Fix: adding new submission action and add a system for it (#403)

* add sort by notes and projects to browse page

* fix chips button component to be clickable again

* make the visibility property in the ontology form required

* extract and reuse group chip component from browse page to ontology form

* add the add new submission to an ontology flow test

* prevent the add new submission form to copy all the old submission vals

.github/workflows/tests-real-data-stageportal.yml

@@ -8,7 +8,7 @@ name: "Run remote API (stageportal) tests CI"
 
 on:
   push:
-  pull_request_target:
+  pull_request:
     types: [ opened, reopened ]
 env:
   API_URL: https://data.stageportal.lirmm.fr/ # or ${{ secrets.API_URL }}

.github/workflows/tests-real-data-testportal.yml

@@ -8,7 +8,7 @@ name: "Run remote API (testportal) tests CI"
 
 on:
   push:
-  pull_request_target:
+  pull_request:
     types: [ opened, reopened ]
 env:
   API_URL: https://data.testportal.lirmm.fr/ # or ${{ secrets.API_URL }}

.github/workflows/tests-system.yml

@@ -8,7 +8,7 @@ name: "Run system tests CI"
 
 on:
   push:
-  pull_request_target:
+  pull_request:
     types: [ opened, reopened ]
 env:
   API_URL: http://localhost:9393

.github/workflows/tests.yml

@@ -8,7 +8,7 @@ name: "Run local API tests CI"
 
 on:
   push:
-  pull_request_target:
+  pull_request:
     types: [ opened, reopened ]
 env:
   API_URL: http://localhost:9393

app/components/chip_button_component/chip_button_component.html.haml

@@ -1,6 +1,9 @@
 - if @type == "static"
   %span.chip_button_container{@html_options}
     = @text || content
+- elsif !content
+  %a.chip_button_container_clickable{@html_options}
+    = @text
 - else
   %span.chip_button_container_clickable{@html_options}
-    = @text || content
+    = content

app/controllers/concerns/ontology_updater.rb

@@ -7,7 +7,13 @@ def update_existent_ontology(acronym)
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first
     return nil if @ontology.nil?
 
-    [@ontology, @ontology.update(values: ontology_params)]
+    new_values = ontology_params
+    new_values.each do |key, values|
+      @ontology.send("#{key}=", values)
+    rescue StandardError
+      next
+    end
+    [@ontology, @ontology.update(values: new_values)]
   end
 
   def ontology_from_params
@@ -55,20 +61,19 @@ def errors_attributes
     @errors.keys.map(&:to_s) if @errors.is_a?(Hash)
   end
 
-  def new_submission_hash(ontology)
-    @submission = ontology.explore.latest_submission({ display: 'all' })
-
-    submission_params = submission_params(params[:submission])
+  def new_submission_hash(ontology, submission = nil)
+    @submission = submission
+    new_submission_params = submission_params(params[:submission])
 
     if @submission
-      submission_params = submission_params(ActionController::Parameters.new(@submission.to_hash.delete_if do |k, v|
-        v.nil? || v.respond_to?(:empty?) && v.empty?
-      end.merge(submission_params)))
+      old_submission_values = @submission.to_hash.delete_if {  |k, v| !copyable_submission_params?(k, v)}
+      new_submission_params = ActionController::Parameters.new(old_submission_values.merge(new_submission_params))
+      new_submission_params = submission_params(new_submission_params)
     end
 
-    submission_params.delete 'submissionId'
-    submission_params[:ontology] = @ontology.acronym
-    ActionController::Parameters.new(submission_params)
+    new_submission_params.delete 'submissionId'
+    new_submission_params[:ontology] = ontology.acronym
+    ActionController::Parameters.new(new_submission_params)
   end
 
   def update_submission_hash(acronym)
@@ -88,4 +93,14 @@ def reset_agent_attributes
       @submission[attr] = new_values
     end
   end
+
+  def copyable_submission_params?(key, value)
+    return false if value.nil? || (value.respond_to?(:empty?) && value.empty?)
+
+    attr_to_not_copy = [:versionIRI, :version, :deprecated, :valid, :curatedOn,
+                        :pullLocation, :metadataVoc, :hasPriorVersion,
+                        :submissionStatus]
+
+    !attr_to_not_copy.include?(key.to_sym)
+  end
 end

app/controllers/concerns/submission_filter.rb

@@ -32,6 +32,10 @@ def submissions_paginate_filter(params)
       submissions = submissions.sort_by { |x| -x[:popularity] }
     elsif @selected_sort_by.eql?('fair')
       submissions = submissions.sort_by { |x| -x[:fairScore] }
+    elsif @selected_sort_by.eql?('notes')
+      submissions = submissions.sort_by { |x| -x[:note_count] }
+    elsif @selected_sort_by.eql?('projects')
+      submissions = submissions.sort_by { |x| -x[:project_count] }
     end
     submissions
   end
@@ -194,6 +198,8 @@ def ontology_filters_init(categories, groups)
       ['Sort by release date', 'released'],
       ['Sort by FAIR score', 'fair'],
       ['Sort by popularity', 'visits'],
+      ['Sort by notes', 'notes'],
+      ['Sort by projects', 'projects'],
     ]
 
     init_filters(params)

app/controllers/concerns/submission_updater.rb

@@ -116,14 +116,9 @@ def submission_params(params)
     ]
 
     submission_metadata.each do |m|
-
       m_attr = m["attribute"].to_sym
-
-      attributes << if m["enforce"].include?("list")
-                      [{ m_attr => {} }, { m_attr => []}]
-                    else
-                      m_attr
-                    end
+      m_attr =  Array(m["enforce"]).include?("list") ? [{ m_attr => {} }, { m_attr => []}] : m_attr
+      attributes << m_attr
     end
     p = params.permit(attributes.uniq)
     p['pullLocation'] = '' if p['isRemote']&.eql?('3')

app/controllers/submissions_controller.rb

@@ -45,7 +45,8 @@ def create
         return
       end
     end
-    @submission = save_submission(new_submission_hash(@ontology))
+    @submission = @ontology.explore.latest_submission({ display: 'all' })
+    @submission = save_submission(new_submission_hash(@ontology, @submission))
 
     if response_error?(@submission)
       show_new_errors(@submission)

app/helpers/application_helper.rb

@@ -431,6 +431,21 @@ def truncate_with_more(text, options = {})
     output = "<span class='more_less_container'><span class='truncated_more'>#{truncate(text, :length => length, :omission => trailing_text)}" + more + "</span>"
   end
 
+  def chips_component(id: , name: , label: , value: , checked: false , tooltip: nil, &block)
+    content_tag(:div, data: { controller: 'tooltip' }, title: tooltip) do
+      check_input(id: id, name: name, value: value, label: label, checked: checked, &block)
+    end
+  end
+
+  def group_chip_component(id: nil, name: , object: , checked: , value: nil, title: nil, &block)
+    title ||= object["name"]
+    value ||= (object["value"] || object["acronym"] || object["id"])
+
+    chips_component(id: id || value, name: name, label: object["acronym"],
+                    checked: checked,
+                    value: value, tooltip: title, &block)
+  end
+  alias  :category_chip_component :group_chip_component
 
   def add_comment_button(parent_id, parent_type)
     if session[:user].nil?

app/helpers/inputs_helper.rb

@@ -17,8 +17,12 @@ def select_input(name:, values:, id: nil, label: nil, selected: nil, multiple: f
                                       data: data)
   end
 
-  def check_input(id:, name:, value:, label: '', checked: false)
-    render ChipsComponent.new(name: name, id: id, label: label, value: value, checked: checked)
+  def check_input(id:, name:, value:, label: '', checked: false, &block)
+    render ChipsComponent.new(name: name, id: id, label: label, value: value, checked: checked) do |c|
+      if block_given?
+        capture(c, &block)
+      end
+    end
   end
 
   def switch_input(id:, name:, label:, checked: false, value: '', boolean_switch: false, style: nil)

app/helpers/ontologies_helper.rb

@@ -544,7 +544,7 @@ def metadata_formats_buttons
                                     ['JsonLd', 'MOD/json-ld'],
                                     ['XML', 'MOD/rdf-xml']
                                   ]) do |format, label|
-          render ChipButtonComponent.new(type: 'clickable', 'data-action': "metadata-downloader#download#{format}") do
+          render ChipButtonComponent.new(type: 'clickable', 'data-action': "click->metadata-downloader#download#{format}") do
             concat content_tag(:span, label)
             concat content_tag(:span, inline_svg("summary/download.svg", width: '15px', height: '15px'))
           end
@@ -607,7 +607,7 @@ def projects_field(projects, ontology_acronym = @ontology.acronym)
         empty_state_message("No projects using #{ontology_acronym}")
       else
         horizontal_list_container(projects) do |project|
-           render ChipButtonComponent.new(url: project_path(project.acronym), text: project.name, type: "clickable")
+          render ChipButtonComponent.new(url: project_path(project.acronym), text: project.name, type: "clickable")
         end
       end
     end

app/helpers/submission_inputs_helper.rb

@@ -132,7 +132,9 @@ def ontology_categories_input(ontology = @ontology, categories = @categories)
       content_tag(:div, class: 'upload-ontology-chips-container') do
         hidden_field_tag('ontology[hasDomain][]') +
           categories.map do |category|
-            check_input(name: "ontology[hasDomain][]", id: category[:acronym], label: category[:acronym], value: category[:id], checked: ontology.hasDomain&.any? { |x| x.eql?(category[:id]) })
+            category_chip_component(id: category[:acronym], name: "ontology[hasDomain][]",
+                                    object: category, value: category[:id],
+                                    checked: ontology.hasDomain&.any? { |x| x.eql?(category[:id]) })
           end.join.html_safe
       end
     end
@@ -159,7 +161,9 @@ def ontology_groups_input(ontology = @ontology, groups = @groups)
       content_tag(:div, class: 'upload-ontology-chips-container') do
         hidden_field_tag('ontology[group][]') +
           groups.map do |group|
-            check_input(name: "ontology[group][]", id: group[:acronym], label: group[:acronym], value: group[:id], checked: ontology.group&.any? { |x| x.eql?(group[:id]) })
+            group_chip_component(name: "ontology[group][]", id: group[:acronym],
+                                 object: group, value: group[:id],
+                                 checked: ontology.group&.any? { |x| x.eql?(group[:id]) })
           end.join.html_safe
       end
     end
@@ -173,7 +177,9 @@ def ontology_visibility_input(ontology = @ontology)
 
     render(Layout::RevealComponent.new(init_show: ontology.viewingRestriction&.eql?('private'), show_condition: 'private')) do |c|
       c.button do
-        select_input(label: "Visibility", name: "ontology[viewingRestriction]", values: %w[public private], selected: ontology.viewingRestriction)
+        select_input(label: "Visibility", name: "ontology[viewingRestriction]", required: true,
+                     values: %w[public private],
+                     selected: ontology.viewingRestriction)
       end
       content_tag(:div, class: 'upload-ontology-input-field-container') do
         select_input(label: "Add or remove accounts that are allowed to see this ontology in #{portal_name}.", name: "ontology[acl]", values: @user_select_list, selected: ontology.acl, multiple: true)

app/views/ontologies/browser/browse.html.haml

@@ -60,17 +60,13 @@
                   .collapse{id: "browse-#{key}-filter", class: "#{values[2].positive? ? 'show': ''}"}
                     .browse-filter-checks-container
                       - values.first.each do |object|
-                        - title = (key.eql?(:categories) || key.eql?(:groups) ?  object["name"] : '')
-                        - value = (object["value"] || object["acronym"] || object["id"])
-                        %div{data: {controller: 'tooltip'}, title: title}
-                          = render ChipsComponent.new(id: value, name: key, value: value,
-                                    label:  object["acronym"].humanize,
-                                    checked: values[1]&.include?(object["id"])) do |c|
-                            - c.count do
-                              %span.badge.badge-light.ml-1
-                                = turbo_frame_tag "count_#{key}_#{object["id"]}", busy: true
-                                %span.show-if-loading
-                                  = render LoaderComponent.new(small:true)
+                        - title = (key.eql?(:categories) || key.eql?(:groups)) ? nil : ''
+                        = group_chip_component(name: key, object: object, checked: values[1]&.include?(object["id"]), title: title) do |c|
+                          - c.count do
+                            %span.badge.badge-light.ml-1
+                              = turbo_frame_tag "count_#{key}_#{object["id"]}", busy: true
+                              %span.show-if-loading
+                                = render LoaderComponent.new(small:true)
 
         .browse-second-row
           .browse-search-bar

app/views/ontologies/new.html.haml

@@ -27,7 +27,7 @@
                   .upload-ontology-input-field-container
                     = attribute_input('description', long_text: true)
                   - if @is_update_ontology
-                    .upload-ontology-input-field-container
+                    .upload-ontology-input-field-container{id: "submissionnotes_from_group_input"}
                       = attribute_input("notes", label: 'Change notes')
                   .upload-ontology-field-container
                     = render Layout::RevealComponent.new(init_show: @submission.hasOntologyLanguage&.eql?('SKOS'), show_condition: 'SKOS') do |c|
@@ -44,6 +44,7 @@
                       - c.button do
                         = attribute_input("status")
                       .upload-ontology-field-container
+                        - @submission.valid = nil unless @submission.status&.eql?('retired')
                         = attribute_input("valid")
                   .upload-ontology-field-container
                     = render partial: 'ontologies/submission_location_form'
@@ -54,5 +55,5 @@
                       = attribute_input('modificationDate', label: 'Modification date', max_date: Date.today)
                     - else
                       = attribute_input('released',  label: 'Date of original creation',  max_date: Date.today)
-                  .upload-ontology-contact
+                  .upload-ontology-contact{id: "submissioncontact_from_group_input"}
                     = contact_input(show_help: false)