ontoportal-lirmm · Bilelkihal · Jan 12, 2024 · Jul 28, 2023 · Jul 28, 2023 · Jul 28, 2023
diff --git a/Gemfile b/Gemfile
@@ -138,3 +138,5 @@ gem "net-ftp", "~> 0.2.0", require: false
 gem "net-http", "~> 0.3.2"
 
 
+
+gem "bugsnag", "~> 6.26"
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -109,6 +109,8 @@ GEM
       popper_js (>= 1.14.3, < 2)
       sassc-rails (>= 2.0.0)
     brakeman (5.4.1)
+    bugsnag (6.26.0)
+      concurrent-ruby (~> 1.0)
     builder (3.2.4)
     capistrano (3.18.0)
       airbrussh (>= 1.0.0)
@@ -311,12 +313,13 @@ GEM
       racc (~> 1.4)
     nokogiri (1.15.5-x86_64-linux)
       racc (~> 1.4)
-    oauth2 (1.4.11)
+    oauth2 (2.0.9)
       faraday (>= 0.17.3, < 3.0)
       jwt (>= 1.0, < 3.0)
-      multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (>= 1.2, < 4)
+      snaky_hash (~> 2.0)
+      version_gem (~> 1.1)
     oj (3.16.3)
       bigdecimal (>= 3.0)
     omniauth (2.1.1)
@@ -326,11 +329,10 @@ GEM
     omniauth-github (2.0.0)
       omniauth (~> 2.0)
       omniauth-oauth2 (~> 1.7.1)
-    omniauth-google-oauth2 (1.0.1)
+    omniauth-google-oauth2 (0.8.0)
       jwt (>= 2.0)
-      oauth2 (~> 1.1)
-      omniauth (~> 2.0)
-      omniauth-oauth2 (~> 1.7.1)
+      omniauth (>= 1.1.1)
+      omniauth-oauth2 (>= 1.6)
     omniauth-keycloak (1.5.1)
       faraday
       json-jwt (> 1.13.0)
@@ -484,6 +486,9 @@ GEM
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.4)
     smart_properties (1.17.0)
+    snaky_hash (2.0.1)
+      hashie
+      version_gem (~> 1.1, >= 1.1.1)
     spawnling (2.1.5)
     sprockets (4.2.1)
       concurrent-ruby (~> 1.0)
@@ -525,6 +530,7 @@ GEM
       concurrent-ruby (~> 1.0)
     unicode-display_width (2.5.0)
     uri (0.13.0)
+    version_gem (1.1.3)
     view_component (2.82.0)
       activesupport (>= 5.2.0, < 8.0)
       concurrent-ruby (~> 1.0)
@@ -547,12 +553,14 @@ GEM
 PLATFORMS
   x86_64-darwin-23
   x86_64-linux
+  x86_64-linux-musl
 
 DEPENDENCIES
   bcrypt_pbkdf (>= 1.0, < 2.0)
   bootsnap
   bootstrap (~> 4.2.0)
   brakeman
+  bugsnag (~> 6.26)
   capistrano (~> 3.11)
   capistrano-bundler
   capistrano-locally

diff --git a/app/assets/images/icons/arrow-curved-up.svg b/app/assets/images/icons/arrow-curved-up.svg
diff --git a/app/assets/stylesheets/components/regular_button.scss b/app/assets/stylesheets/components/regular_button.scss
@@ -54,7 +54,7 @@
 }
 
 .secondary-button {
-    color: var(--primary-color);
+    color: var(--primary-color) !important;
     border: 1px solid var(--primary-color);
     transition: background-color ease 0.3s;
     background-color: rgba(0, 0, 0, 0) !important;

diff --git a/app/assets/stylesheets/home.scss b/app/assets/stylesheets/home.scss
@@ -226,9 +226,16 @@ i.fa.fa-caret-square-o-down {
 .home-upload-benifits div img{
   margin-top: 3px
 }
-.home-upload-ontology-button{
+.home-ontologies-actions{
+  display: flex;
+  align-items: center;
   margin-top: 30px;
+
+}
+.home-upload-ontology-button{
+
   width: fit-content;
+  margin-right: 20px;
 }
 
 .home-upload-icon {
@@ -249,11 +256,35 @@ i.fa.fa-caret-square-o-down {
 .home-services-buttons{
   background-color: white;
   border-radius: 8px;
-  padding: 20px;
+  padding: 0;
   display: flex;
   justify-content: flex-end;
   align-items: center;
 }
+.home-services-buttons.container{
+  padding: 0 30px 30px 0;
+}
+.home-services-buttons .insert-sample-text-button{
+  display: flex;
+  align-items: center;
+  margin-right: 20px;
+}
+.home-services-buttons .insert-sample-text-button:hover{
+  cursor: pointer;
+}
+.home-services-buttons .insert-sample-text-button div{
+  color: var(--primary-color);
+  margin-right: 5px;
+  font-weight: 500;
+}
+.home-services-buttons .insert-sample-text-button svg{
+  width: 18px;
+  height: 18px;
+}
+.home-services-buttons .insert-sample-text-button svg path{
+  fill: var(--primary-color);
+
+}
 .home-card{
   border-radius: 8px;
   box-shadow: 2px 30px 60px rgba(0, 0, 0, 0.1);
@@ -293,6 +324,9 @@ i.fa.fa-caret-square-o-down {
   color: white !important;
   background-color: var(--primary-color);
 }
+.home-get-recommendations svg path{
+  fill: var(--primary-color)
+}
 .home-get-recommendations:hover .home-play-icon path{
   fill: white;
 }

diff --git a/app/components/search_input_component/search_input_component_controller.js b/app/components/search_input_component/search_input_component_controller.js
@@ -10,7 +10,6 @@ export default class extends Controller {
         itemLinkBase: String,
         idKey: String,
         cache: {type: Boolean, default: true},
-        scrollDown: {type: Boolean, default: true}
     }
 
     connect() {
@@ -39,35 +38,7 @@ export default class extends Controller {
     #useCache() {
         return this.cacheValue
     }
-    #scrollDownEnabled(){
-        return this.scrollDownValue
-    }
 
-    #scrollDown(currentScroll) {
-        const startPosition = window.pageYOffset;
-        const distance = 300 - currentScroll;
-        const duration = 1000;
-        let start = null;
-
-        function scrollAnimation(timestamp) {
-            if (!start) start = timestamp;
-            const progress = timestamp - start;
-            const scrollPosition = startPosition + easeInOutCubic(progress, 0, distance, duration);
-            window.scrollTo(0, scrollPosition);
-            if (progress < duration) {
-                window.requestAnimationFrame(scrollAnimation);
-            }
-        }
-
-        function easeInOutCubic(t, b, c, d) {
-            t /= d / 2;
-            if (t < 1) return c / 2 * t * t * t + b;
-            t -= 2;
-            return c / 2 * (t * t * t + 2) + b;
-        }
-
-        window.requestAnimationFrame(scrollAnimation);
-    }
 
     #fetchItems() {
         if (this.items.length !== 0 && this.#useCache()) {
@@ -130,9 +101,7 @@ export default class extends Controller {
             this.dropDown.style.display = "block";
 
             this.input.classList.add("home-dropdown-active");
-            if ((window.scrollY < 300) && this.#scrollDownEnabled()) {
-                this.#scrollDown(window.scrollY);
-            }
+
 
         } else {
             this.dropDown.style.display = "none";

diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
@@ -41,9 +41,8 @@ def detect_locale
   helper :all # include all helpers, all the time
   helper_method :bp_config_json, :current_license, :using_captcha?
 
-  unless Rails.env.development? || Rails.env.test?
+  if !Rails.env.development? && !Rails.env.test?
     rescue_from ActiveRecord::RecordNotFound, with: :not_found_record
-    #rescue_from StandardError, with: :internal_server_error
   end
 
   # Pull configuration parameters for REST connection.
@@ -811,13 +810,4 @@ def not_found_record(exception)
 
     render 'errors/not_found', status: 404
   end
-
-  def internal_server_error(exception)
-    current_user = session[:user] if defined?(session)
-    request_ip = request.remote_ip if defined?(request)
-    current_url = request.original_url if defined?(request)
-
-    Notifier.error(exception, current_user, request_ip, current_url).deliver_now
-    render 'errors/internal_server_error', status: 500
-  end
 end
diff --git a/app/helpers/metadata_helper.rb b/app/helpers/metadata_helper.rb
@@ -83,7 +83,7 @@ def display_attribute(metadata, value)
     elsif attr_uri?(metadata)
       render LinkFieldComponent.new(value: value)
     elsif input_type?(attr_metadata(metadata), 'contact')
-      display_contact([value]).html_safe
+      display_contact(value)
     else
       render TextAreaFieldComponent.new(value: value.to_s)
     end

diff --git a/app/views/home/index.html.haml b/app/views/home/index.html.haml
@@ -57,20 +57,28 @@
           %img{:src => asset_path("check-outlined.svg")}/
           %p
             = benefit
-
-    %div.home-upload-ontology-button
-      = upload_ontology_button
+    .home-ontologies-actions
+      .home-upload-ontology-button
+        = upload_ontology_button
+      .discover-ontologies
+        = render Buttons::RegularButtonComponent.new(id: 'discover-ontologies-button', value: t('home.discover_ontologies_button'), variant: "secondary", state: "regular", href: "/ontologies") do |btn|
+          - btn.icon_right do
+            - inline_svg_tag "arrow-right.svg"
 
   .home-section
     %h4
       = t('home.recommender_annotator')
     %hr.home-section-line/
     .home-card
       %form{action: "/annotator_recommender_form", method: "post"}
-        %textarea.home-recommendations-and-annotations{rows: "6" , placeholder: t('home.paste_text_prompt'), name: "text"}
+        %textarea.home-recommendations-and-annotations{rows: "4" , placeholder: t('home.paste_text_prompt'), name: "text"}
         %input.d-none{type: "submit", name: "submit_button" ,value: "annotator", id: "annotator_submit"}/
         %input.d-none{type: "submit" , name: "submit_button" ,value: "recommender", id: "recommender_submit"}/
-        .home-services-buttons
+        .home-services-buttons.container
+          .insert-sample-text-button{onclick: "insertSampleText()"}
+            %div
+              Insert sample text
+            = inline_svg_tag 'icons/arrow-curved-up.svg'
           .home-get-recommendations{onclick: "submitRecommender()"}
             %p= t('home.get_recommendations')
             = inline_svg_tag "play.svg", class: "home-play-icon"
@@ -168,20 +176,12 @@
   .home-section
     .home-statistics-container
       .home-support-title
-        %p= t('home.supported_by')
+        %p= t('home.support_and_collaborations')
         %hr.home-section-line/
       .home-support-items
-        - $HOME_PAGE_LOGOS[:supported_by].each do |logo|
+        - $HOME_PAGE_LOGOS.each do |logo|
           %a{href:logo[:url], target: "_blanc"}
             %img{src: asset_path(logo[:img_src])}
-      .home-support-title
-        %p= t('home.with_collaboration')
-        %hr.home-section-line/
-      .home-support-items
-        - $HOME_PAGE_LOGOS[:with_the_collaboration_of].each do |logo|
-          %a{href:logo[:url], target: "_blanc"}
-            %img{src: asset_path(logo[:img_src]), class: 'custom-logo-class'}
-
 
 
 :javascript
@@ -191,4 +191,9 @@
   function submitRecommender(){
   document.getElementById("recommender_submit").click()
   }
+  let recommenderAnnotatorArea = document.querySelector('.home-recommendations-and-annotations');
+
+  function insertSampleText(){
+    recommenderAnnotatorArea.value = 'Melanoma is a malignant tumor of melanocytes found mainly in the skin but also in the intestine and the eye.';
+  }
 
diff --git a/app/views/ontologies/sections/_additional_metadata.html.haml b/app/views/ontologies/sections/_additional_metadata.html.haml
@@ -1,8 +1,18 @@
 = turbo_frame_tag 'application_modal_content' do
+  - sub_hash = @submission_latest.to_hash.except(:context, :links, :ontology)
   %div.card.overflow-hidden{style: 'border-radius: 20px;'}
-    %section{style:'height: 70vh; overflow-y: scroll'}
+    %div
+      = render Display::AlertComponent.new(closable: false) do
+        %div.d-flex.align-items-center
+          %div{style:'width: 50px; height: 50px'}
+            - sub_values = sub_hash.values
+            - count = sub_values.count{|x| !(x.nil? || x.to_s.empty?)}
+            = render CircleProgressBarComponent.new(count: count , max: sub_values.size )
+          %div.mx-1
+            of the  metadata attributes were filled
+    %section.px-4{style:'height: 70vh; overflow-y: scroll'}
       = render SubmissionMetadataComponent.new(submission: @submission_latest, submission_metadata: submission_metadata) unless @submission_latest.nil?
     %div.scroll-message.text-center.py-3.bg-light.text-primary
       %p.scroll-text.mb-0
         Scroll down to see more
-      %i.scroll-icon.fa.fa-chevron-down
+      %i.scroll-icon.fa.fa-chevron-down
diff --git a/config/bioportal_config_env.rb.sample b/config/bioportal_config_env.rb.sample
@@ -135,8 +135,7 @@ $FRONT_NOTICE = ''
 # Site notice appears on all pages and remains closed indefinitely. Stored below as a hash with a unique key and a string message
 # EX: $SITE_NOTICE = { :unique_key => 'Put your message here (can include <a href="/link">html</a> if you use single quotes).' }
 $SITE_NOTICE = {}
-$HOME_PAGE_LOGOS = {
-  supported_by: [
+$HOME_PAGE_LOGOS = [
     {
       img_src: 'logos/supports/numev.png',
       url: 'http://www.lirmm.fr/numev',
@@ -151,9 +150,7 @@ $HOME_PAGE_LOGOS = {
       img_src: 'logos/supports/eu.png',
       url: 'https://commission.europa.eu/research-and-innovation_en',
       target: '_blank'
-    }
-  ],
-  with_the_collaboration_of: [
+    },
     {
       img_src: 'logos/collaboration/d2kab.png',
       url: 'http://d2kab.mystrikingly.com',
@@ -174,8 +171,8 @@ $HOME_PAGE_LOGOS = {
       url: 'https://www.stanford.edu',
       target: '_blank'
     }
-  ]
-}
+]
+
 
 $FOOTER_LINKS = {
   social: [

diff --git a/config/initializers/bugsnag.rb b/config/initializers/bugsnag.rb
@@ -0,0 +1,3 @@
+Bugsnag.configure do |config|
+  config.api_key = "00ccc6304835fbd8f08f6764a6611704"
+end
diff --git a/config/locales/de.yml b/config/locales/de.yml
@@ -118,13 +118,14 @@ de:
     ontology_upload_benefits: 'Indem Sie Ihre Ontologie auf %{site} hochladen, können
       Sie:'
     ontology_upload_button: Ontologie hochladen
+    discover_ontologies_button: Ontdek ontologieën
     ontology_upload_desc: Das Hochladen einer Ontologie ist eine Möglichkeit, Ihr
       Fachwissen mit anderen zu teilen.
     paste_text_prompt: Einfügen eines Textabsatzes oder einiger Schlüsselwörter ...
     recommender_annotator: Empfehlungsgeber und Kommentator
-    supported_by: Unterstützt von
+    support_and_collaborations: Ondersteuning en samenwerkingen
     twitter_news: Nachrichten
-    with_collaboration: In Zusammenarbeit mit der
+
   input: Eingabe
   insert_sample_text: Beispieltext einfügen
   keywords: Schlüsselwörter