Feature: add SPARQL endpoint UI (#427)

* add yasgui dependency to have a SPARQL editor

* add sparql ednpoint proxy action

* add SPARQL section to the admin page

* add SPARQL section to the ontology viewer

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/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/helpers/ontologies_helper.rb

@@ -410,7 +410,7 @@ 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/javascript/controllers/index.js

@@ -70,6 +70,9 @@ application.register("simple-tree", SimpleTreeController)
 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/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)
+}
+

app/views/admin/index.html.haml

@@ -12,12 +12,13 @@
 
 %div
   %div.mx-1
-    - sections = ['Analytics', 'Site Administration','Ontology Administration',  'Licensing', 'Users', 'Metadata Administration', 'Groups', 'Categories', 'Persons & Organizations']
+    - sections = ['Analytics', 'Site Administration','Ontology Administration',  'Licensing', 'Users', 'Metadata Administration', 'Groups', 'Categories', 'Persons & Organizations', 'SPARQL']
+    - selected = params[:section] || sections.first
     = render TabsContainerComponent.new do |t|
       - sections.each do |section_title|
         - t.item(title: section_title,
                      path: '',
-                     selected: section_title.eql?(sections.first),
+                     selected: section_title.downcase.eql?(selected),
                      page_name: '')
       - t.item_content do
         = render 'analytics'
@@ -66,8 +67,6 @@
         %div.ontologies_list_container.mt-3
           %div.mx-auto.w-75
             = render TurboFrameComponent.new(id: 'agents-list', src: '/agents', loading: 'lazy')
-
-      -# Groups tab
-      %div.tab-pane.fade{id: "groups", role: "tabpanel", aria: { labelledby: "groups-admin-tab" }}
-        %div.ontologies_list_container.mt-3
-          %table#adminGroups.zebra{:cellpadding => "0", :cellspacing => "0", :width => "100%"}
+      - t.item_content do
+        %div.container
+          = sparql_query_container

app/views/ontologies/sections/_sparql.html.haml

@@ -0,0 +1,2 @@
+= render TurboFrameComponent.new(id: "sparql", data: {"turbo-frame-target": "frame"} ) do
+  = sparql_query_container(graph: @submission_latest.id )

config/routes.rb

@@ -94,6 +94,8 @@
 
   get '' => 'home#index'
 
+  match 'sparql_proxy', to: 'admin#sparql_endpoint', via: [:get, :post]
+
   # Top-level pages
   match '/feedback', to: 'home#feedback', via: [:get, :post]
   get '/account' => 'home#account'

package.json

@@ -4,6 +4,7 @@
   "dependencies": {
     "@hotwired/stimulus": "^3.0.1",
     "@hotwired/turbo-rails": "^7.1.1",
+    "@triply/yasgui": "^4.2.28",
     "chart.js": "^4.4.1",
     "debounce": "^1.2.1",
     "esbuild": "^0.14.41",