small fixes + dynamic min similarity for fuzzysort technique

frontend/src/js/stringComparison.js

@@ -69,6 +69,7 @@
 
   // string comparison used in source code editors (e.g. Sublime Text)
   function occurrencesFuzzysort ( string, subStrings ) {
+    if (minSimilarity > 0) minSimilarity = FUZZY_SORT_MIN_SIMILARITY;
     var words = (!!string && string != '') ? string.replace(/([^\w\d\s]+)/g, '').replace(/\s(\s+)/g, ' ').split(/\s/) : [];
     var counter = 0;
     var occurrences = [];
@@ -77,7 +78,7 @@
         var entryPrepared = fuzzysort.prepare(entry)
         subStrings.forEach ( function ( subString ) {
           var value = fuzzysort.single(subString, entryPrepared);
-          if (!!value && value.score >= FUZZY_SORT_MIN_SIMILARITY) {
+          if (!!value && value.score >= minSimilarity) {
             counter++;
             var index = -1;
             for ( var i = 0; i < occurrences.length; i++ ) {

frontend/src/landing.html

@@ -53,7 +53,7 @@
 	      users.forEach ( function( item ) {
 				var id = item.id;
 				var name = item.name;
-			   $('#list').append('<div id="'+ id +'" class="list-group-item"><a href="#" name='+name+' id='+id+' class="list-group-item active">'+name +' <span id="stat_'+ id +'" class="badge">14</span> </a></div>')
+			   $('#list').append('<div id="'+ id +'" class="list-group-item"><a href="javascript:void(0)" name='+name+' id='+id+' class="list-group-item active">'+name +' <span id="stat_'+ id +'" class="badge">14</span> </a></div>')
 		  });
 		  PopulateStats();
 	    })
@@ -163,7 +163,7 @@
 	<div class="row">
 		<div class="col-md-6">
 			<div id="list" class="list-group">
-				 <span href="#" class="list-group-item active">Reviewer Account:</span>
+				 <span href="javascript:void(0)" class="list-group-item active">Reviewer Account:</span>
 
 			</div>
 		</div>

frontend/taxonomy/correlationMap/interactive/conceptCorrelations_three_dimensional.html

@@ -292,7 +292,7 @@
           dataType: 'json',
           contentType:'application/json',
           async: true,
-          data: JSON.stringify({text1: text1, text2: text2}),
+          data: JSON.stringify({'taxonomy_id': TAXONOMY_ID, text1: text1, text2: text2}),
           success: function ( citations ) {
             if (!citations) {
              handleError('Cannot get papers from DB.');

frontend/taxonomy/correlationMap/interactive/conceptCorrelations_two_dimensional.html

@@ -557,9 +557,9 @@ <h1 id="bibModalTitle"></h1><br>
               <li style="display:inline-block;"><h4>Paper Import</h4></li>
               <li style="display:inline-block;"><div style="padding:10px;"><label for="selectStringComparisonTechnique">String Comparison Technique: </label></div><div><select id="selectStringComparisonTechnique" style="width:100px;" title="String Comparison Technique">
                 <option title="Exact matching using regular expressions">Regex</option>
-                <option title="Dice's Coefficient calculates string similarity based on the number of bigrams two words have in common">Dice's Coefficient</option>
-                <option title="The Levenshtein distance is the minimal number of insertions, deletions and replacements needed for transforming one string into another one">Levenshtein</option>
-                <option title="SublimeText-like fuzzy search (https://github.com/farzher/fuzzysort)">Fuzzysort</option>
+                <option title="Dice's Coefficient calculates string similarity based on the number of bigrams two words have in common (value between 0 and 1)">Dice's Coefficient</option>
+                <option title="The Levenshtein distance is the minimal number of insertions, deletions and replacements needed for transforming one string into another one (value must be a natural number)">Levenshtein</option>
+                <option title="SublimeText-like fuzzy search (https://github.com/farzher/fuzzysort) (negative value, 0 standing for exact matching)">Fuzzysort</option>
               </select></div></li>
               <li style="display:inline-block;"><div style="padding:10px;"><label for="importMinSimilarity">Min Similarity: </label></div><div><input type="text" id="importMinSimilarity" value="" style="width:50px;" title="Min similarity"></div></li>
               <li style="display:inline-block;"><div style="padding:10px;"><div><label for="importMinOccurrences">Min Occurrences: </label></div><div><input type="text" id="importMinOccurrences" value="1" style="width:50px;" title="Min occurrences"></div></li>

frontend/taxonomy/cytoscape/taxonomyRelations.html

@@ -519,6 +519,108 @@ <h1 id="multiselectTitle"></h1><br>
     }
   }
 
+  function testPerformanceAddNode ( nodeName, count, results, timeoutFactor, callback ) {
+    if (count <= 0) {
+      callback(results);
+      return;
+    }
+    if (!results) results = [];
+    var request = {'taxonomy_id': TAXONOMY_ID};
+    request.x = '';
+    request.y = '';
+    request.xMajor = '';
+    request.yMajor = '';
+    request.major = 0;
+    request.dimension = 'Attack view';
+    var attributeName = 'Test' + nodeName;
+    request.text = attributeName + '_' + count;
+    var startTime = window.performance.now();
+    $.ajax
+      ({
+          type: "POST",
+          url: 'addAttribute',
+          dataType: 'json',
+          contentType:'application/json',
+          async: true,
+          data: JSON.stringify(request),
+          success: function ( result ) {
+            if (!result || !result.success) {
+              handleErrorHelper('Error occurred while adding node.');
+              return;
+            }
+            var endTime = window.performance.now();
+            results.push(endTime - startTime);
+            if (count <= 1) callback(results);
+            else {
+              setTimeout(function () {
+                testPerformanceAddNode(nodeName, count-1, results, timeoutFactor, callback);
+              }, timeoutFactor);
+            }
+          }
+      });
+  }
+
+  function testPerformanceRemoveNode ( nodeName, count, results, timeoutFactor, callback ) {
+    if (count <= 0) {
+      callback(results);
+      return;
+    }
+    if (!results) results = [];
+    var request = {'taxonomy_id': TAXONOMY_ID};
+    var attributeName = 'Test' + nodeName;
+    request.text = attributeName + '_' + count;
+    var startTime = window.performance.now();
+    $.ajax
+      ({
+          type: "POST",
+          url: 'removeAttribute',
+          dataType: 'json',
+          contentType:'application/json',
+          async: true,
+          data: JSON.stringify(request),
+          success: function ( result ) {
+            if (!result || !result.success) {
+              handleErrorHelper('Error occurred while adding node.');
+              return;
+            }
+            var endTime = window.performance.now();
+            results.push(endTime - startTime);
+            if (count <= 1) callback(results);
+            else {
+              setTimeout(function () {
+                testPerformanceRemoveNode(nodeName, count-1, results, timeoutFactor, callback);
+              }, timeoutFactor);
+            }
+          }
+      });
+  }
+
+  function testPerformance ( funct, nodeName, count, timeoutFactor ) {
+    funct(nodeName, count, [], timeoutFactor, function ( results ) {
+      if (!results || results.length == 0) {
+        handleErrorHelper("Cannot calculate average performance.");
+        return;
+      }
+      results.sort( function ( a, b ) {
+        return a < b ? -1 : (a == b ? 0 : 1);
+      });
+      var lengthIsOdd = results.length % 2 == 1;
+      var median = 0;
+      var index = Math.floor(results.length / 2);
+      if (lengthIsOdd) median = results[index];
+      else median = (results[index-1] + results[index]) / 2;
+      var mean = 0;
+      var standardDeviation = 0;
+      for ( var i = 0; i < results.length; i++ ) {
+        mean += results[i];
+        standardDeviation += Math.pow(results[i] - median, 2);
+      }
+      mean /= results.length;
+      standardDeviation = Math.sqrt(standardDeviation / results.length);
+      console.log("median: " + median + ", mean: " + mean + ", deviation: " + standardDeviation);
+    });
+  }
+
   // add concept node
   function addNode ( cy, ele, e, major ) {
     cy.elements().trigger('qtiphide');

frontend/taxonomy/users/modals.html

@@ -1,7 +1,7 @@
 <div class="modal fade" id="login-modal" class="loginmodal" tabindex="-1" role="dialog" aria-labelledby="loginLabel" aria-hidden="true" style="display: none;">
   <div class="modal-dialog">
     <div class="loginmodal-container">
-      <span class="close-btn"><a href="#">X</a></span>
+      <span class="close-btn"><a href="javascript:void(0)">X</a></span>
       <h1>Login</h1><br>
       <form id="loginForm">
         <input type="text" name="email" title="email" placeholder="Email">
@@ -14,7 +14,7 @@ <h1>Login</h1><br>
 <div class="modal fade" id="signup-modal" class="loginmodal" tabindex="-1" role="dialog" aria-labelledby="signupLabel" aria-hidden="true" style="display: none;">
   <div class="modal-dialog">
     <div class="loginmodal-container">
-      <span class="close-btn"><a href="#">X</a></span>
+      <span class="close-btn"><a href="javascript:void(0)">X</a></span>
       <h1>Register</h1><br>
       <form id="signupForm">
         <input type="text" name="email" title="email" placeholder="Email">