Changeset 1757 for extensions/net.sf.basedb.reggie/branches/ticket-422

Timestamp:

Nov 28, 2012, 9:41:46 AM (11 years ago)

Author:

Nicklas Nordborg

Message:

Catching up on trunk revisions 1734 to 1756.

Location:

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

Files:

• . (modified) (1 prop)
• .classpath (modified) (1 diff)
• META-INF/extensions.xml (modified) (1 diff)
• README (modified) (1 diff)
• build.xml (modified) (2 diffs)
• resources/export_monthly_oplist.jsp (modified) (7 diffs)
• resources/index.jsp (modified) (1 diff)
• resources/samplereportgenerator.jsp (modified) (31 diffs)
• src/net/sf/basedb/reggie/Reggie.java (modified) (1 diff)
• src/net/sf/basedb/reggie/Site.java (modified) (1 diff)
• src/net/sf/basedb/reggie/dao/Blood.java (modified) (1 diff)
• src/net/sf/basedb/reggie/plugins/CaliperRunParametersExporter.java (modified) (1 diff)
• src/net/sf/basedb/reggie/plugins/CaliperSampleNameExporter.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/BloodRegistrationServlet.java (modified) (4 diffs)
• src/net/sf/basedb/reggie/servlet/ExportServlet.java (modified) (6 diffs)
• src/net/sf/basedb/reggie/servlet/SampleReportServlet.java (modified) (25 diffs)

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

@@ -6 +6 @@
   <classpathentry kind="lib" path="lib/compile/json_simple-1.1.jar"/>
   <classpathentry kind="lib" path="lib/compile/jdom-1.1.2.jar"/>
-  <classpathentry kind="lib" path="lib/compile/base-core-3.1.0.jar"/>
-  <classpathentry kind="lib" path="lib/compile/base-webclient-3.1.0.jar"/>
-  <classpathentry kind="lib" path="lib/compile/base-webservices-client-3.1.0.jar"/>
+  <classpathentry kind="lib" path="lib/compile/base-core-3.2.0.jar"/>
+  <classpathentry kind="lib" path="lib/compile/base-webclient-3.2.0.jar"/>
+  <classpathentry kind="lib" path="lib/compile/base-webservices-client-3.2.0.jar"/>
   <classpathentry kind="output" path=".build"/>
 </classpath>

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

@@ -7 +7 @@
       and samples.
     </description>
-    <version>2.9-dev</version>
-    <min-base-version>3.1.0</min-base-version>
+    <version>2.10-dev</version>
+    <min-base-version>3.2.0</min-base-version>
     <copyright>BASE development team</copyright>
     <email>basedb-users@lists.sourceforge.net</email>

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

@@ -1 +1 @@
 == Requirements ==
 
- 1. BASE 3.1 or later.
+ 1. BASE 3.2 or later.
  
 == Introduction ==

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

@@ -10 +10 @@
   <!-- variables used -->
   <property name="name" value="reggie" />
-  <property name="version" value="2.9-dev" />
+  <property name="version" value="2.10-dev" />
   <property name="src" location="src" description="Location of source files" />
   <property name="build" location="build" description="Location of compiled files" />
@@ -22 +22 @@
   <property name="javac.encoding" value="UTF-8" />
   <property name="depend.base-version" 
-    value="3.1.0" 
+    value="3.2.0" 
     description="The BASE version that this project depends on."
   />

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

@@ -41 +41 @@
   url += '&time=' + frm.time.value;
   url += '&exportSubtype='+(frm.exportSubtype.checked ? 1 : 0);
+  url += '&exportPatientId='+(frm.exportPatientId.checked ? 1 : 0);
   if (preview) 
   {
@@ -72 +73 @@
     {
       var allLines = request.responseText.split('\n');
-      var numLines = allLines.length - 1;
-      
+      var numCases = allLines.length - 2; // First line is a header line
+      
+      var html = '<tr><th>'+allLines[0].replace(/\t/g, '</th><th>')+'</th></tr>';
       // Check last column for the 'Consent' value. All should be 'YES' for the export to be ok.
       var numNoConsent = 0;
       var numMissingConsent = 0;
-      for (var i = 0 ; i < numLines; i++)
+      for (var i = 1 ; i <= numCases; i++)
       {
         var line = allLines[i];
-        var lastColIdx = line.lastIndexOf('\t');
-        var lastCol = line.substr(lastColIdx+1);
-        
-        if (lastCol != 'YES')
+        var cols = line.split(/\t/);
+        var consent = cols[cols.length-1];
+        var rowClass = '';
+        if (consent != 'YES')
         {
-          if (lastCol == 'MISSING')
+          rowClass = 'consent-warning';
+          if (consent == 'MISSING')
           {
             numMissingConsent++;
@@ -93 +96 @@
             numNoConsent++;
           }
-          allLines[i] = '<span class="consent-warning">'+line+'</span>';
         }
+        html += '<tr class="'+rowClass+'"><td>'+cols.join('</td><td>')+'</td></tr>';
       }
       
@@ -105 +108 @@
       }
       
-      previewTitle.innerHTML = 'Operation dates - ' + frm.time[frm.time.selectedIndex].text + ' (' + numLines + ')';
-      previewList.innerHTML = allLines.join('\n');
+      previewTitle.innerHTML = 'Operation dates - ' + frm.time[frm.time.selectedIndex].text + ' (' + numCases + ')';
+      previewList.innerHTML = '<table>'+html+'</table>';
       Main.show('previewWrapper');
     }
@@ -128 +131 @@
 {
   position: absolute;
-  top: 9em;
+  top: 11em;
   bottom: 1em;
   left: 20px;
@@ -155 +158 @@
 }
 
+#previewList th
+{
+  border-bottom: 1px dotted #A0A0A0;
+}
+
+#previewList td, #previewList th
+{
+  text-align: left;
+  padding-right: 2em;
+  vertical-align: bottom;
+}
+
 .consent-warning
 {
-  font-weight: bold;
   color: #A00000;
   background-color: #F8F8E8;
 }
 
-.consent-warning:after
-{
-  content: url('images/warning_small.png');
-  vertical-align: middle;
+.consent-warning td:last-child
+{
+  background-image: url('images/warning_small.png');
+  background-position: 95% 50%;
+  background-repeat: no-repeat;
 }
 
@@ -229 +244 @@
       </tr>
       
-      <tr>
+      <tr style="vertical-align: top;">
         <td class="prompt">Optional columns</td>
         <td class="input">
           <input type="checkbox" name="exportSubtype" value="1" id="exportSubtype">
-          <label for="exportSubtype">Specimen/NoSpecimen</label>
+          <label for="exportSubtype">Specimen/NoSpecimen</label><br>
+          <input type="checkbox" name="exportPatientId" value="1" id="exportPatientId">
+          <label for="exportPatientId">Patient ID</label>
         </td>
         <td class="help"><span id="subtype.message" class="message" style="display: none;"></span></td>

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

@@ -271 +271 @@
             <li>Sample count report</li> 
             <li>Consent count report</li> 
+            <li>Patient count report</li> 
             </ul>
           </dd>

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

@@ -63 +63 @@
     var frm = document.forms['reggie'];
     frm.reporttype.disabled = true;
+    // Hide sample type pop-up menu
+    document.getElementById("sampleTypeSubSection01").style.display = 'none';
+    document.getElementById("sampleTypeSubSection02").style.display = 'none';
+    document.getElementById("sampleTypeSubSection04").style.display = 'none';
     if (frm.reporttype[frm.reporttype.selectedIndex].value == 'samplecount')
     {
-      Main.show('sampleCountSection');
+      // Set item name for report period text
+      document.getElementById("items01").innerHTML="tubes";
+      // Set item name for report time step text
+      document.getElementById("items02").innerHTML="samples";
+      document.getElementById("items03").innerHTML="samples";
+      document.getElementById("items04").innerHTML="samples";
+      document.getElementById("items05").innerHTML="samples";
+      // Show view type pop-up menu
+      document.getElementById("viewTypeSubSection01").style.display = 'block';
+      document.getElementById("viewTypeSubSection02").style.display = 'block';
+      document.getElementById("viewTypeSubSection04").style.display = 'block';
+      // Show sample type pop-up menu
+      document.getElementById("sampleTypeSubSection01").style.display = 'block';
+      document.getElementById("sampleTypeSubSection02").style.display = 'block';
+      document.getElementById("sampleTypeSubSection04").style.display = 'block';
     }
     else if (frm.reporttype[frm.reporttype.selectedIndex].value == 'consentcount')
     {
-      Main.show('consentCountSection');
-    }
+      // 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';
+    }
+    else if (frm.reporttype[frm.reporttype.selectedIndex].value == 'patientcount')
+    {
+      // Set item name for report period text
+      document.getElementById("items01").innerHTML="patients";
+      // Set item name for report time step text
+      document.getElementById("items02").innerHTML="patients";
+      document.getElementById("items03").innerHTML="patients";
+      document.getElementById("items04").innerHTML="patients";
+      document.getElementById("items05").innerHTML="patients";
+      // Show view type pop-up menu
+      document.getElementById("viewTypeSubSection01").style.display = 'block';
+      document.getElementById("viewTypeSubSection02").style.display = 'block';
+      document.getElementById("viewTypeSubSection04").style.display = 'block';
+    }
+    Main.show('itemCountSection');
         
     Main.show('gocreate');    
@@ -132 +170 @@
     var cellElement = document.getElementById('reportcell');
     var frm = document.forms['reggie'];   
+    var reportType = frm.reporttype[frm.reporttype.selectedIndex].value;    
     frm.fromdate.disabled = true;
     frm.todate.disabled = true;
-    frm.viewtype.disabled = true;
+    var sampleType = frm.sampletype[frm.sampletype.selectedIndex].value;    
+    if (reportType == 'samplecount')
+    {
+      frm.viewtype.disabled = true;
+      frm.sampletype.disabled = true;
+    }
+    if (reportType == 'patientcount')
+    {
+      frm.viewtype.disabled = true;
+    }
     Main.hide('gocreate');
     Main.show('reportSection');
-    var reportType = frm.reporttype[frm.reporttype.selectedIndex].value;    
     var url = 'SampleReport.servlet?ID=<%=ID%>&cmd='+reportType;    
     
+    if (frm.fromdate.value != null) url += '&fdate='+frm.fromdate.value;
+    if (frm.todate.value != null) url += '&tdate='+frm.todate.value;
     if (reportType == 'samplecount')
     {     
-      if (frm.fromdate.value != null) url += '&fdate='+frm.fromdate.value;
-      if (frm.todate.value != null) url += '&tdate='+frm.todate.value;
       if (frm.viewtype.value != null) url += '&vtype='+frm.viewtype.value;
-    }
+      if (frm.sampletype.value != null) url += '&stype='+frm.sampletype.value;
+    }
+    if (reportType == 'patientcount')
+    {     
+      if (frm.viewtype.value != null) url += '&vtype='+frm.viewtype.value;
+    }
+    
     var request = Ajax.getXmlHttpRequest();
     request.open("GET", url, false);
@@ -164 +217 @@
       if ('samplecount' == reportType)
       {     
-        reportTable = createSampleCountReport(report);
+        reportTable = createItemCountReport(report, reportType);
       }
       else if ('consentcount' == reportType)
       {     
         reportTable = createConsentCountReport(report);
+      }
+      if ('patientcount' == reportType)
+      {     
+        reportTable = createItemCountReport(report, reportType);
       }
     }
@@ -182 +239 @@
     setInnerHTML('reportcell', '');
     cellElement.appendChild(reportTable);
+    // Optional extra tables
+    if ('consentcount' == reportType)
+    {
+      var spacer = document.createElement('text');
+      spacer.innerHTML = "<BR>";
+      cellElement.appendChild(spacer);
+      var unknownDateTable = createConsentCountUnknownDateTable(report);
+      cellElement.appendChild(unknownDateTable);
+    }
+    // Summary list
     var summaryList = document.createElement('ul');
     if (unknownSite == null) unknownSite = 0;
     if (unknownCreation == null) unknownCreation = 0;
     if ('samplecount' == reportType)
-    {     
-      summaryList.appendChild(getListElement(unknownSite + ' specimens registered to unknown sites.'));
-      summaryList.appendChild(getListElement(unknownCreation + ' specimens without creation date. These are included in the \'Total\' column.'));
+    {
+      var samples = 'specimens';
+      if ('blood' == sampleType)
+      {
+        samples = 'blood samples';
+      }
+      summaryList.appendChild(getListElement(unknownSite + ' ' + samples + ' registered to unknown sites.'));
+      summaryList.appendChild(getListElement(unknownCreation + ' ' + samples + ' without creation date. These are included in the \'Total\' column.'));
     }
     else if ('consentcount' == reportType)
@@ -203 +275 @@
       }
       summaryList.appendChild(getListElement(unknownSite + ' consents registered to unknown sites.'));
-      summaryList.appendChild(getListElement(unknownCreation + ' consents without known date.'));
+      summaryList.appendChild(getListElement(unknownCreation + ' consents without known date. These are included in the \'Total\' column.'));
       summaryList.appendChild(getListElement(numDuplicates + ' duplicates ignored.'));
 
@@ -215 +287 @@
       summaryList.appendChild(getListElement(patientsWithMultipleDatesText));
     }
+    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.'));
+    }
     cellElement.appendChild(summaryList);
     if ('consentcount' == reportType)
@@ -225 +302 @@
   }
   
-  function createSampleCountReport(report)
+  function createItemCountReport(report, reportType)
   {
     var reportTable = getReportTable();
@@ -254 +331 @@
     
     var viewType = report.viewType;   
+    var sampleType = report.sampleType;
   
     var headerRow = document.createElement('tr');   
@@ -259 +337 @@
     var columnHeaderRow = document.createElement('tr');
     
-    var headerText = '# Specimen by ';
+    var headerText = '# Items by ';
+    if ('samplecount' == reportType)
+    {
+      headerText = '# Specimens by ';
+      if ('blood' == sampleType)
+      {
+        headerText = '# Blood samples by ';
+      }
+    }
+    else if ('patientcount' == reportType)
+    {
+      headerText = '# Patients by ';
+    }
     if (viewType == 'WEEK')
     { 
@@ -280 +370 @@
     else if (viewType == 'QUARTER')
     {
-      //First year
+      // First year (from start quarter to end of year)
       numCols = 4 - Math.floor(periodStartDate.getMonth()/3);
+      // Last year (from start of year to end quarter) 
       numCols += Math.floor(endDate.getMonth()/3)+1;
+      // If first and last year is the same, subtract 4 quarters
+      if (endDate.getFullYear() - periodStartDate.getFullYear() == 0)
+      {
+        numCols -= 4;
+      }
+      // Full years between start and end dates
       if((endDate.getFullYear() - periodStartDate.getFullYear()) > 1)
       {
@@ -350 +447 @@
       headerText += latestDate.getDate();
     }   
-    headerRow.appendChild(getTableCellElement(headerText, 'reportheader', (numCols+4)));
+    headerRow.appendChild(getTableCellElement(headerText, 'reportheader', (numCols+5)));
     
     // Sub headers
@@ -356 +453 @@
     if (viewType != 'YEAR')
     {
-      subHeaderRowYear.appendChild(getTableCellElement('', 'reportsubheader', 2));
+      subHeaderRowYear.appendChild(getTableCellElement('', 'reportsubheader', 3));
       addYearSubHeaders(periodStartDate, endDate, subHeaderRowYear, viewType);      
       subHeaderRowYear.appendChild(getTableCellElement('', 'reportsubheader', 2));
@@ -364 +461 @@
     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);  
     
     if (viewType == 'MONTH') addMonthColumnHeaders(columnHeaderRow, periodStartDate);
@@ -387 +486 @@
     var sitesCombinedRow = document.createElement('tr');
     sitesCombinedRow.appendChild(getTableCellElement('Sites combined', 'colsummary'));
-    sitesCombinedRow.appendChild(getTableCellElement('', 'colsummary'));
+    sitesCombinedRow.appendChild(getTableCellElement('', 'colsummary', 2));
     // Get combined numbers for all sites for each period
     var statistics = report.statistics;
@@ -396 +495 @@
     {
       key = sortedKeyArray[arrayIndex];
-      var data = getJSONData(sitesCombined, key);
+      var data = getJSONData(sitesCombined, key, 0);
       // Add entry with sample sum for site for selected time period
       sitesCombinedRow.appendChild(getTableCellElement(data,'colsummary'));
     }
     // Get total number of samples for site for the selected time period
-    var sum = statistics.sumKey;
+    var sum = getJSONData(statistics, 'sumKey', 0);
     // Add entry with total number of samples for site for the selected time period
     sitesCombinedRow.appendChild(getTableCellElement(sum, 'colsummary'));
     // Get total number of samples for all sites, regardless of creation date
-    var total = statistics.totalKey;
+    var total = getJSONData(statistics, 'totalKey', 0);
     // Add entry with total number of samples for all sites, regardless of creation date
     sitesCombinedRow.appendChild(getTableCellElement(total, 'colsummary'));
@@ -416 +515 @@
   {
     var reportTable = getReportTable();
-/*
     var sdString = report.beginDate;
     var edString = report.endDate;
+/*
     var psdString = report.periodBeginDate;
+*/
     var ldString = report.latestDate;
     var startDate = new Date();
@@ -429 +529 @@
     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)
@@ -441 +543 @@
       latestDate.setDate(ldString.substr(6));
     }   
-    
+
+/*    
     var viewType = report.viewType; 
 */  
@@ -449 +552 @@
     var columnHeaderRow = document.createElement('tr');
     
-    var numCols = 8;
+    var numCols = 5;
     var numDecimals = 0;
     var headerText = '# Consent forms of different types for cases and blood samples';
-    headerRow.appendChild(getTableCellElement(headerText, 'reportheader', (numCols+3)));
+    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+5)));
     
     // Subheader    
-    subHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
-    subHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
-    
-    //subHeaderRow.appendChild(getTableCellElement('Yes', 'reportsubheader'));
-    subHeaderRow.appendChild(getTableCellElement('Yes', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('', 'reportsubheader', 3));
+    
     subHeaderRow.appendChild(getTableCellElement('Yes', 'reportsubheader'));
     subHeaderRow.appendChild(getTableCellElement('Yes', 'reportsubheader'));
     subHeaderRow.appendChild(getTableCellElement('No', 'reportsubheader'));
-    subHeaderRow.appendChild(getTableCellElement('No', 'reportsubheader'));
     subHeaderRow.appendChild(getTableCellElement('Not asked', 'reportsubheader'));
-    subHeaderRow.appendChild(getTableCellElement('Not asked', 'reportsubheader'));
-    //subHeaderRow.appendChild(getTableCellElement('Other', 'reportsubheader'));
-    subHeaderRow.appendChild(getTableCellElement('Missing', 'reportsubheader'));
-    subHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
-    //subHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Unknown date', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('', 'reportsubheader', 2));
 
     // 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(getTableCellElement('Yes', 'reportsubheader'));
-    columnHeaderRow.appendChild(getTableCellElement('date, PAT#', 'reportsubheader'));
-    columnHeaderRow.appendChild(getTableCellElement('date, no PAT#', 'reportsubheader'));
-    columnHeaderRow.appendChild(getTableCellElement('no date', 'reportsubheader'));
-    columnHeaderRow.appendChild(getTableCellElement('date', 'reportsubheader'));
-    columnHeaderRow.appendChild(getTableCellElement('no date', 'reportsubheader'));
-    columnHeaderRow.appendChild(getTableCellElement('date', 'reportsubheader'));
-    columnHeaderRow.appendChild(getTableCellElement('no date', 'reportsubheader'));
-    //columnHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
+    columnHeaderRow.appendChild(latestDateHeader);  
+    
+    columnHeaderRow.appendChild(getTableCellElement('(has PAT#)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('(no PAT#)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('(has date)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('(has date)', 'reportsubheader'));
     columnHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
     columnHeaderRow.appendChild(getTableCellElement('Sum', 'reportsubheader'));
-    //columnHeaderRow.appendChild(getTableCellElement('Total', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('Total', 'reportsubheader'));
 
     // Build table      
@@ -501 +602 @@
     var sitesCombinedRow = document.createElement('tr');
     sitesCombinedRow.appendChild(getTableCellElement('Sites combined', 'colsummary'));
-    sitesCombinedRow.appendChild(getTableCellElement('', '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)
+    {
+      data = getJSONDataWithPercent(sitesCombined, 'yesPatient', sumKey, numDecimals);
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONDataWithPercent(sitesCombined, 'yesNoPatient', sumKey, numDecimals);
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONDataWithPercent(sitesCombined, 'no', sumKey, numDecimals);
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONDataWithPercent(sitesCombined, 'notAsked', sumKey, numDecimals);
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+      data = getJSONDataWithPercent(sitesCombined, noDateKey, sumKey, numDecimals);
+      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+    }
+    // Add entry with total number of consents with chosen restrictions
+    data = getJSONData(sitesCombined, sumKey, 0);
+    sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+    // Add entry with total number of consents, regardless of restrictions
+    var totalKey = 'totalKey';
+    data = getJSONData(sitesCombined, totalKey, 0);
+    sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
+    reportTable.appendChild(sitesCombinedRow);  
+
+    return reportTable;
+  }
+  
+  function createConsentCountUnknownDateTable(report)
+  {
+    var reportTable = getReportTable();
+    var headerRow = document.createElement('tr');   
+    var subHeaderRow = document.createElement('tr');
+    var columnHeaderRow = document.createElement('tr');
+    
+    var numCols = 4;
+    var numDecimals = 0;
+    var headerText = '# Consent forms of different types for cases and blood samples, unknown consent date';
+    headerRow.appendChild(getTableCellElement(headerText, 'reportheader', (numCols+5)));
+    
+    // Subheader    
+    subHeaderRow.appendChild(getTableCellElement('', 'reportsubheader', 3));
+    
+    subHeaderRow.appendChild(getTableCellElement('Yes', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('No', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Not asked', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('Missing', 'reportsubheader'));
+    subHeaderRow.appendChild(getTableCellElement('', 'reportsubheader', 2));
+
+    // 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('(no date)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('(no date)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('(no date)', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('Sum', 'reportsubheader'));
+    columnHeaderRow.appendChild(getTableCellElement('Total', 'reportsubheader'));
+
+    // Build table      
+    reportTable.appendChild(headerRow);
+    reportTable.appendChild(subHeaderRow);
+    reportTable.appendChild(columnHeaderRow);
+          
+    // Data rows      
+    addDataRowsToConsentTableUnknownDate(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 sumKey = 'sumKey';
@@ -508 +687 @@
     if (sitesCombined != null)
     {
-      //data = getJSONDataRightPadded(sitesCombined, 'yes', sumKey, numDecimals);
-      //sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
-      data = getJSONDataWithPercent(sitesCombined, 'yesPatient', sumKey, numDecimals);
-      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
-      data = getJSONDataWithPercent(sitesCombined, 'yesNoPatient', sumKey, numDecimals);
-      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
       data = getJSONDataWithPercent(sitesCombined, 'yesNoDate', sumKey, numDecimals);
-      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
-      data = getJSONDataWithPercent(sitesCombined, 'no', sumKey, numDecimals);
       sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
       data = getJSONDataWithPercent(sitesCombined, 'noNoDate', sumKey, numDecimals);
       sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
-      data = getJSONDataWithPercent(sitesCombined, 'notAsked', sumKey, numDecimals);
-      sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
       data = getJSONDataWithPercent(sitesCombined, 'notAskedNoDate', sumKey, numDecimals);
       sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
-      //data = getJSONDataWithPercent(sitesCombined, 'other', sumKey, numDecimals);
-      //sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
       data = getJSONDataWithPercent(sitesCombined, 'missing', sumKey, numDecimals);
       sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
     }
     // Add entry with total number of consents with chosen restrictions
-    data = getJSONData(sitesCombined, sumKey);
+    var noDateKey = 'noDate';
+    data = getJSONData(sitesCombined, noDateKey, 0);
     sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
-/*
     // Add entry with total number of consents, regardless of restrictions
-    data = getJSONData(sitesCombined, totalKey);
+    var totalKey = 'totalKey';
+    data = getJSONData(sitesCombined, totalKey, 0);
     sitesCombinedRow.appendChild(getTableCellElement(data, 'colsummary'));
-*/
     reportTable.appendChild(sitesCombinedRow);  
 
@@ -542 +709 @@
   }
   
+  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 createConsentTablePatientsWithMultipleDates(report)
   {
@@ -617 +797 @@
     unknownCreation = statistics.noDate;
     unknownSite = statistics.unknownSite;
-    for (namePrefix in sites)
-    {
+    var siteOrderList = report.siteOrderListKey;
+    for (var siteOrderIndex in siteOrderList)
+    {
+      var namePrefix = siteOrderList[siteOrderIndex];   
       if (!sites.hasOwnProperty(namePrefix)) continue;        
       var site = sites[namePrefix];
@@ -628 +810 @@
       
       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, 'yes', sumKey, numDecimals);
-        //tableRow.appendChild(getTableCellElement(data, 'reportdata'));
         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, 'no', sumKey, numDecimals);
         tableRow.appendChild(getTableCellElement(data, 'reportdata'));
         data = getJSONDataWithPercent(siteData, 'noNoDate', sumKey, numDecimals);
         tableRow.appendChild(getTableCellElement(data, 'reportdata'));
-        data = getJSONDataWithPercent(siteData, 'notAsked', sumKey, numDecimals);
-        tableRow.appendChild(getTableCellElement(data, 'reportdata'));
         data = getJSONDataWithPercent(siteData, 'notAskedNoDate', sumKey, numDecimals);
         tableRow.appendChild(getTableCellElement(data, 'reportdata'));
-        //data = getJSONDataWithPercent(siteData, 'other', 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 = 0;
-        if (siteData != null)
-        {
-          if (siteData[sumKey] != null)
-          {
-            siteSum = siteData[sumKey];
-          }
-        }
+        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 = 0;
-      if (siteData != null)
-      {
-        var totalKey = 'totalKey';
-        if (siteData[totalKey] != null)
-        {
-          siteTotal = siteData[totalKey];
-        }
-      }
+      var siteTotal = getJSONData(siteData, totalKey, 0);
       tableRow.appendChild(getTableCellElement(siteTotal, 'rowsummary'));
-*/
       reportTable.appendChild(tableRow);
     }
@@ -718 +935 @@
   function getJSONData(jsonObject, key)
   {
-    var data = '';
+    var data = getJSONData(jsonObject, key, '');
+    return data;
+  }
+
+  function getJSONData(jsonObject, key, defaultChoice)
+  {
+    var data = defaultChoice;
     if (jsonObject != null)
     {
@@ -726 +949 @@
       }
     }
+    /*
     else
     {
       data = 'jsonObject==null';
     }
+    */
     return data;
   }
@@ -885 +1110 @@
     unknownCreation = statistics.noDate;
     unknownSite = statistics.unknownSite;
-    for (namePrefix in sites)
-    {
-      if (!sites.hasOwnProperty(namePrefix)) continue;        
+    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 siteName = site.name;   
       var year = site.startDate.substr(0,4);
       var month = site.startDate.substr(5,2);
@@ -895 +1122 @@
       var siteStartDate = new Date(year, month-1, date);
       
-      var siteData = statistics[namePrefix];      
+      var siteData = statistics[namePrefix];
+      var siteLatestDate = siteData['latestDateKey'];
+      var siteLatestDateStr = '????-??-??';
+      if (siteLatestDate != null)
+      {
+        var siteLatestDateYear = siteLatestDate.substr(0,4);
+        var siteLatestDateMonth = siteLatestDate.substr(4,2);
+        var siteLatestDateDate = siteLatestDate.substr(6,2);
+        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');
       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 columnCounter = 0;
@@ -1140 +1383 @@
                 <option value="samplecount" selected="yes">Sample count report</option>
                 <option value="consentcount">Consent count report</option>
+                <option value="patientcount">Patient count report</option>
               </select>
             </td>
@@ -1153 +1397 @@
       </table>
       
-      <div id="sampleCountSection" style="display:none;">
+      <div id="itemCountSection" style="display:none;">
         <p></p>
         <!-- 2. Report parameters-->
@@ -1173 +1417 @@
               <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 tubes.<br>
+                Define which period the report should cover. Empty fields will include all <text id="items01">items</text>.<br>
               </td>
             </tr> 
-            <tr>          
-              <td valign="top" class="prompt">View type</td>
+            <tr>
+              <td valign="top" class="prompt">
+                <div id="viewTypeSubSection01" style="display:none;">
+                  View type
+                </div>
+              </td>
               <td valign="top" class="input">
-                <select name="viewtype">
-                  <option value="AUTO" selected="yes">Auto</option>
-                  <option value="WEEK">Week</option>
-                  <option value="MONTH">Month</option>
-                  <option value="QUARTER">Quarter</option>
-                  <option value="YEAR">Year</option>
-                </select>
+                <div id="viewTypeSubSection02" style="display:none;">
+                  <select name="viewtype">
+                    <option value="AUTO" selected="yes">Auto</option>
+                    <option value="WEEK">Week</option>
+                    <option value="MONTH">Month</option>
+                    <option value="QUARTER">Quarter</option>
+                    <option value="YEAR">Year</option>
+                  </select>
+                </div>
               </td>
               <td valign="top" class="status" id="displayViewType.status"></td>
               <td class="help">
-                <span id="displayViewType.message" class="message" style="display: none;"></span>
-                Auto will adjust the report depending on the size of the period.
-                <ul>
-                  <li>Period shorter then 3 months - specimens per week</li>
-                  <li>Period shorter then 13 months - specimens per month</li>
-                  <li>Period shorter then 3 year - specimens per quarter</li>
-                  <li>Period is 3 year or greater - specimens per year</li>
-                </ul>                 
+                <div id="viewTypeSubSection04" style="display:none;">
+                  <span id="displayViewType.message" class="message" style="display: none;"></span>
+                  Auto will adjust the report depending on the size of the period.
+                  <ul>
+                    <li>Period shorter than 3 months - <text id="items02">items</text> per week</li>
+                    <li>Period shorter than 13 months - <text id="items03">items</text> per month</li>
+                    <li>Period shorter than 3 years - <text id="items04">items</text> per quarter</li>
+                    <li>Period is 3 years or greater - <text id="items05">items</text> per year</li>
+                  </ul>                 
+                </div>
               </td>
             </tr>
-            </table>
-          </td>
-        </tr>
-        </table>
-      </div>
-      
-      <div id="consentCountSection" style="display:none;">
-        <p></p>
-        <!-- 2. Report parameters-->
-        <table border="0" cellspacing="0" cellpadding="0" class="stepform">
-        <tr>
-          <td rowspan="3" class="stepno">2</td>
-          <td class="steptitle">Report parameters</td>
-        </tr>
-        <tr>
-          <td class="stepfields">
-            <table border="0" cellspacing="0" cellpadding="0" width="100%">           
             <tr>
-              <td valign="top" class="prompt">No report parameters</td>
+              <td valign="top" class="prompt">
+                <div id="sampleTypeSubSection01" style="display:none;">
+                  Sample type
+                </div>
+              </td>
               <td valign="top" class="input">
+                <div id="sampleTypeSubSection02" style="display:none;">
+                  <select name="sampletype">
+                    <option value="specimen" selected="yes">Specimen</option>
+                    <option value="blood">Blood</option>
+                  </select>
+                </div>
               </td>
-              <td valign="top" class="status" id="displayInterval.status"></td>
+              <td valign="top" class="status" id="displaySampleType.status"></td>
               <td class="help">
-                <span id="displayInterval.message" class="message" style="display: none;"></span>
-                Consent report will be generated irrespective of date for consent.<br>
+                <div id="sampleTypeSubSection04" style="display:none;">
+                  <span id="displaySampleType.message" class="message" style="display: none;"></span>
+                  Select sample type for report.
+                </div>
               </td>
-            </tr> 
+            </tr>
             </table>
           </td>

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 = "2.9-dev";
+  public static final String VERSION = "2.10-dev";
 
   

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

@@ -20 +20 @@
   public static final Site LUND         = new Site("11", "Lund", "2010-11-10", true);
   public static final Site HELSINGBORG  = new Site("22", "Helsingborg", "2010-11-01", true);
-  public static final Site HALMSTAD     = new Site("33", "Halmstad", "2010-10-01", false);
+  public static final Site HALMSTAD     = new Site("33", "Halmstad", "2010-10-01", true);
   public static final Site KRISTIANSTAD = new Site("44", "Kristianstad", "2010-09-15", true);
-  public static final Site KARLSKRONA   = new Site("55", "Karlskrona", "2010-10-04", false);
-  public static final Site VÄXJÖ        = new Site("66", "Växjö", "2010-10-01", false);
+  public static final Site KARLSKRONA   = new Site("55", "Karlskrona", "2010-10-04", true);
+  public static final Site VÄXJÖ        = new Site("66", "Växjö", "2010-10-01", true);
   public static final Site MALMÖ        = new Site("77", "Malmö", "2010-08-30", true);
   

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

@@ -187 +187 @@
   }
   
-
-  public String getName()
-  {
-    return getSample().getName();
-  }
-  
   /**
     Verify that the patient has given their permission to participate in the

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

@@ -233 +233 @@
     
   }
+  @Override
   protected void end(boolean success)
   {
     this.dc = null;
   }
+  @Override
   protected String getSuccessMessage()
   {

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

@@ -199 +199 @@
     
   }
+  @Override
   protected void end(boolean success)
   {
     this.dc = null;
   }
+  @Override
   protected String getSuccessMessage()
   {

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

@@ -17 +17 @@
 import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.Application;
+import net.sf.basedb.core.BioMaterialEvent;
 import net.sf.basedb.core.BioSource;
 import net.sf.basedb.core.DbControl;
@@ -195 +196 @@
         blood.setItemSubtype(Subtype.BLOOD.load(dc));
         blood.setName(bloodName);
-        blood.getCreationEvent().setSource(patient);
+        BioMaterialEvent creationEvent = blood.getCreationEvent();
+        creationEvent.setSource(patient);
         dc.saveItem(blood);
 
@@ -203 +205 @@
         String bloodSample = Values.getStringOrNull((String)jsonBlood.get("bloodSample"));
         
-        if (samplingDate != null) Annotationtype.BLOOD_SAMPLING_DATETIME.setAnnotationValue(dc, blood, samplingDate);
-        if (freezerDate != null) Annotationtype.BLOOD_FREEZER_DATETIME.setAnnotationValue(dc, blood, freezerDate);
+        creationEvent.setEventDate(samplingDate);
+        Annotationtype.BLOOD_SAMPLING_DATETIME.setAnnotationValue(dc, blood, samplingDate);
+        Annotationtype.BLOOD_FREEZER_DATETIME.setAnnotationValue(dc, blood, freezerDate);
         Annotationtype.BLOOD_SERUM.setAnnotationValue(dc, blood, jsonBlood.get("serum"));
         Annotationtype.BLOOD_SAMPLE.setAnnotationValue(dc, blood, bloodSample);
@@ -237 +240 @@
         String bloodSample = Values.getStringOrNull((String)jsonBlood.get("bloodSample"));
         
-        if (samplingDate != null) Annotationtype.BLOOD_SAMPLING_DATETIME.setAnnotationValue(dc, blood, samplingDate);
-        if (freezerDate != null) Annotationtype.BLOOD_FREEZER_DATETIME.setAnnotationValue(dc, blood, freezerDate);
+        blood.getCreationEvent().setEventDate(samplingDate);
+        
+        Annotationtype.BLOOD_SAMPLING_DATETIME.setAnnotationValue(dc, blood, samplingDate);
+        Annotationtype.BLOOD_FREEZER_DATETIME.setAnnotationValue(dc, blood, freezerDate);
         Annotationtype.BLOOD_SERUM.setAnnotationValue(dc, blood, jsonBlood.get("serum"));
         Annotationtype.BLOOD_SAMPLE.setAnnotationValue(dc, blood, bloodSample);

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

@@ -60 +60 @@
       {
         boolean exportSubtype = Values.getBoolean(req.getParameter("exportSubtype"));
+        boolean exportPatientId = Values.getBoolean(req.getParameter("exportPatientId"));
         
         // This can be any time point in the desired month/year
@@ -142 +143 @@
                   String opDate = dateFormat.format(s.getCreationEvent().getEventDate());
                   String subtype = exportSubtype ? s.getItemSubtype().getName() : null;
+                  String patientId = exportPatientId ? patient.getName() : null;
                   String caseName = caseNamePattern.matcher(s.getName()).replaceFirst("");
-                  opDates.add(new PersonalOpDate(pnr, opDate, site, laterality, subtype, caseName, consent));
+                  opDates.add(new PersonalOpDate(pnr, opDate, site, laterality, subtype, caseName, consent, patientId));
                 }
               }
@@ -155 +157 @@
         resp.setCharacterEncoding("UTF-8");
         PrintWriter os = resp.getWriter();
-        
+        os.write("PersonalNr\tScanBId\tOpDate\tLaterality\tSite");
+        if (exportSubtype) os.write("\tSpecimen");
+        if (exportPatientId) os.write("\tPatientId");
+        os.write("\tConsent\n");
+
         for (PersonalOpDate pop : opDates)
         {
@@ -188 +194 @@
     private final String caseName;
     private final String consent;
-    
-    PersonalOpDate(String pnr, String opDate, Site site, String laterality, String subtype, String caseName, String consent)
+    private final String patientId;
+    
+    PersonalOpDate(String pnr, String opDate, Site site, String laterality, String subtype, String caseName, String consent, String patientId)
     {
       this.pnr = pnr;
@@ -198 +205 @@
       this.caseName = caseName;
       this.consent = consent;
+      this.patientId = patientId;
     }
     
@@ -203 +211 @@
     public String toString()
     {
-      return pnr + "\t" + caseName + "\t" + opDate + "\t" + 
-          (laterality == null ? "" : laterality) + "\t" + 
-          site.getName() + 
-          (subtype==null ? "" : "\t" + subtype) + "\t" +
-          (consent == null ? "MISSING" : consent.toUpperCase());
+      return pnr + "\t" + caseName + "\t" + opDate + 
+          "\t" + (laterality == null ? "" : laterality) + 
+          "\t" + site.getName() + 
+          (subtype==null ? "" : "\t" + subtype) + 
+          (patientId==null ? "" : "\t"+patientId)+
+          "\t" + (consent == null ? "MISSING" : consent.toUpperCase());
     }
 

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

@@ -10 +10 @@
 import java.util.List;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.Set;
+import java.util.TreeMap;
 
 import javax.servlet.ServletException;
@@ -23 +25 @@
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.ItemResultIterator;
+import net.sf.basedb.core.ItemSubtype;
+import net.sf.basedb.core.MeasuredBioMaterial;
 import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.SessionControl;
@@ -53 +57 @@
   private static final int quarterViewLimit= 3;
   
+  private static final String alphabeticalOrder = "ALPHABETICAL_ORDER";
+  private static final String namePrefixOrder = "NAME_PREFIX_ORDER";
+  private static final String startDateOrder = "START_DATE_ORDER";
+  private static final String nameLengthOrder = "NAME_LENGTH_ORDER";
+
   public SampleReportServlet()
   {}
@@ -111 +120 @@
           viewType = getViewType(startDate, endDate);
         }
-
-        json = createSampleCountReport(dc, json, startDate, endDate, viewType);
+        String sampleType = "specimen";
+        String sampleTypeParameter = Values.getString(req.getParameter("stype"), null);
+        if (sampleTypeParameter != null)
+        {
+          sampleType = sampleTypeParameter;
+        }
+
+        json = createSampleCountReport(dc, json, startDate, endDate, viewType, sampleType);
       }
       else if ("consentcount".equals(cmd))
       {       
-        json = createConsentCountReport(dc, json);
+        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 = createConsentCountReport(dc, json, startDate, endDate);
+      }
+      else if ("patientcount".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 viewType = null;
+        String viewTypeParameter = Values.getString(req.getParameter("vtype"), null);
+        if (viewTypeParameter != null && !viewTypeParameter.equals("AUTO"))
+        {
+          viewType = viewTypeParameter;
+        }
+        else
+        {
+          viewType = getViewType(startDate, endDate);
+        }
+
+        json = createPatientCountReport(dc, json, startDate, endDate, viewType);
       }
     }
@@ -134 +212 @@
   }
   
-  private JSONObject createSampleCountReport(DbControl dc, JSONObject json, Date startDate, Date endDate, String viewType)
+  @SuppressWarnings("unchecked")
+  private JSONObject createSampleCountReport(DbControl dc, JSONObject json, Date startDate, Date endDate, String viewType, String sampleType)
     throws ServletException, IOException 
   { 
@@ -143 +222 @@
     ItemQuery<Sample> sampleQuery = Sample.getQuery();
     sampleQuery.joinPermanent(Hql.innerJoin(null, "creationEvent", "ce", true));
-    Subtype.SPECIMEN.addFilter(dc, sampleQuery);
+    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);        
+    // Store samples that should be processed for report table in list 
+    List<Sample> sampleList = new ArrayList<Sample>();
+    while (sampleIterator.hasNext())
+    {
+      Sample s = sampleIterator.next();
+      sampleList.add(s);
+    }
+                  
+    JSONObject jsonStatistics = createJSONStatistics(sampleList.iterator(), startDate, endDate, viewType);
+    jsonReport.put("statistics", jsonStatistics);       
+    if (viewType == null)
+    {
+      viewType = getViewType(startDate, endDate);
+    }
+    DateToStringConverter date2StringConverter = Reggie.CONVERTER_DATE_TO_STRING;
+    Date periodStartDate = calculatePeriodStartDate(startDate, viewType);
+    jsonReport.put("viewType", viewType);
+    jsonReport.put("sampleType", sampleType);
+    jsonReport.put("beginDate", date2StringConverter.convert(startDate));
+    jsonReport.put("endDate", date2StringConverter.convert(endDate));
+    jsonReport.put("periodBeginDate", date2StringConverter.convert(periodStartDate));
+    // 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 createPatientCountReport(DbControl dc, JSONObject json, Date startDate, Date endDate, String viewType)
+    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', or 'Blood' items
+    sampleQuery.restrict(
+      Restrictions.or(
+        Subtype.SPECIMEN.restriction(dc, null),
+        Subtype.NO_SPECIMEN.restriction(dc, null),
+        Subtype.BLOOD.restriction(dc, null)
+      ));
     sampleQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
     sampleQuery.order(Orders.asc(Hql.property("name")));
@@ -150 +288 @@
     ItemResultIterator<Sample> sampleIterator = sampleQuery.iterate(dc);        
                   
-    JSONObject jsonStatistics = createJSONStatistics(sampleIterator, startDate, endDate, viewType);
+    // Store samples that should be processed for report table in list 
+    List<Sample> sampleList = new ArrayList<Sample>();
+    // Create HashMap to keep track of sample with earliest date for each patient
+    HashMap<String, Sample>patientSampleHashMap = new HashMap<String, Sample>();
+    // Create HashMap to keep track of sample with unknown date for each patient
+    HashMap<String, Sample>patientSampleNoDateHashMap = new HashMap<String, Sample>();
+    // Find earliest sample dates for each patient
+    ItemSubtype subtypeBlood = Subtype.BLOOD.load(dc);
+    while (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
+        patient = s.getParent();
+      }
+      else
+      {
+        // The grandparent is the 'Patient' for specimens and no specimens
+        MeasuredBioMaterial parent = (MeasuredBioMaterial) s.getParent();
+        if (parent != null)
+        {
+          patient = parent.getParent();
+        }
+      }
+      if (patient != null)
+      {
+        String patientName = patient.getName();
+        if (creationDate != null)
+        {
+          patientSampleHashMap = updateStringEarliestSampleHashMap(patientSampleHashMap, patientName, s);
+        }
+        else
+        {
+          patientSampleNoDateHashMap.put(patientName, s);
+        }
+      }
+    }
+    // Create list of samples for report
+    // Add sample with earliest date for patient
+    for (String key: patientSampleHashMap.keySet())
+    {
+      if (key != null && !key.equals(""))
+      {
+        Sample s = patientSampleHashMap.get(key);
+        // Include sample in list of samples for report
+        sampleList.add(s);
+      }
+    }
+    // Add sample with unknown date if no sample with date exists for patient
+    for (String key: patientSampleNoDateHashMap.keySet())
+    {
+      if (key != null && !key.equals(""))
+      {
+        // If no sample with date exists for sample, include sample without date
+        if (!patientSampleHashMap.containsKey(key))
+        {
+          Sample s = patientSampleNoDateHashMap.get(key);
+          // Include sample in list of samples for report
+          sampleList.add(s);
+        }
+      }
+    }
+
+    JSONObject jsonStatistics = createJSONStatistics(sampleList.iterator(), startDate, endDate, viewType);
     jsonReport.put("statistics", jsonStatistics);       
     if (viewType == null)
@@ -165 +372 @@
     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;
   }
     
-  private JSONObject createConsentCountReport(DbControl dc, JSONObject json)
+  @SuppressWarnings({ "unchecked", "rawtypes" })
+  private JSONObject createConsentCountReport(DbControl dc, JSONObject json, Date startDate, Date endDate)
       throws ServletException, IOException 
   { 
@@ -207 +418 @@
     String sumKey = "sumKey";
     String totalKey = "totalKey";
+    String latestDateKey = "latestDateKey";
     String noDateKey = "noDate";
     String duplicateKey = "duplicateKey";
@@ -221 +433 @@
     jsonStatistics = initializeJSONSiteData(jsonStatistics, otherKey);
     jsonStatistics = initializeJSONSiteData(jsonStatistics, missingKey);
-    //jsonStatistics = initializeJSONSiteData(jsonStatistics, sumKey);
-    //jsonStatistics = initializeJSONSiteData(jsonStatistics, totalKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, noDateKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, sumKey);
+    jsonStatistics = initializeJSONSiteData(jsonStatistics, totalKey);
     // Initialize combined data to 0 for the different keys
     jsonSitesCombined.put(yesKey, 0);
@@ -234 +447 @@
     jsonSitesCombined.put(otherKey, 0);
     jsonSitesCombined.put(missingKey, 0);
+    jsonSitesCombined.put(noDateKey, 0);
     jsonSitesCombined.put(sumKey, 0);
     jsonSitesCombined.put(totalKey, 0);
@@ -239 +453 @@
     jsonStatistics.put(noDateKey, 0);
     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();
+    // Create HashMap to keep track of latest consent date for each site
+    HashMap<String, Date> sitePrefixDateHashMap = new HashMap<String, Date>();
     while (sampleIterator.hasNext())
     {
       Sample s = sampleIterator.next();
+/*
       BioMaterialEvent creationEvent = s.getCreationEvent();
       Date creationDate = creationEvent.getEventDate();
+*/
               
       Site site = Site.findByCaseName(s.getName()); 
@@ -267 +486 @@
         // Get consent date
         Date consentDate = (Date) Annotationtype.CONSENT_DATE.getAnnotationValue(dc, manager, s);
-        String key = missingKey;
+        String key = null;
         Boolean duplicate = false;
         if (consent != null)
         {
-          if (consent.equals("Yes"))
-          {
-            key = yesKey;
+          if (consentDate != null)
+          {
             // Check if a consent already exists for the same patient and date
-            if (consentDate != null)
+            // The parent is the 'Patient'
+            BioMaterial patient = s.getParent();
+            if (patient != null)
             {
-              // The parent is the 'Patient'
-              BioMaterial patient = s.getParent();
-              if (patient != null)
+              // Store patient ID value
+              jsonPatientnamePatientid = updateJSONItemnameItemid(jsonPatientnamePatientid, patient);
+              String patientName = patient.getName();
+              if (inStringDateSetHashMap(patientDateSetHashMap, patientName, consentDate))
               {
-                // Store patient ID value
-                jsonPatientnamePatientid = updateJSONItemnameItemid(jsonPatientnamePatientid, patient);
-                key = yesPatientKey;
-                String patientName = patient.getName();
-                if (inStringDateSetHashMap(patientDateSetHashMap, patientName, consentDate))
+                duplicate = true;
+              }
+              else
+              {
+                patientDateSetHashMap = updateStringDateSetHashMap(patientDateSetHashMap, patientName, consentDate);
+              }
+            }
+            if ((consentDate.after(startDate) || consentDate.equals(startDate)) &&
+              (consentDate.before(endDate) || consentDate.equals(endDate)))
+            {
+              if (consent.equals("Yes"))
+              {
+                key = yesKey;
+                if (patient != null)
                 {
-                  duplicate = true;
+                  key = yesPatientKey;
                 }
                 else
                 {
-                  patientDateSetHashMap = updateStringDateSetHashMap(patientDateSetHashMap, patientName, consentDate);
+                  key = yesNoPatientKey;
                 }
+              }
+              else if (consent.equals("No"))
+              {
+                key = noKey;
+              }
+              else if (consent.equals("Not asked"))
+              {
+                key = notAskedKey;
               }
               else
               {
-                key = yesNoPatientKey;
+                key = otherKey;
               }
+              // Find out if current consent date is the latest so far.
+              if (latestDate == null || latestDate.before(consentDate)) 
+              {
+                latestDate = consentDate;
+              }
+            }
+          }
+          else
+          {
+            if (consent.equals("Yes"))
+            {
+              key = yesNoDateKey;
+            }
+            else if (consent.equals("No"))
+            {
+              key = noNoDateKey;
+            }
+            else if (consent.equals("Not asked"))
+            {
+              key = notAskedNoDateKey;
             }
             else
             {
-              key = yesNoDateKey;
+              key = otherKey;
             }
           }
-          else if (consent.equals("No"))
-          {
-            key = noKey;
-            // Check if consent date exists
-            if (consentDate == null)
+          // Keep track of latest consent date for site
+          if (consentDate != null)
+          {
+            Date siteLatestDate = sitePrefixDateHashMap.get(site.getPrefix());
+            if (siteLatestDate == null || siteLatestDate.before(consentDate))
             {
-              key = noNoDateKey;
+              sitePrefixDateHashMap.put(site.getPrefix(), consentDate);
             }
           }
-          else if (consent.equals("Not asked"))
-          {
-            key = notAskedKey;
-            // Check if consent date exists
-            if (consentDate == null)
-            {
-              key = notAskedNoDateKey;
-            }
-          }
-          else
-          {
-            key = otherKey;
-          }
+        }
+        else
+        {
+          key = missingKey;
         }
         // Note that items with duplicate == false include missing consent items
         if (!duplicate)
         {
-          // Update consent counters
-          jsonSite = updateJSONObjectCounter(jsonSite, key);
-          jsonSite = updateJSONObjectCounter(jsonSite, sumKey);
-          jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, key);
-          jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, sumKey);
+          if (key != null)
+          {
+            // Update consent counters
+            jsonSite = updateJSONObjectCounter(jsonSite, key);
+            jsonSite = updateJSONObjectCounter(jsonSite, sumKey);
+            jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, key);
+            jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, sumKey);
+          }
           if (consentDate == null)
           {
+            // Include consents with unknown date 
+            jsonSite = updateJSONObjectCounter(jsonSite, noDateKey);
+            jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, noDateKey);
             jsonStatistics = updateJSONObjectCounter(jsonStatistics, noDateKey);
           }
+          // Increase the counter for total consents for the site, regardless of creation date
+          jsonSite = updateJSONObjectCounter(jsonSite, totalKey);
+
+          // Increase the counter for total consents for all sites
+          jsonSitesCombined = updateJSONObjectCounter(jsonSitesCombined, totalKey);
         }
         else
@@ -346 +606 @@
       }
     }
+    // Add latest consent 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));
     // Create JSONObject (patient, dates) for patients with multiple dates
     JSONObject jsonPatientsWithMultipleDates = createJSONPatientsWithMultipleDates(patientDateSetHashMap);
@@ -356 +631 @@
     //
     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;
@@ -381 +664 @@
   }
 
+  @SuppressWarnings({ "unchecked", "rawtypes" })
   private JSONObject updateJSONItemnameItemid(JSONObject jsonObject, BioMaterial item)
   {
@@ -431 +715 @@
   }
 
-  private int numDatesInStringDateSetHashMap(HashMap<String, Set<Date>> stringDateSetHashMap)
-  {
-    int numDates = 0;
-    if (stringDateSetHashMap != null)
-    {
-      Set<String> stringSet = stringDateSetHashMap.keySet();
-      if (stringSet != null)
-      {
-        for (String string: stringSet)
-        {
-          Set<Date> dateSet = stringDateSetHashMap.get(string);
-          if (dateSet != null)
-          {
-            numDates += dateSet.size();
-          }
-        }
-      }
-    }
-    return numDates;
-  }
-
-  private Set<String> keysWithMultipleDates(HashMap<String, Set<Date>> stringDateSetHashMap)
-  {
-    Set<String> keysWithMultipleDatesSet = new HashSet<String>();
-    if (stringDateSetHashMap != null)
-    {
-      Set<String> stringSet = stringDateSetHashMap.keySet();
-      if (stringSet != null)
-      {
-        for (String string: stringSet)
-        {
-          Set<Date> dateSet = stringDateSetHashMap.get(string);
-          if (dateSet != null && dateSet.size() > 1)
-          {
-            keysWithMultipleDatesSet.add(string);
-          }
-        }
-      }
-    }
-    return keysWithMultipleDatesSet;
-  }
-
+  private HashMap<String, Sample> updateStringEarliestSampleHashMap(HashMap<String, Sample> stringSampleHashMap, String string, Sample sample)
+  {
+    if (stringSampleHashMap == null)
+    {
+      stringSampleHashMap = new HashMap<String, Sample>();
+    }
+    if (string != null && !string.equals(""))
+    {
+      // Store the sample with the earliest date for the item defined by string
+      Sample storedSample = stringSampleHashMap.get(string);
+      Date sampleDate = null;
+      Date storedSampleDate = null;
+      if (sample != null)
+      {
+        BioMaterialEvent creationEvent = sample.getCreationEvent();
+        sampleDate = creationEvent.getEventDate();
+      }
+      if (storedSample != null)
+      {
+        BioMaterialEvent creationEvent = storedSample.getCreationEvent();
+        storedSampleDate = creationEvent.getEventDate();
+      }
+      if (sampleDate != null)
+      {
+        if (storedSampleDate != null)
+        {
+          if (sampleDate.before(storedSampleDate))
+          {
+            // New sample date earlier, store that sample for patient
+            stringSampleHashMap.put(string, sample);
+          }
+        }
+        else
+        {
+          // No stored sample; store new sample for patient
+          stringSampleHashMap.put(string, sample);
+        }
+      }
+    }
+    return stringSampleHashMap;
+  }
+
+  @SuppressWarnings("unchecked")
   private JSONObject createJSONPatientsWithMultipleDates(HashMap<String, Set<Date>> stringDateSetHashMap)
   {
@@ -507 +792 @@
   }
 
-  private JSONObject createJSONStatistics(ItemResultIterator<Sample> sampleIterator, Date startDate, Date endDate, String viewType)
+  @SuppressWarnings("unchecked")
+  private JSONObject createJSONStatistics(Iterator<Sample> sampleIterator, Date startDate, Date endDate, String viewType)
     throws ServletException, IOException 
   { 
@@ -522 +808 @@
     String latestDateKey = "latestDateKey";
     jsonStatistics.put(sitesCombinedKey, jsonSitesCombined);
+    // Create HashMap to keep track of latest sample date for each site
+    HashMap<String, Date> sitePrefixDateHashMap = new HashMap<String, Date>();
     while (sampleIterator.hasNext())
     {
@@ -566 +854 @@
             }
           }
+
+          // Keep track of latest sample date for site
+          Date siteLatestDate = sitePrefixDateHashMap.get(site.getPrefix());
+          if (siteLatestDate == null || siteLatestDate.before(creationDate))
+          {
+            sitePrefixDateHashMap.put(site.getPrefix(), creationDate);
+          }
         }
         else
@@ -580 +875 @@
       }
     }
+    // Add latest sample 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
-    DateToStringConverter date2StringConverter = Reggie.CONVERTER_DATE_TO_STRING;
     jsonStatistics.put(latestDateKey, date2StringConverter.convert(latestDate));
     return jsonStatistics;        
   }
       
+  @SuppressWarnings("unchecked")
   private JSONObject updateJSONObjectCounter(JSONObject jsonObject, String key)
   {
@@ -599 +907 @@
   }
 
+  @SuppressWarnings("unchecked")
   private JSONObject initializeJSONSiteData(JSONObject jsonSiteContainerObject, String key)
   {
@@ -620 +929 @@
   }
 
+  @SuppressWarnings("unchecked")
   private JSONObject initializeJSONPeriodData(JSONObject jsonObject, Date startDate, Date endDate, Date dataStartDate, String viewType)
   {
@@ -644 +954 @@
     }
     return jsonObject;
+  }
+
+  /**
+   *  Creates a JSONObject with order index as key and site prefix as value.
+   *
+   *  @param order String A string indicating desired order (null => alphabetical order)
+   *  @return String A JSONObject with sort index as key and site prefix as value. 
+   */
+  @SuppressWarnings("unchecked")
+  private JSONObject createJSONSiteOrderList(String order)
+  {
+    JSONObject jsonSiteOrderList = new JSONObject();
+    List<String> siteOrderedList = createSiteOrderedList(order);
+    for (int i=0; i < siteOrderedList.size(); i++)
+    {
+      String namePrefix = siteOrderedList.get(i);
+      jsonSiteOrderList.put(i, namePrefix);
+    }
+    return jsonSiteOrderList;
+  }
+
+  /**
+   *  Creates a list of site name prefixes sorted after specified order.
+   *
+   *  @param order String A string indicating desired order (null => alphabetical order)
+   *  @return List<String> list of site name prefixes sorted after specified order.
+   */
+  @SuppressWarnings("rawtypes")
+  private List<String> createSiteOrderedList(String order)
+  {
+    if (order == null || order.equals(""))
+    {
+      order = alphabeticalOrder;
+    }
+    TreeMap<Comparable, String> treeMap = new TreeMap<Comparable, String>();
+    for (Site site: Site.getAllSites())
+    {
+      Comparable comparableObject = null;
+      if (order.equals(alphabeticalOrder))
+      {
+        comparableObject = site.getName();
+      }
+      else if (order.equals(namePrefixOrder))
+      {
+        comparableObject = site.getPrefix();
+      }
+      else if (order.equals(startDateOrder))
+      {
+        comparableObject = site.getStartDate();
+      }
+      else if (order.equals(nameLengthOrder))
+      {
+        comparableObject = site.getName().length();
+      }
+      treeMap.put(comparableObject, site.getPrefix());
+    }
+    List<String> list = new ArrayList<String>();
+    for (Comparable key: treeMap.keySet())
+    {
+      list.add(treeMap.get(key));
+    } 
+    return list;
   }
 
@@ -749 +1121 @@
   }
 
+  @SuppressWarnings("unused")
   private List<Date> createSortedPeriodStartDateList(Date startDate, Date endDate, String viewType)
   {