Fix: Open to add values to some metadata attribute in the submission …

…edit form (#392)

* show ontology groups in the ontology summary page

* updatr account page to show empty state  of Subscriptions,  Submitted and projects

* don't stop the API server after running the tests

* add chrome-server service to run integration test

* add users creation & login  flow tests

* add submission creation system tests

* add system tests CI

* fix development environnement not raising exception

* if submission status icon helper with the correct conditions

* not show the ontology data section if the submission is not ready

* add an alert message in summary page, to give information about this submission statueses

* add remote api of Stageportal tests CI

* add option to the ontoportal script to run test with a remote API

* fix ontologies with no submissions summary page state

* build docker images in github hub  in addition of docker

* add test coverage report

* fix ontology viewer sections order

* fix  summary icons, by  adding publication, title and enforce disabled

* add admin block helper

* add to the ontology viewer private, hasLanguage and  retired badges

* add a title to the json and subscribe button to give their usages

* fix summary usage and methodology properties not showing

* add :award to summary page "usage" block

* add :exampleIdentifier to the summary identifiers block

* add ::associatedMedia, :bugDatabase, :mailingList, :uriRegexPattern to summary links block

* add :toDoList and :notes to summary  methodology block

* add a an admin block in the summary page for the configuration metadata

* lazy load the ontology view section in development mode for better perf

* add the abstract to ontology summary description block

* update the summary page description text to integrate multiple metadata

 alternative, hasLicense, prefix, namespace, metadataVoc

* add ontology edit metadata tests

* fix browse not working in local french

* remove reset button in submission forms

* fix metrics evolution popup title

* add in summary page  show all metrics popup

* don't humanize agent name and show them as saved

* fix the new hasOntologyLanguage badge for the one that are nil

* fix landscape average metrics all NaN

* fix metadata curator returning content missing

* fix subscribe button unwatch state title

* hide topnav "Recently Viewed" if empty

* fix user edit form button style

* add useGuidelines and copyrightHolder to the ontology licenses popup

* add submission hasDomain  to the summary general information block

* fix agent input for single fields

* fix select input not removing the text written after select

* add no list agents input support

* fix missing translate for concept selector in mappings page

* fix recemender insert text missing translation

* use the select component for the relations inputs

* fix ontologies tries not opening for OWL ones

* handle the case of an ontology with no submission

* disable copryright holder editing

* add again remove images that are still used

* add rest_url helper, that clean the give $REST_URL in the configuration

* make the stop_api script also remove the volumes

* add agent creation system tests

* fix submission single agent input ( e.g copyrightHolder )

* open to add ontology relation inputs except hasPriorVersion

* fix the edition of curatedOn metadata and also the display as a list

* update submission flow tests to the remaining tests (agent, curatedOn)

* update some attribute in submission from to be open to add values

* fix switch input for boolean type as Deprecated

* update retired badge to have two state deprecated in orange or retired in red

* add codevoc  generation

* update trancate text to not be hidden but scrollable

* move the alternative and hiddenLabel as tooltip of the ontology name

* add community and content blocks in summary page

* add ontology license badge in the ontology viewer header

* add required option to select input used for hasOntologyLanguage

* auto select person type in the agent from if new

* don't show the cancel button in agent input if the agent is not a list

* add submission description filter to the browse page

* remove a slow call the tree display and fix the language all display

* fix agent input been removed from submission after edited

* add admin agents edition system tests

* fix user subscription if subscribed to a no more existent ontology

Dockerfile

@@ -37,7 +37,7 @@ RUN bundle install
 
 RUN echo "--modules-folder /node_modules" > .yarnrc
 COPY package.json *yarn* ./
-RUN yarn install && yarn build
+RUN yarn install
 
 COPY . .
 

app/assets/stylesheets/bioportal.scss

@@ -49,6 +49,32 @@ body{
 
 }
 
+.disabled-link{
+  color: #888888 !important;
+  span{
+    opacity: 0.6;
+  }
+  a {
+    color: #888888 !important;
+  }
+  svg path{
+    fill: #888888 !important;
+  }
+}
+.text-truncate-scroll{
+  overflow: scroll;
+  white-space: nowrap;
+}
+
+
+.bg-warning-light{
+  background-color: var(--bg-warning-light-color) !important;
+}
+
+.bg-danger-light{
+  background-color: var(--bg-danger-light-color) !important;
+}
+
 @keyframes gradient {
   0% {
     background-position: 0% 50%;

app/assets/stylesheets/components/alert.scss

@@ -3,24 +3,26 @@
     align-items: center;
     padding: 20px;
     border-radius: 5px;
+
+
 }
+
 .alert-container.alert-info-type{
-    background-color: rgba(59, 130, 246, 0.1);
+    background-color:  var(--bg-info-light-color);
 }
 .alert-container.alert-warning-type {
-    background-color: rgba(234, 179, 8, 0.1);
+    background-color: var(--bg-warning-light-color);
 }
 .alert-container.alert-danger-type {
-    background-color: rgba(239, 68, 68, 0.1);
+    background-color: var(--bg-danger-light-color);
 }
 .alert-container.alert-success-type {
-    background-color: rgba(34, 197, 94, 0.1);
+    background-color: var(--bg-success-light-color);
 }
 
 
 
 
-
 .alert-message{
     font-size: 16px;
     margin: 0 10px;
@@ -43,8 +45,6 @@
 }
 
 
-
-
 .alert-icon svg{
     width: 25px;
     margin: 0 !important;

app/assets/stylesheets/theme-variables.scss.erb

@@ -33,7 +33,6 @@
             --primary-color: #5499a4;
             --hover-color: #6B96B7;
             --secondary-color: #ffc107;
-            --light-color: #F0F5F6;
             --admin-color: #145FF4;
             --light-color: #F1F6FA;
             --error-color: #EB4335;
@@ -44,6 +43,16 @@
 
 
 
+// common variables
+:root{
+    --container-max-width: 1248px;
+    --bg-info-light-color: rgba(59, 130, 246, 0.1);
+    --bg-danger-light-color: rgba(239, 68, 68, 0.1);
+    --bg-warning-light-color: rgba(234, 179, 8, 0.1);
+    --bg-success-light-color: rgba(34, 197, 94, 0.1);
+}
+
+
 
 
 

app/components/agent_search_input_component/agent_search_input_component.html.haml

@@ -2,7 +2,7 @@
 = render SearchInputComponent.new(id: 'agent' + @id, name:'agent' + @id, ajax_url: "/ajax/agents?agent_type=#{@agent_type}&name=",
      item_base_url:"/agents/#{@id}?parent_id=#{@parent_id}&edit_on_modal=#{@edit_on_modal}&name_prefix=#{@name_prefix}&deletable=#{@deletable}&agent_id=", id_key: 'id',
      use_cache: false,
-     actions_links: {create_new_agent: {link: "/agents/new?name=&id=#{@id}&parent_id=#{@parent_id}&type=#{@agent_type}&show_affiliations=#{@show_affiliations}&edit_on_modal=#{@edit_on_modal}&name_prefix=#{@name_prefix}[#{@id}]", target:'_self'}}) do |s|
+     actions_links: {create_new_agent: {link: "/agents/new?name=&id=#{@id}&parent_id=#{@parent_id}&type=#{@agent_type}&show_affiliations=#{@show_affiliations}&deletable=#{@deletable}&edit_on_modal=#{@edit_on_modal}&name_prefix=#{@name_prefix}[#{@id}]", target:'_self'}}) do |s|
   - s.template do
     %a{href: "LINK", class: "search-content", 'data-turbo-frame': '_self'}
       %p.search-element.home-searched-ontology

app/components/chip_button_component/chip_button_component.html.haml

@@ -1,5 +1,6 @@
 - if @type == "static"
-    %span.chip_button_container{@html_options}
-        = @text || content
+  %span.chip_button_container{@html_options}
+    = @text || content
 - else
-    %a.chip_button_container_clickable{@html_options}= @text || content
+  %span.chip_button_container_clickable{@html_options}
+    = @text || content

app/components/input/select_component.rb

@@ -2,21 +2,23 @@
 
 class Input::SelectComponent < Input::InputFieldComponent
 
-  def initialize(id: nil, label: '', name:, value: [], selected: '', placeholder: '', error_message: '', helper_text: '', multiple: false, open_to_add_values: false, data: {}, tooltip: nil)
+  def initialize(id: nil, label: '', name:, value: [], selected: '', placeholder: '', error_message: '', helper_text: '', multiple: false, open_to_add_values: false, required: false,  data: {}, tooltip: nil)
     super(label: label, name: name, value: value, placeholder: placeholder, error_message: error_message,
           helper_text: helper_text, data: data)
     @values = value
     @selected = selected
     @open_to_add_values = open_to_add_values
     @multiple = multiple
     @id = id
+    @required = required
   end
 
   def call
     render Input::InputFieldComponent.new(name: @name, error_message: @error_message, helper_text: @helper_text, label: @label) do
       render SelectInputComponent.new(id: @id, name: @name, values: @values, selected: @selected,
-                                      placeholder: @placeholder,
-                                      multiple: @multiple, open_to_add_values: @open_to_add_values, data: @data)
+                                      placeholder: @placeholder, required: @required,
+                                      multiple: @multiple, open_to_add_values: @open_to_add_values,
+                                      data: @data)
     end
   end
 end

app/components/layout/horizontal_list_component.rb

@@ -9,7 +9,7 @@ def call
     content_tag(:div, class: 'd-flex flex-wrap align-items-center') do
       out = ''
       elements.each do |element|
-        out = out +  content_tag(:div, element, class: 'mr-1 mb-1 text-truncate overflow-hidden')
+        out = out +  content_tag(:div, element, class: 'mr-1 mb-1 text-truncate-scroll')
       end
       raw out
     end

app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml

@@ -59,7 +59,7 @@
         %span.mx-1
           = render ChipButtonComponent.new(type: "clickable") do
             = ontology[:format]
-      - if ontology[:deprecated]
+      - if ontology_retired?(ontology)
         %span.mx-1
           = ontology_retired_badge(ontology)
       - if ontology[:viewOfOnt]
@@ -68,8 +68,7 @@
 
       - if session[:user]&.admin?
         %div.mx-1{title: content_tag(:div, debug(ontology), style: 'height: 300px; overflow: scroll'), data:{controller: 'tooltip', 'tooltip-interactive-value': 'true'}}
-          %span.admin-background
-            = render ChipButtonComponent.new(type: "clickable", text: "Debug")
+          = render ChipButtonComponent.new(type: "clickable", text: "Debug" , class: 'admin-background')
 - else
   .browse-ontology-container
     .browse-sket

app/components/select_input_component.rb

@@ -2,7 +2,7 @@
 
 class SelectInputComponent < ViewComponent::Base
 
-  def initialize(id:, name:, values:, selected: nil, multiple: false, open_to_add_values: false, data: {}, placeholder: '')
+  def initialize(id:, name:, values:, selected: nil, multiple: false, open_to_add_values: false, required: false, data: {}, placeholder: '')
     super
     @id = id || ''
     @name = name
@@ -12,21 +12,25 @@ def initialize(id:, name:, values:, selected: nil, multiple: false, open_to_add_
     @open_to_add_values = open_to_add_values
     @placeholder = placeholder
     @data = data
+    @required = required
   end
 
   def call
-    select_input_tag(@id, @name, @values, @selected, multiple: @multiple, open_to_add_values: @open_to_add_values, placeholder: @placeholder)
+    select_input_tag(@id, @name, @values, @selected, multiple: @multiple, open_to_add_values: @open_to_add_values,
+                     placeholder: @placeholder, required: @required)
   end
 
   private
 
   def select_input_tag(id, name, values, selected, options = {})
     multiple = options[:multiple] || false
     open_to_add_values = options[:open_to_add_values] || false
+    required = options[:required] || false
     placeholder = options[:placeholder] || ''
     data = @data.merge({
                          'select-input-multiple-value': multiple,
-                         'select-input-open-add-value': open_to_add_values
+                         'select-input-open-add-value': open_to_add_values,
+                         'select-input-required-value': required,
                        })
     data[:controller] = "#{data[:controller]} select-input"
 

app/components/select_input_component/select_input_component_controller.js

@@ -4,7 +4,8 @@ import {useTomSelect} from "../../javascript/mixins/useTomSelect"
 export default class extends Controller {
     static values = {
         multiple: {type: Boolean, default: false},
-        openAdd: {type: Boolean, default: false}
+        openAdd: {type: Boolean, default: false},
+        required: {type: Boolean, default: false}
     };
 
 
@@ -34,10 +35,14 @@ export default class extends Controller {
             myOptions['create'] = true;
         }
 
-        useTomSelect(this.element, myOptions, this.#triggerChange.bind(this))
+        this.select = useTomSelect(this.element, myOptions, this.#triggerChange.bind(this))
     }
 
     #triggerChange() {
-        document.dispatchEvent(new Event('change', {target: this.element}))
+        if (this.requiredValue && !this.multipleValue && this.select.getValue() === ""){
+            this.select.setValue(Object.keys(this.select.options)[0])
+        }
+
+        document.dispatchEvent(new Event('change', { target: this.element }))
     }
 }

app/components/switch_input_component.rb

@@ -15,7 +15,7 @@ def initialize(id:, name: , label: '', value: '', checked: false, boolean_switch
   end
 
   def boolean_switch_action
-    "this.previousElementSibling.value = this.previousElementSibling.value !== 'true'" if @boolean_switch
+    "this.parentElement.previousElementSibling.value = this.parentElement.previousElementSibling.value !== 'true'" if @boolean_switch
   end
 
   def check_box_name

app/components/switch_input_component/switch_input_component.html.haml

@@ -1,8 +1,8 @@
 %div.switch-filter
-  - if @boolean_switch
-    = hidden_field_tag @name, @value
   - if content || !@label.empty?
     = content_tag(:div, content || @label, style: @style)
+  - if @boolean_switch
+    = hidden_field_tag @name, @value
   %label.switch{for: check_box_id}
     = check_box_tag  check_box_name, @value, @checked, class: '', id:  check_box_id, onChange: "#{boolean_switch_action}"
     %span.slider

app/controllers/agents_controller.rb

@@ -41,31 +41,36 @@ def new
     @agent.name = params[:name]
     @name_prefix = params[:name_prefix] || ''
     @show_affiliations = params[:show_affiliations].nil? || params[:show_affiliations]&.eql?('true')
+    @deletable = params[:deletable]&.eql?('true')
   end
 
   def create
     new_agent = save_agent(agent_params)
     parent_id = params[:parent_id]
     name_prefix = params[:name_prefix]
     alert_id = agent_id_alert_container_id(params[:id], parent_id)
-
+    deletable = params[:deletable]&.eql?('true')
     if new_agent.errors
       render_turbo_stream alert_error(id: alert_id) { JSON.pretty_generate(response_errors(new_agent)) }
     else
       success_message = 'New Agent added successfully'
       streams = [alert_success(id: alert_id) { success_message }]
 
       streams << prepend('agents_table_content', partial: 'agents/show_line', locals: { agent: new_agent })
-      streams << replace_agent_form(new_agent, agent_id: nil, frame_id: params[:id], parent_id: parent_id, name_prefix: name_prefix) if params[:parent_id]
+      streams << replace_agent_form(new_agent, agent_id: nil, frame_id: params[:id],
+                                    parent_id: parent_id, name_prefix: name_prefix,
+                                    deletable: deletable
+      ) if params[:parent_id]
 
       render_turbo_stream(*streams)
     end
   end
 
   def edit
     @agent = LinkedData::Client::Models::Agent.find("#{rest_url}/Agents/#{params[:id]}")
-    @name_prefix = params[:parent_id] || ''
+    @name_prefix = params[:name_prefix] || ''
     @show_affiliations = params[:show_affiliations].nil? || params[:show_affiliations].eql?('true')
+    @deletable = params[:deletable].to_s.eql?('true')
   end
 
   def show_search
@@ -88,18 +93,18 @@ def update
 
     parent_id = params[:parent_id]
     alert_id = agent_alert_container_id(agent, parent_id)
-
+    deletable = params[:deletable]&.eql?('true')
     if response_error?(agent_update)
       render_turbo_stream(alert_error(id: alert_id) { JSON.pretty_generate(response_errors(agent_update)) })
     else
       success_message = 'Agent successfully updated'
       table_line_id = agent_table_line_id(agent_id(agent))
-
+      agent = LinkedData::Client::Models::Agent.find(agent.id)
       streams = [alert_success(id: alert_id) { success_message },
                  replace(table_line_id, partial: 'agents/show_line', locals: { agent: agent })
       ]
 
-      streams << replace_agent_form(agent, parent_id: parent_id) if params[:parent_id]
+      streams << replace_agent_form(agent, agent_id: agent_id(agent.id), name_prefix: params[:name_prefix] , parent_id: parent_id, deletable: deletable) if params[:parent_id]
 
       render_turbo_stream(*streams)
     end
@@ -176,14 +181,14 @@ def destroy
 
   private
 
-  def replace_agent_form(agent, agent_id: nil, frame_id: nil, parent_id:, partial: 'agents/agent_show', name_prefix: '')
+  def replace_agent_form(agent, agent_id: nil, frame_id: nil, parent_id:, partial: 'agents/agent_show', name_prefix: '', deletable: true)
 
     frame_id = frame_id ? agent_id_frame_id(frame_id, parent_id) : agent_frame_id(agent, parent_id)
 
     replace(frame_id, partial: partial, layout: false ,
             locals: { agent_id: agent_id, agent: agent, name_prefix: name_prefix, parent_id: parent_id,
                       edit_on_modal: false,
-                      deletable: true})
+                      deletable: deletable})
   end
 
   def save_agent(params)

app/controllers/concerns/submission_filter.rb

@@ -53,7 +53,7 @@ def filters_params(params, includes: BROWSE_ATTRIBUTES.join(','), page: 1, pages
       isOfType: :isOfType,
       format: :hasOntologyLanguage,
       hasFormalityLevel: :hasFormalityLevel,
-      search: %i[name acronym],
+      search: %i[name acronym description],
       sort_by: :order_by
     }
 

app/controllers/ontologies_controller.rb

@@ -319,13 +319,15 @@ def summary
       ["#{helpers.attr_label(attr, attr_metadata: helpers.attr_metadata(attr), show_tooltip: false)}(#{relation})",
        relation]
     end
-    @config_properties = properties_hash_values([:obsoleteParent] + category_attributes["object description properties"])
-    @methodology_properties = properties_hash_values(category_attributes["methodology"] + [:toDoList, :notes])
+    @config_properties = properties_hash_values(category_attributes["object description properties"])
+    @methodology_properties = properties_hash_values(category_attributes["methodology"])
     @agents_properties = properties_hash_values(category_attributes["persons and organizations"])
     @dates_properties = properties_hash_values(category_attributes["dates"], custom_labels: {released: "Initially created On"})
-    @links_properties = properties_hash_values(category_attributes["links"] + [:associatedMedia, :bugDatabase, :mailingList, :uriRegexPattern])
-    @identifiers = properties_hash_values([:URI, :versionIRI, :identifier, :exampleIdentifier])
-    @projects_properties = properties_hash_values(category_attributes["usage"] + [:award])
+    @links_properties = properties_hash_values(category_attributes["links"])
+    @content_properties = properties_hash_values(category_attributes["content"])
+    @community_properties = properties_hash_values(category_attributes["community"] + [:notes])
+    @identifiers = properties_hash_values([:URI, :versionIRI, :identifier])
+    @projects_properties = properties_hash_values(category_attributes["usage"])
     @ontology_icon_links = [%w[summary/download dataDump],
                             %w[summary/homepage homepage],
                             %w[summary/documentation documentation],

app/controllers/subscriptions_controller.rb

@@ -25,6 +25,8 @@ def create
       # So here we re-generate a new subscription Array (instead of directly updating it, which causes error)
       all_subs = []
       u.subscription.each do |subs|
+        next if subs.ontology.nil?
+
         # Add all subscription to the array, but not the one to be deleted
         if !subs.ontology.split('/').last.eql?(ont.acronym)
           all_subs.push({ontology: subs.ontology, notification_type: subs.notification_type})
@@ -42,6 +44,7 @@ def create
       already_subscribed = false
       all_subs = []
       u.subscription.each do |subs|
+        next if subs.ontology.nil?
         # add all existing subscriptions
         all_subs.push({ontology: subs.ontology, notification_type: subs.notification_type})
         if subs.ontology.split("/").last == ont.acronym && subs.notification_type == "NOTES"