Merge branch 'development' into stage

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_api_ruby_client.git
-  revision: 169afb7c1002f9db2b3276af36d552575cc80ba2
+  revision: 674193220f93d99587e6d3a969adcb384caf0a61
   branch: development
   specs:
     ontologies_api_client (2.2.0)
@@ -99,6 +99,7 @@ GEM
       erubi (~> 1.4)
       parser (>= 2.4)
       smart_properties
+    bigdecimal (3.1.5)
     bindata (2.4.15)
     bindex (0.8.1)
     bootsnap (1.17.0)
@@ -147,9 +148,9 @@ GEM
     daemons (1.4.1)
     dalli (3.2.6)
     date (3.3.4)
-    debug (1.8.0)
-      irb (>= 1.5.0)
-      reline (>= 0.3.1)
+    debug (1.9.0)
+      irb (~> 1.10)
+      reline (>= 0.3.8)
     deepl-rb (2.5.3)
     diff-lcs (1.5.0)
     docile (1.4.0)
@@ -158,7 +159,7 @@ GEM
     erubi (1.12.0)
     erubis (2.7.0)
     eventmachine (1.2.7)
-    excon (0.105.0)
+    excon (0.108.0)
     execjs (2.9.1)
     faraday (2.0.1)
       faraday-net_http (~> 2.0)
@@ -177,7 +178,7 @@ GEM
     flamegraph (0.9.5)
     globalid (1.2.1)
       activesupport (>= 6.1)
-    graphql (2.1.6)
+    graphql (2.1.7)
       racc (~> 1.4)
     graphql-client (0.18.0)
       activesupport (>= 3.0)
@@ -218,8 +219,8 @@ GEM
     inline_svg (1.9.0)
       activesupport (>= 3.0)
       nokogiri (>= 1.6)
-    io-console (0.6.0)
-    irb (1.9.1)
+    io-console (0.7.1)
+    irb (1.10.1)
       rdoc
       reline (>= 0.3.8)
     iso-639 (0.3.6)
@@ -231,7 +232,7 @@ GEM
       railties (>= 3.2.16)
     jsbundling-rails (1.2.1)
       railties (>= 6.0.0)
-    json (2.7.0)
+    json (2.7.1)
     json-jwt (1.16.3)
       activesupport (>= 4.2)
       aes_key_wrap
@@ -319,7 +320,8 @@ GEM
       rack (>= 1.2, < 4)
       snaky_hash (~> 2.0)
       version_gem (~> 1.1)
-    oj (3.16.1)
+    oj (3.16.3)
+      bigdecimal (>= 3.0)
     omniauth (2.1.1)
       hashie (>= 3.4.6)
       rack (>= 2.2.3)
@@ -346,7 +348,7 @@ GEM
       actionpack (>= 4.2)
       omniauth (~> 2.0)
     open_uri_redirections (0.2.1)
-    parallel (1.23.0)
+    parallel (1.24.0)
     parser (3.2.2.4)
       ast (~> 2.4.1)
       racc
@@ -412,7 +414,7 @@ GEM
     recaptcha (5.9.0)
       json
     redcarpet (3.6.0)
-    regexp_parser (2.8.2)
+    regexp_parser (2.8.3)
     reline (0.4.1)
       io-console (~> 0.5)
     rest-client (2.1.0)

app/components/ontology_subscribe_button_component.rb

@@ -1,8 +1,9 @@
 # frozen_string_literal: true
 
 class OntologySubscribeButtonComponent < ViewComponent::Base
-  def initialize(ontology_id:, subscribed:, user_id:, count: 0, link: 'javascript:void(0);')
+  def initialize(id: '', ontology_id:, subscribed:, user_id:, count: 0, link: 'javascript:void(0);')
     super
+    @id = id
     @subscribed = subscribed
     @sub_text = subscribed ? 'UnWatch' : 'Watch'
     @link = link

app/components/ontology_subscribe_button_component/ontology_subscribe_button_component.html.haml

@@ -1,4 +1,4 @@
-%div{@controller_params, style: 'margin-left: 10px;'}
+%div{@controller_params, style: 'margin-left: 10px;', id: @id}
   = render PillButtonComponent.new do
     %a.d-flex.align-items-center{href: @link}
       = inline_svg_tag "eye.svg"

app/controllers/agents_controller.rb

@@ -8,7 +8,7 @@ def index
 
   def show
     # we use :agent_id not :id
-    @agent = LinkedData::Client::Models::Agent.find(params[:agent_id])
+    @agent = LinkedData::Client::Models::Agent.find(params[:agent_id].split('/').last)
     not_found("Agent with id #{params[:agent_id]}") if @agent.nil?
 
     @agent_id = params[:id] || agent_id(@agent)
@@ -67,7 +67,7 @@ def create
   end
 
   def edit
-    @agent = LinkedData::Client::Models::Agent.find("#{rest_url}/Agents/#{params[:id]}")
+    @agent = LinkedData::Client::Models::Agent.find(params[:id].split('/').last)
     @name_prefix = params[:name_prefix] || ''
     @show_affiliations = params[:show_affiliations].nil? || params[:show_affiliations].eql?('true')
     @deletable = params[:deletable].to_s.eql?('true')
@@ -99,7 +99,7 @@ def 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)
+      agent = LinkedData::Client::Models::Agent.find(agent.id.split('/').last)
       streams = [alert_success(id: alert_id) { success_message },
                  replace(table_line_id, partial: 'agents/show_line', locals: { agent: agent })
       ]
@@ -147,7 +147,7 @@ def update_agent_usages
 
   def destroy
     error = nil
-    @agent = LinkedData::Client::Models::Agent.find("#{rest_url}/Agents/#{params[:id]}")
+    @agent = LinkedData::Client::Models::Agent.find(params[:id].split('/').last)
     success_text = ''
 
     if @agent.nil?
@@ -198,7 +198,7 @@ def save_agent(params)
   end
 
   def update_agent(id = params[:id], params)
-    agent = LinkedData::Client::Models::Agent.find("#{rest_url}/Agents/#{id}")
+    agent = LinkedData::Client::Models::Agent.find(id)
 
     params[:creator] = session[:user].id if (agent.creator.nil? || agent.creator.empty?) && (params[:creator] || '').empty?
 

app/controllers/concerns/ontology_updater.rb

@@ -13,7 +13,7 @@ def update_existent_ontology(acronym)
     rescue StandardError
       next
     end
-    [@ontology, @ontology.update(values: new_values)]
+    [@ontology, @ontology.update(values: new_values, cache_refresh_all: false)]
   end
 
   def ontology_from_params
@@ -86,7 +86,7 @@ def update_submission_hash(acronym)
   def reset_agent_attributes
     helpers.agent_attributes.each do |attr|
       current_val = @submission[attr]
-      new_values = Array(current_val).map { |x| LinkedData::Client::Models::Agent.find(x) }
+      new_values = Array(current_val).map { |x| LinkedData::Client::Models::Agent.find(x.split('/').last) }
 
       new_values = new_values.first unless current_val.is_a?(Array)
 

app/controllers/concerns/submission_updater.rb

@@ -12,13 +12,14 @@ def save_submission(new_submission_hash)
     @submission.save(cache_refresh_all: false)
   end
 
-  def update_submission(new_submission_hash, submission_id)
+  def update_submission(new_submission_hash, submission_id , ontology = nil)
 
     convert_values_to_types(new_submission_hash)
 
-    @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(new_submission_hash[:ontology]).first
+    @ontology = ontology || LinkedData::Client::Models::Ontology.find_by_acronym(new_submission_hash[:ontology]).first
     new_submission_hash.delete(:ontology)
-    @submission = @ontology.explore.submissions({ display: 'all' }, submission_id)
+
+    @submission = @ontology.explore.submissions({ include: 'all' }, submission_id)
 
     new_values = new_submission_hash
     new_values.each do |key, values|
@@ -61,8 +62,9 @@ def delete_ontologies_from_object(new_ontologies,old_ontologies,object)
   private
 
   def update_ontology_summary_only(is_remote = @submission.isRemote)
-    @ontology.summaryOnly = is_remote&.eql?('3')
-    @ontology.update
+    if is_remote && @ontology.summaryOnly != is_remote.eql?('3')
+      @ontology.update(values: {summaryOnly: is_remote.eql?('3')}, cache_refresh_all: false)
+    end
   end
 
   def convert_values_to_types(new_submission_hash)

app/controllers/ontologies_controller.rb

@@ -56,17 +56,17 @@ def ontologies_filter
     ] + update_filters_counts
 
     streams =if params[:page].nil?
-               [
-                 prepend('ontologies_list_container', partial: 'ontologies/browser/ontologies'),
-                 prepend('ontologies_list_container') {
-                   helpers.turbo_frame_tag("ontologies_filter_count_request") do
-                     helpers.browser_counter_loader
-                   end
-                 }
-               ]
-             else
-               [replace("ontologies_list_view-page-1", partial: 'ontologies/browser/ontologies')]
-             end
+                [
+                  prepend('ontologies_list_container', partial: 'ontologies/browser/ontologies'),
+                  prepend('ontologies_list_container') {
+                    helpers.turbo_frame_tag("ontologies_filter_count_request") do
+                      helpers.browser_counter_loader
+                    end
+                  }
+                ]
+              else
+                [replace("ontologies_list_view-page-1", partial: 'ontologies/browser/ontologies')]
+              end
 
     render turbo_stream: streams + count_streams
   end
@@ -246,7 +246,7 @@ def show
     # See: https://github.com/ncbo/bioportal_web_ui/issues/133.
     data_pages = KNOWN_PAGES - %w[summary notes]
     if @ontology.summaryOnly && params[:p].present? && data_pages.include?(params[:p].to_s)
-        redirect_to(ontology_path(params[:ontology]), status: :temporary_redirect) and return
+      redirect_to(ontology_path(params[:ontology]), status: :temporary_redirect) and return
     end
 
     #@ob_instructions = helpers.ontolobridge_instructions_template(@ontology)
@@ -346,6 +346,28 @@ def summary
     end
   end
 
+  def subscriptions
+    ontology_id = params[:ontology_id]
+    return not_found if ontology_id.nil?
+
+    ontology_acronym = ontology_id.split('/').last
+
+    if session[:user].nil?
+      link = "/login?redirect=#{request.url}"
+      subscribed = false
+      user_id = nil
+    else
+      user = LinkedData::Client::Models::User.find(session[:user].id)
+      subscribed = helpers.subscribed_to_ontology?(ontology_acronym, user)
+      link = "javascript:void(0);"
+      user_id = user.id
+    end
+
+    count = helpers.count_subscriptions(ontology_id)
+    render inline:  helpers.turbo_frame_tag('subscribe_button') {
+      render_to_string(OntologySubscribeButtonComponent.new(id: 'subscribe_button', ontology_id: ontology_id, subscribed: subscribed, user_id: user_id, count: count, link: link),  layout: nil)
+    }
+  end
 
   def virtual
     redirect_new_api
@@ -362,7 +384,7 @@ def widgets
       render partial: 'ontologies/sections/widgets', layout: 'ontology_viewer'
     end
   end
-  
+
 
   def show_additional_metadata
     @metadata = submission_metadata
@@ -439,12 +461,11 @@ def ontology_relations_data(sub = @submission_latest)
 
         target_id = relation_value
         target_in_portal = false
+        target_ont = nil
         # if we find our portal URL in the ontology URL, then we just keep the ACRONYM to try to get the ontology.
-        relation_value = relation_value.split('/').last if relation_value.include?($UI_URL)
-
-        # Use acronym to get ontology from the portal
-        target_ont = LinkedData::Client::Models::Ontology.find_by_acronym(relation_value).first
-        if target_ont
+        if relation_value.include?(portal_name)
+          relation_value = relation_value.split('/').last
+          target_ont = LinkedData::Client::Models::Ontology.find_by_acronym(relation_value).first
           target_id = target_ont.acronym
           target_in_portal = true
         end

app/controllers/ontologies_metadata_curator_controller.rb

@@ -5,29 +5,16 @@ class OntologiesMetadataCuratorController < ApplicationController
   before_action :submission_metadata, only: [:result, :edit, :update, :show_metadata_by_ontology]
 
   def result
-    @ontologies_ids = params[:ontology] ? params[:ontology][:ontologyId] : []
+    @ontologies_ids = params[:ontology] ? Array(params[:ontology][:ontologyId]) : []
     @metadata_sel = params[:search] ? params[:search][:metadata] : []
     @show_submissions = !params[:show_submissions].nil?
-    @ontologies = []
     @submissions = []
 
-    if @ontologies_ids.nil? || @ontologies_ids.empty?
-      @ontologies = LinkedData::Client::Models::Ontology.all
-    else
-      @ontologies_ids.each do |data|
-        @ontologies << LinkedData::Client::Models::Ontology.find_by_acronym(data).first
-      end
-    end
-
     display_attribute = equivalent_properties(@metadata_sel) + %w[submissionId]
-    @ontologies.each do |ont|
-      if @show_submissions
-        submissions = ont.explore.submissions({ include: display_attribute.join(',') })
-      else
-        submissions = [ont.explore.latest_submission({ include: display_attribute.join(',') })]
-      end
-      submissions.each { |sub| append_submission(ont, sub) }
-    end
+
+    @submissions = LinkedData::Client::Models::OntologySubmission.all(acronym: @ontologies_ids.join('|'), display_links: false, display_context: false, include: display_attribute.join(','), include_status: 'RDF')
+    @submissions.reject!{|x| !@ontologies_ids.include?(x.id.split('/')[-3])} unless @ontologies_ids.empty?
+    @submissions.sort_by!{|x| x.id}
 
     respond_to do |format|
       format.html { redirect_to admin_index_path }

app/controllers/submissions_controller.rb

@@ -88,9 +88,10 @@ def update
     acronym = params[:ontology_id]
     submission_id = params[:id]
     if params[:ontology]
-      @ontology = update_existent_ontology(acronym)
-      if @ontology.nil? || response_error?(@ontology)
-        show_new_errors(@ontology, partial: 'submissions/form_content', id: 'test')
+      @ontology, response = update_existent_ontology(acronym)
+
+      if response.nil? || response_error?(response)
+        show_new_errors(response, partial: 'submissions/form_content', id: 'test')
         return
       end
     end
@@ -100,7 +101,7 @@ def update
                          notice: 'Submission updated successfully'
     end
 
-    @submission, response = update_submission(update_submission_hash(acronym), submission_id)
+    @submission, response = update_submission(update_submission_hash(acronym), submission_id, @ontology)
     if params[:attribute].nil?
       if response_error?(response)
         show_new_errors(response, partial: 'submissions/form_content', id: 'test')