From 1e4204f815c10d50807b5f46ba09ae4e8905ed3e Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Thu, 25 Jul 2024 16:37:49 +0200
Subject: [PATCH 1/5] Feature: Enhance agents search input component (#703)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* make agents search field component results unlimited to only 4

* make agents cherchable by acronym, affiliations, email and home page

* Update the agent search input to display the result in this format Orga name (ACRONYM) – ROR:003vg9w96 and for persons Person Name – ORCID:0000-1524-5487-5487

* chagne display mode value type from string to boolean in search input component

* remove agents search logic from UI side and limit it to only name, acronym and identifiers

* use the endpoint '/search/agents' for the agents search input component
---
 .../stylesheets/components/search_input.scss  |  6 +++++
 .../agent_search_input_component.html.haml    |  4 ++--
 app/components/search_input_component.rb      |  7 +++++-
 .../search_input_component.html.haml          |  5 ++--
 .../search_input_component_controller.js      | 23 +++++++++++--------
 app/controllers/agents_controller.rb          | 16 ++++++-------
 6 files changed, 39 insertions(+), 22 deletions(-)

diff --git a/app/assets/stylesheets/components/search_input.scss b/app/assets/stylesheets/components/search_input.scss
index dd721562a..883899fbc 100644
--- a/app/assets/stylesheets/components/search_input.scss
+++ b/app/assets/stylesheets/components/search_input.scss
@@ -9,6 +9,12 @@
   position: absolute;
 }
 
+.search-container.search-container-scroll{
+  max-height: 400px;
+  overflow-y: auto;
+}
+
+
 .search-content{
   display: flex;
   flex-wrap: wrap;
diff --git a/app/components/agent_search_input_component/agent_search_input_component.html.haml b/app/components/agent_search_input_component/agent_search_input_component.html.haml
index 02b022ae1..9da8101b5 100644
--- a/app/components/agent_search_input_component/agent_search_input_component.html.haml
+++ b/app/components/agent_search_input_component/agent_search_input_component.html.haml
@@ -1,11 +1,11 @@
 = hidden_field_tag  "#{@name_prefix}[#{@id}]"
-= render SearchInputComponent.new(id: 'agent' + @id, name:'agent' + @id, ajax_url: "/ajax/agents?agent_type=#{@agent_type}&name=",
+= render SearchInputComponent.new(id: 'agent' + @id, name:'agent' + @id, ajax_url: "/ajax/agents?query=", display_all: true,
      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}&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
-        NAME (IDENTIFIERS)
+        NAME ACRONYM IDENTIFIERS
       %p.home-result-type
         TYPE
diff --git a/app/components/search_input_component.rb b/app/components/search_input_component.rb
index 941b03d2e..9390797d3 100644
--- a/app/components/search_input_component.rb
+++ b/app/components/search_input_component.rb
@@ -11,7 +11,8 @@ def initialize(id: '',
                  item_base_url:,
                  id_key:,
                  links_target: '_top',
-                 search_icon_type: nil)
+                 search_icon_type: nil,
+                 display_all: false)
     @id = id
     @name = name
     @placeholder = placeholder
@@ -23,6 +24,7 @@ def initialize(id: '',
     @id_key = id_key
     @links_target = links_target
     @search_icon_type = search_icon_type
+    @display_all = display_all
   end
   def action_link_info(value)
     if value.is_a?(Hash)
@@ -34,4 +36,7 @@ def action_link_info(value)
   def nav_icon_class
     @search_icon_type.eql?('nav') ? 'search-input-nav-icon' : ''
   end
+  def display_all_mode_class
+    @display_all ? 'search-container-scroll' : ''
+  end
 end
diff --git a/app/components/search_input_component/search_input_component.html.haml b/app/components/search_input_component/search_input_component.html.haml
index fb0d79f28..9d5e19384 100644
--- a/app/components/search_input_component/search_input_component.html.haml
+++ b/app/components/search_input_component/search_input_component.html.haml
@@ -4,7 +4,8 @@
   'data-search-input-id-key-value': @id_key,
   'data-search-input-cache-value': @use_cache.to_s,
   'data-search-input-scroll-down-value': @scroll_down.to_s,
-  'data-search-input-selected-item-value': 0
+  'data-search-input-selected-item-value': 0,
+  'data-search-input-display-all-value': @display_all
   }
 
   - if @search_icon_type
@@ -21,7 +22,7 @@
   = render Input::InputFieldComponent.new(name: @name, placeholder: @placeholder,
                                             data: {'action': 'input->search-input#search blur->search-input#blur keydown.down->search-input#arrow_down keydown.up->search-input#arrow_up keydown.enter->search-input#enter_key',
                                             'search-input-target': 'input'})
-  .search-container{'data-search-input-target': 'dropDown', 'data-action': 'mousedown->search-input#prevent'}
+  %div{class: "search-container #{display_all_mode_class}", 'data-search-input-target': 'dropDown', 'data-action': 'mousedown->search-input#prevent'}
     - @actions_links.each do |key, value|
       - link, target = action_link_info(value)
       %a.search-content#search-content{href:  link, 'data-turbo-frame': target, 'data-search-input-target': 'actionLink'}
diff --git a/app/components/search_input_component/search_input_component_controller.js b/app/components/search_input_component/search_input_component_controller.js
index 5c8d07cad..957dc6f04 100644
--- a/app/components/search_input_component/search_input_component_controller.js
+++ b/app/components/search_input_component/search_input_component_controller.js
@@ -12,7 +12,8 @@ export default class extends Controller {
         idKey: String,
         cache: {type: Boolean, default: true},
         selectedItem: Number,
-        searchEndpoint: {type: String, default: '/search'}
+        searchEndpoint: {type: String, default: '/search'},
+        displayAll: Boolean
     }
 
     connect() {
@@ -114,14 +115,14 @@ export default class extends Controller {
             this.dropDown.innerHTML = ""
             let breaker = 0
             for (let i = 0; i < this.items.length; i++) {
-                if (breaker === 4) {
+                if (!this.displayAllValue && breaker === 4) {
                     break;
                 }
                 // Get the current item from the ontologies array
                 const item = this.items[i];
 
                 let text =  Object.values(item).reduce((acc, value) => acc + value, "")
-
+                
                 // Check if the item contains the substring
                 if (!this.cacheValue || text.toLowerCase().includes(inputValue.toLowerCase())) {
                     results_list.push(item);
@@ -149,18 +150,22 @@ export default class extends Controller {
 
     #renderLine(item) {
         let template = this.templateTarget.content
-        let newElement = template.firstElementChild
-        let string = newElement.outerHTML
-
+        let newElement = template.firstElementChild.outerHTML
         Object.entries(item).forEach( ([key, value]) => {
             key = key.toString().toUpperCase()
             if (key === 'TYPE'){
                 value  = value.toString().split('/').slice(-1)
             }
+            if (key === 'ACRONYM'){
+                value = value ? `(${value.toString()})` : ''
+            }
+            if (key === 'IDENTIFIERS'){
+                value = value ? `- ${value.toString()}` : ''
+            }
             const regex = new RegExp('\\b' + key + '\\b', 'gi');
-            string =  string.replace(regex, value ? value.toString() : "")
+            newElement =  newElement.replace(regex, value ? value.toString() : "")
         })
-
-        return new DOMParser().parseFromString(string, "text/html").body.firstElementChild
+        
+        return new DOMParser().parseFromString(newElement, "text/html").body.firstElementChild
     }
 }
diff --git a/app/controllers/agents_controller.rb b/app/controllers/agents_controller.rb
index 08411245f..678892a7f 100644
--- a/app/controllers/agents_controller.rb
+++ b/app/controllers/agents_controller.rb
@@ -18,15 +18,15 @@ def show
   end
 
   def ajax_agents
-    filters = { name: params[:name] }
-    filters[:agentType] = params[:agent_type] if params[:agent_type]
-    @agents = LinkedData::Client::Models::Agent.all(filters)
-    agents_json = @agents.map do |x|
+    filters = { query: params[:query]}
+    @agents = LinkedData::Client::HTTP.get('/search/agents', filters)
+    agents_json = @agents.collection.map do |x|
       {
-        id: x.id,
-        name: x.name,
-        type: x.agentType,
-        identifiers: x.identifiers.map { |i| "#{i.schemaAgency}:#{i.notation}" }.join(', ')
+        id: x.resource_id,
+        name: x.name_text,
+        type: x.agentType_t,
+        identifiers: x.identifiers_texts&.join(', '),
+        acronym: x.acronym_text
       }
     end
 

From 4dfcc83dc7b90a8e8fe4e8eb1652784071863243 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Thu, 1 Aug 2024 16:58:20 +0200
Subject: [PATCH 2/5] Fix: saving and cancel button locals text capitalization
 (#724)

---
 config/locales/en.yml | 6 +++---
 config/locales/fr.yml | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/config/locales/en.yml b/config/locales/en.yml
index fd083756c..63fd0b572 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -946,7 +946,7 @@ en:
       synonym: Synonym
       definition: Definition
       parent: Parent
-      save: save
+      save: Save
     note_line:
       alert_text: "Are you sure you want to delete the note <span style='color:red;font-weight:bold;'> ''%{subject}''</span> created by <span style='color:red;font-weight:bold;'>%{creator}</span>?<br/><b>This action CAN NOT be undone!!!</b>"
       delete: Delete
@@ -957,8 +957,8 @@ en:
     reply:
       about_note_decorator: about %{note_decorator}
       comment: Comment
-      save: save
-      cancel: cancel
+      save: Save
+      cancel: Cancel
   ontolobridge:
     problem_of_creating_new_term: "Problem creating a new term %{endpoint}: %{class} - %{message}"
     new_term_instructions_saved: New term request instructions for %{acronym} saved
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index fd6bde39e..e83bd927c 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -964,7 +964,7 @@ fr:
       synonym: Synonyme
       definition: Définition
       parent: Parent
-      save: sauvegarder
+      save: Sauvegarder
     note_line:
       alert_text: "Êtes-vous sûr de vouloir supprimer la note <span style='color:red;font-weight:bold;'> ''%{subject}''</span> créée par <span style='color:red;font-weight:bold;'>%{creator}</span>?<br/><b>Cette action NE PEUT PAS être annulée !!!</b>"
       delete: Supprimer
@@ -975,8 +975,8 @@ fr:
     reply:
       about_note_decorator: à propos de %{note_decorator}
       comment: Commentaire
-      save: sauvegarder
-      cancel: annuler
+      save: Sauvegarder
+      cancel: Annuler
 
   ontolobridge:
     problem_of_creating_new_term: "Problème de création d'un nouveau terme %{endpoint} : %{class} - %{message}"

From 49a4c43a0e649dc87d45b066248fcd5217dc15fe Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Fri, 2 Aug 2024 12:10:46 +0200
Subject: [PATCH 3/5] Feature: add qf param in agents search (#727)

---
 app/controllers/agents_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/controllers/agents_controller.rb b/app/controllers/agents_controller.rb
index 678892a7f..652e01a40 100644
--- a/app/controllers/agents_controller.rb
+++ b/app/controllers/agents_controller.rb
@@ -18,7 +18,7 @@ def show
   end
 
   def ajax_agents
-    filters = { query: params[:query]}
+    filters = { query: params[:query], qf: "identifiers_texts^20 acronym_text^15 name_text^10 email_text^10"}
     @agents = LinkedData::Client::HTTP.get('/search/agents', filters)
     agents_json = @agents.collection.map do |x|
       {

From c6d7c8ec63a58e8f0695e182e039b54e642f77ac Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Sun, 4 Aug 2024 09:54:16 +0200
Subject: [PATCH 4/5] Fix: Hide affiliations when agent is organization in
 agent form (#696)

* Hide affiliations when the agent is an organization in the agents form

* Change the name of the function affliations? to is_organization? to make it more clear

* fix submission flows test after the fix of the PR #713

* fix agent tests after changing the behavior of displaying affiliations

---------

Co-authored-by: Syphax <gs_bouazzouni@esi.dz>
---
 app/helpers/agent_helper.rb          | 16 ++++-----
 app/views/agents/_form.html.haml     | 10 +++---
 bin/run_api                          |  4 +--
 test/application_system_test_case.rb | 10 +++---
 test/fixtures/agents.yml             | 53 ----------------------------
 test/fixtures/ontologies.yml         |  7 ++--
 test/system/agent_flows_test.rb      | 10 +++---
 test/system/submission_flows_test.rb |  9 +++--
 8 files changed, 35 insertions(+), 84 deletions(-)

diff --git a/app/helpers/agent_helper.rb b/app/helpers/agent_helper.rb
index af3902fbd..513854f0f 100644
--- a/app/helpers/agent_helper.rb
+++ b/app/helpers/agent_helper.rb
@@ -69,7 +69,7 @@ def agent_search_input(id, agent_type, parent_id: , name_prefix:, deletable: fal
   end
 
 
-  def affiliation?(agent)
+  def is_organization?(agent)
     agent.agentType.eql?('organization')
   end
 
@@ -163,7 +163,7 @@ def display_agent(agent, link: true)
   def agent_tooltip(agent)
     name = agent.name
     email = agent.email
-    type = agent.agentType 
+    type = agent.agentType
     identifiers = display_identifiers(agent.identifiers, link: false)
     identifiers = orcid_number(identifiers)
     if agent.affiliations && agent.affiliations != []
@@ -203,7 +203,7 @@ def generate_agent_tooltip(agent_icon, name, email = nil, identifiers = nil, aff
       end
     end
   end
-  
+
 
   def agent_chip_component(agent)
     person_icon = inline_svg_tag 'icons/person.svg' , class: 'agent-type-icon'
@@ -219,16 +219,16 @@ def agent_chip_component(agent)
       title = agent_tooltip(agent)
     end
     render_chip_component(title, agent_icon, name)
-  end 
+  end
 
 
   def render_chip_component(title,agent_icon,name)
-    render ChipButtonComponent.new(type: "static",'data-controller':' tooltip', title: title , class: 'text-truncate', style: 'max-width: 280px; display:block; line-height: unset') do 
+    render ChipButtonComponent.new(type: "static",'data-controller':' tooltip', title: title , class: 'text-truncate', style: 'max-width: 280px; display:block; line-height: unset') do
       content_tag(:div, class: 'agent-chip') do
         content_tag(:div, agent_icon, class: 'agent-chip-circle') +
         content_tag(:div, name, class: 'agent-chip-name text-truncate')
-      end   
-    end 
+      end
+    end
   end
 
   def orcid_number(orcid)
@@ -236,5 +236,5 @@ def orcid_number(orcid)
   end
 
 
-  
+
 end
diff --git a/app/views/agents/_form.html.haml b/app/views/agents/_form.html.haml
index 60b02f33e..20c35857d 100644
--- a/app/views/agents/_form.html.haml
+++ b/app/views/agents/_form.html.haml
@@ -9,7 +9,7 @@
   = hidden_field_tag :deletable, deletable if deletable
   = hidden_field_tag agent_field_name(:id, name_prefix), agent.id if agent.id
 
-  - if affiliation?(agent) &&  params[:parent_id]
+  - if is_organization?(agent) &&  params[:parent_id]
     = hidden_field_tag agent_field_name(:agentType, name_prefix), agent.agentType
   - else
     %tr
@@ -30,19 +30,19 @@
       %span.asterik *
     %td.top
       = text_field_tag agent_field_name(:name, name_prefix), agent.name, class: "form-control"
-  %tr{'data-form-options-display-target':"option1",  class: affiliation?(agent) && 'd-none'}
+  %tr{'data-form-options-display-target':"option1",  class: is_organization?(agent) && 'd-none'}
     %th
       = t("agents.form.email")
       %span.asterik
     %td.top
       = email_field_tag agent_field_name(:email, name_prefix), agent.email, class: "form-control"
-  %tr{'data-form-options-display-target':"option2",  class: !affiliation?(agent) && 'd-none'}
+  %tr{'data-form-options-display-target':"option2",  class: !is_organization?(agent) && 'd-none'}
     %th
       = t("agents.form.acronym")
       %span.asterik
     %td.top
       = text_field_tag agent_field_name(:acronym, name_prefix), agent.acronym,class: "form-control"
-  %tr{'data-form-options-display-target':"option2",  class: !affiliation?(agent) && 'd-none'}
+  %tr{'data-form-options-display-target':"option2",  class: !is_organization?(agent) && 'd-none'}
     %th
       = t("agents.form.homepage")
     %td.top
@@ -78,7 +78,7 @@
                   - values = %w[ORCID ROR ISNI GRID]
                   = render SelectInputComponent.new(id: "#{name_prefix}_identifiers_schemaAgency_#{i.to_s.upcase}", name: agent_identifier_name(i.to_s.upcase, :schemaAgency, name_prefix), values: values, selected: identifier.schemaAgency)
   - if show_affiliations
-    %tr
+    %tr{'data-form-options-display-target':"option1",  class: is_organization?(agent) && 'd-none'}
       %th
         = t("agents.form.affiliations")
       %td.top.agents-affiliations.agents-inputs
diff --git a/bin/run_api b/bin/run_api
index 8ed4d11dc..5d1634b2f 100755
--- a/bin/run_api
+++ b/bin/run_api
@@ -52,7 +52,7 @@ image_tag="${image_tag:-$API_IMAGE_TAG}"
 starter_ontology="${starter_ontology:-$STARTER_ONTOLOGY}"
 remote_api_url="${remote_api_url:-$OP_API_URL}"
 
-if curl -sSf http://localhost:9393 > /dev/null 2>&1;  then
+if curl -sSf http://localhost:9393 > /dev/null 2>&1; then
   echo "API is already running in http://localhost:9393"
   exit 0
 fi
@@ -62,7 +62,7 @@ docker compose ls -a --filter "name=ontoportal_docker" | grep -q "ontoportal_doc
 (
   cd tmp/ontoportal_docker || exit 1
   command="./run -k $api_key -r $image_repository -t $image_tag -s $starter_ontology -u $remote_api_url"
-  [ "$no_provision" = true ] && command="$command --no-provision"
+  [ "$no_provision" = true ] && command="$command"
   echo "Run: $command"
   eval "$command"
 )
diff --git a/test/application_system_test_case.rb b/test/application_system_test_case.rb
index b4457f965..a33ff79e4 100644
--- a/test/application_system_test_case.rb
+++ b/test/application_system_test_case.rb
@@ -151,11 +151,11 @@ def agent_search(name)
 
   end
 
-  def agent_fill(agent, parent_id: nil, enable_affiliations: true)
+  def agent_fill(agent, parent_id: nil, is_affiliation: false)
     id = agent.id ? "/#{agent.id}": ''
     form = all("form[action=\"/agents#{id}\"]").first
     within form  do
-      choose "", option: agent.agentType, allow_label_click: true if enable_affiliations
+      choose "", option: agent.agentType, allow_label_click: true  unless is_affiliation
       fill_in 'name', with: agent.name
 
       if agent.agentType.eql?('organization')
@@ -171,8 +171,9 @@ def agent_fill(agent, parent_id: nil, enable_affiliations: true)
       list_inputs ".agents-identifiers",
                   "[identifiers]", agent.identifiers
 
-      unless enable_affiliations
+      if is_affiliation || agent.agentType.eql?('organization')
         refute_selector ".agents-affiliations"
+        click_on "Save" if agent.agentType.eql?('organization')
         return
       end
 
@@ -184,8 +185,7 @@ def agent_fill(agent, parent_id: nil, enable_affiliations: true)
           agent_id = agent_search(aff.name)
           id = parent_id && !parent_id.eql?('NEW_RECORD') ? "#{parent_id}_#{agent_id}" : agent_id
           within "turbo-frame[id=\"#{id}\"]" do
-            agent_fill(aff, enable_affiliations: false)
-            click_on "Save"
+            agent_fill(aff, is_affiliation: true)
             sleep 1
           end
         end
diff --git a/test/fixtures/agents.yml b/test/fixtures/agents.yml
index ce32845e0..7c1a33704 100644
--- a/test/fixtures/agents.yml
+++ b/test/fixtures/agents.yml
@@ -97,25 +97,6 @@ organization1:
     agentType: "organization"
     identifiers:
         - notation: "1234-5678"
-    affiliations:
-      - name: "Research Consortium A"
-        agentType: "organization"
-        identifiers:
-          - notation: "9876-5432"
-        affiliations: [ ]
-        email: "contact@researchconsortiumA.com"
-        acronym: "RCA"
-        homepage: "https://www.researchconsortiumA.com/"
-
-      - name: "Innovation Hub B"
-        agentType: "organization"
-        identifiers:
-          - notation: "3456-7890"
-        affiliations: [ ]
-        email: "info@innovationhubb.com"
-        acronym: "IHB"
-        homepage: "https://www.innovationhubb.com/"
-
     email: "info@techsolutionsgroup.com"
     acronym: "TSG"
     homepage: "https://www.techsolutionsgroup.com/"
@@ -125,23 +106,6 @@ organization2:
   agentType: "organization"
   identifiers:
     - notation: "5678-9012"
-  affiliations:
-    - name: "Space Exploration Consortium"
-      agentType: "organization"
-      identifiers:
-        - notation: "1234-1234"
-      affiliations: []
-      email: "contact@spaceconsortium.com"
-      acronym: "SEC"
-      homepage: "https://www.spaceconsortium.com/"
-    - name: "Tech Innovators Guild"
-      agentType: "organization"
-      identifiers:
-        - notation: "7890-1234"
-      affiliations: []
-      email: "info@techinnovatorsguild.com"
-      acronym: "TIG"
-      homepage: "https://www.techinnovatorsguild.com/"
   email: "info@quantumdynamics.com"
   acronym: "QDS"
   homepage: "https://www.quantumdynamics.com/"
@@ -151,23 +115,6 @@ organization3:
   agentType: "organization"
   identifiers:
     - notation: "2345-6789"
-  affiliations:
-    - name: "Health Research Alliance"
-      agentType: "organization"
-      identifiers:
-        - notation: "5678-9012"
-      affiliations: []
-      email: "contact@healthresearchalliance.com"
-      acronym: "HRA"
-      homepage: "https://www.healthresearchalliance.com/"
-    - name: "GreenTech Innovations"
-      agentType: "organization"
-      identifiers:
-        - notation: "8901-2345"
-      affiliations: []
-      email: "info@greentechinnovations.com"
-      acronym: "GTI"
-      homepage: "https://www.greentechinnovations.com/"
   email: "info@biotechsolutions.com"
   acronym: "BSI"
   homepage: "https://www.biotechsolutions.com/"
diff --git a/test/fixtures/ontologies.yml b/test/fixtures/ontologies.yml
index 1d9fa0daf..100d00b3a 100644
--- a/test/fixtures/ontologies.yml
+++ b/test/fixtures/ontologies.yml
@@ -83,10 +83,10 @@ resource_content_formats:
         "metadata_def:mappingSameURI":
           "@id": "ns0:T071"
         "metadata_def:mappingLoom": "entity"
-      - "@id": "ns0:T077"
+      - "@id": "ns0:T072"
         "rdfs:subClassOf":
           "@id": "ns0:T071"
-      - "@id": "ns0:T072"
+      - "@id": "ns0:T077"
         "rdfs:subClassOf":
           "@id": "ns0:T071"
   
@@ -119,9 +119,10 @@ resource_content_formats:
     <http://purl.bioontology.org/ontology/STY/T071> <http://www.w3.org/2004/02/skos/core#notation> "T071" .
     <http://purl.bioontology.org/ontology/STY/T071> <http://data.bioontology.org/metadata/def/mappingSameURI> <http://purl.bioontology.org/ontology/STY/T071> .
     <http://purl.bioontology.org/ontology/STY/T071> <http://data.bioontology.org/metadata/def/mappingLoom> "entity" .
+    <http://purl.bioontology.org/ontology/STY/T072> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.bioontology.org/ontology/STY/T071> .
     <http://purl.bioontology.org/ontology/STY/T077> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.bioontology.org/ontology/STY/T071> .
     <http://purl.bioontology.org/ontology/STY/T071> <http://data.bioontology.org/metadata/def/mappingSameURI> <http://purl.bioontology.org/ontology/STY/T071> .
-    <http://purl.bioontology.org/ontology/STY/T072> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://purl.bioontology.org/ontology/STY/T071> .
+
   
   turtle: |
     @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
diff --git a/test/system/agent_flows_test.rb b/test/system/agent_flows_test.rb
index 91be5fc8b..953c4d2e4 100644
--- a/test/system/agent_flows_test.rb
+++ b/test/system/agent_flows_test.rb
@@ -41,7 +41,7 @@ def teardown
     click_on "Persons & organizations"
 
     # Creation test
-    create_agent_flow(@new_organization, person_count: 0, organization_count: 3)
+    create_agent_flow(@new_organization, person_count: 0, organization_count: 1)
 
     # Edition test
     @new_organization2 = fixtures(:agents)[:organization2]
@@ -50,7 +50,7 @@ def teardown
     @new_organization2.id = edit_link['href'].split('/')[-2]
     edit_link.click
 
-    edit_agent_flow(@new_organization2, person_count: 0, organization_count: 5)
+    edit_agent_flow(@new_organization2, person_count: 0, organization_count: 1)
   end
 
 
@@ -61,7 +61,7 @@ def create_agent_flow(new_agent, person_count: , organization_count:)
     # Creation test
     click_on "Create New Agent"
     wait_for_text "TYPE"
-    agent_fill(new_agent)
+    agent_fill(new_agent, is_affiliation: false)
     sleep 1
     assert_text "New Agent added successfully"
     find('.close').click
@@ -75,7 +75,7 @@ def create_agent_flow(new_agent, person_count: , organization_count:)
       assert_text 'person', count: person_count
       assert_text 'organization', count: organization_count
 
-      new_agent.affiliations.map do |aff|
+      Array(new_agent.affiliations).map do |aff|
         aff["identifiers"] = aff["identifiers"].each{|x| x["schemaAgency"] = 'ORCID'}
         assert_text aff['name']
       end
@@ -97,7 +97,7 @@ def edit_agent_flow(agent, person_count: , organization_count: )
       assert_text 'person', count: person_count
       assert_text 'organization', count: organization_count
 
-      agent.affiliations.map do |aff|
+      Array(agent.affiliations).map do |aff|
         aff["identifiers"] = aff["identifiers"].each{|x| x["schemaAgency"] = 'ORCID'}
         assert_text aff['name']
       end
diff --git a/test/system/submission_flows_test.rb b/test/system/submission_flows_test.rb
index 635045cda..54adbeab5 100644
--- a/test/system/submission_flows_test.rb
+++ b/test/system/submission_flows_test.rb
@@ -203,12 +203,15 @@ class SubmissionFlowsTest < ApplicationSystemTestCase
     open_dropdown "#projects_section"
     usage_properties = [
       :coverage, :knownUsage,
-      :hasDomain, :example
+      :example
     ]
     usage_properties.each do |property|
       Array(submission_2[property]).each { |v| assert_text v } # check
     end
 
+    has_domain_values = ["Has Domain2.1", "Has Domain2.2", "Has Domain2.3"]
+    has_domain_values.each { |v| assert_text v }
+
     submission_2.designedForOntologyTask.each do |task|
       assert_text task.delete(' ') # TODO fix in the UI the disaply of taskes
     end
@@ -329,7 +332,7 @@ class SubmissionFlowsTest < ApplicationSystemTestCase
     assert_equal existent_submission.pullLocation, find_field('submission[pullLocation]').value
 
     click_button 'Next'
-    
+
     assert_equal Date.parse(existent_submission.modificationDate).to_s, find('[name="submission[modificationDate]"]', visible: false).value
     assert_equal existent_submission.contact.map(&:values).flatten.sort, all('[name^="submission[contact]"]').map(&:value).sort
 
@@ -651,4 +654,4 @@ def fill_ontology(new_ontology, new_submission, add_submission: false)
       click_button 'Finish'
     end
   end
-end
\ No newline at end of file
+end

From 5925571f01326e98880d30e6f70a058e66b1c95a Mon Sep 17 00:00:00 2001
From: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>
Date: Sun, 4 Aug 2024 11:46:47 +0200
Subject: [PATCH 5/5] Feature: Make agent indentifiers field set by default
 based on agent type (#721)

* remove the restriction for certain submission fields to create only organization type or person type agents

* make orcid or ror default input based on agent type in agent form

* fix disappeared signup form icons

* fix nested agents creation

* fix agent form not filling saved identifier values

* create an agent identifier input helper

* disable cookie banner in development and test  mode

* fix agent tests after enforcing ROR for organizations

---------

Co-authored-by: Syphax <gs_bouazzouni@esi.dz>
---
 app/assets/stylesheets/agents.scss   | 19 ++++++++
 app/controllers/agents_controller.rb |  4 ++
 app/helpers/agent_helper.rb          | 18 +++++++
 app/views/agents/_form.html.haml     | 36 +++++++-------
 app/views/layouts/_header.html.erb   | 72 +++++++++++++++++-----------
 app/views/users/_form.html.haml      |  4 +-
 test/system/agent_flows_test.rb      |  4 +-
 7 files changed, 110 insertions(+), 47 deletions(-)

diff --git a/app/assets/stylesheets/agents.scss b/app/assets/stylesheets/agents.scss
index df7b74d71..bed9b6b14 100644
--- a/app/assets/stylesheets/agents.scss
+++ b/app/assets/stylesheets/agents.scss
@@ -31,4 +31,23 @@
   display: flex !important;
   flex-direction: column;
   justify-content: center;
+}
+.agent-input-with-icon{
+  padding: 8px;
+  margin-bottom: 0px;
+  border-radius: 5px;
+  width: 100%;
+  color: #5f6573;
+  outline: none;
+  font-size: 15px;
+  font-weight: 500;
+  border: 1px solid #d7d7d7;
+  padding-left: 45px;
+}
+.agent-input-icon{
+  height: 20px;
+  width: 20px;
+  position: absolute;
+  padding: 11px 17px;
+  box-sizing: unset;
 }
\ No newline at end of file
diff --git a/app/controllers/agents_controller.rb b/app/controllers/agents_controller.rb
index 652e01a40..7ee6f3808 100644
--- a/app/controllers/agents_controller.rb
+++ b/app/controllers/agents_controller.rb
@@ -273,6 +273,10 @@ def agent_params
         v
       end
     end
+    identifiers_schemaAgency = params[:agentType].eql?('person') ? 'ORCID' : 'ROR'
+    p[:identifiers]&.each_value do |identifier|
+      identifier[:schemaAgency] = identifiers_schemaAgency
+    end
     p[:identifiers] = (p[:identifiers] || {}).values
     p[:affiliations] = (p[:affiliations] || {}).values
     p[:affiliations].each do |affiliation|
diff --git a/app/helpers/agent_helper.rb b/app/helpers/agent_helper.rb
index 513854f0f..6c5366bf7 100644
--- a/app/helpers/agent_helper.rb
+++ b/app/helpers/agent_helper.rb
@@ -82,6 +82,24 @@ def identifier_link(link, link_to: true)
 
   end
 
+
+  def agent_identifier_input(index, name_prefix, value = '', is_organization: true)
+
+    content_tag :div, id: index, class: 'd-flex' do
+      content_tag(:div, class: 'w-100') do
+
+        concat hidden_field_tag(agent_identifier_name(index , :creator, name_prefix), session[:user].id)
+        if is_organization
+          concat inline_svg_tag 'icons/ror.svg', class: 'agent-input-icon'
+        else
+          concat inline_svg_tag('orcid.svg', class: 'agent-input-icon')
+        end
+        concat text_field_tag(agent_identifier_name(index, :notation, name_prefix), value, class: 'agent-input-with-icon')
+      end
+    end
+  end
+
+
   def display_identifiers(identifiers, link: true)
     schemes_urls = { ORCID: 'https://orcid.org/', ISNI: 'https://isni.org/', ROR: 'https://ror.org/', GRID: 'https://www.grid.ac/' }
     Array(identifiers).map do |i|
diff --git a/app/views/agents/_form.html.haml b/app/views/agents/_form.html.haml
index 20c35857d..2e8aa35d4 100644
--- a/app/views/agents/_form.html.haml
+++ b/app/views/agents/_form.html.haml
@@ -9,7 +9,7 @@
   = hidden_field_tag :deletable, deletable if deletable
   = hidden_field_tag agent_field_name(:id, name_prefix), agent.id if agent.id
 
-  - if is_organization?(agent) &&  params[:parent_id]
+  - if is_organization?(agent) && params[:parent_id]
     = hidden_field_tag agent_field_name(:agentType, name_prefix), agent.agentType
   - else
     %tr
@@ -56,27 +56,31 @@
     %th
       = t("agents.form.identifiers")
     %td.top
-      %div.agents-identifiers
+      %div.agents-identifiers{'data-form-options-display-target':"option1",  class: is_organization?(agent) && 'd-none'}
         = render NestedFormInputsComponent.new do |c|
           - c.template do
-            %div.d-flex{id: 'NEW_RECORD'}
-              %div.w-100
-                = hidden_field_tag agent_identifier_name('NEW_RECORD' , :creator, name_prefix), session[:user].id
-                = text_field_tag agent_identifier_name('NEW_RECORD' , :notation, name_prefix), '', class: "form-control"
-              %div{style:'width: 15%'}
-                - values = %w[ORCID ROR ISNI GRID]
-                = render SelectInputComponent.new(id: "agent_identifiers_schemaAgency_NEW_RECORD", name: agent_identifier_name('NEW_RECORD', :schemaAgency, name_prefix), values: values, selected: 'ORCID')
+            = agent_identifier_input('NEW_RECORD', name_prefix)
+
           - c.empty_state do
             = hidden_field_tag agent_field_name('',  name_prefix+"[#{Array(agent.identifiers).size}]")
+
           - Array(agent.identifiers).each_with_index do |identifier, i|
             - c.row do
-              %div.d-flex{id: identifier.id}
-                %div.w-100
-                  = hidden_field_tag agent_identifier_name(i.to_s.upcase, :creator, name_prefix), session[:user].id
-                  = text_field_tag agent_identifier_name(i.to_s.upcase, :notation, name_prefix), identifier.notation, class: "form-control"
-                %div{style:'width: 15%'}
-                  - values = %w[ORCID ROR ISNI GRID]
-                  = render SelectInputComponent.new(id: "#{name_prefix}_identifiers_schemaAgency_#{i.to_s.upcase}", name: agent_identifier_name(i.to_s.upcase, :schemaAgency, name_prefix), values: values, selected: identifier.schemaAgency)
+              = agent_identifier_input(i.to_s.upcase, name_prefix, identifier.notation)
+
+      %div.agents-identifiers{'data-form-options-display-target':"option2",  class: !is_organization?(agent) && 'd-none'}
+        = render NestedFormInputsComponent.new do |c|
+          - c.template do
+            = agent_identifier_input('NEW_RECORD', name_prefix, is_organization: false)
+
+          - c.empty_state do
+            = hidden_field_tag agent_field_name('',  name_prefix+"[#{Array(agent.identifiers).size}]")
+
+          - Array(agent.identifiers).each_with_index do |identifier, i|
+            - c.row do
+              = agent_identifier_input(i.to_s.upcase, name_prefix, identifier.notation, is_organization: false)
+
+
   - if show_affiliations
     %tr{'data-form-options-display-target':"option1",  class: is_organization?(agent) && 'd-none'}
       %th
diff --git a/app/views/layouts/_header.html.erb b/app/views/layouts/_header.html.erb
index 244d0a15b..07d28d73d 100644
--- a/app/views/layouts/_header.html.erb
+++ b/app/views/layouts/_header.html.erb
@@ -1,25 +1,28 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" <%="xml:lang=\"#{I18n.locale}\""%> lang="<%=I18n.locale%>">
+<html xmlns="http://www.w3.org/1999/xhtml" <%= "xml:lang=\"#{I18n.locale}\"" %> lang="<%= I18n.locale %>">
 <head>
-	<%= render partial: 'ga_tracking' %>
-	<meta http-equiv="content-type" content="text/html;charset=UTF-8" />
+  <%= render partial: 'ga_tracking' %>
+  <meta http-equiv="content-type" content="text/html;charset=UTF-8"/>
 
-	<!-- Force IE to use latest rendering engine -->
-	<meta http-equiv="X-UA-Compatible" content="IE=Edge"/>
+  <!-- Force IE to use latest rendering engine -->
+  <meta http-equiv="X-UA-Compatible" content="IE=Edge"/>
 
-	<% unless Rails.env.appliance? %>
+  <% unless Rails.env.appliance? %>
     <!-- Google Webmaster Tools verifications -->
-  	<meta name="google-site-verification" content="IBxfKu6VbYH9atd5OLu2zXVD2ZRWi9SgMKTi8nvw3ks" />
+    <meta name="google-site-verification" content="IBxfKu6VbYH9atd5OLu2zXVD2ZRWi9SgMKTi8nvw3ks"/>
   <% end %>
-	<meta name="turbo-cache-control" content="no-cache">
-	<%= csrf_meta_tag %>
-
-	<title><%if @title.nil?%><%=$ORG_SITE%><%else%><%="#{@title} | #{$ORG_SITE}"%><%end%></title>
-
-	<link rel="shortcut icon" href="/fav.ico" type="image/x-icon" />
-	<!-- Fonts -->
-	<link href='//fonts.googleapis.com/css?family=Droid+Sans:400' rel='stylesheet' type='text/css'>
-	<!-- CSS -->
+  <meta name="turbo-cache-control" content="no-cache">
+  <%= csrf_meta_tag %>
+
+  <title>
+    <% if @title.nil? %><%= $ORG_SITE %>
+    <% else %><%= "#{@title} | #{$ORG_SITE}" %>
+    <% end %></title>
+
+  <link rel="shortcut icon" href="/fav.ico" type="image/x-icon"/>
+  <!-- Fonts -->
+  <link href='//fonts.googleapis.com/css?family=Droid+Sans:400' rel='stylesheet' type='text/css'>
+  <!-- CSS -->
   <%= stylesheet_link_tag "https://use.fontawesome.com/releases/v5.2.0/css/all.css", integrity: "sha384-hWVjflwFxL6sNzntih27bfxkr27PmbbK/iSvJ+a4+0owXq79v+lsFkW54bOGbiDQ", crossorigin: "anonymous" %>
   <%= stylesheet_link_tag "application" %>
 
@@ -27,19 +30,34 @@
   <%= javascript_include_tag "vendor" %>
 
   <script>
-    jQuery(document).data({bp: {config: <%=bp_config_json.html_safe%>, user: <%=(session[:user] || {}).to_hash.to_json.html_safe%>}});
-    jQuery(document).data().bp.ontology = <%=@ontology.to_json.html_safe%> || {};
-    jQuery(document).data().bp.submission_latest = <%=@submission_latest.to_json.html_safe%> || {};
-    jQuery(document).data().bp.ontolobridge_ontologies = <%=$NEW_TERM_REQUEST_ONTOLOGIES.to_json.html_safe%> || [];
-    jQuery(document).data().bp.ont_viewer = {};
-    jQuery(document).data().bp.ont_chart = {};
+      jQuery(document).data({
+          bp: {
+              config: <%=bp_config_json.html_safe%>,
+              user: <%=(session[:user] || {}).to_hash.to_json.html_safe%>
+          }
+      });
+      jQuery(document).data().bp.ontology =
+      <%=@ontology.to_json.html_safe%> ||
+      {
+      }
+      ;
+      jQuery(document).data().bp.submission_latest =
+      <%=@submission_latest.to_json.html_safe%> ||
+      {
+      }
+      ;
+      jQuery(document).data().bp.ontolobridge_ontologies =
+      <%=$NEW_TERM_REQUEST_ONTOLOGIES.to_json.html_safe%> ||
+      [];
+      jQuery(document).data().bp.ont_viewer = {};
+      jQuery(document).data().bp.ont_chart = {};
   </script>
 
-  <!-- BioPortal-specific JavaScript is loaded in _footer.html.erb. -->  
+  <!-- BioPortal-specific JavaScript is loaded in _footer.html.erb. -->
 </head>
 <body class="<%= controller_name %> <%= action_name %>">
-  <%=render partial: 'layouts/topnav'%>
-	<%= turbo_frame_tag :cookies_modal, src: cookies_path if session[:cookies_accepted].nil? %>
+<%= render partial: 'layouts/topnav' %>
+<%= turbo_frame_tag :cookies_modal, src: cookies_path if session[:cookies_accepted].nil? && !(Rails.env.development? || Rails.env.test?) %>
 
-	<div class="flex-grow-1">
-    <%=render partial: 'layouts/notices'%>
\ No newline at end of file
+<div class="flex-grow-1">
+<%= render partial: 'layouts/notices' %>
\ No newline at end of file
diff --git a/app/views/users/_form.html.haml b/app/views/users/_form.html.haml
index 3a2f38b52..02fde4988 100644
--- a/app/views/users/_form.html.haml
+++ b/app/views/users/_form.html.haml
@@ -27,13 +27,13 @@
       ORCID ID
       %font.register-optional 
       = t('register.optional')
-    %img.register-input-icon{:src => "#{asset_path("orcid.svg")}"}/
+    = inline_svg_tag 'orcid.svg', class: 'register-input-icon'
     = text_field :user, :orcidId, value: @user.orcidId, class: "register-input-long register-input-with-icon"
     %p.register-input-title
       Github ID
       %font.register-optional 
       = t('register.optional')
-    %img.register-input-icon{:src => "#{asset_path("github-icon.svg")}"}/
+    = inline_svg_tag 'github-icon.svg', class: 'register-input-icon'
     = text_field :user, :githubId, value: @user.githubId, class: "register-input-long register-input-with-icon"
     %p.register-input-title
       = t('register.email')
diff --git a/test/system/agent_flows_test.rb b/test/system/agent_flows_test.rb
index 953c4d2e4..5eeb72055 100644
--- a/test/system/agent_flows_test.rb
+++ b/test/system/agent_flows_test.rb
@@ -68,7 +68,7 @@ def create_agent_flow(new_agent, person_count: , organization_count:)
     within "table#admin_agents" do
       assert_selector '.human',  count: person_count + organization_count #  all created  agents
       assert_text new_agent.name
-      new_agent.identifiers.map{|x| "https://orcid.org/#{x["notation"]}"}.each do |orcid|
+      new_agent.identifiers.map{|x| "https://#{new_agent.agentType.eql?('organization') ? 'ror' : 'orcid'}.org/#{x["notation"]}"}.each do |orcid|
         assert_text orcid
       end
 
@@ -91,7 +91,7 @@ def edit_agent_flow(agent, person_count: , organization_count: )
     within "table#admin_agents" do
       assert_selector '.human',  count: person_count + organization_count # all created  agents
       assert_text agent.name
-      agent.identifiers.map{|x| "https://orcid.org/#{x["notation"]}"}.each do |orcid|
+      agent.identifiers.map{|x| "https://#{agent.agentType.eql?('organization') ? 'ror' : 'orcid'}.org/#{x["notation"]}"}.each do |orcid|
         assert_text orcid
       end
       assert_text 'person', count: person_count