Merge branch 'development' into stage

app/assets/stylesheets/admin.scss

@@ -22,6 +22,13 @@
   }
 }
 
+.yasgui .autocompleteWrapper, .yasgui .tabContextButton{
+  display: none !important;
+}
+.yasqe .yasqe_buttons .yasqe_share{
+  display: none !important;
+}
+
 .alert-box span {
   font-weight: bold;
   text-transform: uppercase;

app/assets/stylesheets/application.css.scss.erb

@@ -49,6 +49,7 @@
 @import "tom-select/dist/scss/tom-select";
 @import "tippy.js/dist/tippy";
 @import 'tippy.js/themes/light-border';
+@import '@triply/yasgui/build/yasgui.min';
 @import "feedback";
 @import "login";
 @import "components/index";

app/assets/stylesheets/home.scss

@@ -153,7 +153,7 @@ i.fa.fa-caret-square-o-down {
 .home-statistics-container{
   border-radius: 8px;
   box-shadow: 2px 0px 60px rgba(0, 0, 0, 0.10);
-  padding: 30px 40px;
+  padding: 30px 40px 10px 40px;
 
 }
 .home-statistics-container > div {

app/controllers/admin_controller.rb

@@ -1,5 +1,5 @@
 class AdminController < ApplicationController
-  include TurboHelper, HomeHelper
+  include TurboHelper, HomeHelper, SparqlHelper
   layout :determine_layout
   before_action :cache_setup
 
@@ -10,6 +10,20 @@ class AdminController < ApplicationController
   PARSE_LOG_URL = lambda { |acronym| "#{ONTOLOGY_URL.call(acronym)}/log" }
   REPORT_NEVER_GENERATED = "NEVER GENERATED"
 
+
+  def sparql_endpoint
+    graph = params["named-graph-uri"]
+    if !session[:user]&.admin? && !graph.blank?
+      acronym = graph.split('/')[-3]
+      @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first
+      render(inline: 'Query not permitted') && return  if @ontology.nil? || @ontology.errors
+    end
+
+    response = helpers.ontology_sparql_query(params[:query], graph)
+
+    render inline:  response
+  end
+
   def index
     @users = LinkedData::Client::Models::User.all
     @ontology_visits = ontology_visits_data

app/controllers/ontologies_controller.rb

@@ -10,6 +10,7 @@ class OntologiesController < ApplicationController
   include MappingStatistics
   include OntologyUpdater
   include TurboHelper
+  include SparqlHelper
   include SubmissionFilter
 
   require 'multi_json'
@@ -22,7 +23,7 @@ class OntologiesController < ApplicationController
 
   before_action :authorize_and_redirect, :only => [:edit, :update, :create, :new]
   before_action :submission_metadata, only: [:show]
-  KNOWN_PAGES = Set.new(["terms", "classes", "mappings", "notes", "widgets", "summary", "properties", "instances", "schemes", "collections"])
+  KNOWN_PAGES = Set.new(["terms", "classes", "mappings", "notes", "widgets", "summary", "properties", "instances", "schemes", "collections", "sparql"])
   EXTERNAL_MAPPINGS_GRAPH = "http://data.bioontology.org/metadata/ExternalMappings"
   INTERPORTAL_MAPPINGS_GRAPH = "http://data.bioontology.org/metadata/InterportalMappings"
 
@@ -208,6 +209,14 @@ def collections
     end
   end
 
+
+  def sparql
+    if request.xhr?
+      render partial: 'ontologies/sections/sparql', layout: false
+    else
+      render partial: 'ontologies/sections/sparql', layout: 'ontology_viewer'
+    end
+  end
   # GET /ontologies/ACRONYM
   # GET /ontologies/1.xml
   def show
@@ -240,7 +249,7 @@ def show
 
     # Note: find_by_acronym includes ontology views
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
-    ontology_not_found(params[:ontology]) if @ontology.nil?
+    ontology_not_found(params[:ontology]) if @ontology.nil? || @ontology.errors
 
     # Handle the case where an ontology is converted to summary only.
     # See: https://github.com/ncbo/bioportal_web_ui/issues/133.
@@ -288,6 +297,8 @@ def show
       self.schemes
     when 'collections'
       self.collections
+    when 'sparql'
+      self.sparql
     else
       self.summary
     end

app/controllers/statistics_controller.rb

@@ -0,0 +1,14 @@
+class StatisticsController < ApplicationController
+  include StatisticsHelper, ComponentsHelper
+
+  layout :determine_layout
+
+  def index
+    projects = LinkedData::Client::Models::Project.all({include: 'created'})
+    users = LinkedData::Client::Models::User.all({include: 'created'})
+    year_month_count,  @year_month_visits =  ontologies_by_year_month
+    @merged_data = merge_time_evolution_data([group_by_year_month(users),
+                                              group_by_year_month(projects),
+                                              year_month_count])
+  end
+end

app/helpers/application_helper.rb

@@ -25,11 +25,8 @@ module ApplicationHelper
 
 
   def ontologies_analytics
-    LinkedData::Client::Analytics.all.to_h.map do |key, ontology_analytics|
-      next if key.eql?(:links) || key.eql?(:context)
-
-      [key.to_s, ontology_analytics.to_h.values.map { |x| x&.values }.flatten.compact.sum]
-    end.compact.to_h
+    data = LinkedData::Client::Analytics.last_month.onts
+    data.map{|x| [x[:ont].to_s, x[:views]]}.to_h
   end
 
   def get_apikey

app/helpers/components_helper.rb

@@ -17,17 +17,19 @@ def tree_close_icon
   end
 
 
-  def chart_component(title: '', type: , labels: , datasets: , index_axis: 'x')
+  def chart_component(title: '', type: , labels: , datasets: , index_axis: 'x', show_legend: false)
       data =  {
         controller: 'load-chart',
         'load-chart-type-value': type,
         'load-chart-title-value': title,
         'load-chart-labels-value': labels,
         'load-chart-index-axis-value': index_axis,
-        'load-chart-datasets-value': datasets
+        'load-chart-datasets-value': datasets,
+        'load-chart-legend-value': show_legend,
       }
       content_tag(:canvas, nil, data: data)
   end
+
   def info_tooltip(text)
     render Display::InfoTooltipComponent.new(text: text)
   end

app/helpers/ontologies_helper.rb

@@ -149,7 +149,7 @@ def classes_link(ontology, count)
 
   def metadata_filled_count(submission = @submission_latest, ontology = @ontology)
     return if submission.nil?
-    
+
     reject = [:csvDump, :dataDump, :openSearchDescription, :metrics, :prefLabelProperty, :definitionProperty,
               :definitionProperty, :synonymProperty, :authorProperty, :hierarchyProperty, :obsoleteProperty,
               :ontology, :endpoint, :submissionId, :submissionStatus, :uploadFilePath, :context, :links, :ontology]
@@ -384,18 +384,23 @@ def lazy_load_section(section_title, &block)
   end
 
   def visits_chart_dataset(visits_data)
-    [
+    visits_chart_dataset_array({'Visits': visits_data})
+  end
+
+  def visits_chart_dataset_array(visits_data, fill: true)
+    visits_data = visits_data.map do |label , x|
       {
-        label: 'Visits',
-        data: visits_data,
+        label: label,
+        data: x,
         borderWidth: 2,
         borderRadius: 5,
         borderSkipped: false,
         cubicInterpolationMode: 'monotone',
         tension: 0.4,
-        fill: true
+        fill: fill
       }
-    ].to_json
+    end
+    visits_data.to_json
   end
 
   def submission_ready?(submission)
@@ -410,7 +415,7 @@ def sections_to_show
       sections += %w[properties]
       sections += %w[schemes collections] if skos?
       sections += %w[instances] unless skos?
-      sections += %w[notes mappings widgets]
+      sections += %w[notes mappings widgets sparql]
     end
     sections
   end

app/helpers/sparql_helper.rb

@@ -0,0 +1,67 @@
+module SparqlHelper
+  def change_from_clause(query, graph)
+    unless graph.blank?
+      graph = graph.gsub($REST_URL, 'http://data.bioontology.org')
+
+      if query.match?(/FROM <[^>]+>/i)
+        # Use a regular expression to replace all instances of FROM <uri>
+        query = query.gsub(/FROM <[^>]+>/i, "")
+      else
+        query = query.gsub("WHERE", "FROM <#{graph}> WHERE")
+      end
+
+      query = query.gsub(/GRAPH <[^>]+>/i, "")
+    end
+    query
+  end
+  def ontology_sparql_query(query, graph = '')
+    query = change_from_clause(query, graph)
+    sparql_query(query)
+  end
+  def is_allowed_query?(sparql_query)
+    forbidden_operations = [
+      'INSERT DATA',
+      'DELETE DATA',
+      'DELETE/INSERT',
+      'DELETE',
+      'INSERT',
+      'DELETE WHERE',
+      'LOAD',
+      'CLEAR',
+      'CREATE',
+      'DROP',
+      'COPY',
+      'MOVE',
+      'ADD'
+    ]
+
+    # Define a regular expression to match SELECT queries
+    select_query_regex = /\A\s*SELECT\b/m
+
+    # Check if the query contains any forbidden operations outside SELECT queries
+    return false if forbidden_operations.any? { |op| sparql_query.upcase.include?(op) && !sparql_query.match(select_query_regex) }
+
+    true
+  end
+
+  def sparql_query(query)
+    return 'No SPARQL endpoint configured' if $SPARQL_URL.blank?
+    return 'INSERT Queries not permitted' unless  is_allowed_query?(query)
+    endpoint = $SPARQL_URL.gsub('test', 'sparql')
+    begin
+      conn = Faraday.new do |conn|
+        conn.options.timeout = 60
+      end
+      response = conn.get("#{endpoint}?query=#{encode_param(query)}")
+      response.body.force_encoding('ISO-8859-1').encode('UTF-8')
+    rescue
+      "Query timeout"
+    end
+  end
+  def sparql_query_container(graph: nil)
+    content_tag(:div, '', data: {controller: 'sparql',
+                                 'sparql-proxy-value': '/sparql_proxy/',
+                                 'sparql-graph-value': graph})
+  end
+
+end

app/helpers/statistics_helper.rb

@@ -0,0 +1,60 @@
+module StatisticsHelper
+
+  def ontologies_by_year_month
+    data = LinkedData::Client::Analytics.all.to_h
+    data.delete(:links)
+    data.delete(:context)
+    year_month_count = {}
+    year_month_visits = {}
+    acronyms = []
+    data.each do |acronym, ont|
+      ont.each do |year, months|
+        next if year.eql?(:links) || year.eql?(:context)
+        months.each do |month, count|
+          next if month.eql?(:links) || month.eql?(:context)
+          year_month_count[[year.to_s.to_i, month.to_s.to_i]] ||= []
+          year_month_visits[[year.to_s.to_i, month.to_s.to_i]] = count + (year_month_visits[[year.to_s.to_i, month.to_s.to_i]] || 0)
+
+          if !count.zero? && !acronyms.include?(acronym)
+            year_month_count[[year.to_s.to_i, month.to_s.to_i]] << acronym
+            acronyms << acronym
+          end
+        end
+      end
+    end
+    year_month_visits = year_month_visits.sort_by { |(year, month), _| [year, month] }.to_h
+    [year_month_count, year_month_visits]
+  end
+
+  def string_year_month(year, month)
+    DateTime.parse("#{year}/#{month}").strftime("%b %Y")
+  end
+  def group_by_year_month(data)
+    data.group_by{|x| [Date.parse(x.created).year, Date.parse(x.created).month] }.sort_by { |(year, month), _| [year, month] }.to_h
+  end
+
+  def merge_time_evolution_data(data)
+    min_year =  data.map{|x| x.keys.first.first}.min
+    old = data.size.times.map { |x|  0 }
+
+    visits_data = { visits: data.size.times.map { |x|  [] }, labels: [] }
+
+    (min_year..Date.today.year).each do |year|
+      (1..12).each do |month|
+        data.each_with_index do |x , i|
+          old[i] += x[[year, month]]&.size || 0
+        end
+
+        next if old.sum.zero?
+
+        data.each_index do |i|
+          visits_data[:visits][i] << old[i]
+        end
+
+        visits_data[:labels] << string_year_month(year, month)
+      end
+    end
+    visits_data
+  end
+
+end

app/javascript/controllers/index.js

@@ -69,6 +69,9 @@ application.register("show-modal", ShowModalController)
 import SkosCollectionColorsController from "./skos_collection_colors_controller"
 application.register("skos-collection-colors", SkosCollectionColorsController)
 
+import SparqlController from "./sparql_controller"
+application.register("sparql", SparqlController)
+
 import TextTruncateController from "./text_truncate_controller"
 application.register("text-truncate", TextTruncateController)
 

app/javascript/controllers/load_chart_controller.js

@@ -9,7 +9,8 @@ export default class extends Controller {
     datasets: Array,
     type: { type: String, default: 'line' },
     title: String,
-    indexAxis: { type: String, default: 'x' }
+    indexAxis: { type: String, default: 'x' },
+    legend: { type: Boolean, default: false }
   }
 
   connect () {
@@ -34,7 +35,7 @@ export default class extends Controller {
             text: this.titleValue
           },
           legend: {
-            display: false
+            display: this.legendValue
           }
         },
         responsive: true,

app/javascript/controllers/sparql_controller.js

@@ -0,0 +1,25 @@
+import { Controller } from '@hotwired/stimulus'
+import { getYasgui } from '../mixins/useYasgui'
+
+// Connects to data-controller="sparql"
+export default class extends Controller {
+  static  values = {
+    proxy: String,
+    graph: String,
+  }
+  connect () {
+    localStorage.removeItem('yagui__config');
+    this.yasgui = getYasgui(this.element,
+      {
+        corsProxy: this.proxyValue,
+        copyEndpointOnNewTab: true,
+        requestConfig: {
+          endpoint: this.proxyValue,
+          acceptHeaderGraph: false,
+          acceptHeaderUpdate: false,
+          namedGraphs: [this.graphValue],
+        }
+      })
+
+  }
+}

app/javascript/mixins/useYasgui.js

@@ -0,0 +1,6 @@
+import Yasgui from "@triply/yasgui";
+
+export const getYasgui = (elem, config) => {
+    return new Yasgui(elem, config)
+}
+