adjusted query examples;added method to direct onto uris to bioportal

application.rb

@@ -70,11 +70,16 @@
 end
 
 # sparql endpoint access
-get '/sparql/:query?' do
+#get '/sparql/:query?' do
+get '/sparql/?' do
+  halt 400, "Missing query parameter.\n" unless params[:query]
+  halt 400, "Missing query parameter.\n" if params[:query].empty?
   sparqlstring = params[:query]
   halt 400, "Not allowed SPARQL keyword.\n" if !!(sparqlstring =~ /\b(delete|insert|load|clear)\b/i)
   type = request.env["HTTP_ACCEPT"]
-  if (sparqlstring =~ /^select/i ? @accepted_select.include?(type) : @accepted_construct.include?(type) )
+
+  #if (sparqlstring =~ /^select/i ? @accepted_select.include?(type) : @accepted_construct.include?(type) )
+  if ( @accepted_select.include?(type) || @accepted_construct.include?(type) )
     RestClient::Resource.new(URI.encode("#{$service_uri}/sparql/?query=#{sparqlstring}"), :verify_ssl => 0, :headers => {:accept => type } ).get do |response,request,result|
       if response.code == 400
         halt response.code, "malformed query\n"
@@ -91,12 +96,12 @@
 
 # sparql result as file download in various formats
 get "/download" do
-  type = params[:query_type]
-  sparqlstring = params[:queryfield]
+  type = params[:queryType]
+  sparqlstring = params[:queryField]
   halt 400, "Not allowed SPARQL keyword.\n" if !!(sparqlstring =~ /\b(delete|insert|load|clear)\b/i)
   file = Tempfile.new("enm")
-
-  if (sparqlstring =~ /\b(select)\b/i ? @accepted_select.include?(type) : @accepted_construct.include?(type) )
+  #TODO check for SELECT keyword else return a message instead wrong type
+  if ( @accepted_select.include?(type) || @accepted_construct.include?(type) )
     RestClient::Resource.new(URI.encode("#{$service_uri}/sparql/?query=#{sparqlstring}"), :verify_ssl => 0, :headers => {:accept => type}).get do |response, request, result|
       if response.code == 400
         halt response.code, "malformed query\n"

config.ru

@@ -4,6 +4,6 @@ require File.expand_path './application.rb'
 require "sinatra/reloader" if development?
 FileUtils.mkdir_p 'log' unless File.exists?('log')
 log = File.new("log/enm-ontoviewer.log", "a")
-$stdout.reopen(log)
+#$stdout.reopen(log)
 #$stderr.reopen(log)
 run Sinatra::Application

help.md

@@ -8,4 +8,4 @@ Please also note the part `{,5}` which is a [property path](https://www.w3.org/T
 
 ---
 #### Sparql
-This page allows you to write [SPARQL](https://www.w3.org/TR/rdf-sparql-query/) queries without any restrictions and with full [SPARQL](https://www.w3.org/TR/rdf-sparql-query/) syntax support including subqueries. The result can be downloaded to your computer. Please choose one of the output formats from the drop-down list.
+This page allows you to write [SPARQL](https://www.w3.org/TR/rdf-sparql-query/) queries without any restrictions and with full [SPARQL](https://www.w3.org/TR/rdf-sparql-query/) syntax support including subqueries. The result can be downloaded to your computer. Please choose one of the output formats from the drop-down list. There is also an option to render results as HTML table to the page.

public/examples/example1

@@ -12,8 +12,9 @@ SELECT DISTINCT ?resource ?epLabel ?value ?unit WHERE {
       obo:OBI_0000299 ?endpoint .
     ?endpoint sio:has-value ?value ;
               sio:has-unit ?unit ;
-              rdfs:label ?epLabel.
+              rdfs:label ?endpLabel.
   }
   BIND("PARTICLE SIZE" AS ?epLabel)
   FILTER(BOUND(?endpoint))
+  FILTER(?unit ="nm")
 }

public/examples/example3

@@ -12,8 +12,9 @@ SELECT DISTINCT ?resource ?epLabel ?value ?unit WHERE {
       obo:OBI_0000299 ?endpoint .
     ?endpoint sio:has-value ?value ;
               sio:has-unit ?unit ;
-              rdfs:label ?epLabel.
+              rdfs:label ?endpLabel.
   }
   BIND("ZETA POTENTIAL" AS ?epLabel)
-  FILTER(!BOUND(?endpoint))
+  FILTER(BOUND(?endpoint))
+  FILTER(?unit ="mV")
 }

views/query.haml

@@ -1,4 +1,15 @@
 :javascript
+  $(document).ready(function() {
+    $('#selType').on('change', function() {
+      var el = document.getElementById('selType');
+      var button = document.getElementById('submitRender');
+      if (el.value == "text/html"){
+        button.style.display='inline';
+      }else{
+        button.style.display='none';
+      }
+    });
+  });
   var HttpClient = function() {
     this.get = function(aUrl, aCallback) {
     var anHttpRequest = new XMLHttpRequest();
@@ -14,14 +25,23 @@
   function renderResponse() {
     var type = "text/html";
     var query = d3.select("#sparqlDownload").property("value");
-    var uri = "#{to("/download?query_type=")}"+type+"&queryfield="+escape(query);
+    var uri = "#{to("/download?queryType=")}"+type+"&queryField="+escape(query);
     var div = document.getElementById("render");
         div.innerHTML = "";
-    aClient = new HttpClient();
-    aClient.get(uri, function(response) {
-      var el = document.createElement("response");
-      el.innerHTML = response;
-      document.getElementById("render").appendChild(el);
+        aClient = new HttpClient();
+        aClient.get(uri, function(response) {
+        var el = document.createElement("response");
+        el.innerHTML = response;
+        document.getElementById("render").appendChild(el);
+        $(".sparql a").click(function() {
+          var t = $(this).text();
+          $(this).attr('alt', 'Link opens in new window.');
+          $(this).attr('title', 'Link opens in new window.');
+          $(this).attr('target', '_blank');
+          if (t.includes("onto")){
+            $(this).attr('href', 'http://bioportal.bioontology.org/ontologies/ENM/?p=classes&conceptid='+escape(t));
+          };
+        });
     });
   }  
 
@@ -89,11 +109,11 @@
 #query{:style => "margin: 10px"}
   %ul.nav.nav-tabs
     %li.active
-      %a{:href=>"#viewer", :data=>{:toggle=>"tab"}, :onclick=>"clearView();"} Viewer
+      %a{:href=>"#viewer", :data=>{:toggle=>"tab"}, :onclick=>"clearView();"} VIEWER
     %li
-      %a{:href=>"#download", :data=>{:toggle=>"tab"}, :onclick=>"clearView();"} Sparql
+      %a{:href=>"#download", :data=>{:toggle=>"tab"}, :onclick=>"clearView();"} SPARQL
     %li
-      %a{:href=>"#help", :data=>{:toggle=>"tab"}, :onclick=>"clearView();"} Help
+      %a{:href=>"#help", :data=>{:toggle=>"tab"}, :onclick=>"clearView();"} HELP
 
   %div.tab-content{:style=>"padding-top:2em;"}
     %input#endpoint{:size=>"50",:type => "text", :value => to("/search/"), :disabled=>"disabled", :style=>"display:none;"}
@@ -146,16 +166,17 @@
               #{File.read(File.join("public/examples/"+example[0]))}
         %form.form-inline.col-md-12{:id=>"form2", :role=>"form", :action=> to("/download"), :method=>"get", :style=>"padding:0;"}
           %div.form-group
-            %select.form-control{:id=>"selType", :autocomplete=>"off", :name=>"query_type",:value=>""}
+            %select.form-control{:id=>"selType", :autocomplete=>"off", :name=>"queryType",:value=>""}
               %optgroup{:label=>"SELECT"}
               - @accepted_select.sort.each do |type|
-                %option{:value => type}= type
+                %option{:value => type, :style => ("color:green;" if type == "text/html")}= type
               %optgroup{:label=>"CONSTRUCT"}
               - @accepted_construct.sort.each do |type|
                 %option{:value => type}= type
-            %input#inputquery{:type=>"hidden",:name=>"queryfield", :value=>""}
+            %input#inputquery{:type=>"hidden",:name=>"queryField", :value=>""}
             %input#renderType{:type=>"hidden",:name=>"renderType", :value=>""}
-          %button.btn.btn-default{:id=>"submitSubmit", :type=>"button", :title=>"render as HTML table", :onclick=>"renderResponse();"} render
+          %button.btn.btn-default{:id=>"submitRender", :type=>"button", :title=>"render as HTML table", :onclick=>"renderResponse();", :style=>"display:none;color:green;"} render
+          -#%button.btn.btn-default{:id=>"submitRender", :type=>"submit", :title=>"download as file", :onclick=>"sparqlValue('inline');"} render
           %button.btn.btn-default{:id=>"submitDownload", :type=>"submit", :title=>"download as file", :onclick=>"sparqlValue('attachment');"} download
 
       %div.col-md-6{:style=>"padding:0;"}
@@ -164,10 +185,8 @@
           %p Physico-Chemical Characteristics
           %fieldset
             - @examples.each_with_index do |example, idx|
-              %input{:id=> idx, :type=>"radio", :name=>"examples", :value=>"", :onclick=>"refresh_template(#{idx})"}
-                = example[0]
-              %br
-              %label{:for=>example[0]}
+              %input{:id=> idx, :type=>"radio", :name=>"examples", :value=>idx, :onclick=>"refresh_template(#{idx})"}
+              %label{:for=>idx}
                 = example[1]
               %br
       #render.col-md-12{:style=>"padding:0;margin-top:50px;minwidth:100%;maxwidth:100%;"}