<%=render partial: 'layouts/notices'%>
\ No newline at end of file
diff --git a/app/views/layouts/_topnav.html.haml b/app/views/layouts/_topnav.html.haml
index 4ae87baeb..8ce7afe78 100644
--- a/app/views/layouts/_topnav.html.haml
+++ b/app/views/layouts/_topnav.html.haml
@@ -1,61 +1,74 @@
-%nav.navbar.navbar-expand-lg.navbar-dark.navbar-custom
- = link_to(image_tag("logos/ontoportal-logo.png") + content_tag(:span, $SITE, class: 'site-name'), root_path(), class: "navbar-brand")
- = button_tag(type: "button", class: "navbar-toggler", data: {toggle: "collapse", target: "#topNavigationToggler"}, aria: {controls: "topNavigationToggler", expanded: "false", label: "Toggle navigation"}) do
- %span.navbar-toggler-icon
+.nav-container.text-white{data: {controller:"topnav-responsiveness"}}
+ %nav.top-nav
+ .nav-responsiveness-container
+ %a.nav-logo{href: "/"}
+ %img{:src => asset_path("logo-white.svg")}/
+ %p
+ = portal_name
+ %input#nav-menu{:type => "checkbox", 'data-topnav-responsiveness-target': 'navMenu'}
+ %label.menu-btn{:for => "nav-menu"}
+ %i.fas.fa-bars
+ .nav-items
+ %ul.top-nav-ul
+ - navitems.each do |navItem|
+ %li.nav-ul-li
+ %a{href: navItem[0], class: ("active" if current_page?(navItem[0]))} #{navItem[1]}
+ %div.d-flex.align-items-center.justify-content-between{style:'min-width: 40%'}
+ - if current_page?('/')
+ .nav-search-container{style:'visibility: hidden'}
+ %input
+ - else
+ .nav-search-container{'data-controller': "home-search"}
+ %input.nav-input{:placeholder => "Search in "+portal_name+" ...", :type => "text", :name => "search", 'data-home-search-target': 'input', 'data-action': 'input->home-search#search blur->home-search#blur'}
+ #home-search-drop-down.nav-search-drop-down{'data-home-search-target': 'dropDown', 'data-action': 'mousedown->home-search#prevent'}
+ %a.home-search-ontology-content#home-search-ontology-content{href: "#", 'data-home-search-target': 'searchOntologyContent'}
+ %p#seached-ontology{'data-home-search-target': 'ontology'}
+ %div
+ %img{src: asset_path("loop.svg")}/
+ %p Search ontology content
+ %a.home-search-ontology-content#home-search-ontologies{href: "#", 'data-home-search-target': 'homeSearchOntologies'}
+ %p#seached-ontologies{'data-home-search-target': 'searchedOntologies'}
+ %div
+ %img{src: asset_path("loop.svg")}/
+ %p See all ontologies
- %div#topNavigationToggler.navbar-collapse.collapse.justify-content-between
- %ul.navbar-nav
- %li.nav-item
- = link_to(t('layout.header.browse'), ontologies_path(), class: "nav-link")
- %li.nav-item
- = link_to(t('layout.header.search'), "/search", class: "nav-link")
- %li.nav-item
- = link_to(t('layout.header.mappings'), mappings_path(), class: "nav-link")
- %li.nav-item
- = link_to(t('layout.header.recommender'), recommender_index_path, class: "nav-link")
- %li.nav-item
- = link_to(t('layout.header.annotator'), annotator_index_path(), class: "nav-link")
- - if $NCBO_ANNOTATORPLUS_ENABLED == true
- %li.nav-item
- = link_to(t('layout.header.ncbo_annotator_plus'), '/ncbo_annotatorplus', class: "nav-link")
- %li.nav-item
- = link_to(t('layout.header.projects'), projects_path(), class: "nav-link")
- %li.nav-item
- = link_to(t('layout.header.landscape'), '/landscape', class: "nav-link")
- -if (!session[:user].nil? && session[:user].admin?)
- %li.nav-item
- = link_to(t('layout.header.admin'), admin_index_path, class: "nav-link")
- %ul.navbar-nav
- %li.nav-item{ style: "margin-right: 10px;" }
- %select#language-select.form-control{ data: { controller: "platform-language", action: "change->platform-language#handleLangChanged" } }
- %option{ value: "en" } English
- %option{ value: "fr" } Français
-
- - if session[:user].nil?
- %li.nav-item
- = link_to(t(:_login), login_index_path(redirect: request.original_url), class: "btn btn-bp-login mr-md-2")
- - else
- -# Account menu
- %li.nav-item.dropdown
- = link_to("#", id: "accountMenuDropdownLink", class: "nav-link dropdown-toggle", role: "button", data: {toggle: "dropdown"}, aria: {haspopup: "true", expanded: "false"}) do
- = session[:user].username
- %div.dropdown-menu.dropdown-menu-right{aria: {labelledby: "accountMenuDropdownLink"}}
- = link_to(t(:_account_setting), "/account", class: "dropdown-item")
- - unless session[:ontologies].nil?
- %div.dropdown-divider
- %h6.dropdown-header Recently Viewed
+ - if session[:user].nil?
+ %a.nav-a{:href => "/login"} Login
+ - else
+ = render DropdownButtonComponent.new do |d|
+ - d.header do
+ = session[:user].username
+ - d.with_section(divide: false) do |s|
+ - s.item do
+ = link_to(t(:_account_setting), "/account")
+ - d.with_section do |s|
+ - s.header do
+ Recently Viewed
- for ont in session[:ontologies]
- = link_to(ont.ontology_name, "/ontologies/#{ont.ontology_acronym}/?p=classes&conceptid=#{CGI.escape(ont.concept)}", class: "dropdown-item")
- %div.dropdown-divider
- = link_to("Logout", logout_path, class: "dropdown-item")
- -# Support menu
- %li.nav-item.dropdown
- = link_to("#", id: "supportMenuDropdownLink", class: "nav-link dropdown-toggle", role: "button", data: {toggle: "dropdown"}, aria: {haspopup: "true", expanded: "false"}) do
- Support
- %div.dropdown-menu.dropdown-menu-right{aria: {labelledby: "supportMenuDropdownLink"}}
- = link_to(t(:submit_feedback), feedback_path(location: encode_param(request.url)), id: "submitFeedbackMenuItem", class: "dropdown-item pop_window")
- %div.dropdown-divider
- %h6.dropdown-header Documentation
- = link_to(t(:_help), "#{$WIKI_HELP_PAGE}", target: "_blank", class: "dropdown-item")
- = link_to(t(:_release_notes), "#{$RELEASE_NOTES}", target: "_blank", class: "dropdown-item")
- = link_to(t(:_publications), $PUBLICATIONS_URL, target: "_blank", class: "dropdown-item")
+ - s.item do
+ = link_to(ont.ontology_name, "/ontologies/#{ont.ontology_acronym}/?p=classes&conceptid=#{CGI.escape(ont.concept)}")
+ - d.with_section do |s|
+ - s.item do
+ = link_to("Logout", logout_path)
+
+ = select_tag('language', options_for_select([['EN','en'],['FR','fr']]), id: 'language-select', class: 'nav-language',
+ data: { controller: "platform-language", action: "change->platform-language#handleLangChanged" })
+
+ = render DropdownButtonComponent.new do |d|
+ - d.header do
+ = link_to("#", id: "supportMenuDropdownLink", class: "nav-link top-nav-nav-link supportMenuDropdownLink", role: "button") do
+ Support
+ - d.with_section(divide: false) do |s|
+ - s.item do
+ = link_to(t(:submit_feedback), feedback_path(location: encode_param(request.url)), id: "submitFeedbackMenuItem", class: "pop_window")
+ - d.with_section do |s|
+ - s.header do
+ Documentation
+ - s.item do
+ = link_to(t(:_help), "#{$WIKI_HELP_PAGE}", target: "_blank")
+ - s.item do
+ = link_to(t(:_release_notes), "#{$RELEASE_NOTES}", target: "_blank")
+ - s.item do
+ = link_to(t(:_publications), $PUBLICATIONS_URL, target: "_blank")
+
+
diff --git a/app/views/recommender/index.html.haml b/app/views/recommender/index.html.haml
index 8dddc3846..0cb71e46e 100644
--- a/app/views/recommender/index.html.haml
+++ b/app/views/recommender/index.html.haml
@@ -31,7 +31,7 @@
-# Input text or keywords
%div.form-group.mt-4
- = text_area_tag("inputText", nil, rows: 10, class: "form-control default", placeholder: t('paste_input_text'), aria: {describedby: "inputTextHelpBlock"})
+ = text_area_tag("inputText", @text, rows: 10, class: "form-control default", placeholder: "Paste a paragraph of text or some keywords to use in calculating ontology recommendations", aria: {describedby: "inputTextHelpBlock"})
%div.card#inputTextHighlighted
%div.card-body
%small#inputTextHelpBlock.form-text
@@ -107,3 +107,14 @@
%div.col
%h5#resultsHeader
%div#recommender-results.mb-5
+
+:javascript
+ window.addEventListener("load", function() {
+ const value = document.getElementById("inputText").value
+ document.getElementById("inputText").click();
+ document.getElementById("inputText").value = value
+ if(document.getElementById("inputText").value != ''){
+ document.getElementById("recommenderButton").click()
+ window.scrollBy(0, 1080);
+ }
+ });
\ No newline at end of file
diff --git a/app/views/users/show.html.haml b/app/views/users/show.html.haml
index ecd788660..bf3657498 100644
--- a/app/views/users/show.html.haml
+++ b/app/views/users/show.html.haml
@@ -111,8 +111,8 @@
%h4.account-page-card-title Submitted ontologies
.account-page-small-cards-container
- @admin_ontologies.each do |ont|
- .account-page-submitted-ontology
- %a{href: "/ontologies/#{ont.acronym}"}= ont.name
+ .account-page-submitted-ontology{data: {controller: 'tooltip'}, title: ont.name}
+ %a{href: "/ontologies/#{ont.acronym}"}= ont.acronym
- unless @user_projects.nil? || @user_projects.empty?
- no_ontologies = false
.account-page-card
diff --git a/config/locales/en.yml b/config/locales/en.yml
index b19e00522..ae4ebeeae 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -184,9 +184,9 @@ en:
index:
find_ontology_placeholder: Start typing the ontology name, then choose from
query_placeholder: Enter a class, eg Melanoma
- tagline: the world's most comprehensive repository of biomedical ontologies
+ tagline: The home of vocabularies and ontologies in agronomy and related fields.
title: Welcome to the %{organization}
- welcome: Welcome to the %{site},
+ welcome: Welcome to %{site},
help:
welcome: Welcome to the %{site} of the National Center for Biomedical Ontology. %{site} is a web application for accessing and sharing biomedical ontologies.
getting_started: >
@@ -270,61 +270,63 @@ en:
sample_text: Melanoma is a malignant tumor of melanocytes found mainly in the skin but also in the intestine and the eye.
ontology_details:
- header:
- last_uploaded: "Last uploaded:"
- sections:
- summary: "Summary"
- concepts: "Concepts"
- classes: "Classes"
- properties: "Properties"
- notes: "Notes"
- mappings: "Mappings"
- schemes: "Schemes"
- collections: "Collections"
- widgets: "Widgets"
- metadata:
- details: "Details"
- acronym: "Acronym"
- visibility: "Visibility"
- viewing_restriction: "Viewing Restriction"
- view_of_ontology: "View of ontology"
- description: "Description"
- status: "Status"
- format: "Format"
- contact: "Contact"
- categories: "Categories"
- groups: "Groups"
- pull_url: "Pull URL"
- submissions: "Submissions"
- links: "Links"
- add_submission: "Add Submission"
- views_of: "Views of"
- create_new_view: "Create a new view"
- no_views_of: "No views of %{name} available"
- go_to_rest_api_json_entry: "Go to REST API JSON Entry"
- get_my_metadata_back: "Get my metadata back"
- n_triple: "N-Triple"
- json_ld: "JSON-LD"
- rdf_xml: "RDF/XML"
- view_individual_metrics_definitions: "View individual metrics definitions"
- metrics: "Metrics"
- metrics_not_calculated_yet: "We have not yet calculated metrics for"
- classes: "Classes"
- individuals: "Individuals"
- properties: "Properties"
- max_depth: "Maximum depth"
- max_children: "Maximum number of children"
- avg_children: "Average number of children"
- single_child_classes: "Classes with a single child"
- many_children_classes: "Classes with more than 25 children"
- no_definition_classes: "Classes without definition"
- visits: "Visits"
- download_as_csv: "Download as CSV"
- projects_using: "Projects Using"
- no_projects_using: "No projects are using"
- create_new_project: "Create a new project"
- additional_metadata: "Additional Metadata"
+ metadata:
+ details: "Details"
+ acronym: "Acronym"
+ visibility: "Visibility"
+ viewing_restriction: "Viewing Restriction"
+ view_of_ontology: "View of ontology"
+ description: "Description"
+ status: "Status"
+ format: "Format"
+ contact: "Contact"
+ categories: "Categories"
+ groups: "Groups"
+ pull_url: "Pull URL"
+ submissions: "Submissions"
+ links: "Links"
+ add_submission: "Add Submission"
+ views_of: "Views of"
+ create_new_view: "Create a new view"
+ no_views_of: "No views of %{name} available"
+ go_to_rest_api_json_entry: "Go to REST API JSON Entry"
+ get_my_metadata_back: "Get my metadata back"
+ n_triple: "N-Triple"
+ json_ld: "JSON-LD"
+ rdf_xml: "RDF/XML"
+ view_individual_metrics_definitions: "View individual metrics definitions"
+ metrics: "Metrics"
+ metrics_not_calculated_yet: "We have not yet calculated metrics for"
+ classes: "Classes"
+ individuals: "Individuals"
+ properties: "Properties"
+ max_depth: "Maximum depth"
+ max_children: "Maximum number of children"
+ avg_children: "Average number of children"
+ single_child_classes: "Classes with a single child"
+ many_children_classes: "Classes with more than 25 children"
+ no_definition_classes: "Classes without definition"
+ visits: "Visits"
+ download_as_csv: "Download as CSV"
+ projects_using: "Projects Using"
+ no_projects_using: "No projects are using"
+ create_new_project: "Create a new project"
+ additional_metadata: "Additional Metadata"
+ concept:
+ no_preferred_name_for_selected_language: "No preferred name for selected language."
+ no_synonym_name_for_selected_language: "No Synonym for selected language."
+ no_definitions_for_selected_language: "No Definitions for selected language."
+ preferred_name: "Preferred name"
+ id: "ID"
+ synonyms: "Synonyms"
+ definitions: "Definitions"
+ obsolete: "Obsolete"
+ member_of: "Member of"
+ in_schemes: "In Schemes"
+ type: "Type"
+ no_value_for_selected_language: "No value for selected language."
+
layout:
header:
browse: "Browse"
diff --git a/config/locales/fr.yml b/config/locales/fr.yml
index 95940640f..3992efa92 100644
--- a/config/locales/fr.yml
+++ b/config/locales/fr.yml
@@ -1,4 +1,5 @@
fr:
+
nbco_annotatosplus:
score_help: "Annotations de score suivant la mesure NCBO 2009 précédente (ancienne) ou Annotations de score suivant la mesure C-Value (cvalue) ou Annotations de score suivant la mesure C-Value avec expansion de la hiérarchie (cvalueh)"
start_typing_to_select: "Commencez à taper pour sélectionner %{type} ou laissez vide pour tout utiliser"
@@ -190,8 +191,7 @@ fr:
projects: "Projets"
users: "Utilisateurs"
no_recent_notes: "Aucune note récente n'a été soumise"
- supported_by: "Avec le soutien de"
- with_collaboration: "Avec la collaboration de"
+
index:
find_ontology_placeholder: Commencez à taper le nom de l'ontologie, puis choisissez dans
query_placeholder: Entrez une classe, par exemple Melanoma
@@ -281,22 +281,9 @@ fr:
sample_text: Le mélanome est une tumeur maligne des mélanocytes qui se trouvent principalement dans la peau mais aussi dans l'intestin et l'œil.
ontology_details:
- header:
- last_uploaded: "Dernière mise à jour:"
- sections:
- summary: "Résumé"
- concepts: "Concepts"
- classes: "Classes"
- properties: "Propriétés"
- notes: "Notes"
- mappings: "Mappings"
- schemes: "Schemes"
- collections: "Collections"
- widgets: "Widgets"
-
metadata:
details: "Détails"
- acronym: "Acronyme"
+ acronym: "Acronym"
visibility: "Visibilité"
viewing_restriction: "Restriction de visualisation"
view_of_ontology: "Vue de l'ontologie"
@@ -337,6 +324,23 @@ fr:
create_new_project: "Créer un nouveau projet"
additional_metadata: "Métadonnées supplémentaires"
+ concept:
+ no_preferred_name_for_selected_language: "Pas de nom préféré pour la langue sélectionnée."
+ no_synonym_name_for_selected_language : "Aucun synonyme pour la langue sélectionnée."
+ no_definitions_for_selected_language : "Aucune définition pour la langue sélectionnée."
+ preferred_name: "Nom préféré"
+ id: "Identifiant"
+ synonyms: "Synonymes"
+ definitions: "Définitions"
+ obsolete: "Obsolète"
+ member_of: "Membre de"
+ in_schemes: "Dans les schémas"
+ type: "Type"
+ no_value_for_selected_language: "Pas de valeur pour la langue sélectionnée."
+
+
+
+
layout:
header:
browse: "Parcourir"
@@ -354,24 +358,7 @@ fr:
release_notes: "Notes de version"
publications: "Publications"
footer:
- products: Produits
- ontoportal: OntoPortal
- release_notes: Notes de version
- api: API
- sparql: SPARQL
- support: Support
- contact_us: Nous contacter
- wiki: Wiki
- documentation: Documentation
- agreements: Accords
- terms: Conditions d'utilisation
- privacy_policy: Politique de confidentialité
- cite_us: Nous citer
- acknowledgments: Remerciements
- about: À propos
- about_us: À propos de nous
- projects: Projets
- team: Équipe
+ products: "Produits"
copyright_html: Droit d'auteur &copie; 2005‑2022, Conseil d'administration de l'Université Leland Stanford Junior. Tous les droits sont réservés.
grant_html: >
%{site} est actuellement développé dans le cadre du
projet ANR D2KAB (
ANR-18-CE23-0017). Il reçoit ou a également reçu le soutien du
projet ANR SIFR (
ANR-12-JS02-0010), Union Européenne
Projet H2020-MSCA SIFRm (
N° 701771), le
Labex NUMEV (ANR-10-LABX-20), le
projet IBC de Montpellier (ANR-11-BINF0002) , l'Agro Labex (ANR-10-LABX-0001) ainsi que de l'Université de Montpellier et du CNRS.
@@ -448,8 +435,8 @@ fr:
formats:
year_month_day_concise: "%Y-%m-%d" # 2017-03-01
month_day_year: "%b %-d, %Y" # Mar 1, 2017
- monthfull_day_year: "%-d %B %Y" # March 1, 2017
-
+ monthfull_day_year: "%B %-d, %Y" # March 1, 2017
+
ontologies:
self: "Ontologies"
loading: Chargement des ontologies
@@ -571,3 +558,5 @@ fr:
paste_input_text: "Collez un paragraphe de texte ou des mots-clés à utiliser dans le calcul des recommandations d'ontologie"
get_recommendations: "Obtenir des recommandations"
select_ontologies_list: "Sélectionnez les ontologies"
+
+
\ No newline at end of file
diff --git a/config/routes.rb b/config/routes.rb
index 4862b94cc..5090016ec 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -89,6 +89,7 @@
get '/about' => 'home#about'
get '/site_config' => 'home#site_config'
get '/validate_ontology_file' => 'home#validate_ontology_file_show'
+ post '/annotator_recommender_form' => 'home#annotator_recommender_form'
match '/validate_ontology_file' => 'home#validate_ontology_file', via: [:get, :post]
get '/layout_partial/:partial' => 'home#render_layout_partial'
match '/visits', to: 'visits#index', via: :get
@@ -151,6 +152,7 @@
get '/ajax/fair_score/json' => 'fair_score#details_json'
get '/ajax/:ontology/instances' => 'instances#index_by_ontology'
get '/ajax/:ontology/classes/:conceptid/instances' => 'instances#index_by_class', :constraints => { conceptid: /[^\/?]+/ }
+ get '/ajax/ontologies' , to:"ontologies#ajax_ontologies"
# User
get '/logout' => 'login#destroy', :as => :logout
diff --git a/test/components/previews/alert_message_component_preview.rb b/test/components/previews/alert_message_component_preview.rb
new file mode 100644
index 000000000..4efb845e9
--- /dev/null
+++ b/test/components/previews/alert_message_component_preview.rb
@@ -0,0 +1,10 @@
+class AlertMessageComponentPreview < ViewComponent::Preview
+
+ # @param message text
+ # @param type select [error, info, success, warning]
+
+ def default(message: "Here we can type a success or failure message to the user", type: "info", closeable: true )
+ render(AlertMessageComponent.new(message: message, type: type, closeable: closeable))
+ end
+
+end
\ No newline at end of file
diff --git a/test/components/previews/card_message_component_preview.rb b/test/components/previews/card_message_component_preview.rb
index 02c17f200..522031669 100644
--- a/test/components/previews/card_message_component_preview.rb
+++ b/test/components/previews/card_message_component_preview.rb
@@ -2,11 +2,29 @@ class CardMessageComponentPreview < ViewComponent::Preview
# @param message text
# @param button_text text
- # @param type select [success, failure]
# @param button_link text
- def default(message: "Here we can type a success or failure message to the user", button_text: "Do action", type: "success", button_link: "/" )
- render(CardMessageComponent.new(message: message, button_text: button_text, type: type, button_link: button_link))
+ def default(message: "Here we can type a success or failure message to the user", button_text: "Do action", button_link: "/" )
+ render(CardMessageComponent.new(message: message, button_text: button_text, type: "success", button_link: button_link))
end
- end
\ No newline at end of file
+
+ # @param message text
+ # @param button_text text
+ # @param button_link text
+
+ def warning(message: "Here we can type a success or failure message to the user", button_text: "Do action", button_link: "/" )
+ render(CardMessageComponent.new(message: message, button_text: button_text, type: "warning", button_link: button_link))
+ end
+
+
+ # @param message text
+ # @param button_text text
+ # @param button_link text
+
+ def failure(message: "Here we can type a success or failure message to the user", button_text: "Do action", button_link: "/" )
+ render(CardMessageComponent.new(message: message, button_text: button_text, type: "failure", button_link: button_link))
+ end
+
+
+end
\ No newline at end of file
diff --git a/test/components/previews/chip_button_component_preview.rb b/test/components/previews/chip_button_component_preview.rb
new file mode 100644
index 000000000..ab5dedab2
--- /dev/null
+++ b/test/components/previews/chip_button_component_preview.rb
@@ -0,0 +1,19 @@
+class ChipButtonComponentPreview < ViewComponent::Preview
+
+ # @param url text
+ # @param text text
+
+ def standard(url: "nil", text: "text")
+ render(ChipButtonComponent.new(url: url, text: text, type: "static"))
+ end
+
+ # @param url text
+ # @param text text
+
+ def clickable(url: "nil", text: "text")
+ render(ChipButtonComponent.new(url: url, text: text, type: "clickable"))
+ end
+
+
+
+end
\ No newline at end of file
diff --git a/test/components/previews/chips_component_preview.rb b/test/components/previews/chips_component_preview.rb
index 55ff1b5bc..8f806211c 100644
--- a/test/components/previews/chips_component_preview.rb
+++ b/test/components/previews/chips_component_preview.rb
@@ -7,4 +7,4 @@ def default(name: "name", value: "value")
render(ChipsComponent.new(name: name, value: value))
end
- end
\ No newline at end of file
+end
\ No newline at end of file
diff --git a/test/components/previews/rounded_button_component_preview.rb b/test/components/previews/rounded_button_component_preview.rb
new file mode 100644
index 000000000..1ba6584f1
--- /dev/null
+++ b/test/components/previews/rounded_button_component_preview.rb
@@ -0,0 +1,14 @@
+class RoundedButtonComponentPreview < ViewComponent::Preview
+
+ # @param icon text
+ # @param link text
+ # @param size select [small, medium, big]
+
+ def default(icon: "json.svg", link: "text", size: "small")
+ render(RoundedButtonComponent.new(icon: icon, link: link, size: size))
+ end
+
+
+
+
+end
\ No newline at end of file