#{child.explore.ontology.acronym}/concepts/?id=#{CGI.escape(child.id)}&language=#{language}"
-
-    if child.prefLabel.nil?
-      prefLabelHTML =  child.id.split('/').last
-    else
-      prefLabelLang, prefLabelHTML = select_language_label(child.prefLabel)
-      prefLabelLang = prefLabelLang.to_s.upcase
-      tooltip = prefLabelLang.eql?("@NONE") ? "" : "data-controller='tooltip' data-tooltip-position-value='right' title='#{prefLabelLang}'";
-    end
-
     link = <<-EOS
-        <a id='#{child.id}' 
-        data-conceptid='#{child.id}'
-        data-turbo=true data-turbo-frame='concept_show' href='#{href}' 
-        data-collections-value='#{child.memberOf || []}'
-        data-active-collections-value='#{child.isInActiveCollection || []}'
-        data-skos-collection-colors-target='collection'
-        class='#{muted_style} #{active_style}'
-        #{tooltip}
-          >
-            #{ prefLabelHTML }
-            
+        <a id='#{child.id}' data-conceptid='#{child.id}'
+           data-turbo=true data-turbo-frame='concept_show' href='#{href}' 
+           data-collections-value='#{child.memberOf || []}'
+           data-active-collections-value='#{child.isInActiveCollection || []}'
+           data-skos-collection-colors-target='collection'
+            class='#{muted_style} #{active_style}' #{muted_title}>
+            #{child.prefLabel ? child.prefLabel({ use_html: true }) : child.id}
         </a>
     EOS
 
     "<li #{open} id='#{li_id}'>#{link} #{icons}"
   end
 
-  def tree_link_to_children(child:, concept_schemes: [])
+
+  def tree_link_to_children(child:, acronym: ,concept_schemes: nil)
     language = request_lang
     li_id = child.id.eql?('bp_fake_root') ? 'bp_fake_root' : short_uuid
-    concept_schemes = concept_schemes.map{|x| CGI.escape(x)}.join(',')
-    link = "<a id='#{child.id}' href='/ajax_concepts/#{child.explore.ontology.acronym}/?conceptid=#{CGI.escape(child.id)}&concept_schemes=#{concept_schemes}&callback=children&language=#{language}'>ajax_class</a>"
+    concept_schemes = "&concept_schemes=#{concept_schemes.map{|x| CGI.escape(x)}.join(',')}" if concept_schemes
+
+    link = "<a id='#{child.id}' href='/ajax_concepts/#{acronym}/?conceptid=#{CGI.escape(child.id)}#{concept_schemes}&callback=children&language=#{language}'>ajax_class</a>"
     "<ul class='ajax'><li id='#{li_id}'>#{link}</li></ul>"
   end
 

app/services/issue_creator_service.rb

@@ -3,13 +3,15 @@
 class IssueCreatorService < ApplicationService
   class QueryError < StandardError; end
 
+
   def initialize(params)
     @title = params[:content][:title]
     @body = params[:content][:body]
     @repo = Rails.configuration.change_request.dig(:ontologies, params[:ont_acronym].to_sym, :repository)
   end
 
   def call
+
     findRepoQuery = GitHub::Client.parse <<-'GRAPHQL'
     query ($owner: String!, $name: String!) {
       repository(owner: $owner, name: $name) {
@@ -19,23 +21,22 @@ def call
     GRAPHQL
 
     createIssueMutation = GitHub::Client.parse <<-'GRAPHQL'
-      mutation ($repositoryId: ID!, $title: String!, $body: String) {
-        createIssue(input: {repositoryId: $repositoryId, title: $title, body: $body}) {
-          issue {
-            bodyText,
-            createdAt,
-            id,
-            number,
-            repository {
-              nameWithOwner
-            },
-            title,
-            url
-          }
+    mutation ($repositoryId: ID!, $title: String!, $body: String) {
+      createIssue(input: {repositoryId: $repositoryId, title: $title, body: $body}) {
+        issue {
+          bodyText,
+          createdAt,
+          id,
+          number,
+          repository {
+            nameWithOwner
+          },
+          title,
+          url
         }
       }
-    GRAPHQL
-
+    }
+  GRAPHQL
     data = query(findRepoQuery, variables: { owner: repo_owner, name: repo_name })
     data = query(createIssueMutation, variables: { repositoryId: data.repository.id, title: @title, body: @body })
     data.to_h.dig('createIssue', 'issue')

app/views/concepts/_child_nodes.html.haml

@@ -1,7 +1,7 @@
 - output =""
 - for child in @children
-  - output << tree_link_to_concept(child: child, ontology_acronym: child.explore.ontology.acronym, active_style: '', node: @concept)
+  - output << tree_link_to_concept(child: child, ontology_acronym: @ontology.acronym, active_style: '', node: @concept, skos: [email protected]?)
   - if child.hasChildren
-    - output << tree_link_to_children(child: child, concept_schemes: @schemes)
+    - output << tree_link_to_children(child: child, acronym: @ontology.acronym, concept_schemes: @schemes)
   - output << "</li>"
 = raw output

app/views/ontologies/_treeview.html.haml

@@ -5,6 +5,6 @@
                         action: 'clicked->history#updateURL'}}
       %li.root
         %ul
-          = draw_tree(@root, @concept.id, (params[:concept_schemes] || '').split(','))
+          = draw_tree(@root, params[:ontology], @concept.id, params[:concept_schemes]&.split(','))
 
 

app/views/ontologies/concepts_browsers/_concepts_tree.html.haml

@@ -15,7 +15,13 @@
                        data: {action: 'changed->skos-collection-colors#updateCollectionTags' ,
                         'chosen-enable-colors-value': 'true'}}
   -# Class tree
-  %div#sd_content.py-3{style: 'overflow-y: scroll; height: 60vh;'}
-    = render TurboFrameComponent.new(id: 'concepts_tree_view',
-                                     src: "/ajax/classes/treeview?ontology=#{@ontology.acronym}&conceptid=#{escape(@concept.id)}&concept_schemes=#{params[:concept_schemes]}&auto_click=false&language=#{request_lang}",
-                                     data: {'turbo-frame-target': 'frame'})
+  %div#sd_content.card.p-1.py-3{style: 'overflow-y: scroll; height: 60vh;'}
+    - if skos? && @roots&.empty?
+      %div.text-wrap
+        = render AlertMessageComponent.new do
+          Missing roots for #{@ontology.acronym} (skos:topConceptOf)
+    - else
+      - concept_schemes = skos? ? "&concept_schemes=#{params[:concept_schemes]}" : ''
+      = render TurboFrameComponent.new(id: 'concepts_tree_view',
+                                     src: "/ajax/classes/treeview?ontology=#{@ontology.acronym}&conceptid=#{escape(@concept.id)}#{concept_schemes}&auto_click=false",
+                                     data: {'turbo-frame-target': 'frame'})                          

vendor/assets/javascripts/jquery.simple.tree.js.erb

@@ -156,11 +156,8 @@ $.fn.simpleTree = function(opt){
 			.bind('selectstart', function() {
 				return false;
 			}).click(function(){
-				$('.active',TREE).attr('class','text');
-				if(this.className=='text')
-				{
-					this.className='active';
-				}
+				$('.active',TREE).removeClass('active');
+				this.classList.add('active');
 				if(typeof TREE.option.afterClick == 'function')
 				{
 					TREE.option.afterClick($(this).parent());
@@ -177,11 +174,8 @@ $.fn.simpleTree = function(opt){
 				// added by Erik Dohmen (2BinBusiness.nl) to make context menu actions
 				// available
 			}).bind("contextmenu",function(){
-				$('.active',TREE).attr('class','text');
-				if(this.className=='text')
-				{
-					this.className='active';
-				}
+				$('.active',TREE).removeClass('active');
+				this.classList.add('active');
 				if(typeof TREE.option.afterContextMenu == 'function')
 				{
 					TREE.option.afterContextMenu($(this).parent());