Changeset 1782

Timestamp:

Dec 12, 2012, 3:05:23 PM (11 years ago)

Author:

Nicklas Nordborg

Message:

Catching up on trunk revisions 1755 to 1781.

Location:

extensions/net.sf.basedb.reggie/branches/ticket-422

Files:

• . (modified) (1 prop)
• META-INF/extensions.xml (modified) (1 diff)
• README (modified) (1 diff)
• build.xml (modified) (1 diff)
• resources/bloodform.jsp (modified) (13 diffs)
• resources/css/reggie.css (modified) (1 diff)
• resources/histology_block.jsp (modified) (3 diffs)
• resources/histology_glass.jsp (modified) (16 diffs)
• resources/histology_protocol2.jsp (modified) (1 diff)
• resources/images/new.png (copied) (copied from extensions/net.sf.basedb.reggie/trunk/resources/images/new.png)
• resources/index.jsp (modified) (1 diff)
• resources/persinfo.jsp (modified) (14 diffs)
• resources/samplereportgenerator.jsp (modified) (25 diffs)
• resources/specimentube.jsp (modified) (1 diff)
• src/net/sf/basedb/reggie/Reggie.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/BloodRegistrationServlet.java (modified) (8 diffs)
• src/net/sf/basedb/reggie/servlet/HistologyServlet.java (modified) (14 diffs)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/PersonalRegistrationServlet.java (modified) (3 diffs)
• src/net/sf/basedb/reggie/servlet/SampleReportServlet.java (modified) (4 diffs)

extensions/net.sf.basedb.reggie/branches/ticket-422/META-INF/extensions.xml

@@ -7 +7 @@
       and samples.
     </description>
-    <version>2.10-dev</version>
+    <version>2.11-dev</version>
     <min-base-version>3.2.1</min-base-version>
     <copyright>BASE development team</copyright>

extensions/net.sf.basedb.reggie/branches/ticket-422/README

@@ -84 +84 @@
 
  * Histology wizards
-   TODO
+   Three wizards used in the process of creating H&E stained glass
+   slides. The first wizard creates a printable lab tracking protocol
+   for the current batch biomaterial items that are about to be
+   processed. The second wizard records the paraffin embedding step,
+   and the last wizard records the H&E staining step.
 
  * RNA quality control wizards

extensions/net.sf.basedb.reggie/branches/ticket-422/build.xml

@@ -10 +10 @@
   <!-- variables used -->
   <property name="name" value="reggie" />
-  <property name="version" value="2.10-dev" />
+  <property name="version" value="2.11-dev" />
   <property name="src" location="src" description="Location of source files" />
   <property name="build" location="build" description="Location of compiled files" />

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/bloodform.jsp

@@ -71 +71 @@
     if (frm.allFirstNames.value == '')
     {
-      setInputStatus('allFirstNames', 'Missing', 'invalid');
-      frm.allFirstNames.focus();
+      setInputStatus('allFirstNames', 'Missing', 'warning');
       formOk = false;
     }
@@ -82 +81 @@
     if (frm.familyName.value == '')
     {
-      setInputStatus('familyName', 'Missing', 'invalid');
-      frm.familyName.focus();
+      setInputStatus('familyName', 'Missing', 'warning');
       formOk = false;
     }
@@ -104 +102 @@
   return formOk;
 }
+
+function step2IsAcceptable()
+{
+  var formOk = true;
+  var frm = document.forms['reggie'];
+  // New patient only
+  if (!patientInfo.id)
+  {
+    formOk = frm.patientCode.value != '';
+  }
+  return formOk;
+}
+
 
 function step3IsValid()
@@ -141 +152 @@
   else if (currentStep == 2)
   {
-    if (step2IsValid()) gotoStep3();
+    if (step2IsValid()) 
+    {
+      gotoStep3();
+    }
+    else if (step2IsAcceptable())
+    {
+      if (manual)
+      {
+        gotoStep3();
+      }
+      else
+      {
+        setInnerHTML('gonext.message', 'Missing name(s). Click \'Next\' to continue registration.');
+      }
+    }
   }
 }
@@ -220 +245 @@
   setInputStatus('pnr', '', 'valid');
   pnrIsValid = true;
+}
+
+function nameOnChange(event)
+{
+  var field = event.target;
+  if (field.value == '')
+  {
+    setInputStatus(field.name, 'Missing', 'warning');
+  }
+  else
+  {
+    setInputStatus(field.name, '', 'valid');
+  }
 }
 
@@ -435 +473 @@
       Forms.selectListOption(frm.bloodSample, bloodInfo.bloodSample);
     }
+    if (bloodInfo.otherPathNote)
+    {
+      frm.otherPathNote.value = bloodInfo.otherPathNote;
+    }
   }
   else
@@ -481 +523 @@
   bloodInfo.serum = frm.serum.checked ? "Yes" : "No";
   bloodInfo.bloodSample = frm.bloodSample[frm.bloodSample.selectedIndex].value;
+  bloodInfo.otherPathNote = frm.otherPathNote.value;
   if (frm.copyConsent.checked && frm.copyConsent.value)
   {
@@ -491 +534 @@
   frm.freezerTime.disabled = true;
   frm.bloodSample.disabled = true;
+  frm.otherPathNote.disabled = true;
 
   var updateMode = bloodInfo.id;
@@ -601 +645 @@
         <td class="prompt">Family name</td>
         <td class="input"><input type="text" name="familyName" 
-          value="" size="35" maxlength="255"
+          value="" size="35" maxlength="255" onblur="nameOnChange(event)"
           onkeypress="focusOnEnter(event, 'allFirstNames')"></td>
         <td class="status" id="familyName.status"></td>
@@ -608 +652 @@
       <tr valign="top">
         <td class="prompt">All first names</td>
-        <td class="input"><input type="text" name="allFirstNames" 
+        <td class="input"><input type="text" name="allFirstNames" onblur="nameOnChange(event)"
           size="35" maxlength="255" onkeypress="doOnTabOrEnter(event, goNextAuto)"></td>
         <td class="status" id="allFirstNames.status"></td>
@@ -709 +753 @@
         <td class="subprompt">Plasma/serum</td>
         <td class="input">
-          <input type="checkbox" name="serum" id="serum" value="1"><label for="serum">Yes</label>
+          <input type="checkbox" name="serum" id="serum" value="1" checked="checked"><label for="serum">Yes</label>
         <td class="status" id="serum.status"></td>
         <td class="help">Mark the check box if serum/plasma is available.</td>
@@ -716 +760 @@
         <td class="prompt" id="bloodSample.prompt">Blood sample</td>
         <td class="input" id="bloodSample.input">
-          <select name="bloodSample">
+          <select onkeypress="focusOnEnter(event, 'otherPathNote')" 
+            name="bloodSample"
+          >
             <option selected value="">unknown
             <option value="PreNeo">PreNeo
@@ -724 +770 @@
         <td class="status" id="bloodSample.status"></td>
         <td class="help"><span id="bloodSample.message" class="message" style="display: none;"></span></td>
+      </tr>
+      <tr>
+        <td class="prompt" id="otherPathNote.prompt">Other path note</td>
+        <td class="input" id="otherPathNote.input"><textarea rows="3" cols="30" 
+          name="otherPathNote" value="" onkeypress="doOnTab(event, goNextAuto)"></textarea></td>
+        <td class="status" id="otherPathNote.status"></td>
+        <td class="help"><span id="otherPathNote.message" class="message" style="display: none;"></span></td>
       </tr>
       <tr id="copyConsentSection" style="display: none;">

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/css/reggie.css

@@ -155 +155 @@
 {
   content: url('../images/ok.png');
+}
+.status.new:before
+{
+  content: url('../images/new.png');
 }
 .success ul

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/histology_block.jsp

@@ -213 +213 @@
   html += '<th>Paraffin block</th>';
   html += '<th>Storage box</th>';
+  html += '<th>Comment</th>';
   html += '</tr>';
   html += '</thead>';
@@ -223 +224 @@
 
     html += '<tr>';
-    html += '<td style="width: 150px;">' + block.name + '</td>';
+    html += '<td style="width: 120px;">' + block.name + '</td>';
     html += '<td><input type="text" name="blockBox'+blockNo+'" value="<%=lastBlockBox%>" onblur="blockBoxOnChange('+blockNo+')"';
     html += ' onkeypress="' + nextStep + '" size="10" ></td>';
+    html += '<td><input type="text" name="blockComment'+blockNo+'" value="" size="35"></td>';
     html += '</tr>';
   }
@@ -278 +280 @@
     var block = workList.blocks[blockNo];
     block.storageBox = frm['blockBox'+blockNo].value;
+    block.comment = frm['blockComment'+blockNo].value;
     frm['blockBox'+blockNo].disabled = true;
+    frm['blockComment'+blockNo].disabled = true;
   }
 

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/histology_glass.jsp

@@ -35 +35 @@
 
 var paraffinBlock;
+var existingNumberOfHEGlass = 0;
 var stainDateIsValid = false;
+var numHEGlassIsValid = false;
 
 function init()
@@ -221 +223 @@
   
   setInnerHTML('blockName', paraffinBlock.name);
-
+  frm.comment.value = paraffinBlock.comment;
+  if (heGlass) 
+  {
+    frm.numberOfHEGlass.value = heGlass.length;
+    existingNumberOfHEGlass = heGlass.length;
+  }
+  
   var numWells = 0;
   for (var i = 0; i < paraffinBlock.bioWells.length; i++)
@@ -263 +271 @@
   
   stainDateOnChange();
-  frm['idx.0.0'].focus();
+  frm['numberOfHEGlass'].focus();
 }
 
@@ -325 +333 @@
 function step2IsValid()
 {
-  
-  var frm = document.forms['reggie'];
-  
+  var frm = document.forms['reggie'];
+  if (!numHEGlassIsValid)
+  {
+    frm.numberOfHEGlass.focus();
+    return false;
+  }
+  
+  var numHEGlass = parseInt(frm.numberOfHEGlass.value, 10);
   var allValid = true;
   for (var i = 0; i < wells.length; i++)
   {
     var field = frm[wells[i]];
-    if (!(parseInt(field.value, 10) > 0))
+    var indexValue = parseInt(field.value, 10);
+    if (!indexValue || indexValue <= 0 || indexValue > numHEGlass)
     {
       setInputStatus(field.name, null, 'invalid');
@@ -338 +352 @@
       allValid = false;
     }
+    else
+    {
+      setInputStatus(field.name, null, 'valid');
+    }
   }
   
   if (!allValid)
   {
-    setInputStatus('index', 'Value must be >= 1', 'invalid');
+    setInputStatus('index', 'Value must be between 1–' + numHEGlass, 'invalid');
     return false;
   }
@@ -358 +376 @@
 {
   var frm = document.forms['reggie'];
-  if (!(parseInt(frm[field].value, 10) > 0))
-  {
-    frm[field].focus();
+  
+  var numHEGlass = parseInt(frm.numberOfHEGlass.value, 10) || 1;
+  var indexValue = parseInt(frm[field].value, 10);
+
+  if (!indexValue || indexValue <= 0 || indexValue > numHEGlass)
+  {
     setInputStatus(field, null, 'invalid');
+    setInputStatus('index', 'Must be between 1–'+numHEGlass, '');
     return;
   }
 
   setInputStatus(field, null, 'valid');
-  
+  setInputStatus('index', '', '');
+}
+
+function checkNumHEGlass()
+{
+  var frm = document.forms['reggie'];
+  numHEGlassIsValid = false;
+  
+  var numHEGlass = parseInt(frm.numberOfHEGlass.value, 10) || 0;
+  var limit = Math.max(1, existingNumberOfHEGlass);
+  if (numHEGlass < limit)
+  {
+    setInputStatus('numberOfHEGlass', 'Must be a value &gt;= ' + limit, 'invalid');
+    return;
+  }
+  
+  setInputStatus('numberOfHEGlass', '', 'valid');
+  numHEGlassIsValid = true;
+  
+  for (var i = 0; i < wells.length; i++)
+  {
+    checkIndexValue(wells[i]);
+  }
+
 }
 
@@ -374 +419 @@
 
   var frm = document.forms['reggie'];
-  
-  var maxIndex = 1;
+  frm.stainDate.disabled = true;
+  frm.stainingProtocol.disabled = true;
+  frm.comment.disabled = true;
+  frm.numberOfHEGlass.disabled = true;
+  
+  var numHEGlass = parseInt(frm.numberOfHEGlass.value, 10);
   for (var i = 0; i < wells.length; i++)
   {
     var field = frm[wells[i]];
     field.disabled = true;
-    if (parseInt(field.value, 10) > maxIndex)
-    {
-      maxIndex = parseInt(field.value, 10);
-    }
   }
 
@@ -407 +452 @@
   var heGlass = paraffinBlock.heGlass;
   
-  for (var glassNo = 0; glassNo < maxIndex; glassNo++)
-  {
-    var nextStep = glassNo < (maxIndex-1) ? 'focusOnEnter(event, \'glassNo'+(glassNo+1)+'\')' : '';
+  for (var glassNo = 0; glassNo < numHEGlass; glassNo++)
+  {
+    var nextStep = glassNo < (numHEGlass-1) ? 'focusOnEnter(event, \'glassBox'+(glassNo+1)+'\');' : '';
     var heSlide = new Object();
     
@@ -440 +485 @@
     }
 
-    html += '<tr>';
-    html += '<td style="width: 150px;">' + heSlide.name + '</td>';
+    html += '<tr style="border-top: 1px dotted #A0A0A0;">';
+    html += '<td style="width: 120px;">' + heSlide.name + '</td>';
     html += '<td><input type="text" name="glassBox'+glassNo+'" value="'+heSlide.storageBox+'" onblur="glassBoxOnChange('+glassNo+')"';
     html += ' onkeypress="focusOnEnter(event, \'position'+glassNo+'\'); return Numbers.integerOnly(event)" size="10" ></td>';
     html += '<td><input type="text" name="position'+glassNo+'" value="'+heSlide.position+'" onblur="glassBoxOnChange('+glassNo+')"';
-    html += ' onkeypress="' + nextStep + '; return Numbers.integerOnly(event)" size="10" ></td>';
+    html += ' onkeypress="'+nextStep+' return Numbers.integerOnly(event)" size="10" ></td>';
     html += '<td class="status" id="glassBox'+glassNo+'.status"></td>';
+    html += '</tr>';
+    
+    html += '<tr>';
+    html += '<td style="width: 120px;" class="subprompt">- comment</td>';
+    html += '<td colspan="2"><input type="text" name="comment'+glassNo+'" value="" style="width: 100%;"></td>';
+    html += '<td class="status"></td>';
     html += '</tr>';
   }
@@ -453 +504 @@
   setInnerHTML('glassBoxInput', html);
   
+  for (var glassNo = 0; glassNo < numHEGlass; glassNo++)
+  {
+    if (heGlass && heGlass[glassNo])
+    {
+      frm['comment'+glassNo].value = heGlass[glassNo].comment;
+      glassBoxOnChange(glassNo);
+    }
+    else
+    {
+      setInputStatus('glassBox'+glassNo, null, 'new');
+    }
+  }
+  
   frm.glassBox0.focus();
 }
@@ -462 +526 @@
   if (frm['glassBox'+glassNo].value == '')
   {
-    setInputStatus('glassBox'+glassNo, null, 'invalid');
+    setInputStatus('glassBox'+glassNo, 'Missing storage box', 'invalid');
     return;
   }
   if (frm['position'+glassNo].value == '')
   {
-    setInputStatus('glassBox'+glassNo, null, 'invalid');
+    setInputStatus('glassBox'+glassNo, 'Missing position', 'invalid');
     return;
   }
@@ -554 +618 @@
     heGlass.storageBox = frm['glassBox'+glassNo].value;
     heGlass.position = frm['position'+glassNo].value;
+    heGlass.comment = frm['comment'+glassNo].value;
     glassNo++;
   }
@@ -560 +625 @@
   paraffinBlock.stainDate = frm.stainDate.value;
   paraffinBlock.protocolId = parseInt(frm.stainingProtocol[frm.stainingProtocol.selectedIndex].value, 10);
+  paraffinBlock.comment = frm.comment.value;
   submitInfo.paraffinBlock = paraffinBlock;
   
@@ -652 +718 @@
   {
     padding: 2px;
-    text-align: left;
   }
 
@@ -730 +795 @@
         <tr valign="top">
           <td class="prompt">Protocol</td>
-          <td class="input"><select style="width:90%" name="stainingProtocol" id="stainingProtocol" 
+          <td class="input"><select style="width:95%" name="stainingProtocol" id="stainingProtocol" 
             ></select></td>
           <td class="status" id="stainingProtocol.status"></td>
@@ -742 +807 @@
           <td class="status" id="paraffinblock.status"></td>
           <td class="help"></td>
+        </tr>
+        <tr valign="top">
+          <td class="subprompt">- comment</td>
+          <td class="input"><textarea name="comment" rows="2" style="width: 95%;"></textarea></td>
+          <td class="status" id="comment.status"></td>
+          <td class="help"></td>
+        </tr>
+        <tr valign="top">
+          <td class="prompt">HE slides created</td>
+          <td class="input"><input type="text" size="4"
+            name="numberOfHEGlass" value="2" 
+            onblur="checkNumHEGlass()"
+            onkeypress="focusOnEnter(event, 'idx.0.0'); return Numbers.integerOnly(event)">
+          </td>
+          <td class="status" id="numberOfHEGlass.status"></td>
+          <td class="help"><span id="numberOfHEGlass.message" class="message" style="display: none;"></span>
+            Enter the total number of HE glass slides that has been created from the selected paraffin block.
+          </td>
         </tr>
         

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/histology_protocol2.jsp

@@ -147 +147 @@
   function downloadHEGlassLabels()
   {
-    var numLabelsPerBlock = prompt('Number of labels per block?', 5);
+    var numLabelsPerBlock = prompt('Number of labels per block?', 3);
     if (numLabelsPerBlock == null) return;
     

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/index.jsp

@@ -272 +272 @@
             <li>Consent count report</li> 
             <li>Patient count report</li> 
+            <li>Overview report</li> 
+            <li>Missing sample data report</li> 
             </ul>
           </dd>

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/persinfo.jsp

@@ -74 +74 @@
     if (frm.allFirstNames.value == '')
     {
-      setInputStatus('allFirstNames', 'Missing', 'invalid');
-      frm.allFirstNames.focus();
+      setInputStatus('allFirstNames', 'Missing', 'warning');
       formOk = false;
     }
@@ -85 +84 @@
     if (frm.familyName.value == '')
     {
-      setInputStatus('familyName', 'Missing', 'invalid');
-      frm.familyName.focus();
+      setInputStatus('familyName', 'Missing', 'warning');
       formOk = false;
     }
@@ -109 +107 @@
     if (frm.existingAllFirstNames.value == '')
     {
-      setInputStatus('existingAllFirstNames', 'Missing', 'invalid');
-      frm.existingAllFirstNames.focus();
+      setInputStatus('existingAllFirstNames', 'Missing', 'warning');
       formOk = false;
     }
@@ -120 +117 @@
     if (frm.existingFamilyName.value == '')
     {
-      setInputStatus('existingFamilyName', 'Missing', 'invalid');
-      frm.existingFamilyName.focus();
+      setInputStatus('existingFamilyName', 'Missing', 'warning');
       formOk = false;
     }
@@ -132 +128 @@
   return formOk;
 }
+
+function step2IsAcceptable()
+{
+  var formOk = true;
+  var frm = document.forms['reggie'];
+  // New patient only
+  if (!patientInfo.id)
+  {
+    formOk = frm.patientCode.value != '';
+  }
+  return formOk;
+}
+
+
 
 function step3IsValid()
@@ -173 +183 @@
   else if (currentStep == 2)
   {
-    if (step2IsValid()) gotoStep3();
+    if (step2IsValid()) 
+    {
+      gotoStep3();
+    }
+    else if (step2IsAcceptable())
+    {
+      if (manual)
+      {
+        gotoStep3();
+      }
+      else
+      {
+        setInnerHTML('gonext.message', 'Missing name(s). Click \'Next\' to continue registration.');
+      }
+    }
   }
 }
@@ -253 +277 @@
 }
 
+function nameOnChange(event)
+{
+  var field = event.target;
+  if (field.value == '')
+  {
+    setInputStatus(field.name, 'Missing', 'warning');
+  }
+  else
+  {
+    setInputStatus(field.name, '', 'valid');
+  }
+}
+
 function lateralityOnChange()
 {
@@ -351 +388 @@
     }
     
-    if (!Dates.isDate(samplingDate, 'yyyyMMdd'))
+    if (samplingDate != '' && !Dates.isDate(samplingDate, 'yyyyMMdd'))
     {
       setInputStatus('samplingDate', 'Not a valid date', 'invalid');
@@ -366 +403 @@
       }
     }
-    setInputStatus('samplingDate', '', 'valid');
+    if (samplingDate == '')
+    {
+      setInputStatus('samplingDate', 'Missing', 'warning');
+    }
+    else
+    {
+      setInputStatus('samplingDate', '', 'valid');
+    }
   }
   samplingDateIsValid = true;
@@ -409 +453 @@
   {
     var samplingTimestamp = Dates.parseString(frm.samplingDate.value + ' ' + frm.samplingTime.value, 'yyyyMMdd Hmm');
-    if (samplingTimestamp && rnaLaterTimestamp.getDate() != samplingTimestamp.getDate())
-    {
-      setInputStatus('rnaLaterDate', 'Sampling and RNA later dates are different', 'warning');
+    if (samplingTimestamp)
+    {
+      if (rnaLaterTimestamp.getDate() != samplingTimestamp.getDate())
+      {
+        setInputStatus('rnaLaterDate', 'Sampling and RNA later dates are different', 'warning');
+      }
+      else if (rnaLaterTimestamp.getTime() < samplingTimestamp.getTime())
+      {
+        setInputStatus('rnaLaterDate', 'RNA later time is before Sampling time', 'warning');
+      }
     }
   }
@@ -929 +980 @@
         <td class="prompt">Family name</td>
         <td class="input"><input type="text" name="familyName" 
-          value="" size="35" maxlength="255"
+          value="" size="35" maxlength="255" onblur="nameOnChange(event)"
           onkeypress="focusOnEnter(event, 'allFirstNames')"></td>
         <td class="status" id="familyName.status"></td>
@@ -936 +987 @@
       <tr valign="top">
         <td class="prompt">All first names</td>
-        <td class="input"><input type="text" name="allFirstNames" 
+        <td class="input"><input type="text" name="allFirstNames" onblur="nameOnChange(event)"
           size="35" maxlength="255" onkeypress="doOnTabOrEnter(event, goNextAuto)"></td>
         <td class="status" id="allFirstNames.status"></td>
@@ -977 +1028 @@
         <td class="prompt">Family name</td>
         <td class="input"><input type="text" name="existingFamilyName" 
-          value="" size="35" maxlength="255"
+          value="" size="35" maxlength="255" onblur="nameOnChange(event)"
           onkeypress="focusOnEnter(event, 'existingAllFirstNames')"></td>
         <td class="status" id="existingFamilyName.status"></td>
@@ -984 +1035 @@
       <tr valign="top">
         <td class="prompt">All first names</td>
-        <td class="input"><input type="text" name="existingAllFirstNames" 
+        <td class="input"><input type="text" name="existingAllFirstNames" onblur="nameOnChange(event)"
           size="35" maxlength="255" onkeypress="doOnTabOrEnter(event, goNextAuto)"></td>
         <td class="status" id="existingAllFirstNames.status"></td>

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/samplereportgenerator.jsp

@@ -34 +34 @@
   var unknownSite = 0;
   var unknownCreation;
+  var numPatientsNoSamples = 0;
   
   var month=new Array(12);
@@ -63 +64 @@
     var frm = document.forms['reggie'];
     frm.reporttype.disabled = true;
+    // Hide report period input fields
+    document.getElementById("reportPeriodSubSection01").style.display = 'none';
+    document.getElementById("reportPeriodSubSection02").style.display = 'none';
+    document.getElementById("reportPeriodSubSection04").style.display = 'none';
+    // Hide view type pop-up menu
+    document.getElementById("viewTypeSubSection01").style.display = 'none';
+    document.getElementById("viewTypeSubSection02").style.display = 'none';
+    document.getElementById("viewTypeSubSection04").style.display = 'none';
     // Hide sample type pop-up menu
     document.getElementById("sampleTypeSubSection01").style.display = 'none';
@@ -69 +78 @@
     if (frm.reporttype[frm.reporttype.selectedIndex].value == 'samplecount')
     {
-      // Set item name for report period text
-      document.getElementById("items01").innerHTML="tubes";
+      // Show report period input fields
+      document.getElementById("reportPeriodSubSection01").style.display = 'block';
+      document.getElementById("reportPeriodSubSection02").style.display = 'block';
+      document.getElementById("reportPeriodSubSection04").style.display = 'block';
+      document.getElementById("reportPeriodSubSection01Header").innerHTML="Report period";
+      document.getElementById("reportPeriodSubSection04HelpText").innerHTML="Define which period the report should cover. Empty fields will include all tubes.";
       // Set item name for report time step text
       document.getElementById("items02").innerHTML="samples";
@@ -87 +100 @@
     else if (frm.reporttype[frm.reporttype.selectedIndex].value == 'consentcount')
     {
-      // Set item name for report period text
-      document.getElementById("items01").innerHTML="consents";
-      // Hide view type pop-up menu
-      document.getElementById("viewTypeSubSection01").style.display = 'none';
-      document.getElementById("viewTypeSubSection02").style.display = 'none';
-      document.getElementById("viewTypeSubSection04").style.display = 'none';
+      // Show report period input fields
+      document.getElementById("reportPeriodSubSection01").style.display = 'block';
+      document.getElementById("reportPeriodSubSection02").style.display = 'block';
+      document.getElementById("reportPeriodSubSection04").style.display = 'block';
+      document.getElementById("reportPeriodSubSection01Header").innerHTML="Report period";
+      document.getElementById("reportPeriodSubSection04HelpText").innerHTML="Define which period the report should cover. Empty fields will include all consents.";
     }
     else if (frm.reporttype[frm.reporttype.selectedIndex].value == 'patientcount')
     {
-      // Set item name for report period text
-      document.getElementById("items01").innerHTML="patients";
+      // Show report period input fields
+      document.getElementById("reportPeriodSubSection01").style.display = 'block';
+      document.getElementById("reportPeriodSubSection02").style.display = 'block';
+      document.getElementById("reportPeriodSubSection04").style.display = 'block';
+      document.getElementById("reportPeriodSubSection01Header").innerHTML="Report period";
+      document.getElementById("reportPeriodSubSection04HelpText").innerHTML="Define which period the report should cover. Empty fields will include all patients.";
       // Set item name for report time step text
       document.getElementById("items02").innerHTML="patients";
@@ -108 +125 @@
       document.getElementById("viewTypeSubSection04").style.display = 'block';
     }
+    else if (frm.reporttype[frm.reporttype.selectedIndex].value == 'overviewreport')
+    {
+      // Set parameters (report period) help text
+      document.getElementById("reportPeriodSubSection01").style.display = 'block';
+      document.getElementById("reportPeriodSubSection04").style.display = 'block';
+      document.getElementById("reportPeriodSubSection01Header").innerHTML="No report parameters";
+      document.getElementById("reportPeriodSubSection04HelpText").innerHTML="Overview report will be generated irrespective of date for items.";
+    }
+    else if (frm.reporttype[frm.reporttype.selectedIndex].value == 'missingsampledatareport')
+    {
+      // Show sample type pop-up menu
+      document.getElementById("sampleTypeSubSection01").style.display = 'block';
+      document.getElementById("sampleTypeSubSection02").style.display = 'block';
+      document.getElementById("sampleTypeSubSection04").style.display = 'block';
+    }
     Main.show('itemCountSection');
         
@@ -179 +211 @@
       frm.sampletype.disabled = true;
     }
-    if (reportType == 'patientcount')
+    else if (reportType == 'patientcount')
     {
       frm.viewtype.disabled = true;
+    }
+    else if (reportType == 'missingsampledatareport')
+    {
+      frm.sampletype.disabled = true;
     }
     Main.hide('gocreate');
@@ -194 +230 @@
       if (frm.sampletype.value != null) url += '&stype='+frm.sampletype.value;
     }
-    if (reportType == 'patientcount')
+    else if (reportType == 'patientcount')
     {     
       if (frm.viewtype.value != null) url += '&vtype='+frm.viewtype.value;
+    }
+    else if (reportType == 'missingsampledatareport')
+    {     
+      if (frm.sampletype.value != null) url += '&stype='+frm.sampletype.value;
     }
     
@@ -211 +251 @@
     }
     var report = response.report;
+    var permissionDeniedForPatientName = report.permissionDeniedForPatientName;
     var reportTable;
     
@@ -223 +264 @@
         reportTable = createConsentCountReport(report);
       }
-      if ('patientcount' == reportType)
+      else if ('patientcount' == reportType)
       {     
         reportTable = createItemCountReport(report, reportType);
+      }
+      else if ('overviewreport' == reportType)
+      {     
+        reportTable = createOverviewReport(report);
+      }
+      else if ('missingsampledatareport' == reportType)
+      {     
+        reportTable = createMissingSampleDataReport(report);
       }
     }
@@ -248 +297 @@
       cellElement.appendChild(unknownDateTable);
     }
+    else if ('overviewreport' == reportType)
+    {
+      var spacer = document.createElement('text');
+      spacer.innerHTML = "<BR>";
+      cellElement.appendChild(spacer);
+      var patientDetailedTable = createOverviewPatientDetailedTable(report);
+      cellElement.appendChild(patientDetailedTable);
+    }
     // Summary list
     var summaryList = document.createElement('ul');
@@ -255 +312 @@
     {
       var samples = 'specimens';
-      if ('blood' == sampleType)
+      if ('nospecimen' == sampleType)
+      {
+        samples = '"no specimens"';
+      }
+      else if ('blood' == sampleType)
       {
         samples = 'blood samples';
@@ -288 +349 @@
     }
     else if ('patientcount' == reportType)
-    {     
+    {
       summaryList.appendChild(getListElement(unknownSite + ' patients registered to unknown sites.'));
       summaryList.appendChild(getListElement(unknownCreation + ' patients without creation date. These are included in the \'Total\' column.'));
+    }
+    else if ('overviewreport' == reportType)
+    {
+      summaryList.appendChild(getListElement(unknownSite + ' patients registered to unknown sites.'));
+      summaryList.appendChild(getListElement(numPatientsNoSamples + ' patients with no samples.'));
+      summaryList.appendChild(getListElement('Note: Consents of type "Yes" include consents without patient id (PAT#) or date.'));
+    }
+    else if ('missingsampledatareport' == reportType)
+    {
+      summaryList.appendChild(getListElement('Note: Patient name is considered missing if either "all first names" or "family name" is missing.'));
+      if ('true' == permissionDeniedForPatientName)
+      {
+        var patientNamePermissionWarningIconWithMessage = document.createElement('img');
+        patientNamePermissionWarningIconWithMessage.innerHTML = '<img src="images/warning.png"> Sorry, logged-in user does not have permission to check patient names.</img>';
+        var patientNamePermissionWarningListElement = document.createElement('li');
+        patientNamePermissionWarningListElement.appendChild(patientNamePermissionWarningIconWithMessage);
+        summaryList.appendChild(patientNamePermissionWarningListElement);
+      }
     }
     cellElement.appendChild(summaryList);
@@ -309 +388 @@
     var psdString = report.periodBeginDate;
     var ldString = report.latestDate;
-    var startDate = new Date();
-    startDate.setYear(sdString.substr(0,4));
-    startDate.setMonth(sdString.substr(4,2)-1);
-    startDate.setDate(sdString.substr(6));
-    var endDate = new Date();
-    endDate.setYear(edString.substr(0,4));
-    endDate.setMonth(edString.substr(4,2)-1);
-    endDate.setDate(edString.substr(6));
-    var periodStartDate = new Date();
-    periodStartDate.setYear(psdString.substr(0,4));
-    periodStartDate.setMonth(psdString.substr(4,2)-1);
-    periodStartDate.setDate(psdString.substr(6));
-    var latestDate;
-    if (ldString != null)
-    {
-      latestDate = new Date();
-      latestDate.setYear(ldString.substr(0,4));
-      latestDate.setMonth(ldString.substr(4,2)-1);
-      latestDate.setDate(ldString.substr(6));
-    }   
+    var startDate = dateStrToDate(sdString);
+    var endDate = dateStrToDate(edString);
+    var periodStartDate = dateStrToDate(psdString);
+    var latestDate = dateStrToDate(ldString);
     
     var viewType = report.viewType;   
@@ -338 +401 @@
     
     var headerText = '# Items by ';
+    var startDateStr = addHyphensToDateString(sdString);
+    var endDateStr = addHyphensToDateString(edString);
+    var latestDateStr = addHyphensToDateString(ldString);
     if ('samplecount' == reportType)
     {
       headerText = '# Specimens by ';
-      if ('blood' == sampleType)
+      if ('nospecimen' == sampleType)
+      {
+        headerText = '# "No specimens" by ';
+      }
+      else if ('blood' == sampleType)
       {
         headerText = '# Blood samples by ';
@@ -393 +463 @@
       
     // Set table header
-    headerText += ' (between ' + startDate.getFullYear()+'-';
-    if ((startDate.getMonth()+1) < 10)
-    {
-      headerText += '0' + (startDate.getMonth()+1);
-    }
-    else
-    {
-      headerText += (startDate.getMonth()+1);
-    }
-    headerText += '-';
-    if (startDate.getDate() < 10)
-    {
-      headerText += '0' + startDate.getDate();
-    }
-    else
-    {
-      headerText += startDate.getDate();
-    }
-    headerText += ' and ';
-    headerText += endDate.getFullYear()+'-';
-    if ((endDate.getMonth()+1) < 10)
-    {
-      headerText += '0' + (endDate.getMonth()+1);
-    }
-    else
-    {
-      headerText += (endDate.getMonth()+1);
-    }
-    headerText += '-';
-    if (endDate.getDate() < 10)
-    {
-      headerText += '0' + endDate.getDate();
-    }
-    else
-    {
-      headerText += endDate.getDate();
-    }
-    headerText += ')';
+    headerText += ' (between ' + startDateStr + ' and ' + endDateStr + ')';
     if (latestDate != null)
     {
-      headerText += '\nLast registration ' + latestDate.getFullYear();
-      headerText += '-';
-      if ((latestDate.getMonth()+1) < 10)
-      {
-        headerText += '0';
-      }
-      headerText += (latestDate.getMonth()+1);
-      headerText += '-';
-      if (latestDate.getDate()<10)
-      {
-        headerText += '0';
-      }
-      headerText += latestDate.getDate();
+      headerText += '\nLast registration ' + latestDateStr;
     }   
     headerRow.appendChild(getTableCellElement(headerText, 'reportheader', (numCols+5)));
@@ -517 +538 @@
     var sdString = report.beginDate;
     var edString = report.endDate;
-/*
-    var psdString = report.periodBeginDate;
-*/
     var ldString = report.latestDate;
-    var startDate = new Date();
-    startDate.setYear(sdString.substr(0,4));
-    startDate.setMonth(sdString.substr(4,2)-1);
-    startDate.setDate(sdString.substr(6));
-    var endDate = new Date();
-    endDate.setYear(edString.substr(0,4));
-    endDate.setMonth(edString.substr(4,2)-1);
-    endDate.setDate(edString.substr(6));
-/*
-    var periodStartDate = new Date();
-    periodStartDate.setYear(psdString.substr(0,4));
-    periodStartDate.setMonth(psdString.substr(4,2)-1);
-    periodStartDate.setDate(psdString.substr(6));
-*/
-    var latestDate;
-    if (ldString != null)
-    {
-      latestDate = new Date();
-      latestDate.setYear(ldString.substr(0,4));
-      latestDate.setMonth(ldString.substr(4,2)-1);
-      latestDate.setDate(ldString.substr(6));
-    }   
-
-/*    
-    var viewType = report.viewType; 
-*/  
-  
+    var startDate = dateStrToDate(sdString);
+    var endDate = dateStrToDate(edString);
+    var latestDate = dateStrToDate(ldString);
+
     var headerRow = document.createElement('tr');   
     var subHeaderRow = document.createElement('tr');
@@ -677 +672 @@
     addDataRowsToConsentTableUnknownDate(report, reportTable);
       
-    // Add a row with the combined numbers for all sites for each period
+    // Add a row with the combined numbers for all sites
     var sitesCombinedRow = document.createElement('tr');
     sitesCombinedRow.appendChild(getTableCellElement('Sites combined', 'colsummary'));
     sitesCombinedRow.appendChild(getTableCellElement('', 'colsummary', 2));
-    // Get combined numbers for all sites for each period
+    // Get combined numbers for all sites
     var sumKey = 'sumKey';
     var statistics = report.statistics;
@@ -709 +704 @@
   }
   
-  function addHyphensToDateString(yyyymmddStr)
-  {
-    var dateWithHyphensStr = '????-??-??';
-    if (yyyymmddStr != null)
-    {
-      var yyyyStr = yyyymmddStr.substr(0,4);
-      var mmStr   = yyyymmddStr.substr(4,2);
-      var ddStr = yyyymmddStr.substr(6);
-      dateWithHyphensStr = yyyyStr + '-' + mmStr + '-' + ddStr;
-    }
-    return dateWithHyphensStr;
-  }
-
+  function createOverviewReport(report)
+  {
+    var reportTable = getReportTable();
+    var sdString = report.beginDate;
+    var edString = report.endDate;
+    var ldString = report.latestDate;
+    var startDate = dateStrToDate(sdString);
+    var endDate = dateStrToDate(edString);
+    var latestDate = dateStrToDate(ldString);
+  
+    var headerRow = document.createElement('tr');   
+    var subHeaderRow = document.createElement('tr');
+    var subHeader2Row = document.createElement('tr');
+    var columnHeaderRow = document.createElement('tr');
+    
+    var numCols = 6;
+    var numDecimals = 0;
+    var headerText = 'Number of items of different kinds';
+    var startDateStr = addHyphensToDateString(sdString);
+    var endDateStr = addHyphensToDateString(edString);
+    var latestDateStr = addHyphensToDateString(ldString);
+    headerText += ' (betweeen ' + startDateStr + ' and ' + endDateStr + ')';
+    if (latestDate != null)
+    {
+        headerText += '\nLast registration ' + latestDateStr;
+    }
+    headerRow.appendChild(getTableCellElement(headerText, 'reportheader', (numCols+3)));
+    
+    // Subheader
+    subHeaderRow.appendChild(getTableCellElement('', 'reportsubheader', 3));
+    
+    subHeaderRow.appendChild(getTableCellElement('Patients', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Blood', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Specimens', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('No specimens', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Consents', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Consents', 'reportsubheader'));
+
+    // Columnsheader    
+    var siteHeader = getTableCellElement('Site', 'reportsubheader');      
+    var startDateHeader = getTableCellElement('Start date','reportsubheader');
+    var latestDateHeader = getTableCellElement('Latest date','reportsubheader');
+    columnHeaderRow.appendChild(siteHeader);
+    columnHeaderRow.appendChild(startDateHeader); 
+    columnHeaderRow.appendChild(latestDateHeader);  
+    
+    columnHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('samples', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('(Yes)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('missing', 'reportsubheader'));
+
+    // Build table      
+    reportTable.appendChild(headerRow);
+    reportTable.appendChild(subHeaderRow);
+    reportTable.appendChild(subHeader2Row);
+    reportTable.appendChild(columnHeaderRow);
+          
+    // Data rows      
+    addDataRowsToOverviewTable(report, reportTable);
+      
+    // Add a row with the combined numbers for all sites for each period
+    var sitesCombinedRow = document.createElement('tr');
+    sitesCombinedRow.appendChild(getTableCellElement('Sites combined', 'colsummary'));
+    sitesCombinedRow.appendChild(getTableCellElement('', 'colsummary', 2));
+    // Get combined numbers for all sites for each period
+    var noDateKey = 'noDate';
+    var sumKey = 'sumKey';
+    var statistics = report.statistics;
+    // Get values for use in summary section
+    numPatientsNoSamples = statistics.patientNoSamples;
+    var sitesCombined = statistics.sitesCombinedKey;
+    if (sitesCombined != null)
+    {
+      data = getJSONData(sitesCombined, 'patient');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONData(sitesCombined, 'bloodSample');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONData(sitesCombined, 'specimen');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONData(sitesCombined, 'noSpecimen');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONData(sitesCombined, 'consentYes');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONData(sitesCombined, 'consentMissing');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+    }
+    reportTable.appendChild(sitesCombinedRow);  
+
+    return reportTable;
+  }
+  
+  function createOverviewPatientDetailedTable(report)
+  {
+    var reportTable = getReportTable();
+    var sdString = report.beginDate;
+    var edString = report.endDate;
+    var ldString = report.latestDate;
+    var startDate = dateStrToDate(sdString);
+    var endDate = dateStrToDate(edString);
+  
+    var headerRow = document.createElement('tr');   
+    var subHeaderRow = document.createElement('tr');
+    var subHeader2Row = document.createElement('tr');
+    var columnHeaderRow = document.createElement('tr');
+    
+    var numCols = 8;
+    var numDecimals = 0;
+    var headerText = 'Patient records of different kinds';
+    var startDateStr = addHyphensToDateString(sdString);
+    var endDateStr = addHyphensToDateString(edString);
+    var latestDateStr = addHyphensToDateString(ldString);
+    headerText += ' (betweeen ' + startDateStr + ' and ' + endDateStr + ')';
+/*
+    if (latestDate != null)
+    {
+        headerText += '\nLast registration ' + latestDateStr;
+    }
+*/
+    headerRow.appendChild(getTableCellElement(headerText, 'reportheader', (numCols+2)));
+    
+    // Subheader
+    subHeaderRow.appendChild(getTableCellElement('', 'reportsubheader', 2));
+    
+    subHeaderRow.appendChild(getTableCellElement('Patients', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Patients', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Patients', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Patients', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Patients', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Patients', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Patients', 'reportsubheader'));
+    //subHeaderRow.appendChild(getTableCellElement('Patients', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
+
+    // Subheader 2
+    subHeader2Row.appendChild(getTableCellElement('', 'reportsubheader', 2));
+    
+    subHeader2Row.appendChild(getTableCellElement('(blood', 'reportsubheader'));
+    subHeader2Row.appendChild(getTableCellElement('(spec.', 'reportsubheader'));
+    subHeader2Row.appendChild(getTableCellElement('(no spec.', 'reportsubheader'));
+    subHeader2Row.appendChild(getTableCellElement('(blood and', 'reportsubheader'));
+    subHeader2Row.appendChild(getTableCellElement('(blood and', 'reportsubheader'));
+    subHeader2Row.appendChild(getTableCellElement('(spec. and', 'reportsubheader'));
+    subHeader2Row.appendChild(getTableCellElement('(blood, spec.,', 'reportsubheader'));
+    //subHeader2Row.appendChild(getTableCellElement('(no samples)', 'reportsubheader'));
+    subHeader2Row.appendChild(getTableCellElement('', 'reportsubheader'));
+
+    // Columnsheader    
+    var siteHeader = getTableCellElement('Site', 'reportsubheader');      
+    var startDateHeader = getTableCellElement('Start date','reportsubheader');
+    //var latestDateHeader = getTableCellElement('Latest date','reportsubheader');
+    columnHeaderRow.appendChild(siteHeader);
+    columnHeaderRow.appendChild(startDateHeader); 
+    //columnHeaderRow.appendChild(latestDateHeader);  
+    
+    columnHeaderRow.appendChild(getTableCellElement('only)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('only)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('only)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('specimens)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('no spec.)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('no spec.)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('and no spec.)', 'reportsubheader'));
+    //columnHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
+
+    columnHeaderRow.appendChild(getTableCellElement('Sum', 'reportsubheader'));
+
+    // Build table      
+    reportTable.appendChild(headerRow);
+    reportTable.appendChild(subHeaderRow);
+    reportTable.appendChild(subHeader2Row);
+    reportTable.appendChild(columnHeaderRow);
+          
+    // Data rows      
+    addDataRowsToOverviewPatientDetailedTable(report, reportTable);
+      
+    // Add a row with the combined numbers for all sites
+    var sitesCombinedRow = document.createElement('tr');
+    sitesCombinedRow.appendChild(getTableCellElement('Sites combined', 'colsummary'));
+    sitesCombinedRow.appendChild(getTableCellElement('', 'colsummary'));
+    // Get combined numbers for all sites
+    var noDateKey = 'noDate';
+    var sumKey = 'sumKey';
+    var statistics = report.statistics;
+    // Get values for use in summary section
+    numPatientsNoSamples = statistics.patientNoSamples;
+    var sitesCombined = statistics.sitesCombinedKey;
+    if (sitesCombined != null)
+    {
+      data = getJSONData(sitesCombined, 'patientBloodSampleOnly');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONData(sitesCombined, 'patientSpecimenOnly');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONData(sitesCombined, 'patientNoSpecimenOnly');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONData(sitesCombined, 'patientBloodSampleAndSpecimen');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONData(sitesCombined, 'patientBloodSampleAndNoSpecimen');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONData(sitesCombined, 'patientSpecimenAndNoSpecimen');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONData(sitesCombined, 'patientBloodSampleAndSpecimenAndNoSpecimen');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      //data = getJSONData(sitesCombined, 'patientNoSamples');
+      //sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONData(sitesCombined, 'sumKey');
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+    }
+    reportTable.appendChild(sitesCombinedRow);  
+
+    return reportTable;
+  }
+  
+  function createMissingSampleDataReport(report)
+  {
+    var reportTable = getReportTable();
+    var sdString = report.beginDate;
+    var edString = report.endDate;
+    var ldString = report.latestDate;
+    var startDate = dateStrToDate(sdString);
+    var endDate = dateStrToDate(edString);
+    var latestDate = dateStrToDate(ldString);
+
+    var sampleType = report.sampleType;
+    var permissionDeniedForPatientName = report.permissionDeniedForPatientName;
+
+    var headerRow = document.createElement('tr');   
+    var subHeaderRow = document.createElement('tr');
+    var subHeader2Row = document.createElement('tr');
+    var columnHeaderRow = document.createElement('tr');
+    
+    var numCols = 5;
+    if (sampleType == 'specimen')
+    {
+      numCols = 5;
+    }
+    else if (sampleType == 'nospecimen')
+    {
+      numCols = 2;
+    }
+    else if (sampleType == 'blood')
+    {
+      numCols = 3;
+    }
+    var numDecimals = 0;
+    var headerText = 'Number of missing specimen items of different kinds';
+    if ('nospecimen' == sampleType)
+    {
+      headerText = 'Number of missing "no specimen" items of different kinds';
+    }
+    else if ('blood' == sampleType)
+    {
+      headerText = 'Number of missing blood sample items of different kinds';
+    }
+    var startDateStr = addHyphensToDateString(sdString);
+    var endDateStr = addHyphensToDateString(edString);
+    var latestDateStr = addHyphensToDateString(ldString);
+    headerText += ' (betweeen ' + startDateStr + ' and ' + endDateStr + ')';
+    if (latestDate != null)
+    {
+        headerText += '\nLast registration ' + latestDateStr;
+    }
+    headerRow.appendChild(getTableCellElement(headerText, 'reportheader', (numCols+3)));
+    
+    // Subheader
+    subHeaderRow.appendChild(getTableCellElement('', 'reportsubheader', 3));
+    
+    subHeaderRow.appendChild(getTableCellElement('Patient', 'reportsubheader'));
+    if (sampleType == 'specimen')
+    {
+      subHeaderRow.appendChild(getTableCellElement('PAD', 'reportsubheader'));
+      subHeaderRow.appendChild(getTableCellElement('Laterality', 'reportsubheader'));
+      subHeaderRow.appendChild(getTableCellElement('Sampling', 'reportsubheader'));
+      subHeaderRow.appendChild(getTableCellElement('RNALater', 'reportsubheader'));
+    }
+    else if (sampleType == 'nospecimen')
+    {
+      subHeaderRow.appendChild(getTableCellElement('Sampling', 'reportsubheader'));
+    }
+    else if (sampleType == 'blood')
+    {
+      subHeaderRow.appendChild(getTableCellElement('Blood sampling', 'reportsubheader'));
+      subHeaderRow.appendChild(getTableCellElement('Blood freezer', 'reportsubheader'));
+    }
+
+    // Columnsheader    
+    var siteHeader = getTableCellElement('Site', 'reportsubheader');      
+    var startDateHeader = getTableCellElement('Start date','reportsubheader');
+    var latestDateHeader = getTableCellElement('Latest date','reportsubheader');
+    columnHeaderRow.appendChild(siteHeader);
+    columnHeaderRow.appendChild(startDateHeader); 
+    columnHeaderRow.appendChild(latestDateHeader);  
+    
+    columnHeaderRow.appendChild(getTableCellElement('name', 'reportsubheader'));
+    if (sampleType == 'specimen')
+    {
+      columnHeaderRow.appendChild(getTableCellElement('reference', 'reportsubheader'));
+      columnHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
+      columnHeaderRow.appendChild(getTableCellElement('date', 'reportsubheader'));
+      columnHeaderRow.appendChild(getTableCellElement('date', 'reportsubheader'));
+    }
+    else if (sampleType == 'nospecimen')
+    {
+      columnHeaderRow.appendChild(getTableCellElement('date', 'reportsubheader'));
+    }
+    else if (sampleType == 'blood')
+    {
+      columnHeaderRow.appendChild(getTableCellElement('date', 'reportsubheader'));
+      columnHeaderRow.appendChild(getTableCellElement('date', 'reportsubheader'));
+    }
+
+    // Build table      
+    reportTable.appendChild(headerRow);
+    reportTable.appendChild(subHeaderRow);
+    reportTable.appendChild(columnHeaderRow);
+          
+    // Data rows      
+    addDataRowsToMissingSampleDataTable(report, reportTable);
+      
+    // Add a row with the combined numbers for all sites for each period
+    var sitesCombinedRow = document.createElement('tr');
+    sitesCombinedRow.appendChild(getTableCellElement('Sites combined', 'colsummary'));
+    sitesCombinedRow.appendChild(getTableCellElement('', 'colsummary', 2));
+    // Get combined numbers for all sites for each period
+    var noDateKey = 'noDate';
+    var sumKey = 'sumKey';
+    var statistics = report.statistics;
+    var sitesCombined = statistics.sitesCombinedKey;
+    if (sitesCombined != null)
+    {
+      if ('false' == permissionDeniedForPatientName)
+      {
+        data = getJSONData(sitesCombined, 'missingPatientName');
+        sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      }
+      else
+      {
+        data = '-';
+        sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      }
+      if (sampleType == 'specimen')
+      {
+        data = getJSONData(sitesCombined, 'missingPadReference');
+        sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+        data = getJSONData(sitesCombined, 'missingLaterality');
+        sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+        data = getJSONData(sitesCombined, 'missingSamplingDateTime');
+        sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+        data = getJSONData(sitesCombined, 'missingRnaLaterDateTime');
+        sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      }
+      else if (sampleType == 'nospecimen')
+      {
+        data = getJSONData(sitesCombined, 'missingSamplingDateTime');
+        sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      }
+      else if (sampleType == 'blood')
+      {
+        data = getJSONData(sitesCombined, 'missingBloodSamplingDateTime');
+        sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+        data = getJSONData(sitesCombined, 'missingBloodFreezerDateTime');
+        sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      }
+    }
+    reportTable.appendChild(sitesCombinedRow);  
+
+    return reportTable;
+  }
+  
   function createConsentTablePatientsWithMultipleDates(report)
   {
@@ -803 +1154 @@
       if (!sites.hasOwnProperty(namePrefix)) continue;        
       var site = sites[namePrefix];
-      var siteName = site.name;       
-      var year = site.startDate.substr(0,4);
-      var month = site.startDate.substr(5,2);
-      var date = site.startDate.substr(8,2);      
-      var siteStartDate = new Date(year, month-1, date);
+      var siteName = site.name;
+      var siteStartDate = dateStrToDate(site.startDate);
+      var siteStartDateStr = addHyphensToDateString(site.startDate);
       
       var siteData = statistics[namePrefix];      
       var siteLatestDate = siteData['latestDateKey'];
-      var siteLatestDateYear = siteLatestDate.substr(0,4);
-      var siteLatestDateMonth = siteLatestDate.substr(4,2);
-      var siteLatestDateDate = siteLatestDate.substr(6,2);
-      var siteLatestDateStr = siteLatestDateYear + '-' + siteLatestDateMonth + '-' + siteLatestDateDate;
+      var siteLatestDateStr = addHyphensToDateString(siteLatestDate);
       var tableRow = document.createElement('tr');
       var tableCol = getTableCellElement(siteName, 'rowtitle');
       tableRow.appendChild(tableCol);
-      tableRow.appendChild(getTableCellElement(year+'-'+(month)+'-'+date, 'reportdata'));
+      tableRow.appendChild(getTableCellElement(siteStartDateStr, 'reportdata'));
+      tableRow.appendChild(getTableCellElement(siteLatestDateStr, 'reportdata'));
+      var noDateKey = 'noDate';
+      var sumKey = 'sumKey';
+      var totalKey = 'totalKey';
+      if (siteData != null)
+      {
+        data = getJSONDataWithPercent(siteData, 'yesPatient', sumKey, numDecimals);
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONDataWithPercent(siteData, 'yesNoPatient', sumKey, numDecimals);
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONDataWithPercent(siteData, 'no', sumKey, numDecimals);
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONDataWithPercent(siteData, 'notAsked', sumKey, numDecimals);
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONDataWithPercent(siteData, noDateKey, sumKey, numDecimals);
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        // Add column with summed values for site
+        var siteSum = getJSONData(siteData, sumKey, 0);
+        tableRow.appendChild(getTableCellElement(siteSum, 'rowsummary'));
+      }
+      // Add column with total number of samples for site, regardless of creation date
+      var siteTotal = getJSONData(siteData, totalKey, 0);
+      tableRow.appendChild(getTableCellElement(siteTotal, 'rowsummary'));
+      reportTable.appendChild(tableRow);
+    }
+  }
+
+  function addDataRowsToConsentTableUnknownDate(report, reportTable, numDecimals)
+  {
+    var sites = report.sites;   
+    var statistics = report.statistics;
+    unknownCreation = statistics.noDate;
+    unknownSite = statistics.unknownSite;
+    var siteOrderList = report.siteOrderListKey;
+    for (var siteOrderIndex in siteOrderList)
+    {
+      var namePrefix = siteOrderList[siteOrderIndex];   
+      if (!sites.hasOwnProperty(namePrefix)) continue;        
+      var site = sites[namePrefix];
+      var siteName = site.name;
+      var siteStartDate = dateStrToDate(site.startDate);
+      var siteStartDateStr = addHyphensToDateString(site.startDate);
+      
+      var siteData = statistics[namePrefix];      
+      var siteLatestDate = siteData['latestDateKey'];
+      var siteLatestDateStr = addHyphensToDateString(siteLatestDate);
+      var tableRow = document.createElement('tr');
+      var tableCol = getTableCellElement(siteName, 'rowtitle');
+      tableRow.appendChild(tableCol);
+      tableRow.appendChild(getTableCellElement(siteStartDateStr, 'reportdata'));
+      tableRow.appendChild(getTableCellElement(siteLatestDateStr, 'reportdata'));
+      var noDateKey = 'noDate';
+      var sumKey = 'sumKey';
+      var totalKey = 'totalKey';
+      if (siteData != null)
+      {
+        data = getJSONDataWithPercent(siteData, 'yesNoDate', sumKey, numDecimals);
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONDataWithPercent(siteData, 'noNoDate', sumKey, numDecimals);
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONDataWithPercent(siteData, 'notAskedNoDate', sumKey, numDecimals);
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONDataWithPercent(siteData, 'missing', sumKey, numDecimals);
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        // Add column with summed values for site
+        var siteSum = getJSONData(siteData, noDateKey, 0);
+        tableRow.appendChild(getTableCellElement(siteSum, 'rowsummary'));
+      }
+      // Add column with total number of samples for site, regardless of creation date
+      var siteTotal = getJSONData(siteData, totalKey, 0);
+      tableRow.appendChild(getTableCellElement(siteTotal, 'rowsummary'));
+      reportTable.appendChild(tableRow);
+    }
+  }
+
+  function addDataRowsToOverviewTable(report, reportTable)
+  {
+    var sites = report.sites;   
+    var statistics = report.statistics;
+    unknownCreation = statistics.noDate;
+    unknownSite = statistics.unknownSite;
+    var siteOrderList = report.siteOrderListKey;
+    for (var siteOrderIndex in siteOrderList)
+    {
+      var namePrefix = siteOrderList[siteOrderIndex];   
+      if (!sites.hasOwnProperty(namePrefix)) continue;        
+      var site = sites[namePrefix];
+      var siteName = site.name;       
+      var siteStartDate = dateStrToDate(site.startDate);
+      var siteStartDateStr = addHyphensToDateString(site.startDate);
+      
+      var siteData = statistics[namePrefix];      
+      var siteLatestDate = siteData['latestDateKey'];
+      var siteLatestDateStr = addHyphensToDateString(siteLatestDate);
+      var tableRow = document.createElement('tr');
+      var tableCol = getTableCellElement(siteName, 'rowtitle');
+      tableRow.appendChild(tableCol);
+      tableRow.appendChild(getTableCellElement(siteStartDateStr, 'reportdata'));
+      tableRow.appendChild(getTableCellElement(siteLatestDateStr, 'reportdata'));
+      var noDateKey = 'noDate';
+      var sumKey = 'sumKey';
+      var totalKey = 'totalKey';
+      if (siteData != null)
+      {
+        data = getJSONData(siteData, 'patient');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONData(siteData, 'bloodSample');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONData(siteData, 'specimen');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONData(siteData, 'noSpecimen');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONData(siteData, 'consentYes');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONData(siteData, 'consentMissing');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+      }
+      reportTable.appendChild(tableRow);
+    }
+  }
+
+  function addDataRowsToOverviewPatientDetailedTable(report, reportTable)
+  {
+    var sites = report.sites;   
+    var statistics = report.statistics;
+    unknownCreation = statistics.noDate;
+    unknownSite = statistics.unknownSite;
+    var siteOrderList = report.siteOrderListKey;
+    for (var siteOrderIndex in siteOrderList)
+    {
+      var namePrefix = siteOrderList[siteOrderIndex];   
+      if (!sites.hasOwnProperty(namePrefix)) continue;        
+      var site = sites[namePrefix];
+      var siteName = site.name;       
+      var siteStartDate = dateStrToDate(site.startDate);
+      var siteStartDateStr = addHyphensToDateString(site.startDate);
+      
+      var siteData = statistics[namePrefix];
+/*    
+      var siteLatestDate = siteData['latestDateKey'];
+      var siteLatestDateStr = addHyphensToDateString(siteLatestDate);
+*/
+      var tableRow = document.createElement('tr');
+      var tableCol = getTableCellElement(siteName, 'rowtitle');
+      tableRow.appendChild(tableCol);
+      tableRow.appendChild(getTableCellElement(siteStartDateStr, 'reportdata'));
+/*
+      tableRow.appendChild(getTableCellElement(siteLatestDateStr, 'reportdata'));
+*/
+      var noDateKey = 'noDate';
+      var sumKey = 'sumKey';
+      var totalKey = 'totalKey';
+      if (siteData != null)
+      {
+        data = getJSONData(siteData, 'patientBloodSampleOnly');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONData(siteData, 'patientSpecimenOnly');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONData(siteData, 'patientNoSpecimenOnly');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONData(siteData, 'patientBloodSampleAndSpecimen');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONData(siteData, 'patientBloodSampleAndNoSpecimen');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONData(siteData, 'patientSpecimenAndNoSpecimen');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONData(siteData, 'patientBloodSampleAndSpecimenAndNoSpecimen');
+        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        //data = getJSONData(siteData, 'patientNoSamples');
+        //tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        data = getJSONData(siteData, 'sumKey');
+        tableRow.appendChild(getTableCellElement(data, 'rowsummary'));
+      }
+      reportTable.appendChild(tableRow);
+    }
+  }
+
+  function addDataRowsToMissingSampleDataTable(report, reportTable)
+  {
+    var sites = report.sites;   
+    var statistics = report.statistics;
+    var sampleType = report.sampleType;
+    var permissionDeniedForPatientName = report.permissionDeniedForPatientName;
+    var unknownCreation = statistics.noDate;
+    var unknownSite = statistics.unknownSite;
+    var siteOrderList = report.siteOrderListKey;
+    for (var siteOrderIndex in siteOrderList)
+    {
+      var namePrefix = siteOrderList[siteOrderIndex];   
+      if (!sites.hasOwnProperty(namePrefix)) continue;        
+      var site = sites[namePrefix];
+      var siteName = site.name;
+      var siteStartDate = dateStrToDate(site.startDate);
+      var siteStartDateStr = addHyphensToDateString(site.startDate);
+      
+      var siteData = statistics[namePrefix];      
+      var siteLatestDate = siteData['latestDateKey'];
+      var siteLatestDateStr = addHyphensToDateString(siteLatestDate);
+      var tableRow = document.createElement('tr');
+      var tableCol = getTableCellElement(siteName, 'rowtitle');
+      tableRow.appendChild(tableCol);
+      tableRow.appendChild(getTableCellElement(siteStartDateStr, 'reportdata'));
       tableRow.appendChild(getTableCellElement(siteLatestDateStr, 'reportdata'));
       //var currentDate = new Date(periodStartDate.getFullYear(), periodStartDate.getMonth(), periodStartDate.getDate());     
@@ -826 +1374 @@
       if (siteData != null)
       {
-        data = getJSONDataWithPercent(siteData, 'yesPatient', sumKey, numDecimals);
-        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
-        data = getJSONDataWithPercent(siteData, 'yesNoPatient', sumKey, numDecimals);
-        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
-        data = getJSONDataWithPercent(siteData, 'no', sumKey, numDecimals);
-        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
-        data = getJSONDataWithPercent(siteData, 'notAsked', sumKey, numDecimals);
-        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
-        data = getJSONDataWithPercent(siteData, noDateKey, sumKey, numDecimals);
-        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
-        // Add column with summed values for site
-        var siteSum = getJSONData(siteData, sumKey, 0);
-        tableRow.appendChild(getTableCellElement(siteSum, 'rowsummary'));
-      }
-      // Add column with total number of samples for site, regardless of creation date
-      var siteTotal = getJSONData(siteData, totalKey, 0);
-      tableRow.appendChild(getTableCellElement(siteTotal, 'rowsummary'));
-      reportTable.appendChild(tableRow);
-    }
-  }
-
-  function addDataRowsToConsentTableUnknownDate(report, reportTable, numDecimals)
-  {
-    var sites = report.sites;   
-    var statistics = report.statistics;
-    unknownCreation = statistics.noDate;
-    unknownSite = statistics.unknownSite;
-    var siteOrderList = report.siteOrderListKey;
-    for (var siteOrderIndex in siteOrderList)
-    {
-      var namePrefix = siteOrderList[siteOrderIndex];   
-      if (!sites.hasOwnProperty(namePrefix)) continue;        
-      var site = sites[namePrefix];
-      var siteName = site.name;
-      var year = site.startDate.substr(0,4);
-      var month = site.startDate.substr(5,2);
-      var date = site.startDate.substr(8,2);      
-      var siteStartDate = new Date(year, month-1, date);
-      
-      var siteData = statistics[namePrefix];      
-      var siteLatestDate = siteData['latestDateKey'];
-      var siteLatestDateYear = siteLatestDate.substr(0,4);
-      var siteLatestDateMonth = siteLatestDate.substr(4,2);
-      var siteLatestDateDate = siteLatestDate.substr(6,2);
-      var siteLatestDateStr = siteLatestDateYear + '-' + siteLatestDateMonth + '-' + siteLatestDateDate;
-      var tableRow = document.createElement('tr');
-      var tableCol = getTableCellElement(siteName, 'rowtitle');
-      tableRow.appendChild(tableCol);
-      tableRow.appendChild(getTableCellElement(year+'-'+(month)+'-'+date, 'reportdata'));
-      tableRow.appendChild(getTableCellElement(siteLatestDateStr, 'reportdata'));
-      //var currentDate = new Date(periodStartDate.getFullYear(), periodStartDate.getMonth(), periodStartDate.getDate());     
-      var noDateKey = 'noDate';
-      var sumKey = 'sumKey';
-      var totalKey = 'totalKey';
-      if (siteData != null)
-      {
-        data = getJSONDataWithPercent(siteData, 'yesNoDate', sumKey, numDecimals);
-        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
-        data = getJSONDataWithPercent(siteData, 'noNoDate', sumKey, numDecimals);
-        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
-        data = getJSONDataWithPercent(siteData, 'notAskedNoDate', sumKey, numDecimals);
-        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
-        data = getJSONDataWithPercent(siteData, 'missing', sumKey, numDecimals);
-        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
-        // Add column with summed values for site
-        var siteSum = getJSONData(siteData, noDateKey, 0);
-        tableRow.appendChild(getTableCellElement(siteSum, 'rowsummary'));
-      }
-      // Add column with total number of samples for site, regardless of creation date
-      var siteTotal = getJSONData(siteData, totalKey, 0);
-      tableRow.appendChild(getTableCellElement(siteTotal, 'rowsummary'));
+        if ('false' == permissionDeniedForPatientName)
+        {
+          data = getJSONData(siteData, 'missingPatientName');
+          tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        }
+        else
+        {
+          data = '-';
+          tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        }
+        if (sampleType == 'specimen')
+        {
+          data = getJSONData(siteData, 'missingPadReference');
+          tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+          data = getJSONData(siteData, 'missingLaterality');
+          tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+          data = getJSONData(siteData, 'missingSamplingDateTime');
+          tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+          data = getJSONData(siteData, 'missingRnaLaterDateTime');
+          tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        }
+        else if (sampleType == 'nospecimen')
+        {
+          data = getJSONData(siteData, 'missingSamplingDateTime');
+          tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        }
+        else if (sampleType == 'blood')
+        {
+          data = getJSONData(siteData, 'missingBloodSamplingDateTime');
+          tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+          data = getJSONData(siteData, 'missingBloodFreezerDateTime');
+          tableRow.appendChild(getTableCellElement(data, 'reportdata'));
+        }
+      }
       reportTable.appendChild(tableRow);
     }
@@ -1132 +1643 @@
         siteLatestDateStr = siteLatestDateYear + '-' + siteLatestDateMonth + '-' + siteLatestDateDate;
       }
-/*
-      var siteLatestDateYear = siteLatestDate.substr(0,4);
-      var siteLatestDateMonth = siteLatestDate.substr(4,2);
-      var siteLatestDateDate = siteLatestDate.substr(6,2);
-      var siteLatestDateStr = siteLatestDateYear + '-' + siteLatestDateMonth + '-' + siteLatestDateDate;
-*/
       var tableRow = document.createElement('tr');
       var tableCol = getTableCellElement(siteName, 'rowtitle');
@@ -1326 +1831 @@
   }
 
+  /**
+   *  addHyphensToDateStr()
+   *
+   *  Adds hyphens to date string in yyyymmdd format to
+   *  get yyyy-mm-dd format. If input string already contains
+   *  hyphen(s), the input string is returned unchanged.
+   *  If input string is null or empty, '????-??-??' is returned.
+   *
+   *  @param dateStr String Input date string in yyyy-mm-dd or yyyymmdd format.
+   *  @return String Date string in yyyy-mm-dd format.
+   */
+  function addHyphensToDateString(dateStr)
+  {
+    var dateWithHyphensStr = '????-??-??';
+    if (dateStr != null && dateStr != '')
+    {
+      // Check if input string already contains hyphen
+      if (dateStr.indexOf("-") >= 0)
+      {
+        // Date already has hyphen(s)
+        dateWithHyphensStr = dateStr;
+      }
+      else
+      {
+        // Date in yyyymmdd format
+        var yearStr = dateStr.substr(0,4);
+        var monthStr = dateStr.substr(4,2);
+        var dayStr = dateStr.substr(6,2);     
+        dateWithHyphensStr = yearStr + '-' + monthStr + '-' + dayStr;
+      }
+    }
+    return dateWithHyphensStr;
+  }
+
+  /**
+   *  dateStrToDate()
+   *
+   *  Takes an input date string in yyyy-mm-dd or yyyymmdd format
+   *  and returns a date corresponding to the date string.
+   *  If input string is null or empty, null is returned.
+   *
+   *  @param dateStr String Input date string in yyyy-mm-dd or yyyymmdd format.
+   *  @return Date Date corresponding to input date string.
+   */
+  function dateStrToDate(dateStr)
+  {
+    var date = null;
+    if (dateStr != null && dateStr != '')
+    {
+      // Check if input string already contains hyphen
+      if (dateStr.indexOf("-") >= 0)
+      {
+        // Date in yyyy-mm-dd format
+        var yearStr = dateStr.substr(0,4);
+        var monthStr = dateStr.substr(5,2);
+        var dayStr = dateStr.substr(8,2);     
+        var date = new Date(parseInt(yearStr, 10), parseInt(monthStr, 10)-1, parseInt(dayStr, 10));
+      }
+      else
+      {
+        // Date in yyyymmdd format
+        var yearStr = dateStr.substr(0,4);
+        var monthStr = dateStr.substr(4,2);
+        var dayStr = dateStr.substr(6,2);     
+        var date = new Date(parseInt(yearStr, 10), parseInt(monthStr, 10)-1, parseInt(dayStr, 10));
+      }
+    }
+    return date;
+  }
+
   /*
-   * Get the ISO week number for a given date
+   *  Get the ISO week number for a given date
    * 
-   * Based on code at http://stackoverflow.com/questions/6117814/get-week-of-year-in-javascript-like-in-php
+   *  Based on code at http://stackoverflow.com/questions/6117814/get-week-of-year-in-javascript-like-in-php
+   *
+   *  @param date String Input date to get ISO week number for.
+   *  @return int ISO week number for input date.
    */
   function getISOWeekNumber(date)
@@ -1384 +1962 @@
                 <option value="consentcount">Consent count report</option>
                 <option value="patientcount">Patient count report</option>
+                <option value="overviewreport">Overview report</option>
+                <option value="missingsampledatareport">Missing sample data report</option>
               </select>
             </td>
@@ -1409 +1989 @@
             <table border="0" cellspacing="0" cellpadding="0" width="100%">           
             <tr>
-              <td valign="top" class="prompt">Report period</td>
+              <td valign="top" class="prompt">
+                <div id="reportPeriodSubSection01" style="display:none;">
+                  <text id="reportPeriodSubSection01Header">Report period</text>
+                </div>
+              </td>
               <td valign="top" class="input">
-                From<input type="text" onChange="dateOnChange()" size=7 name="fromdate"/>&nbsp;
-                To<input type="text" onChange="dateOnChange()" size=7 name="todate" />
+                <div id="reportPeriodSubSection02" style="display:none;">
+                  From<input type="text" onChange="dateOnChange()" size=7 name="fromdate"/>&nbsp;
+                  To<input type="text" onChange="dateOnChange()" size=7 name="todate" />
+                </div>
               </td>
               <td valign="top" class="status" id="displayInterval.status"></td>
               <td class="help">
-                <span id="displayInterval.message" class="message" style="display: none;"></span>
-                Define which period the report should cover. Empty fields will include all <text id="items01">items</text>.<br>
+                <div id="reportPeriodSubSection04" style="display:none;">
+                  <span id="displayInterval.message" class="message" style="display: none;"></span>
+                  <!--
+                  Define which period the report should cover. Empty fields will include all <text id="items01">items</text>.<br>
+                  -->
+                  <text id="reportPeriodSubSection04HelpText">Parameter help text</text><br>
+                </div>
               </td>
             </tr> 
@@ -1461 +2052 @@
                   <select name="sampletype">
                     <option value="specimen" selected="yes">Specimen</option>
+                    <option value="nospecimen">No specimen</option>
                     <option value="blood">Blood</option>
                   </select>

extensions/net.sf.basedb.reggie/branches/ticket-422/resources/specimentube.jsp

@@ -613 +613 @@
       if (samplingTimestamp)
       {
-        if (rnaLaterTimestamp.getDate() == samplingTimestamp.getDate() && rnaLaterTimestamp.getTime()<samplingTimestamp.getTime())
-        {
-          setInputStatus('rnaLaterDate', 'RNA-later date+time must later then Sampling date+time','invalid');
-          return;
-        }
         if (rnaLaterTimestamp.getDate() != samplingTimestamp.getDate())
         {
           setInputStatus('rnaLaterDate', 'Sampling and RNA later dates are different', 'invalid');
+          return;
+        }
+        if (rnaLaterTimestamp.getTime() < samplingTimestamp.getTime())
+        {
+          setInputStatus('rnaLaterDate', 'RNA later time must be later than Sampling time','invalid');
           return;
         }

extensions/net.sf.basedb.reggie/branches/ticket-422/src/net/sf/basedb/reggie/Reggie.java

@@ -30 +30 @@
     The current version of this package.
   */
-  public static final String VERSION = "2.10-dev";
+  public static final String VERSION = "2.11-dev";
 
   

extensions/net.sf.basedb.reggie/branches/ticket-422/src/net/sf/basedb/reggie/servlet/BloodRegistrationServlet.java

@@ -14 +14 @@
 import org.json.simple.parser.JSONParser;
 
-import net.sf.basedb.core.AnnotationSet;
-import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.Application;
 import net.sf.basedb.core.BioMaterialEvent;
@@ -24 +22 @@
 import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.reggie.Site;
+import net.sf.basedb.reggie.converter.StringToDateConverter;
 import net.sf.basedb.reggie.dao.Annotationtype;
 import net.sf.basedb.reggie.dao.Blood;
@@ -87 +86 @@
           blood.loadAnnotations(dc, "serum", Annotationtype.BLOOD_SERUM, null);
           blood.loadAnnotations(dc, "bloodSample", Annotationtype.BLOOD_SAMPLE, null);
+          blood.loadAnnotations(dc, "otherPathNote", Annotationtype.OTHER_PATH_NOTE, null);
 
           // Wrap what we have so far up into JSON objects
@@ -204 +204 @@
         Date freezerDate = Reggie.CONVERTER_STRING_TO_DATETIME.convert((String)jsonBlood.get("freezerDate"));
         String bloodSample = Values.getStringOrNull((String)jsonBlood.get("bloodSample"));
+        String otherPathNote = Values.getStringOrNull((String)jsonBlood.get("otherPathNote"));
         
         creationEvent.setEventDate(samplingDate);
@@ -210 +211 @@
         Annotationtype.BLOOD_SERUM.setAnnotationValue(dc, blood, jsonBlood.get("serum"));
         Annotationtype.BLOOD_SAMPLE.setAnnotationValue(dc, blood, bloodSample);
+        Annotationtype.OTHER_PATH_NOTE.setAnnotationValue(dc, blood, otherPathNote);
 
         Number copyConsentId = (Number)jsonBlood.get("copyConsent");
@@ -239 +241 @@
         Date freezerDate = Reggie.CONVERTER_STRING_TO_DATETIME.convert((String)jsonBlood.get("freezerDate"));
         String bloodSample = Values.getStringOrNull((String)jsonBlood.get("bloodSample"));
+        String otherPathNote = Values.getStringOrNull((String)jsonBlood.get("otherPathNote"));
         
         blood.getCreationEvent().setEventDate(samplingDate);
@@ -246 +249 @@
         Annotationtype.BLOOD_SERUM.setAnnotationValue(dc, blood, jsonBlood.get("serum"));
         Annotationtype.BLOOD_SAMPLE.setAnnotationValue(dc, blood, bloodSample);
+        Annotationtype.OTHER_PATH_NOTE.setAnnotationValue(dc, blood, otherPathNote);
 
         jsonMessages.add("Blood '" + blood.getName() + "' updated successfully.");
@@ -288 +292 @@
       patient.setName((String)jsonPat.get("name"));
       String pnr = (String)jsonPat.get("personalNumber");
-      String dateOfBirth = (String)jsonPat.get("dateOfBirth");
-      String gender = (String)jsonPat.get("gender");
-      
-      AnnotationType personalNumberType = Annotationtype.PERSONAL_NUMBER.load(dc);
-      AnnotationType familyNameType = Annotationtype.FAMILY_NAME.load(dc);
-      AnnotationType allFirstNamesType = Annotationtype.ALL_FIRST_NAMES.load(dc);
-      AnnotationType genderType = Annotationtype.GENDER.load(dc);
-      AnnotationType dateOfBirthType = Annotationtype.DATE_OF_BIRTH.load(dc);
-      
-      AnnotationSet as = patient.getAnnotationSet();
-      as.getAnnotation(personalNumberType).setValue(pnr);
-      as.getAnnotation(familyNameType).setValue((String)jsonPat.get("familyName"));
-      as.getAnnotation(allFirstNamesType).setValue((String)jsonPat.get("allFirstNames"));
-      if (gender != null) as.getAnnotation(genderType).setValue(gender);
-      if (dateOfBirth != null)
-      {
-        SimpleDateFormat df = new SimpleDateFormat("yyyy-MM-dd");
-        df.setLenient(false);
-        as.getAnnotation(dateOfBirthType).setValue(df.parse(dateOfBirth));
-      }
+      StringToDateConverter dateConverter = new StringToDateConverter(new SimpleDateFormat("yyyy-MM-dd"));
+      Date dateOfBirth = dateConverter.convert((String)jsonPat.get("dateOfBirth"));
+      String gender = Values.getStringOrNull((String)jsonPat.get("gender"));
+      String familyName = Values.getStringOrNull((String)jsonPat.get("familyName"));
+      String allFirstNames = Values.getStringOrNull((String)jsonPat.get("allFirstNames"));
+
+      Annotationtype.PERSONAL_NUMBER.setAnnotationValue(dc, patient, pnr);
+      Annotationtype.FAMILY_NAME.setAnnotationValue(dc, patient, familyName);
+      Annotationtype.ALL_FIRST_NAMES.setAnnotationValue(dc, patient, allFirstNames);
+      Annotationtype.GENDER.setAnnotationValue(dc, patient, gender);
+      Annotationtype.DATE_OF_BIRTH.setAnnotationValue(dc, patient, dateOfBirth);
+    
       if (gender == null || dateOfBirth == null)
       {

extensions/net.sf.basedb.reggie/branches/ticket-422/src/net/sf/basedb/reggie/servlet/HistologyServlet.java

@@ -7 +7 @@
 import java.util.Set;
 import java.util.TreeSet;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import javax.servlet.ServletException;
@@ -209 +207 @@
         ReactionPlate paraffinBlock = ReactionPlate.getById(dc, bioPlateId, BioplateType.PARAFFIN_BLOCK);
         paraffinBlock.loadBioWells(dc, true);
+        paraffinBlock.setAnnotation("comment", paraffinBlock.getBioPlate().getDescription());
         
         // Load child HEglass plates
         List<ReactionPlate> heGlassPlates = paraffinBlock.findChildPlates(dc, BioplateType.HE_GLASS);
-        
-        Pattern storagePattern = Pattern.compile("Stored in glass box\\: (\\d+)\\; position\\: (\\d+)");
-        
+                
         if (heGlassPlates.size() > 0)
         {
@@ -220 +217 @@
           for (ReactionPlate heGlass : heGlassPlates)
           {
+            BioPlate hePlate = heGlass.getBioPlate();
             heGlass.loadBioWells(dc, true);
             heGlass.loadBioMaterialAnnotations(dc, "GoodStain", Annotationtype.GOOD_STAIN, null);
-            
-            BioPlate hePlate = heGlass.getBioPlate();
-            
-            if (hePlate.getDescription() != null)
+            heGlass.setAnnotation("comment", hePlate.getDescription());
+            
+            if (hePlate.getTray() != null && hePlate.getPosition() != null)
             {
-              Matcher m = storagePattern.matcher(hePlate.getDescription());
-              if (m.matches())
-              {
-                heGlass.setAnnotation("storageBox", m.group(1));
-                heGlass.setAnnotation("position", m.group(2));
-              }
+              heGlass.setAnnotation("storageBox", hePlate.getTray());
+              heGlass.setAnnotation("position", hePlate.getPosition());
             }
             
@@ -257 +250 @@
         {
           BioPlate heGlass = result.get(0);
-          if (heGlass.getDescription() != null)
-          {
-            Pattern storagePattern = Pattern.compile("Stored in glass box\\: (\\d+)\\; position\\: (\\d+)");
-            Matcher m = storagePattern.matcher(heGlass.getDescription());
-            if (m.matches())
-            {
-              json.put("storageBox", Integer.parseInt(m.group(1)));
-              json.put("position", Integer.parseInt(m.group(2)));
-            }
+          if (heGlass.getTray() != null && heGlass.getPosition() != null)
+          {
+            json.put("storageBox", Values.getInt(heGlass.getTray()));
+            json.put("position", Values.getInt(heGlass.getPosition()));
           }
         }
@@ -406 +394 @@
         Date moveDate = Reggie.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("moveDate"));
         Number protocolId = (Number)jsonReq.get("protocolId");
-        String storageBox = "";
+        String storageBox = null;
         
         dc = sc.newDbControl();
@@ -456 +444 @@
           {
             JSONObject jsonBlock = (JSONObject)jsonBlocks.get(blockNo);
-            storageBox = (String)jsonBlock.get("storageBox");
+            storageBox = Values.getStringOrNull((String)jsonBlock.get("storageBox"));
             Number blockId = (Number)jsonBlock.get("id");
             blockPos = 0;
@@ -463 +451 @@
             paraffinBlock = BioPlate.getById(dc, blockId.intValue());
             paraffinBlock.setEventDate(moveDate);
-            paraffinBlock.setDescription("Stored in block box: " + storageBox);
+            paraffinBlock.setTray(storageBox);
+            paraffinBlock.setDescription(Values.getStringOrNull((String)jsonBlock.get("comment")));
             
             // Attach the new paraffin block to the PLACE-ON-PLATE event
@@ -471 +460 @@
             int numSamples = remainingBioMaterial > Histology.SAMPLES_PER_BLOCK ? Histology.SAMPLES_PER_BLOCK : remainingBioMaterial;
             
-            jsonMessages.add("Moved " + numSamples + " samples to '" + paraffinBlock.getName() + "' (" + paraffinBlock.getDescription() + ")");
+            jsonMessages.add("Moved " + numSamples + " samples to '" + paraffinBlock.getName() + "'");
           }
           
@@ -495 +484 @@
         // Mark the work list as removed
         workList.setRemoved(true);
-        sc.setUserClientSetting("net.sf.basedb.reggie.histology.last-block-box", storageBox);
+        if (storageBox != null)
+        {
+          sc.setUserClientSetting("net.sf.basedb.reggie.histology.last-block-box", storageBox);
+        }
 
         dc.commit();
@@ -516 +508 @@
         // and find the max "goodStain" value
         BioPlate pb = BioPlate.getById(dc, plateId.intValue());
-        int maxGoodStain = 1; 
+        pb.setDescription(Values.getStringOrNull((String)jsonPlate.get("comment")));
+        int numHeGlass = jsonHeGlass.size(); 
         for (int i = 0; i < jsonWells.size(); ++i)
         {
@@ -527 +520 @@
           {
             jsonWell.put("histology", histology);
-            Number goodStain = (Number)jsonWell.get("GoodStain");
-            if (goodStain.intValue() > maxGoodStain) 
-            {
-              maxGoodStain = goodStain.intValue();
-            }
           }
         }
@@ -547 +535 @@
         // Create required number of child glass plates
         int numNewHEGlass = 0;
-        for (int stainNo = 1; stainNo <= maxGoodStain; ++stainNo)
+        for (int stainNo = 1; stainNo <= numHeGlass; ++stainNo)
         {
           JSONObject jsonGlass = (JSONObject)jsonHeGlass.get(stainNo-1);
-          String storageBox = (String)jsonGlass.get("storageBox");
-          String position = (String)jsonGlass.get("position");
+          String storageBox = Values.getStringOrNull((String)jsonGlass.get("storageBox"));
+          String position = Values.getStringOrNull((String)jsonGlass.get("position"));
+          String comment = Values.getStringOrNull((String)jsonGlass.get("comment"));
           
           // Try to find an existing HE glass
@@ -575 +564 @@
           }
           
-          heGlass.setDescription("Stored in glass box: " + storageBox + "; position: " + position);
+          heGlass.setTray(storageBox);
+          heGlass.setPosition(position);
+          heGlass.setDescription(comment);
           
           int numGoodStains = 0;
@@ -628 +619 @@
           if (hePlate == null)
           {
-            jsonMessages.add("Created '" + heGlass.getName() + "' with " +  numGoodStains + " good stains. (" + heGlass.getDescription() + ")");
+            jsonMessages.add("Created '" + heGlass.getName() + "' with " +  numGoodStains + " good stains.");
           }
           else

extensions/net.sf.basedb.reggie/branches/ticket-422/src/net/sf/basedb/reggie/servlet/InstallServlet.java

@@ -237 +237 @@
             Annotationtype.CONSENT, Annotationtype.CONSENT_DATE,
             Annotationtype.BLOOD_SAMPLING_DATETIME, Annotationtype.BLOOD_FREEZER_DATETIME,
-            Annotationtype.BLOOD_SERUM, Annotationtype.BLOOD_SAMPLE));
+            Annotationtype.BLOOD_SERUM, Annotationtype.BLOOD_SAMPLE,
+            Annotationtype.OTHER_PATH_NOTE));
         
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.SPECIMEN, createIfMissing, 

extensions/net.sf.basedb.reggie/branches/ticket-422/src/net/sf/basedb/reggie/servlet/PersonalRegistrationServlet.java

@@ -26 +26 @@
 import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.reggie.Site;
+import net.sf.basedb.reggie.converter.StringToDateConverter;
 import net.sf.basedb.reggie.dao.Annotationtype;
 import net.sf.basedb.reggie.dao.Blood;
@@ -543 +544 @@
     Number patientId = (Number)jsonPat.get("id");
     BioSource patient = null;
-    AnnotationType familyNameType = Annotationtype.FAMILY_NAME.load(dc);
-    AnnotationType allFirstNamesType = Annotationtype.ALL_FIRST_NAMES.load(dc);
-    
+    String familyName = Values.getStringOrNull((String)jsonPat.get("familyName"));
+    String allFirstNames = Values.getStringOrNull((String)jsonPat.get("allFirstNames"));
     if (patientId != null)
     {
       patient = BioSource.getById(dc, patientId.intValue());
       // Update names
-      AnnotationSet as = patient.getAnnotationSet();
-      as.getAnnotation(familyNameType).setValue((String)jsonPat.get("familyName"));
-      as.getAnnotation(allFirstNamesType).setValue((String)jsonPat.get("allFirstNames"));
+      Annotationtype.FAMILY_NAME.setAnnotationValue(dc, patient, familyName);
+      Annotationtype.ALL_FIRST_NAMES.setAnnotationValue(dc, patient, allFirstNames);
     }
     else
@@ -561 +560 @@
       patient.setName((String)jsonPat.get("name"));
       String pnr = (String)jsonPat.get("personalNumber");
-      String dateOfBirth = (String)jsonPat.get("dateOfBirth");
-      String gender = (String)jsonPat.get("gender");
-      
-      AnnotationType personalNumberType = Annotationtype.PERSONAL_NUMBER.load(dc);
-      AnnotationType genderType = Annotationtype.GENDER.load(dc);
-      AnnotationType dateOfBirthType = Annotationtype.DATE_OF_BIRTH.load(dc);
-      
-      AnnotationSet as = patient.getAnnotationSet();
-      as.getAnnotation(personalNumberType).setValue(pnr);
-      as.getAnnotation(familyNameType).setValue((String)jsonPat.get("familyName"));
-      as.getAnnotation(allFirstNamesType).setValue((String)jsonPat.get("allFirstNames"));
-      if (gender != null) as.getAnnotation(genderType).setValue(gender);
-      if (dateOfBirth != null)
-      {
-        SimpleDateFormat df = new SimpleDateFormat("yyyy-MM-dd");
-        df.setLenient(false);
-        as.getAnnotation(dateOfBirthType).setValue(df.parse(dateOfBirth));
-      }
+      StringToDateConverter dateConverter = new StringToDateConverter(new SimpleDateFormat("yyyy-MM-dd"));
+      Date dateOfBirth = dateConverter.convert((String)jsonPat.get("dateOfBirth"));
+      String gender = Values.getStringOrNull((String)jsonPat.get("gender"));
+      
+      Annotationtype.PERSONAL_NUMBER.setAnnotationValue(dc, patient, pnr);
+      Annotationtype.FAMILY_NAME.setAnnotationValue(dc, patient, familyName);
+      Annotationtype.ALL_FIRST_NAMES.setAnnotationValue(dc, patient, allFirstNames);
+      Annotationtype.GENDER.setAnnotationValue(dc, patient, gender);
+      Annotationtype.DATE_OF_BIRTH.setAnnotationValue(dc, patient, dateOfBirth);
+      
       if (gender == null || dateOfBirth == null)
       {

extensions/net.sf.basedb.reggie/branches/ticket-422/src/net/sf/basedb/reggie/servlet/SampleReportServlet.java

@@ -27 +27 @@
 import net.sf.basedb.core.ItemSubtype;
 import net.sf.basedb.core.MeasuredBioMaterial;
+import net.sf.basedb.core.PermissionDeniedException;
 import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.SessionControl;
@@ -196 +197 @@
         json = createPatientCountReport(dc, json, startDate, endDate, viewType);
       }
+      else if ("overviewreport".equals(cmd))
+      {
+        String startDateParameter = Values.getString(req.getParameter("fdate"), null);
+        String endDateParameter = Values.getString(req.getParameter("tdate"), null);
+
+        Date startDate = Reggie.CONVERTER_STRING_TO_DATE.convert(startDateParameter);
+        Date endDate = Reggie.CONVERTER_STRING_TO_DATE.convert(endDateParameter);
+        
+        if (startDate == null)
+        {
+          // Get the when the first site started
+          for (Site s : Site.getAllSites())
+          {
+            Date siteDate = Reggie.CONVERTER_STRING_TO_DATE.convert(s.getStartDate().replaceAll("-", ""));
+            if (siteDate != null && (startDate == null || startDate.after(siteDate))) 
+            {
+              startDate = siteDate;           
+            }
+          }
+        }
+        if (endDate == null) 
+        {
+          // Get the date for today
+          endDate = new Date();
+        }
+
+        json = createOverviewReport(dc, json, startDate, endDate);
+      }
+      else if ("missingsampledatareport".equals(cmd))
+      {
+        String startDateParameter = Values.getString(req.getParameter("fdate"), null);
+        String endDateParameter = Values.getString(req.getParameter("tdate"), null);
+
+        Date startDate = Reggie.CONVERTER_STRING_TO_DATE.convert(startDateParameter);
+        Date endDate = Reggie.CONVERTER_STRING_TO_DATE.convert(endDateParameter);
+        
+        if (startDate == null)
+        {
+          // Get the when the first site started
+          for (Site s : Site.getAllSites())
+          {
+            Date siteDate = Reggie.CONVERTER_STRING_TO_DATE.convert(s.getStartDate().replaceAll("-", ""));
+            if (siteDate != null && (startDate == null || startDate.after(siteDate))) 
+            {
+              startDate = siteDate;           
+            }
+          }
+        }
+        if (endDate == null) 
+        {
+          // Get the date for today
+          endDate = new Date();
+        }
+
+        String sampleType = "specimen";
+        String sampleTypeParameter = Values.getString(req.getParameter("stype"), null);
+        if (sampleTypeParameter != null)
+        {
+          sampleType = sampleTypeParameter;
+        }
+
+        json = createMissingSampleDataReport(dc, json, startDate, endDate, sampleType);
+      }
     }
     catch (Throwable t)
@@ -222 +286 @@
     ItemQuery<Sample> sampleQuery = Sample.getQuery();
     sampleQuery.joinPermanent(Hql.innerJoin(null, "creationEvent", "ce", true));
-    if (sampleType.equals("blood"))
+    if (sampleType.equals("nospecimen"))
+    {
+      Subtype.NO_SPECIMEN.addFilter(dc, sampleQuery);
+    }
+    else if (sampleType.equals("blood"))
     {
       Subtype.BLOOD.addFilter(dc, sampleQuery);
@@ -643 +711 @@
   }
 
+  @SuppressWarnings({ "unchecked", "rawtypes" })
+  private JSONObject createOverviewReport(DbControl dc, JSONObject json, Date startDate, Date endDate)
+      throws ServletException, IOException 
+  { 
+    JSONObject jsonReport = new JSONObject();
+    jsonReport.put("sites", getJSONSites());
+    
+    ItemQuery<Sample> sampleQuery = Sample.getQuery();
+    sampleQuery.joinPermanent(Hql.innerJoin(null, "creationEvent", "ce", true));
+    // ...only include 'Specimen', 'No Specimen', 'Blood', or 'Case' items
+    sampleQuery.restrict(
+      Restrictions.or(
+        Subtype.SPECIMEN.restriction(dc, null),
+        Subtype.NO_SPECIMEN.restriction(dc, null),
+        Subtype.BLOOD.restriction(dc, null),
+        Subtype.CASE.restriction(dc, null)
+      ));
+    sampleQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+    sampleQuery.order(Orders.asc(Hql.property("name")));
+    sampleQuery.order(Orders.asc(Hql.property("ce", "eventDate")));
+    sampleQuery.setCacheResult(true);
+    ItemResultIterator<Sample> sampleIterator = sampleQuery.iterate(dc);        
+    // Use stored annotation snapshots for performance reasons
+    SnapshotManager manager = new SnapshotManager();        
+
+    JSONObject jsonStatistics = new JSONObject();
+    JSONObject jsonSitesCombined = new JSONObject();
+    String patientKey = "patient";
+    String bloodSampleKey = "bloodSample";
+    String specimenKey = "specimen";
+    String noSpecimenKey = "noSpecimen";
+    String patientBloodSampleOnlyKey = "patientBloodSampleOnly";
+    String patientSpecimenOnlyKey = "patientSpecimenOnly";
+    String patientNoSpecimenOnlyKey = "patientNoSpecimenOnly";
+    String patientBloodSampleAndSpecimenKey = "patientBloodSampleAndSpecimen";
+    String patientBloodSampleAndNoSpecimenKey = "patientBloodSampleAndNoSpecimen";
+    String patientSpecimenAndNoSpecimenKey = "patientSpecimenAndNoSpecimen";
+    String patientBloodSampleAndSpecimenAndNoSpecimenKey = "patientBloodSampleAndSpecimenAndNoSpecimen";
+    String patientNoSamplesKey = "patientNoSamples";
+    String consentYesKey = "consentYes";
+    String consentMissingKey = "consentMissing";
+    String sitesCombinedKey = "sitesCombinedKey";
+    String sumKey = "sumKey";
+    String latestDateKey = "latestDateKey";
+    String duplicateKey = "duplicateKey";
+    jsonStatistics.put(sitesCombinedKey, jsonSitesCombined);
+    // Initialize site data to 0 for the different keys
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, patientKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, bloodSampleKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, specimenKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, noSpecimenKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, patientBloodSampleOnlyKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, patientSpecimenOnlyKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, patientNoSpecimenOnlyKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, patientBloodSampleAndSpecimenKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, patientBloodSampleAndNoSpecimenKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, patientSpecimenAndNoSpecimenKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, patientBloodSampleAndSpecimenAndNoSpecimenKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, consentYesKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, consentMissingKey);
+    // Initialize combined data to 0 for the different keys
+    jsonSitesCombined.put(patientKey, 0);
+    jsonSitesCombined.put(bloodSampleKey, 0);
+    jsonSitesCombined.put(specimenKey, 0);
+    jsonSitesCombined.put(noSpecimenKey, 0);
+    jsonSitesCombined.put(patientBloodSampleOnlyKey, 0);
+    jsonSitesCombined.put(patientSpecimenOnlyKey, 0);
+    jsonSitesCombined.put(patientNoSpecimenOnlyKey, 0);
+    jsonSitesCombined.put(patientBloodSampleAndSpecimenKey, 0);
+    jsonSitesCombined.put(patientBloodSampleAndNoSpecimenKey, 0);
+    jsonSitesCombined.put(patientSpecimenAndNoSpecimenKey, 0);
+    jsonSitesCombined.put(patientBloodSampleAndSpecimenAndNoSpecimenKey, 0);
+    jsonSitesCombined.put(consentYesKey, 0);
+    jsonSitesCombined.put(consentMissingKey, 0);
+    jsonSitesCombined.put(patientNoSamplesKey, 0);
+    // Initialize other data to 0 for different keys
+    jsonStatistics.put(duplicateKey, 0);
+    Date latestDate = null;
+    // Create HashMap to keep track of processed dates for each patient
+    HashMap<String, Set<Date>>patientDateSetHashMap = new HashMap<String, Set<Date>>();
+    //JSONObject jsonPatientnamePatientid = new JSONObject();
+    // HashMap of patient id's and site prefixes
+    HashMap<String, String> patientHashMap = new HashMap<String, String>();
+    // Set of patient id's for patients with blood samples
+    Set<String> patientsWithBloodSamplesSet = new HashSet<String>();
+    // Set of patient id's for patients with specimens
+    Set<String> patientsWithSpecimensSet = new HashSet<String>();
+    // Set of patient id's for patients with no specimens
+    Set<String> patientsWithNoSpecimensSet = new HashSet<String>();
+    // Create HashMap to keep track of latest item date for each site
+    HashMap<String, Date> sitePrefixDateHashMap = new HashMap<String, Date>();
+    // Get item subtype constants for later use
+    ItemSubtype subtypeSpecimen = Subtype.SPECIMEN.load(dc);
+    ItemSubtype subtypeNoSpecimen = Subtype.NO_SPECIMEN.load(dc);
+    ItemSubtype subtypeBlood = Subtype.BLOOD.load(dc);
+    ItemSubtype subtypeCase = Subtype.CASE.load(dc);
+    //
+    while (sampleIterator != null && sampleIterator.hasNext())
+    {
+      Sample s = sampleIterator.next();
+      BioMaterialEvent creationEvent = s.getCreationEvent();
+      Date creationDate = creationEvent.getEventDate();
+
+      // Find patient id
+      BioMaterial patient = null;
+      if (s.getItemSubtype().equals(subtypeBlood))
+      {
+        // The parent is the 'Patient' for blood samples and cases
+        patient = s.getParent();
+      }
+      else if (s.getItemSubtype().equals(subtypeSpecimen) || s.getItemSubtype().equals(subtypeNoSpecimen))
+      {
+        // The grandparent is the 'Patient' for specimens and no specimens
+        MeasuredBioMaterial parent = (MeasuredBioMaterial) s.getParent();
+        if (parent != null)
+        {
+          patient = parent.getParent();
+        }
+      }
+
+      // Update statistics for specimens, blood samples, and consents
+      Site site = Site.findByCaseName(s.getName()); 
+      if (site == Site.UNKNOWN)
+      {
+        String key = "unknownSite";
+        jsonStatistics = updateJSONObjectCounter(jsonStatistics, key);
+      }
+      else
+      {
+        // Get site info            
+        JSONObject jsonSite = (JSONObject)jsonStatistics.get(site.getPrefix());
+        if (jsonSite == null)
+        {
+          jsonSite = new JSONObject();
+          jsonStatistics.put(site.getPrefix(), jsonSite);
+        }
+
+        // Store patient data for later processing
+        String patientId = null;
+        if (patient != null)
+        {
+          patientId = patient.getName();
+          if (patientId != null && !patientId.equals(""))
+          {
+            // Add patient id to patient HashMap for site
+            patientHashMap.put(patientId, site.getPrefix());
+
+            if (s.getItemSubtype().equals(subtypeSpecimen))
+            {
+              // Add patient to patients with specimens set
+              patientsWithSpecimensSet.add(patientId);
+            }
+
+            if (s.getItemSubtype().equals(subtypeNoSpecimen))
+            {
+              // Add patient to patients with no specimens set
+              patientsWithNoSpecimensSet.add(patientId);
+            }
+
+            if (s.getItemSubtype().equals(subtypeBlood))
+            {
+              // Add patient to patients with blood samples set
+              patientsWithBloodSamplesSet.add(patientId);
+            }
+          }
+        }
+
+        // Update specimen data
+        if (s.getItemSubtype().equals(subtypeSpecimen))
+        {
+          jsonSite = updateJSONObjectCounter(jsonSite, specimenKey);
+          jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, specimenKey);
+        }
+        // Update no specimen data
+        if (s.getItemSubtype().equals(subtypeNoSpecimen))
+        {
+          jsonSite = updateJSONObjectCounter(jsonSite, noSpecimenKey);
+          jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, noSpecimenKey);
+        }
+        // Update blood sample data
+        if (s.getItemSubtype().equals(subtypeBlood))
+        {
+          jsonSite = updateJSONObjectCounter(jsonSite, bloodSampleKey);
+          jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, bloodSampleKey);
+        }
+
+        // Keep track of latest item date for site
+        if (creationDate != null)
+        {
+          Date siteLatestDate = sitePrefixDateHashMap.get(site.getPrefix());
+          if (siteLatestDate == null || siteLatestDate.before(creationDate))
+          {
+            sitePrefixDateHashMap.put(site.getPrefix(), creationDate);
+          }
+          // Keep track of latest item date so far
+          if (latestDate == null || latestDate.before(creationDate)) 
+          {
+            latestDate = creationDate;
+          }
+        }
+
+        // Process consents
+        String consent = null;
+        Date consentDate = null;
+        if (s.getItemSubtype().equals(subtypeBlood) || s.getItemSubtype().equals(subtypeCase))
+        {
+          // Get consent
+          consent = (String) Annotationtype.CONSENT.getAnnotationValue(dc, manager, s);
+          // Get consent date
+          consentDate = (Date) Annotationtype.CONSENT_DATE.getAnnotationValue(dc, manager, s);
+
+          String key = null;
+          Boolean duplicate = false;
+          if (consent != null)
+          {
+            if (consentDate != null)
+            {
+              // The parent is the 'Patient' for blood samples and cases
+              patient = s.getParent();
+
+              // Check if a consent already exists for the same patient and date
+              if (patient != null)
+              {
+                patientId = patient.getName();
+                if (patientId != null && !patientId.equals(""))
+                {
+                  if (inStringDateSetHashMap(patientDateSetHashMap, patientId, consentDate))
+                  {
+                    duplicate = true;
+                  }
+                  else
+                  {
+                    patientDateSetHashMap = updateStringDateSetHashMap(patientDateSetHashMap, patientId, consentDate);
+                  }
+                }
+              }
+            }
+            // Count approved consents, including consents without patient id (PAT#) or date
+            if (consent.equals("Yes"))
+            {
+              key = consentYesKey;
+              if (consentDate != null)
+              {
+                // Keep track of latest item date for site
+                Date siteLatestDate = sitePrefixDateHashMap.get(site.getPrefix());
+                if (siteLatestDate == null || siteLatestDate.before(consentDate))
+                {
+                  sitePrefixDateHashMap.put(site.getPrefix(), consentDate);
+                }
+                // Keep track of latest item date so far
+                if (latestDate == null || latestDate.before(consentDate)) 
+                {
+                  latestDate = consentDate;
+                }
+              }
+            }
+          }
+          else
+          {
+            key = consentMissingKey;
+          }
+          // Note that items with duplicate == false include missing consent items
+          if (!duplicate)
+          {
+            if (key != null)
+            {
+              // Update consent counters
+              jsonSite = updateJSONObjectCounter(jsonSite, key);
+              jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, key);
+            }
+          }
+          else
+          {
+            jsonStatistics = updateJSONObjectCounter(jsonStatistics, duplicateKey);
+          }
+        }
+      }
+    }
+
+    // Process patients
+    for (String patId: patientHashMap.keySet())
+    {
+      if (patId != null && !patId.equals(""))
+      {
+        // Get site info
+        String sitePrefix = patientHashMap.get(patId);
+        JSONObject jsonSite = (JSONObject)jsonStatistics.get(sitePrefix);
+        if (jsonSite == null)
+        {
+          jsonSite = new JSONObject();
+          jsonStatistics.put(sitePrefix, jsonSite);
+        }
+        // Update patient data
+        jsonSite = updateJSONObjectCounter(jsonSite, patientKey);
+        jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, patientKey);
+        if (patientsWithSpecimensSet.contains(patId))
+        {
+          if (patientsWithNoSpecimensSet.contains(patId))
+          {
+            if (patientsWithBloodSamplesSet.contains(patId))
+            {
+              // Patient with both specimens, no specimens, and blood samples
+              jsonSite = updateJSONObjectCounter(jsonSite, patientBloodSampleAndSpecimenAndNoSpecimenKey);
+              jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, patientBloodSampleAndSpecimenAndNoSpecimenKey);
+            }
+            else
+            {
+              // Patient with both specimens and no specimens
+              jsonSite = updateJSONObjectCounter(jsonSite, patientSpecimenAndNoSpecimenKey);
+              jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, patientSpecimenAndNoSpecimenKey);
+            }
+          }
+          else
+          {
+            if (patientsWithBloodSamplesSet.contains(patId))
+            {
+              // Patient with both specimens and blood samples
+              jsonSite = updateJSONObjectCounter(jsonSite, patientBloodSampleAndSpecimenKey);
+              jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, patientBloodSampleAndSpecimenKey);
+            }
+            else
+            {
+              // Patient with specimens only
+              jsonSite = updateJSONObjectCounter(jsonSite, patientSpecimenOnlyKey);
+              jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, patientSpecimenOnlyKey);
+            }
+          }
+        }
+        else
+        {
+          if (patientsWithNoSpecimensSet.contains(patId))
+          {
+            if (patientsWithBloodSamplesSet.contains(patId))
+            {
+              // Patient with both blood samples and no specimens
+              jsonSite = updateJSONObjectCounter(jsonSite, patientBloodSampleAndNoSpecimenKey);
+              jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, patientBloodSampleAndNoSpecimenKey);
+            }
+            else
+            {
+              // Patient with no specimens only
+              jsonSite = updateJSONObjectCounter(jsonSite, patientNoSpecimenOnlyKey);
+              jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, patientNoSpecimenOnlyKey);
+            }
+          }
+          else
+          {
+            if (patientsWithBloodSamplesSet.contains(patId))
+            {
+              // Patient with blood samples only
+              jsonSite = updateJSONObjectCounter(jsonSite, patientBloodSampleOnlyKey);
+              jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, patientBloodSampleOnlyKey);
+            }
+            else
+            {
+              // Patient with no sample
+              jsonSite = updateJSONObjectCounter(jsonSite, patientNoSamplesKey);
+              jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, patientNoSamplesKey);
+            }
+          }
+        }
+        // Update summed patient data
+        jsonSite = updateJSONObjectCounter(jsonSite, sumKey);
+        jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, sumKey);
+      }
+    }
+
+    // Add latest item date for site to site JSON object
+    DateToStringConverter date2StringConverter = Reggie.CONVERTER_DATE_TO_STRING;
+    for (Site s: Site.getAllSites())
+    {
+      JSONObject jsonSite = (JSONObject) jsonStatistics.get(s.getPrefix());
+      if (jsonSite == null)
+      {
+        jsonSite = new JSONObject();
+        jsonStatistics.put(s.getPrefix(), jsonSite);
+      }
+      Date siteLatestDate = sitePrefixDateHashMap.get(s.getPrefix());
+      jsonSite.put(latestDateKey, date2StringConverter.convert(siteLatestDate));
+    }
+    // Add latest date for further transfer to other JSON object
+    jsonStatistics.put(latestDateKey, date2StringConverter.convert(latestDate));
+    // Add number of patients with no samples
+    Integer numPatientsNoSamples = (Integer) jsonSitesCombined.get(patientNoSamplesKey);
+    if (numPatientsNoSamples == null)
+    {
+      numPatientsNoSamples = 0;
+    }
+    jsonStatistics.put(patientNoSamplesKey, numPatientsNoSamples);
+    // Add number of patients with both specimens and no specimens 
+    Integer numPatientsSpecimensAndNoSpecimens = (Integer) jsonSitesCombined.get(patientSpecimenAndNoSpecimenKey);
+    if (numPatientsSpecimensAndNoSpecimens == null)
+    {
+      numPatientsSpecimensAndNoSpecimens = 0;
+    }
+    jsonStatistics.put(patientSpecimenAndNoSpecimenKey, numPatientsSpecimensAndNoSpecimens);
+    // Add number of patients with both blood samples, specimens, and no specimens
+    Integer numPatientsBloodSamplesAndSpecimensAndNoSpecimens = (Integer) jsonSitesCombined.get(patientBloodSampleAndSpecimenAndNoSpecimenKey);
+    if (numPatientsBloodSamplesAndSpecimensAndNoSpecimens == null)
+    {
+      numPatientsBloodSamplesAndSpecimensAndNoSpecimens = 0;
+    }
+    jsonStatistics.put(patientBloodSampleAndSpecimenAndNoSpecimenKey, numPatientsBloodSamplesAndSpecimensAndNoSpecimens);
+    //
+    jsonReport.put("statistics", jsonStatistics);       
+    jsonReport.put("beginDate", date2StringConverter.convert(startDate));
+    jsonReport.put("endDate", date2StringConverter.convert(endDate));
+    // Transfer latest date from jsonStatistics to jsonReport
+    String latestDateStr = (String) jsonStatistics.get("latestDateKey");
+    jsonReport.put("latestDate", latestDateStr);
+    String siteOrder = alphabeticalOrder;
+    JSONObject jsonSiteOrderList = createJSONSiteOrderList(siteOrder);
+    jsonReport.put("siteOrderListKey", jsonSiteOrderList);
+    json.put("report", jsonReport);
+    return json;
+  }
+
+  @SuppressWarnings({ "unchecked", "rawtypes" })
+  private JSONObject createMissingSampleDataReport(DbControl dc, JSONObject json, Date startDate, Date endDate, String sampleType)
+      throws ServletException, IOException 
+  { 
+    JSONObject jsonReport = new JSONObject();
+    jsonReport.put("sites", getJSONSites());
+    
+    ItemQuery<Sample> sampleQuery = Sample.getQuery();
+    sampleQuery.joinPermanent(Hql.innerJoin(null, "creationEvent", "ce", true));
+    // Select what sample subtype to include in database search 
+    if (sampleType.equals("nospecimen"))
+    {
+      Subtype.NO_SPECIMEN.addFilter(dc, sampleQuery);
+    }
+    else if (sampleType.equals("blood"))
+    {
+      Subtype.BLOOD.addFilter(dc, sampleQuery);
+    }
+    else
+    {
+      Subtype.SPECIMEN.addFilter(dc, sampleQuery);
+    }
+    sampleQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+    sampleQuery.order(Orders.asc(Hql.property("name")));
+    sampleQuery.order(Orders.asc(Hql.property("ce", "eventDate")));
+    sampleQuery.setCacheResult(true);
+    ItemResultIterator<Sample> sampleIterator = sampleQuery.iterate(dc);        
+    // Use stored annotation snapshots for performance reasons
+    SnapshotManager manager = new SnapshotManager();        
+
+    JSONObject jsonStatistics = new JSONObject();
+    JSONObject jsonSitesCombined = new JSONObject();
+    String missingPatientNameKey = "missingPatientName";
+    String missingPadReferenceKey = "missingPadReference";
+    String missingLateralityKey = "missingLaterality";
+    String missingSamplingDateTimeKey = "missingSamplingDateTime";
+    String missingRnaLaterDateTimeKey = "missingRnaLaterDateTime";
+    String missingBloodSamplingDateTimeKey = "missingBloodSamplingDateTime";
+    String missingBloodFreezerDateTimeKey = "missingBloodFreezerDateTime";
+    String permissionDeniedForPatientNameKey = "permissionDeniedForPatientName";
+    String sitesCombinedKey = "sitesCombinedKey";
+    String sumKey = "sumKey";
+    String latestDateKey = "latestDateKey";
+    String duplicateKey = "duplicateKey";
+    jsonStatistics.put(sitesCombinedKey, jsonSitesCombined);
+    // Initialize site data to 0 for the different keys
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, missingPatientNameKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, missingPadReferenceKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, missingLateralityKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, missingSamplingDateTimeKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, missingRnaLaterDateTimeKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, missingBloodSamplingDateTimeKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, missingBloodFreezerDateTimeKey);
+    // Initialize combined data to 0 for the different keys
+    jsonSitesCombined.put(missingPatientNameKey, 0);
+    jsonSitesCombined.put(missingPadReferenceKey, 0);
+    jsonSitesCombined.put(missingLateralityKey, 0);
+    jsonSitesCombined.put(missingSamplingDateTimeKey, 0);
+    jsonSitesCombined.put(missingRnaLaterDateTimeKey, 0);
+    jsonSitesCombined.put(missingBloodSamplingDateTimeKey, 0);
+    jsonSitesCombined.put(missingBloodFreezerDateTimeKey, 0);
+    // Initialize other data to 0 for different keys
+    jsonStatistics.put(duplicateKey, 0);
+    Date latestDate = null;
+    // Create HashMap to keep track of latest item date for each site
+    HashMap<String, Date> sitePrefixDateHashMap = new HashMap<String, Date>();
+    // Get item subtype constants for later use
+    ItemSubtype subtypeSpecimen = Subtype.SPECIMEN.load(dc);
+    ItemSubtype subtypeNoSpecimen = Subtype.NO_SPECIMEN.load(dc);
+    ItemSubtype subtypeBlood = Subtype.BLOOD.load(dc);
+    Boolean permissionDeniedForPatientName = false;
+    //
+    while (sampleIterator != null && sampleIterator.hasNext())
+    {
+      Sample s = sampleIterator.next();
+      BioMaterialEvent creationEvent = s.getCreationEvent();
+      Date creationDate = creationEvent.getEventDate();
+
+      // Find patient id
+      BioMaterial patient = null;
+      if (s.getItemSubtype().equals(subtypeBlood))
+      {
+        // The parent is the 'Patient' for blood samples and cases
+        patient = s.getParent();
+      }
+      else if (s.getItemSubtype().equals(subtypeSpecimen) || s.getItemSubtype().equals(subtypeNoSpecimen))
+      {
+        // The grandparent is the 'Patient' for specimens and no specimens
+        MeasuredBioMaterial parent = (MeasuredBioMaterial) s.getParent();
+        if (parent != null)
+        {
+          patient = parent.getParent();
+        }
+      }
+
+      // Initialize sample data
+      String allFirstNames = null;
+      String familyName = null;
+      String pad = null;
+      String laterality = null;
+      Date samplingDate = null;
+      Date rnaLaterDate = null;
+      Date bloodSamplingDate = null;
+      Date bloodFreezerDate = null;
+
+      if (patient != null)
+      {
+        try
+        {
+          // Get patient all first names
+          allFirstNames = (String) Annotationtype.ALL_FIRST_NAMES.getAnnotationValue(dc, manager, patient);
+          // Get patient family name
+          familyName = (String) Annotationtype.FAMILY_NAME.getAnnotationValue(dc, manager, patient);
+        }
+        catch (PermissionDeniedException e)
+        {
+          permissionDeniedForPatientName = true;
+        }
+      }
+      if (sampleType.equals("specimen"))
+      {
+        // Get PAD reference
+        pad = (String) Annotationtype.PAD.getAnnotationValue(dc, manager, s);
+        // Get laterality
+        laterality = (String) Annotationtype.LATERALITY.getAnnotationValue(dc, manager, s);
+        // Get sampling date
+        samplingDate = (Date) Annotationtype.SAMPLING_DATETIME.getAnnotationValue(dc, manager, s);
+        // Get RNALater date
+        rnaLaterDate = (Date) Annotationtype.RNALATER_DATETIME.getAnnotationValue(dc, manager, s);
+      }
+      else if (sampleType.equals("nospecimen"))
+      {
+        // Get sampling date
+        samplingDate = (Date) Annotationtype.SAMPLING_DATETIME.getAnnotationValue(dc, manager, s);
+      }
+      else if (sampleType.equals("blood"))
+      {
+        // Get blood sampling date
+        bloodSamplingDate = (Date) Annotationtype.BLOOD_SAMPLING_DATETIME.getAnnotationValue(dc, manager, s);
+        // Get blood freezer date
+        bloodFreezerDate = (Date) Annotationtype.BLOOD_FREEZER_DATETIME.getAnnotationValue(dc, manager, s);
+      }
+      // Update statistics for sample type
+      Site site = Site.findByCaseName(s.getName()); 
+      if (site == Site.UNKNOWN)
+      {
+        String key = "unknownSite";
+        jsonStatistics = updateJSONObjectCounter(jsonStatistics, key);
+      }
+      else
+      {
+        // Get site info            
+        JSONObject jsonSite = (JSONObject)jsonStatistics.get(site.getPrefix());
+        if (jsonSite == null)
+        {
+          jsonSite = new JSONObject();
+          jsonStatistics.put(site.getPrefix(), jsonSite);
+        }
+
+        if (patient != null)
+        {
+          // Update missing first names data and family name data
+          if (allFirstNames == null || allFirstNames.equals("")
+              || familyName == null || familyName.equals(""))
+          {
+            // Update missing patient name data, provided the user has permission to check it
+            if (!permissionDeniedForPatientName)
+            {
+              jsonSite = updateJSONObjectCounter(jsonSite, missingPatientNameKey);
+              jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, missingPatientNameKey);
+            }
+          }
+        }
+        if (sampleType.equals("specimen"))
+        {
+          // Update missing PAD reference data
+          if (pad == null || pad.equals(""))
+          {
+            jsonSite = updateJSONObjectCounter(jsonSite, missingPadReferenceKey);
+            jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, missingPadReferenceKey);
+          }
+          // Update missing laterality data
+          if (laterality == null || laterality.equals(""))
+          {
+            jsonSite = updateJSONObjectCounter(jsonSite, missingLateralityKey);
+            jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, missingLateralityKey);
+          }
+          // Update missing sampling date data
+          if (samplingDate == null)
+          {
+            jsonSite = updateJSONObjectCounter(jsonSite, missingSamplingDateTimeKey);
+            jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, missingSamplingDateTimeKey);
+          }
+          // Update missing RNALater date data
+          if (rnaLaterDate == null)
+          {
+            jsonSite = updateJSONObjectCounter(jsonSite, missingRnaLaterDateTimeKey);
+            jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, missingRnaLaterDateTimeKey);
+          }
+        }
+        else if (sampleType.equals("nospecimen"))
+        {
+          // Update missing sampling date data
+          if (samplingDate == null)
+          {
+            jsonSite = updateJSONObjectCounter(jsonSite, missingSamplingDateTimeKey);
+            jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, missingSamplingDateTimeKey);
+          }
+        }
+        else if (sampleType.equals("blood"))
+        {
+          // Update missing blood sampling date data
+          if (bloodSamplingDate == null)
+          {
+            jsonSite = updateJSONObjectCounter(jsonSite, missingBloodSamplingDateTimeKey);
+            jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, missingBloodSamplingDateTimeKey);
+          }
+          // Update missing blood freezer date data
+          if (bloodFreezerDate == null)
+          {
+            jsonSite = updateJSONObjectCounter(jsonSite, missingBloodFreezerDateTimeKey);
+            jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, missingBloodFreezerDateTimeKey);
+          }
+        }
+
+        // Keep track of latest item date for site
+        if (creationDate != null)
+        {
+          Date siteLatestDate = sitePrefixDateHashMap.get(site.getPrefix());
+          if (siteLatestDate == null || siteLatestDate.before(creationDate))
+          {
+            sitePrefixDateHashMap.put(site.getPrefix(), creationDate);
+          }
+          // Keep track of latest item date so far
+          if (latestDate == null || latestDate.before(creationDate)) 
+          {
+            latestDate = creationDate;
+          }
+        }
+      }
+    }
+    // Add latest item date for site to site JSON object
+    DateToStringConverter date2StringConverter = Reggie.CONVERTER_DATE_TO_STRING;
+    for (Site s: Site.getAllSites())
+    {
+      JSONObject jsonSite = (JSONObject) jsonStatistics.get(s.getPrefix());
+      if (jsonSite == null)
+      {
+        jsonSite = new JSONObject();
+        jsonStatistics.put(s.getPrefix(), jsonSite);
+      }
+      Date siteLatestDate = sitePrefixDateHashMap.get(s.getPrefix());
+      jsonSite.put(latestDateKey, date2StringConverter.convert(siteLatestDate));
+    }
+    // Add latest date for further transfer to other JSON object
+    jsonStatistics.put(latestDateKey, date2StringConverter.convert(latestDate));
+    //
+    jsonReport.put("statistics", jsonStatistics);       
+    jsonReport.put("sampleType", sampleType);
+    jsonReport.put("beginDate", date2StringConverter.convert(startDate));
+    jsonReport.put("endDate", date2StringConverter.convert(endDate));
+    // Transfer latest date from jsonStatistics to jsonReport
+    String latestDateStr = (String) jsonStatistics.get("latestDateKey");
+    jsonReport.put("latestDate", latestDateStr);
+    jsonReport.put(permissionDeniedForPatientNameKey, permissionDeniedForPatientName.toString());
+    String siteOrder = alphabeticalOrder;
+    JSONObject jsonSiteOrderList = createJSONSiteOrderList(siteOrder);
+    jsonReport.put("siteOrderListKey", jsonSiteOrderList);
+    json.put("report", jsonReport);
+    return json;
+  }
+
   private Boolean inStringDateSetHashMap(HashMap<String, Set<Date>> stringDateSetHashMap, String string, Date date)
   {