Merge branch 'feature/federate-search-page' into test

ontoportal-lirmm · Sep 12, 2024 · 8f3385c · 8f3385c
2 parents 93fe2a8 + d1b228a
commit 8f3385c
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diff --git a/Gemfile.lock b/Gemfile.lock
@@ -420,7 +420,7 @@ GEM
       json
     redcarpet (3.6.0)
     regexp_parser (2.9.2)
-    reline (0.5.9)
+    reline (0.5.10)
       io-console (~> 0.5)
     request_store (1.7.0)
       rack (>= 1.4)
@@ -433,7 +433,7 @@ GEM
     rouge (4.3.0)
     rspec-core (3.13.1)
       rspec-support (~> 3.13.0)
-    rspec-expectations (3.13.2)
+    rspec-expectations (3.13.3)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
     rspec-mocks (3.13.1)
@@ -448,17 +448,17 @@ GEM
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
     rspec-support (3.13.1)
-    rubocop (1.66.0)
+    rubocop (1.66.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 2.4, < 3.0)
-      rubocop-ast (>= 1.32.1, < 2.0)
+      rubocop-ast (>= 1.32.2, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.32.2)
+    rubocop-ast (1.32.3)
       parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.5)
@@ -489,7 +489,7 @@ GEM
     simplecov-cobertura (2.1.0)
       rexml
       simplecov (~> 0.19)
-    simplecov-html (0.12.3)
+    simplecov-html (0.13.1)
     simplecov_json_formatter (0.1.4)
     snaky_hash (2.0.1)
       hashie
@@ -502,11 +502,12 @@ GEM
       actionpack (>= 6.1)
       activesupport (>= 6.1)
       sprockets (>= 3.0.0)
-    sshkit (1.23.0)
+    sshkit (1.23.1)
       base64
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
       net-ssh (>= 2.8.0)
+      ostruct
     stimulus-rails (1.3.4)
       railties (>= 6.0.0)
     string-similarity (2.1.0)
@@ -518,7 +519,7 @@ GEM
       execjs (>= 0.3.0, < 3)
     thor (1.3.2)
     tilt (2.4.0)
-    time (0.3.0)
+    time (0.4.0)
       date
     timeout (0.4.1)
     turbo-rails (2.0.6)
@@ -550,7 +551,7 @@ GEM
     will_paginate (3.3.1)
     xpath (3.2.0)
       nokogiri (~> 1.8)
-    yard (0.9.36)
+    yard (0.9.37)
     zeitwerk (2.6.18)
 
 PLATFORMS

diff --git a/app/assets/images/icons/slices.svg b/app/assets/images/icons/slices.svg
diff --git a/app/assets/stylesheets/application.css.scss.erb b/app/assets/stylesheets/application.css.scss.erb
@@ -58,6 +58,7 @@
 @import "agent_tooltip";
 @import "content_finder";
 @import "tools";
+@import "taxonomy";
 @import "portal_configuration";
 
 /* Bootstrap and Font Awesome */

diff --git a/app/assets/stylesheets/taxonomy.scss b/app/assets/stylesheets/taxonomy.scss
@@ -0,0 +1,101 @@
+.taxonomy-page-container {
+    display: flex;
+    justify-content: center;
+  }
+.taxonomy-page-subcontainer {
+    width: 1248px;
+    padding: 20px 50px;
+}
+.taxonomy-page-title .text{
+    font-size: 25px;
+    font-weight: 700;
+}
+
+.taxonomy-page-title .line{
+    height: 2px;
+    width: 57px;
+    background-color: var(--primary-color);
+    border-radius: 10px;
+}
+.taxonomy-page-decription{
+    color: #888888;
+    margin: 20px 0;
+}
+.taxonomy-section{
+    display: flex;
+}
+.taxonomy-section .second-row{
+    margin-left: 10px;
+}
+.taxonomy-card{
+    border: 1px solid #DFDFDF;
+    padding: 15px 20px;
+    width: 569px;
+    border-radius: 5px;
+    margin-top: 10px;
+}
+
+.taxonomy-card .title-bar{
+    display: flex;
+    justify-content: space-between;
+    align-items: center;
+}
+.taxonomy-card .title{
+    color: var(--primary-color);
+    font-size: 18px;
+    font-weight: bold;
+}
+
+.taxonomy-card .ontologies{
+    display: flex;
+    align-items: center;
+    color: var(--primary-color);
+    margin: 3px 0;
+}
+.taxonomy-card .ontologies svg{
+    width: 15px;
+    height: 15px;
+    margin-right: 10px;
+}
+
+.taxonomy-card .ontologies svg path{
+    fill: var(--primary-color);
+}
+.taxonomy-card .description{
+    color: #666666;
+    padding-bottom: 5px;
+}
+.taxonomy-slice-svg{
+    width: 35px;
+    height: 35px;
+    margin-bottom: 2px;
+}
+
+.taxonomy-children-reveal{
+    display: flex;
+    align-items: center;
+    cursor: pointer;
+    color: var(--primary-color);
+}
+.taxonomy-children-reveal svg{
+    margin-left: 5px;
+    margin-top: 3px;
+}
+
+.taxonomy-children .taxonomy-card{
+    border: none;
+    padding: 0px 18px;
+    width: unset;
+}
+
+.taxonomy-children-container{
+    display: flex;
+    margin-top: 10px
+}
+
+.taxonomy-children-line{
+    width: 1px;
+    background-color: var(--primary-color);
+}
+
+
diff --git a/app/components/display/search_result_component.rb b/app/components/display/search_result_component.rb
@@ -33,9 +33,9 @@ def reuses_id
 
   def details_button
       link_to_modal(nil, "/ajax/class_details?modal=true&ontology=#{@ontology_acronym}&conceptid=#{@uri}&styled=false", data: { show_modal_title_value: @title, show_modal_size_value: 'modal-xl' }) do
-        content_tag(:div, class: 'button', style: @portal_color ? "background-color: #{@portal_light_color} !important" : '') do
+        content_tag(:div, class: 'button') do
           concat inline_svg_tag('icons/details.svg')
-          concat content_tag(:div, class: 'text', style: @portal_color ? "color: #{@portal_color} !important" : '') { t('search.result_component.details') }
+          concat content_tag(:div, class: 'text') { t('search.result_component.details') }
         end
       end
   end
@@ -57,9 +57,9 @@ def mappings_button
 
   def visualize_button
       link_to_modal(nil, "/ajax/biomixer/?ontology=#{@ontology_acronym}&conceptid=#{@uri}", data: { show_modal_title_value: @title, show_modal_size_value: 'modal-xl' }) do
-        content_tag(:div, class: 'button', style: @portal_color ? "background-color: #{@portal_light_color} !important" : '') do
+        content_tag(:div, class: 'button') do
           concat inline_svg_tag('icons/visualize.svg')
-          concat content_tag(:div, class: 'text', style: @portal_color ? "color: #{@portal_color} !important" : '') { t('search.result_component.visualize') }
+          concat content_tag(:div, class: 'text') { t('search.result_component.visualize') }
         end
       end
   end

diff --git a/app/components/display/taxonomy_card_component.rb b/app/components/display/taxonomy_card_component.rb
@@ -0,0 +1,10 @@
+class Display::TaxonomyCardComponent < ViewComponent::Base
+  def initialize(taxonomy: , ontologies_names: )
+    @taxonomy = taxonomy
+    @ontologies_names = ontologies_names
+  end
+
+  def reveal_id
+    @taxonomy.id
+  end
+end
diff --git a/app/components/display/taxonomy_card_component/taxonomy_card_component.html.haml b/app/components/display/taxonomy_card_component/taxonomy_card_component.html.haml
@@ -0,0 +1,26 @@
+.taxonomy-card{'data-controller': 'reveal-component'}
+  .title-bar
+    .title
+      = "#{@taxonomy.name} (#{@taxonomy.acronym})"
+    %a{href: "https://#{@taxonomy.acronym}.#{$UI_URL.sub("https://", "")}"}
+      = inline_svg_tag('icons/slices.svg', class: "taxonomy-slice-svg #{@taxonomy.is_slice ? '' : 'd-none'}")
+  %a.ontologies{href: "/ontologies?#{@taxonomy.id.split('/')[-2]}=#{@taxonomy.acronym}"}
+    = inline_svg_tag('icons/ontology.svg')
+    .number-of-ontologies
+      = "#{@taxonomy.ontologies.length} ontologies"
+  .description
+    = render TextAreaFieldComponent.new(value: @taxonomy.description)
+  .ontologies-cards
+    - @taxonomy.ontologies.each do |ontology|
+      = render ChipButtonComponent.new(url: "/ontologies/#{ontology.split('/').last}", text: ontology.split('/').last, tooltip: @ontologies_names[ontology], type: "clickable")
+
+  - if @taxonomy.children
+    .taxonomy-children-reveal{'data-action': "click->reveal-component#toggle", 'data-id': reveal_id}
+      .text
+        = t('taxonomy.show_sub_categories')
+      = inline_svg_tag 'icons/arrow-down.svg'
+    .taxonomy-children-container
+      .taxonomy-children-line
+      .taxonomy-children.d-none{id: reveal_id}
+        - @taxonomy.children.each do |child|
+          = render Display::TaxonomyCardComponent.new(taxonomy: child, ontologies_names: @ontologies_names)
diff --git a/app/components/ontology_browse_card_component.rb b/app/components/ontology_browse_card_component.rb
@@ -17,11 +17,7 @@ def ontology
   end
 
   def external_ontology?
-    !@portal_name.blank?
-  end
-
-  def external_portal_name
-    @portal_name
+    !internal_ontology?(@ontology[:id]) || (Array(@ontology[:sources]).size > 1)
   end
 
   def onto_link

diff --git a/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml b/app/components/ontology_browse_card_component/ontology_browse_card_component.html.haml
@@ -18,7 +18,7 @@
             = t('components.show_more')
 
 
-          - unless ontology[:fairScore].nil? ||  ontology[:fairScore].zero?  || ontology[:acronym] == 'AGROVOC'
+          - unless ontology[:fairScore].nil? || ontology[:fairScore].zero? || ontology[:acronym] == 'AGROVOC'
             .browse-fair
               %p.browse-fair-title
                 = t('components.fair_score')

diff --git a/app/controllers/admin/categories_controller.rb b/app/controllers/admin/categories_controller.rb
@@ -15,7 +15,6 @@ def index
 
   def new
     @category = LinkedData::Client::Models::Category.new
-
     respond_to do |format|
       format.html { render "new", :layout => false }
     end

diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
@@ -183,33 +183,6 @@ def request_portals
     helpers.request_portals
   end
 
-  def check_http_file(url)
-    session = Net::HTTP.new(url.host, url.port)
-    session.use_ssl = true if url.port == 443
-    session.start do |http|
-      response_valid = http.head(url.request_uri).code.to_i < 400
-      return response_valid
-    end
-  end
-
-  def check_ftp_file(uri)
-    ftp = Net::FTP.new(uri.host, uri.user, uri.password)
-    ftp.login
-    begin
-      file_exists = ftp.size(uri.path) > 0
-    rescue
-      # Check using another method
-      path = uri.path.split("/")
-      filename = path.pop
-      path = path.join("/")
-      ftp.chdir(path)
-      files = ftp.dir
-      # Dumb check, just see if the filename is somewhere in the list
-      files.each { |file| return true if file.include?(filename) }
-    end
-    file_exists
-  end
-
   def parse_response_body(response)
     return nil if response.nil?
 

diff --git a/app/controllers/concerns/search_aggregator.rb b/app/controllers/concerns/search_aggregator.rb
@@ -29,7 +29,7 @@ def aggregate_results(query, results, is_federate)
     ontologies = aggregate_by_ontology(results)
     grouped_results = add_subordinate_ontologies(query, ontologies)
 
-    all_ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym,name', include_views: true, display_links: false, display_context: false, federate: is_federate)
+    all_ontologies = LinkedData::Client::Models::Ontology.all(include: 'acronym,name', include_views: true, display_links: false, display_context: false)
 
     search_results = grouped_results.map do |group|
       format_search_result(group, all_ontologies)
@@ -77,7 +77,7 @@ def search_result_elem(class_object, ontology_acronym, title)
     portal_name = portal_name_from_uri(class_object.links['ui'])
     {
       uri: class_object.id.to_s,
-      title: title.empty? ? label : "#{label} - #{title}",
+      title: title.nil? || title.empty? ? "#{label} - #{ontology_acronym}" : "#{label} - #{title}",
       ontology_acronym: ontology_acronym,
       link: link,
       definition:  class_object.definition,
@@ -93,7 +93,7 @@ def is_federation_external_class(class_object)
 
   def ontology_name_acronym(ontologies, selected_acronym)
     ontology = ontologies.select { |x| x.acronym.eql?(selected_acronym.split('/').last) }.first
-    "#{ontology.name} (#{ontology.acronym})"
+    "#{ontology.name} (#{ontology.acronym})" if ontology
   end
 
   def aggregate_by_ontology(results)

diff --git a/app/controllers/concerns/submission_filter.rb b/app/controllers/concerns/submission_filter.rb
@@ -59,8 +59,8 @@ def submissions_paginate_filter(params)
     [@page.collection, @page.totalCount, count, filter_params]
   end
 
-  def ontologies_filter_url(filters, page: 1, count: false)
-    helpers.ontologies_filter_url(filters, page: page, count: count)
+  def ontologies_with_filters_url(filters, page: 1, count: false)
+    helpers.ontologies_with_filters_url(filters, page: page, count: count)
   end
 
   private

diff --git a/app/controllers/home_controller.rb b/app/controllers/home_controller.rb
@@ -47,7 +47,7 @@ def index
   end
 
   def set_cookies
-    session[:cookies_accepted] = params[:cookies] if params[:cookies]
+    cookies.permanent[:cookies_accepted] = params[:cookies] if params[:cookies]
     render 'cookies', layout: nil
   end