Merge pull request #234 from ncbo/kgcl-change-requests

Add initial support for ontology change requests

Gemfile

@@ -27,6 +27,7 @@ gem 'select2-rails'
 gem 'cube-ruby', require: 'cube'
 gem 'dalli'
 gem 'flamegraph'
+gem 'graphql-client'
 gem 'haml', '~> 5.1'
 gem 'i18n'
 gem 'iconv'

Gemfile.lock

@@ -141,6 +141,10 @@ GEM
     flamegraph (0.9.5)
     globalid (1.0.0)
       activesupport (>= 5.0)
+    graphql (2.0.9)
+    graphql-client (0.18.0)
+      activesupport (>= 3.0)
+      graphql
     haml (5.2.2)
       temple (>= 0.8.0)
       tilt
@@ -353,6 +357,7 @@ DEPENDENCIES
   dalli
   ed25519 (>= 1.2, < 2.0)
   flamegraph
+  graphql-client
   haml (~> 5.1)
   html2haml
   i18n

app/assets/javascripts/application.js

@@ -28,6 +28,7 @@
 //= require bp_admin
 //= require bp_recommender
 //= require bp_property_tree
+//= require concepts
 //= require home
 //= require ontologies
 //= require projects

app/assets/javascripts/concepts.js

@@ -0,0 +1,7 @@
+jQuery(document).ready(function() {
+
+  jQuery('#changeRequestModal').on('submit', function() {
+    $('#changeRequestModal').modal('hide');
+  });
+
+});

app/assets/stylesheets/application.css.scss

@@ -27,6 +27,7 @@
 @import "admin";
 @import "annotator";
 @import "bioportal";
+@import "concepts";
 @import "footer";
 @import "home";
 @import "mappings";

app/assets/stylesheets/bioportal.scss

@@ -547,27 +547,6 @@ li.ac_over > .obsolete_class {
   cursor: inherit;  /*override the help cursor for selection menus*/
 }
 
-.concept_details p {
-  margin-bottom: .5em;
-}
-
-.concept_details .label {
-  vertical-align: top;
-  width: 180px;
-  max-width: 200px;
-}
-
-.concept_details tbody td {
-  padding: 0.6em 0.8em 0 !important;
-  white-space: normal; /* css-3 */
-  white-space: -moz-normal; /* Mozilla, since 1999 */
-  word-wrap: break-word; /* Internet Explorer 5.5+ */
-}
-
-.concept_details td:nth-child(1) {
-  white-space: nowrap;
-}
-
 #format_specific_options td {
   border-top: 1px solid #C1DAD7;
 }

app/assets/stylesheets/concepts.scss

@@ -0,0 +1,33 @@
+.concept_details .label {
+  vertical-align: top;
+  width: 180px;
+  max-width: 200px;
+}
+
+.concept_details tbody td {
+  white-space: normal; /* css-3 */
+  white-space: -moz-normal; /* Mozilla, since 1999 */
+  word-wrap: break-word; /* Internet Explorer 5.5+ */
+
+  p {
+    margin-bottom: 0;
+  }
+
+  a.btn.btn-link {
+    padding: 0;  
+  }
+}
+
+.concept_details td:nth-child(1) {
+  white-space: nowrap;
+}
+
+div.synonym-change-request {
+  display: flex;
+  column-gap: 5px;
+  justify-content: flex-end;
+}
+
+div.synonym-change-request button {
+  padding: 0px;
+}

app/controllers/change_requests_controller.rb

@@ -0,0 +1,37 @@
+# frozen_string_literal: true
+
+class ChangeRequestsController < ApplicationController
+  def create_synonym
+    @concept_label = params[:concept_label]
+    @concept_id = params[:concept_id]
+    @ont_acronym = params[:ont_acronym]
+    @username = session[:user].username
+
+    respond_to :js
+  end
+
+  def create
+    params[:curie] = generate_curie(params[:ont_acronym], params[:concept_id])
+    params[:content] = KGCL::IssueContentGenerator.call(params)
+    @issue = IssueCreatorService.call(params)
+    flash.now.notice = helpers.change_request_success_message if @issue['id'].present?
+
+    respond_to :js
+  end
+
+  private
+
+  def generate_curie(ont_acronym, concept_id)
+    ontology = LinkedData::Client::Models::Ontology.find_by_acronym(ont_acronym).first
+    query_string = { display: 'notation,prefixIRI', display_links: false, display_context: false }
+    concept = ontology.explore.single_class(query_string, concept_id)
+
+    if concept.notation
+      concept.notation
+    elsif concept.prefixIRI
+      concept.prefixIRI
+    else
+      concept_id
+    end
+  end
+end

app/helpers/application_helper.rb

@@ -392,16 +392,13 @@ def xmldatetime_to_date(xml_date_time_str)
   end
 
   def flash_class(level)
-    case level
-    when "notice" 
-      "alert alert-info"
-    when "success" 
-      "alert alert-success"
-    when "error"
-      "alert alert-danger"
-    when "alert" 
-      "alert alert-error"
-    end
+    bootstrap_alert_class = {
+      'notice' => 'alert-info',
+      'success' => 'alert-success',
+      'error' => 'alert-danger',
+      'alert' => 'alert-danger'
+    }
+    bootstrap_alert_class[level]
   end
 
   ###BEGIN ruby equivalent of JS code in bp_ajax_controller.

app/helpers/change_requests_helper.rb

@@ -0,0 +1,12 @@
+# frozen_string_literal: true
+
+module ChangeRequestsHelper
+  def change_request_success_message
+    url = link_to 'details', @issue['url'], target: '_blank', class: 'alert-link'
+    "Your change request was successfully submitted! View the #{url} on GitHub.".html_safe
+  end
+
+  def change_request_alert_context
+    flash.notice.present? ? 'alert-success' : 'alert-danger'
+  end
+end

app/helpers/concepts_helper.rb

@@ -1,27 +1,29 @@
-module ConceptsHelper
+# frozen_string_literal: true
 
+module ConceptsHelper
   def exclude_relation?(relation_to_check, ontology = nil)
-    excluded_relations = [ "type", "rdf:type", "[R]", "SuperClass", "InstanceCount" ]
+    excluded_relations = %w[type rdf:type [R] SuperClass InstanceCount]
 
     # Show or hide property based on the property and ontology settings
     if ontology
       # TODO_REV: Handle obsolete classes
       # Hide owl:deprecated if a user has set class or property based obsolete checking
-      # if !ontology.obsoleteParent.nil? && relation_to_check.include?("owl:deprecated") || !ontology.obsoleteProperty.nil? && relation_to_check.include?("owl:deprecated")
+      # if !ontology.obsoleteParent.nil? && relation_to_check.include?("owl:deprecated") ||
+      #    !ontology.obsoleteProperty.nil? && relation_to_check.include?("owl:deprecated")
       #   return true
       # end
     end
 
     excluded_relations.each do |relation|
       return true if relation_to_check.include?(relation)
     end
-    return false
+    false
   end
 
   def concept_properties2hash(properties)
     # NOTE: example properties
     #
-    #properties
+    # properties
     #=> #<struct
     #  http://www.w3.org/2000/01/rdf-schema#label=
     #    [#<struct
@@ -47,32 +49,83 @@ def concept_properties2hash(properties)
     #  links=nil,
     #  context=nil>
     properties_data = {}
-    keys = properties.members  # keys is an array of symbols
+    keys = properties.members # keys is an array of symbols
     for key in keys
-      next if properties[key].nil?  # ignore :context and :links when nil.
+      next if properties[key].nil? # ignore :context and :links when nil.
+
       # Shorten the key into a simple label
       k = key.to_s if key.kind_of?(Symbol)
       k ||= key
       if k.start_with?("http")
         label = LinkedData::Client::HTTP.get("/ontologies/#{@ontology.acronym}/properties/#{CGI.escape(k)}/label").label rescue ""
         if label.nil? || label.empty?
-          k = k.gsub(/.*#/,'')  # greedy regex replace everything up to last '#'
-          k = k.gsub(/.*\//,'') # greedy regex replace everything up to last '/'
+          k = k.gsub(/.*#/, '')  # greedy regex replace everything up to last '#'
+          k = k.gsub(/.*\//, '') # greedy regex replace everything up to last '/'
           # That might take care of nearly everything to be shortened.
           label = k
         end
       end
       begin
         # Try to simplify the property values, when they are a struct.
-        values = properties[key].map {|v| v.string }
+        values = properties[key].map { |v| v.string }
       rescue
         # Each value is probably a simple datatype already.
         values = properties[key]
       end
-      data = { :key => key, :values => values }
+      data = { key: key, values: values }
       properties_data[label] = data
     end
-    return properties_data
+    properties_data
+  end
+
+  def add_synonym_button
+    return unless change_requests_enabled?(@ontology.acronym)
+
+    if session[:user].nil?
+      link_to(login_index_path(redirect: concept_redirect_path),
+              role: 'button',
+              class: 'btn btn-link',
+              aria: { label: 'Create synonym' }) do
+        content_tag(:i, '', class: 'fas fa-plus-circle fa-lg', aria: { hidden: 'true' }).html_safe
+      end
+    else
+      link_to(change_requests_create_synonym_path(concept_id: @concept.id, concept_label: @concept.prefLabel,
+                                                  ont_acronym: @ontology.acronym),
+              role: 'button',
+              class: 'btn btn-link',
+              aria: { label: 'Create synonym' },
+              data: { toggle: 'modal', target: '#changeRequestModal' },
+              remote: 'true') do
+        content_tag(:i, '', class: 'fas fa-plus-circle fa-lg', aria: { hidden: 'true' }).html_safe
+      end
+    end
   end
 
+  def remove_synonym_button
+    return unless change_requests_enabled?(@ontology.acronym)
+
+    if session[:user].nil?
+      link_to(login_index_path(redirect: concept_redirect_path),
+              role: 'button',
+              class: 'btn btn-link',
+              aria: { label: 'Remove a synonym' }) do
+        content_tag(:i, '', class: 'fas fa-minus-circle fa-lg', aria: { hidden: 'true' }).html_safe
+      end
+    else
+      link_to('#', role: 'button', class: 'btn btn-link', aria: { label: 'Remove a synonym' }) do
+        content_tag(:i, '', class: 'fas fa-minus-circle fa-lg', aria: { hidden: 'true' }).html_safe
+      end
+    end
+  end
+
+  def synonym_qualifier_select(form)
+    options = [%w[exact exact], %w[narrow narrow], %w[broad broad], %w[related related]]
+    form.select :qualifier, options_for_select(options, 0), {}, { class: 'form-control' }
+  end
+
+  private
+
+  def concept_redirect_path
+    ontology_path(@ontology.acronym, p: 'classes', conceptid: @concept.id)
+  end
 end