source: extensions/net.sf.basedb.reggie/trunk/resources/reports/case_summary.jsp @ 2098

<%@ page
  pageEncoding="UTF-8"
  session="false"
  import="net.sf.basedb.core.Application"
  import="net.sf.basedb.core.User"
  import="net.sf.basedb.core.Role"
  import="net.sf.basedb.core.Group"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.SessionControl"
  import="net.sf.basedb.core.SystemItems"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.query.Expressions"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.core.query.Restrictions"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
  import="net.sf.basedb.util.Values"
  import="java.util.List"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
<%
final SessionControl sc = Base.getExistingSessionControl(request, true);
final String ID = sc.getId();
final float scale = Base.getScale(sc);
final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
DbControl dc = null;
try
{
  dc = sc.newDbControl();
  final User user = User.getById(dc, sc.getLoggedInUserId());
  
  boolean isAdmin = user.getId() == SystemItems.getId(User.ROOT);
  boolean isPatientCurator = false;
  if (!isAdmin)
  {
    try
    {
      Role admin = Role.getById(dc, SystemItems.getId(Role.ADMINISTRATOR));
      isAdmin = sc.isMemberOf(admin);
    }
    catch (RuntimeException ex)
    {}
  }
  try
  {
    ItemQuery<Group> query = Group.getQuery();
    query.restrict(Restrictions.eq(Hql.property("name"), Expressions.string("PatientCurator")));
    List<Group> result = query.list(dc);
    if (result.size() == 1)
    {
      isPatientCurator = sc.isMemberOf(result.get(0));
    }
  }
  catch (RuntimeException ex)
  {}
  
  final String caseName = request.getParameter("caseName");
  final String pageType = Values.getString(request.getParameter("pageType"), "default");
  
  boolean iframe = "iframe".equals(pageType);
  boolean popup = "popup".equals(pageType);
  boolean fullPage = !iframe && !popup;
%>
<base:page type="<%=pageType %>" >
<base:head scripts="ajax.js" styles="path.css">
  <link rel="stylesheet" type="text/css" href="../css/reggie.css">
  <link rel="stylesheet" type="text/css" href="../css/case_summary.css">
  <script language="JavaScript" src="../reggie.js" type="text/javascript" charset="UTF-8"></script>

<script language="JavaScript">

var debug = false;
var ID = '<%=ID%>';

var TRUNCATE_SIZE = [-1, 30, 20, 15];

// Style the message as a warning message
function asWarning(message)
{
  message = '<span class="warning">' + message + '</span>';
  return message;
}

// Style the message as a 'no information' message
function asNoInfo(message)
{
  message = '<span class="no-info">' + message + '</span>';
  return message;
}

// Generte a 'Missing' warning if the value is missing
function warnIfMissing(value)
{
  var message = value ? value : asWarning('Missing');
  return message;
}

// Style the message as a 'flag information' message
function asFlagInfo(message, icon)
{
  message = '<span class="flag-info">' + message + '&nbsp;' + '<img src="../images/'+icon+'"></span>';
  return message;
}

// Style the message as a 'fail information' message
function asFailInfo(message, icon)
{
  message = '<span class="fail-info">' + message + '&nbsp;' + '<img src="../images/'+icon+'"></span>';
  return message;
}

function asConsent(consent, consentDate)
{
  var warn = !consent || !consentDate;
  var message;
  if (!consent)
  {
    message = 'Missing' + (consentDate ? ', ' + consentDate : '');
  }
  else
  {
    message = consent + ', ' + (consentDate ? consentDate : 'Missing date');
    
  }
  return warn ? asWarning(message) : message
}

function asBioPlateLocation(well)
{
  if (!well) return '';
  var plate = well.bioPlate;
  var text = makeLink('BIOPLATE', plate)  + ' ' + well.location;
  if (plate.storage)
  {
    var storage = plate.storage;
    var tmp = [];
    if (storage.name) tmp[tmp.length] = storage.name;
    if (storage.section) tmp[tmp.length] = 'section: ' +storage.section;
    if (storage.tray) tmp[tmp.length] = 'tray: ' +storage.tray;
    if (storage.position) tmp[tmp.length] = 'position: ' +storage.position;

    text = '<span class="more-info" title="' + tmp.join('; ')+'">' + text + ' </span>';
  }
  return text;
}

// Set the content of the element 'id' to the value
function setValue(id, value)
{
  setInnerHTML(id, value);
}

function truncate(value, maxLength)
{
  if (!value) return value;
  if (maxLength > 2 && value.length > maxLength) 
  {
    var tmp = '<span class="truncated" title="'+value+'">'+value.substring(0, maxLength-2) + '...</span>';
    value = tmp;
  }
  return value;
}

function addColumn(id, value)
{
  var tr = document.getElementById(id);
  var td = document.createElement('td');
  if (tr.hasAddedColumns)
  {
    td.className = 'extra-column';
    tr.childNodes[tr.childNodes.length-1].className += ' fixed-column';
  }
  tr.hasAddedColumns = true;
  if (value != null)
  {
    td.innerHTML = value == '' ? '&nbsp;' : value;
    if (tr.className.indexOf('dynamic-column') >= 0)
    {
      tr.style.display = 'table-row';
    }
  }
  else
  {
    td.innerHTML = '&nbsp;';
  }
  tr.appendChild(td);
}

function makeLink(itemType, item, maxLength)
{
  var link = '';
  if (item)
  {
    var name = truncate(item.name, maxLength);
    if (item.id)
    {
      link = '<span class="link" onclick="Main.itemOnClick(event, ID, \''+itemType+'\', '+item.id+', '+item.editable+')">';
      link += name + '</span>';
    }
    else
    {
      link = name;
    }
  }
  return link;
}

function asFileLink(file, icon)
{
  var link = '';
  if (file)
  {
    link = '<span class="link filelink" onclick="Main.viewFile(ID,'+file.id+')"><img src="../images/'+icon+'"></span>';
  }
  return link;
}

function asCaseList(allCases, mainCase)
{
  var html = '';
  for (var i = 0; i < allCases.length; i++)
  {
    var cse = allCases[i];
    if (html != '') html += ', ';
    if (cse != mainCase)
    {
      html += '<span class="link" onclick="caseSummary(\''+cse + '\')" title="Show summary of case #'+cse+'">'+cse+'</span>';
    }
    else
    {
      html += '<b>' + cse + '</b>';
    }
  }
  return allCases.length > 1 ? html : null;
}

function formatDate(value)
{
  if (!value) return '';
  if (value.length == 8)
  {
    value = value.substr(0, 4) + '-' + value.substr(4, 2) + '-' + value.substr(6, 2);
  }
  return value;
}


function formatDateTime(value, compareToDate)
{
  if (!value) return '';
  if (value.length == 8)
  {
    value = formatDate(value);
  }
  else if (value.length == 13)
  {
    // If the compareToDate is the same day as the 'value' date, skip the date and replace with white-space
    if (compareToDate && value.substr(0, 8) == compareToDate.substr(0, 8))
    {
      value = '<span class="invisible">'+formatDate(value.substr(0, 8)) + '</span> ' + value.substr(9, 2) + ':'+value.substr(11, 2)
    }
    else
    {
      value = formatDate(value.substr(0, 8)) + ' ' + value.substr(9, 2) + ':'+value.substr(11, 2);
    }
  }
  return value;
}

function formatQuantity(value, scale, unit)
{
  var result = '';
  if (value != null)
  {
    if (scale) value = value / scale;
    result = formatNumber(value, unit, 2);
  }
  return result;
}

function init()
{
  var frm = document.forms['reggie'];
  if (frm.caseName) frm.caseName.focus();
  
  var caseName = '<%=HTML.javaScriptEncode(caseName)%>';
  var isAdmin = <%=isAdmin ? "true" : "false"%>;
  var isPatientCurator = <%=isPatientCurator ? "true" : "false"%>;
  
  var url = '../CaseSummary.servlet?ID=<%=ID%>&cmd=GetCaseInfo';
  url += '&caseName=<%=HTML.urlEncode(caseName)%>';
  var request = Ajax.getXmlHttpRequest();
  request.open("GET", url, false); 
  request.send(null);
  
  if (debug) Main.debug(request.responseText);

  var response = JSON.parse(request.responseText);
  if (response.status != 'ok')
  {
    setFatalError(response.message);
    return false;
  }
  
  Main.show('all-info');
  
  var caseInfo = response.caseInfo;
  var site = response.site;
  var consentOk = true;
  
  if (caseInfo)
  {
    consentOk = !caseInfo.consent || caseInfo.consent == 'Yes';
    addColumn('case.name', makeLink('SAMPLE', caseInfo));
    addColumn('case.registrationDate', formatDate(caseInfo.registrationDate));
    addColumn('case.site', site ? site.name : null);
    addColumn('case.consent', asConsent(caseInfo.consent, formatDate(caseInfo.consentDate)));
    addColumn('case.laterality', consentOk ? warnIfMissing(caseInfo.laterality) : null);
    addColumn('case.comment', caseInfo.comment);
  }
  else
  {
    addColumn('case.name', asNoInfo('No case information has been registered'));
    Main.hide('case-details');
  }
  
  var patient = response.patient;
  if (patient)
  {
    if (consentOk)
    {
      addColumn('patient.name', makeLink('BIOSOURCE', patient));
      addColumn('patient.registrationDate', formatDate(patient.registrationDate));
      addColumn('patient.personalNumber', warnIfMissing(patient.personalNumber));
      addColumn('patient.allFirstNames', warnIfMissing(patient.allFirstNames));
      addColumn('patient.familyName', warnIfMissing(patient.familyName));
      addColumn('patient.gender', patient.gender);
      addColumn('patient.allCases', asCaseList(patient.allCases, caseName));
    }
    else
    {
      Main.hide('patient-info');
    }
  }
  else
  {
    addColumn('patient.name', asNoInfo('No patient information has been registered'));
    Main.hide('patient-details');
  }
  
  var blood = consentOk ? response.blood : null;
  if (blood && blood.length > 0)
  {
    for (var i = 0; i < blood.length; i++)
    {
      var b = blood[i];
      addColumn('blood.name', makeLink('SAMPLE', b));
      addColumn('blood.registrationDate', formatDate(b.registrationDate));
      addColumn('blood.consent', asConsent(b.consent, formatDate(b.consentDate)));
      addColumn('blood.bloodSample', b.bloodSample);
      addColumn('blood.samplingDate', warnIfMissing(formatDateTime(b.samplingDate)));
      addColumn('blood.freezerDate', warnIfMissing(formatDateTime(b.freezerDate, b.samplingDate)));
      addColumn('blood.serum', b.serum);
      addColumn('blood.comment', b.comment);
    }
  }
  else
  {
    if (consentOk)
    {
      addColumn('blood.name', asNoInfo('No blood information has been registered'));
      Main.hide('blood-details');
    }
    else
    {
      Main.hide('blood-info');
    }
  }
  
  var specimen = consentOk ? response.specimen : null;
  var noSpecimen = consentOk ? response.noSpecimen : null;
  var numSpecimenOrNoSpecimen = 0;
  if (specimen && specimen.length > 0)
  {
    var truncateAt = TRUNCATE_SIZE[Math.min(specimen.length-1, TRUNCATE_SIZE.length)];
    for (var i = 0; i < specimen.length; i++)
    {
      var s = specimen[i];
      addColumn('specimen.name', makeLink('SAMPLE', s));
      addColumn('specimen.registrationDate', formatDate(s.registrationDate));
      addColumn('specimen.storageBox', asBioPlateLocation(s.bioWell));
      addColumn('specimen.laterality', warnIfMissing(s.laterality));
      addColumn('specimen.samplingDate', warnIfMissing(formatDateTime(s.samplingDate)));
      addColumn('specimen.rnaLaterDate', warnIfMissing(formatDateTime(s.rnaLaterDate, s.samplingDate)));
      addColumn('specimen.pad', warnIfMissing(s.pad));
      addColumn('specimen.biopsyType', s.biopsyType);
      addColumn('specimen.remainingQuantity', formatQuantity(s.remainingQuantity, 1000, ' mg'));
      addColumn('specimen.originalQuantity', formatQuantity(s.originalQuantity, 1000, ' mg'));
      addColumn('specimen.nofPieces', s.nofPieces);
      addColumn('specimen.partitionComment', truncate(s.partitionComment, truncateAt));
      addColumn('specimen.comment', truncate(s.comment, truncateAt));
      numSpecimenOrNoSpecimen++;
    }
    if (!noSpecimen || noSpecimen.length == 0)
    {
      Main.hide('nospecimen-info');
    }
  }
  if (noSpecimen && noSpecimen.length > 0)
  {
    for (var i = 0; i < noSpecimen.length; i++)
    {
      var s = noSpecimen[i];
      addColumn('nospecimen.name', makeLink('SAMPLE', s));
      addColumn('nospecimen.registrationDate', formatDate(s.registrationDate));
      addColumn('nospecimen.laterality', warnIfMissing(s.laterality));
      addColumn('nospecimen.samplingDate', warnIfMissing(formatDate(s.samplingDate)));
      addColumn('nospecimen.pad', warnIfMissing(s.pad));
      addColumn('nospecimen.reasonIfNoSpecimen', s.reasonIfNoSpecimen);
      addColumn('nospecimen.comment', truncate(s.comment, truncateAt));
      numSpecimenOrNoSpecimen++;
    }
    if (!specimen || specimen.length == 0)
    {
      addColumn('specimen.name', asNoInfo('No specimen received; see below for details'));
      Main.hide('specimen-details');
    }
  }
  if (numSpecimenOrNoSpecimen == 0)
  {
    if (consentOk)
    {
      addColumn('specimen.name', asNoInfo('No specimen information has been registered'));
      Main.hide('specimen-details');
    }
    else
    {
      Main.hide('specimen-info'); 
    }
    Main.hide('nospecimen-info');
  }
  
  var histology = consentOk ? response.histology : null;
  if (histology && histology.length > 0)
  {
    var truncateAt = TRUNCATE_SIZE[Math.min(histology.length-1, TRUNCATE_SIZE.length)];
    for (var i = 0; i < histology.length; i++)
    {
      var h = histology[i];
      addColumn('histology.name', makeLink('SAMPLE', h));
      addColumn('histology.registrationDate', formatDate(h.registrationDate));
      addColumn('histology.partitionDate', formatDate(h.partitionDate));
      addColumn('histology.usedQuantity', formatQuantity(h.originalQuantity, 1000, ' mg'));

      var embedded = h.embedDate ? true : false;
      addColumn('histology.embedded', embedded ? formatDate(h.embedDate) : 'No');
      addColumn('histology.embedProtocol', embedded ? makeLink('PROTOCOL', h.embedProtocol, truncateAt) : null);
      addColumn('histology.paraffinBlock', embedded ? asBioPlateLocation(h.bioWell) : null);
      addColumn('histology.storageBox', embedded ? null : asBioPlateLocation(h.bioWell));

      var stained = h.stainDate ? true : false;
      addColumn('histology.stained', stained ? formatDate(h.stainDate) : 'No');
      addColumn('histology.nofSlides', stained ? h.numStains : null);
      addColumn('histology.heGlass', stained ? asBioPlateLocation(h.bestStain) : null);
      addColumn('histology.stainProtocol', stained ? makeLink('PROTOCOL', h.stainProtocol, truncateAt) : null);
    }
  }
  else
  {
    if (consentOk)
    {
      addColumn('histology.name', asNoInfo('No histology information has been registered'));
      Main.hide('histology-details');
    }
    else
    {
      Main.hide('histology-info');
    }
  }
  
  
  var lysate = consentOk ? response.lysate : null;
  if (lysate && lysate.length > 0)
  {
    var truncateAt = TRUNCATE_SIZE[Math.min(lysate.length-1, TRUNCATE_SIZE.length)];
    for (var i = 0; i < lysate.length; i++)
    {
      var lys = lysate[i];
      addColumn('lysate.name', makeLink('EXTRACT', lys));
      addColumn('lysate.registrationDate', formatDate(lys.registrationDate));
      addColumn('lysate.partitionDate', formatDate(lys.partitionDate));
      addColumn('lysate.usedQuantity', formatQuantity(lys.usedQuantity, 1000, ' mg'));
      addColumn('lysate.multiplePieces', lys.multiplePieces ? 'Yes' : 'No');
      addColumn('lysate.comment', truncate(lys.comment, truncateAt));
      
      var lysis = lys.lysisDate ? true : false;
      addColumn('lysate.lysisDate', lysis ? formatDate(lys.lysisDate) : 'No');
      addColumn('lysate.storageBox', lysis ? asBioPlateLocation(lys.bioWell) : null);
      addColumn('lysate.lysisProtocol', lysis ? makeLink('PROTOCOL', lys.lysisProtocol, truncateAt) : null);
      addColumn('lysate.remainingQuantity', lysis ? formatQuantity(lys.remainingQuantity, null, ' µg') : null);
      addColumn('lysate.originalQuantity', lysis ? formatQuantity(lys.originalQuantity, null, ' µg') : null);
    }
  }
  else
  {
    if (consentOk)
    {
      addColumn('lysate.name', asNoInfo('No lysate information has been registered'));
      Main.hide('lysate-details');
    }
    else
    {
      Main.hide('lysate-info');
    }
  }

  
  var rna = consentOk ? response.rna : null;
  if (rna && rna.length > 0)
  {
    var truncateAt = TRUNCATE_SIZE[Math.min(rna.length-1, TRUNCATE_SIZE.length)];
    for (var i = 0; i < rna.length; i++)
    {
      var r = rna[i];
      addColumn('rna.name', makeLink('EXTRACT', r));
      addColumn('rna.flag', r.flag ? asFlagInfo(r.flag, 'flag.png') : null);
      addColumn('rna.registrationDate', formatDate(r.registrationDate));
      addColumn('rna.storageBox', asBioPlateLocation(r.bioWell));
      addColumn('rna.usedQuantity', formatQuantity(r.usedQuantity, null, ' µg'));
      addColumn('rna.extractionDate', formatDate(r.extractionDate));
      addColumn('rna.extractionProtocol', makeLink('PROTOCOL', r.extractionProtocol, truncateAt));
      addColumn('rna.remainingQuantity', formatQuantity(r.remainingQuantity, null, ' µg'));
      addColumn('rna.originalQuantity', formatQuantity(r.originalQuantity, null, ' µg'));
      addColumn('rna.ndConc', formatQuantity(r.ndConc, null, ' ng/µl'));
      addColumn('rna.comment', truncate(r.comment, truncateAt));
      
      var hasQc = r.nofQc ? true : false;
      addColumn('rna.qc', hasQc ? (r.qcDate ? formatDate(r.qcDate) : asNoInfo('Waiting for Caliper...')) : 'No');
      addColumn('rna.nofQc', hasQc ? r.nofQc : null);
      addColumn('rna.qcProtocol', hasQc ? makeLink('PROTOCOL', r.qcProtocol, truncateAt) : null);
      addColumn('rna.qcPlate', hasQc ? asBioPlateLocation(r.qcPlate)+asFileLink(r.qcPdf, 'pdffile.png') : null);
      addColumn('rna.qcRqs', hasQc && r.qcRqs ? formatNumber(r.qcRqs, null, 1) : null);
      addColumn('rna.qcRin', hasQc && r.qcRin ? formatNumber(r.qcRin, null, 1) : null);
      addColumn('rna.qcComment', hasQc ? truncate(r.qcComment, truncateAt) : null);
    }
  }
  else
  {
    if (consentOk)
    {
      addColumn('rna.name', asNoInfo('No RNA information has been registered'));
      Main.hide('rna-details');
    }
    else
    {
      Main.hide('rna-info');
    }
  }

  var dna = consentOk ? response.dna : null;
  if (dna && dna.length > 0)
  {
    var truncateAt = TRUNCATE_SIZE[Math.min(dna.length-1, TRUNCATE_SIZE.length)];
    for (var i = 0; i < dna.length; i++)
    {
      var d = dna[i];
      addColumn('dna.name', makeLink('EXTRACT', d));
      addColumn('dna.registrationDate', formatDate(d.registrationDate));
      addColumn('dna.storageBox', asBioPlateLocation(d.bioWell));
      addColumn('dna.extractionDate', formatDate(d.extractionDate));
      addColumn('dna.extractionProtocol', makeLink('PROTOCOL', d.extractionProtocol, truncateAt));
      addColumn('dna.remainingQuantity', formatQuantity(d.remainingQuantity, null, ' µg'));
      addColumn('dna.originalQuantity', formatQuantity(d.originalQuantity, null, ' µg'));
      addColumn('dna.ndConc', formatQuantity(d.ndConc, null, ' ng/µl'));
      addColumn('dna.comment', truncate(d.comment, truncateAt));
    }
  }
  else
  {
    if (consentOk)
    {
      addColumn('dna.name', asNoInfo('No DNA information has been registered'));
      Main.hide('dna-details');
    }
    else
    {
      Main.hide('dna-info');
    }
  }

  var ft = consentOk ? response.flowThrough : null;
  if (ft && ft.length > 0)
  {
    var truncateAt = TRUNCATE_SIZE[Math.min(ft.length-1, TRUNCATE_SIZE.length)];
    for (var i = 0; i < ft.length; i++)
    {
      var f = ft[i];
      addColumn('ft.name', makeLink('EXTRACT', f));
      addColumn('ft.registrationDate', formatDate(f.registrationDate));
      addColumn('ft.storageBox', asBioPlateLocation(f.bioWell));
      addColumn('ft.extractionDate', formatDate(f.extractionDate));
      addColumn('ft.extractionProtocol', makeLink('PROTOCOL', f.extractionProtocol, truncateAt));
      addColumn('ft.remainingQuantity', formatQuantity(f.remainingQuantity, null, ' µg'));
      addColumn('ft.originalQuantity', formatQuantity(f.originalQuantity, null, ' µg'));
      addColumn('ft.comment', truncate(f.comment, truncateAt));
    }
  }
  else
  {
    if (consentOk)
    {
      addColumn('ft.name', asNoInfo('No FlowThrough information has been registered'));
      Main.hide('ft-details');
    }
    else
    {
      Main.hide('ft-info');
    }
  }

  
  var mrna = consentOk ? response.mrna : null;
  if (mrna && mrna.length > 0)
  {
    var truncateAt = TRUNCATE_SIZE[Math.min(mrna.length-1, TRUNCATE_SIZE.length)];
    for (var i = 0; i < mrna.length; i++)
    {
      var r = mrna[i];
      addColumn('mrna.name', makeLink('EXTRACT', r));
      addColumn('mrna.registrationDate', formatDate(r.registrationDate));
      addColumn('mrna.storageBox', asBioPlateLocation(r.bioWell)+asFileLink(r.platePdf, 'pdffile.png'));
      addColumn('mrna.result', (r.result && r.result != 'Successful') ? asFailInfo(r.result, 'error.png') : null);
      addColumn('mrna.extractionDate', formatDate(r.extractionDate));
      addColumn('mrna.usedQuantity', formatQuantity(r.usedQuantity, null, ' µg'));
    }
  }
  else
  {
    if (consentOk)
    {
      addColumn('mrna.name', asNoInfo('No mRNA information has been registered'));
      Main.hide('mrna-details');
    }
    else
    {
      Main.hide('mrna-info');
    }
  }


  var cdna = consentOk ? response.cdna : null;
  if (cdna && cdna.length > 0)
  {
    var truncateAt = TRUNCATE_SIZE[Math.min(cdna.length-1, TRUNCATE_SIZE.length)];
    for (var i = 0; i < cdna.length; i++)
    {
      var r = cdna[i];
      addColumn('cdna.name', makeLink('EXTRACT', r));
      addColumn('cdna.registrationDate', formatDate(r.registrationDate));
      addColumn('cdna.storageBox', asBioPlateLocation(r.bioWell));
      addColumn('cdna.result', (r.result && r.result != 'Successful') ? asFailInfo(r.result, 'error.png') : null);
      addColumn('cdna.extractionDate', formatDate(r.extractionDate));
    }
  }
  else
  {
    if (consentOk)
    {
      addColumn('cdna.name', asNoInfo('No cDNA information has been registered'));
      Main.hide('cdna-details');
    }
    else
    {
      Main.hide('cdna-info');
    }
  }


  var lib = consentOk ? response.lib : null;
  if (lib && lib.length > 0)
  {
    var truncateAt = TRUNCATE_SIZE[Math.min(lib.length-1, TRUNCATE_SIZE.length)];
    for (var i = 0; i < lib.length; i++)
    {
      var r = lib[i];
      addColumn('lib.name', makeLink('EXTRACT', r));
      addColumn('lib.registrationDate', formatDate(r.registrationDate));
      addColumn('lib.storageBox', asBioPlateLocation(r.bioWell));
      addColumn('lib.result', (r.result && r.result != 'Successful') ? asFailInfo(r.result, 'error.png') : null);
      addColumn('lib.extractionDate', formatDate(r.extractionDate));
      addColumn('lib.remainingQuantity', formatQuantity(r.remainingQuantity, 0.001, ' ng'));
      addColumn('lib.originalQuantity', formatQuantity(r.originalQuantity, 0.001, ' ng'));
      addColumn('lib.barcode.name', r.barcode.name);
      addColumn('lib.ca_size', formatQuantity(r.ca_size, null, ''));
      addColumn('lib.ca_molarity', formatQuantity(r.ca_molarity, null, ' nM'));
      addColumn('lib.qubitconc', formatQuantity(r.qubitconc, null, ' ng/µl'));
    }
  }
  else
  {
    if (consentOk)
    {
      addColumn('lib.name', asNoInfo('No library information has been registered'));
      Main.hide('lib-details');
    }
    else
    {
      Main.hide('lib-info');
    }
  }


  var pooledLib = consentOk ? response.pooledlib : null;
  if (pooledLib && pooledLib.length > 0)
  {
    var truncateAt = TRUNCATE_SIZE[Math.min(pooledLib.length-1, TRUNCATE_SIZE.length)];
    for (var i = 0; i < pooledLib.length; i++)
    {
      var r = pooledLib[i];
      addColumn('pooledlib.name', makeLink('EXTRACT', r));
      addColumn('pooledlib.registrationDate', formatDate(r.registrationDate));
      addColumn('pooledlib.extractionDate', formatDate(r.extractionDate));
      addColumn('pooledlib.remainingQuantity', formatQuantity(r.remainingQuantity, 0.001, ' ng'));
      addColumn('pooledlib.originalQuantity', formatQuantity(r.originalQuantity, 0.001, ' ng'));
      addColumn('pooledlib.poolmolarity', formatQuantity(r.poolmolarity, null, ' nM'));
      addColumn('pooledlib.poolconc', formatQuantity(r.poolconc, null, ' ng/µl'));
    }
  }
  else
  {
    if (consentOk)
    {
      addColumn('pooledlib.name', asNoInfo('No pooled library information has been registered'));
      Main.hide('pooledlib-details');
    }
    else
    {
      Main.hide('pooledlib-info');
    }
  }
}

function caseSummary(caseName)
{
  var frm = document.forms['reggie'];
  if (!caseName)
  {
    caseName = frm.caseName.value;
    if (!caseName)
    {
      alert('Please enter a 7-digit case id');
      return;
    }
  }
  location.href = 'case_summary.jsp?ID=<%=ID%>&caseName='+encodeURIComponent(caseName);
}

function showConfidentialOnChange()
{
  var frm = document.forms['reggie'];
  if (frm.showConfidential.checked)
  {
    Main.removeClass(document.getElementById('all-info'), 'hide-confidential');
  }
  else
  {
    Main.addClass(document.getElementById('all-info'), 'hide-confidential');
  }
}

function goPrint()
{
  var printNote = '<b>Note!</b> For better printing set page orientation to <i>portrait</i>.<br>';
  printNote += ' You may have to <i>scale down</i> to fit everything on the width of the page.';
  openPrintWindow('<%=ID%>', 'all-content', 'Case summary - <%=HTML.encodeTags(caseName)%>', 'portrait', printNote, '../', 'case_summary.css');
}

</script>
<style>

</style>
</base:head>

<base:body onload="init()">
  <div id="all-content">
  <%
  if (fullPage)
  {
    %>
    <p:path><p:pathelement id="path-reggie" clazz="noprint"
      title="Reggie" href="<%="../index.jsp?ID="+ID%>"
      /><p:pathelement id="path-case-summary" title="<%="Case summary - " + HTML.encodeTags(caseName)%>" 
      /></p:path>
    <%
  }
  else if (popup)
  {
    %>
    <h1>Case summary - <%= HTML.encodeTags(caseName)%></h1>
    <%
  }
  %>
  <div class="content">
  <form name="reggie" onsubmit="return false;">
  <%
  if (fullPage || popup)
  {
    %>
    <div class="filled noprint" id="toolbar">
      <table>
      <tr>
        <th style="padding: 0.5em 0.75em 0.5em 0.75em;">Find another case</th>
        <td><input type="text" class="text" style="width: 25em;"
          name="caseName" title="Please enter a 7-digit case id"
          onkeypress="if (event.keyCode==13 && this.value) caseSummary()"></td>
        <td style="padding-left: 0.5em; padding-right: 0.5em; border-right: 1px dotted #A0A0A0; "><base:icon image="<%=home+"/images/gonext.png"%>" onclick="caseSummary()"></base:icon></td>
        <%
        if (isAdmin || isPatientCurator)
        {
          %>
          <th style="padding-left: 0.5em; padding-right: 0.5em; border-right: 1px dotted #A0A0A0;">
            <label for="showConfidential">Show confidential information</label>
            <input type="checkbox" id="showConfidential" name="showConfidential" onchange="showConfidentialOnChange()">
          </th>
          <%
        }
        %>
        <th style="padding-left: 0.5em; padding-right: 0.5em; border-right: 1px dotted #A0A0A0;">
          <span id="printButton" class="link" onclick="goPrint()"><img src="../images/print.png" style="padding-right: 0.5em;">Print version&hellip;</span>
        </th>
      </tr>
      </table>
    </div>
    <%
  }
  %>
  <div class="hide-confidential" id="all-info" style="display: none;">
    <div id="left-column">
      <div>
        <%
        if (sc.getActiveProjectId() == 0)
        {
          %>
          <div class="messagecontainer note" style="margin-bottom: 20px; font-weight: bold; color: #cc0000;">
            No project has been selected. You may not be able to see all registered information.
          </div>
          <%
        }
        %>
        <div class="info-section" id="case-info">
          <div>
          <table class="info-table">
          <thead>
            <tr id="case.name">
              <th>Case</th>
            </tr>
          </thead>
          <tbody id="case-details">
            <tr id="case.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="case.site">
              <th>Site</th>
            </tr>
            <tr id="case.laterality" class="dynamic-column">
              <th>Laterality</th>
            </tr>
            <tr id="case.consent">
              <th>Consent</th>
            </tr>
            <tr id="case.comment" class="comment dynamic-column">
              <th>Comment</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>

        <div class="info-section" id="patient-info">
          <div>
          <table class="info-table">
          <thead>
            <tr id="patient.name">
              <th>Patient</th>
            </tr>
          </thead>
          <tbody id="patient-details">
            <tr id="patient.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="patient.personalNumber" class="confidential">
              <th>Personal number</th>
            </tr>
            <tr id="patient.allFirstNames" class="confidential">
              <th>All first names</th>
            </tr>
            <tr id="patient.familyName" class="confidential">
              <th>Family name</th>
            </tr>
            <tr id="patient.gender">
              <th>Gender</th>
            </tr>
            <tr id="patient.allCases" class="dynamic-column">
              <th>All cases</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>

        <div class="info-section" id="blood-info">
          <div>
          <table class="info-table">
          <thead>
            <tr id="blood.name">
              <th>Blood</th>
            </tr>
          </thead>
          <tbody id="blood-details">
            <tr id="blood.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="blood.consent">
              <th>Consent</th>
            </tr>
            <tr id="blood.bloodSample">
              <th>Blood sample</th>
            </tr>
            <tr id="blood.samplingDate">
              <th>Sampling date</th>
            </tr>
            <tr id="blood.freezerDate">
              <th>Freezer date</th>
            </tr>
            <tr id="blood.serum">
              <th>Serum</th>
            </tr>
            <tr id="blood.comment" class="comment dynamic-column">
              <th>Comment</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>
        
        <div class="info-section" id="specimen-info">
          <div>
          <table class="info-table">
          <thead>
            <tr id="specimen.name">
              <th>Specimen</th>
            </tr>
          </thead>
          <tbody id="specimen-details">
            <tr id="specimen.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="specimen.storageBox">
              <th>Storage box</th>
            </tr>
            <tr id="specimen.laterality">
              <th>Laterality</th>
            </tr>
            <tr id="specimen.samplingDate">
              <th>Sampling date</th>
            </tr>
            <tr id="specimen.rnaLaterDate">
              <th>RNA later date</th>
            </tr>
            <tr id="specimen.pad">
              <th>PAD</th>
            </tr>
            <tr id="specimen.biopsyType">
              <th>Biopsy type</th>
            </tr>
            <tr id="specimen.remainingQuantity">
              <th>Remaining quantity</th>
            </tr>
            <tr id="specimen.originalQuantity">
              <th>Original quantity</th>
            </tr>
            <tr id="specimen.nofPieces">
              <th>No. pieces</th>
            </tr>
            <tr id="specimen.partitionComment">
              <th>Partition comment</th>
            </tr>
            <tr id="specimen.comment" class="comment dynamic-column">
              <th>Comment</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>
        
        <div class="info-section" id="nospecimen-info">
          <div>
          <table class="info-table">
          <thead>
            <tr id="nospecimen.name">
              <th>NoSpecimen</th>
            </tr>
          </thead>
          <tbody id="nospecimen-details">
            <tr id="nospecimen.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="nospecimen.laterality">
              <th>Laterality</th>
            </tr>
            <tr id="nospecimen.samplingDate">
              <th>Sampling date</th>
            </tr>
            <tr id="nospecimen.pad">
              <th>PAD</th>
            </tr>
            <tr id="nospecimen.reasonIfNoSpecimen" class="comment">
              <th>Reason</th>
            </tr>
            <tr id="nospecimen.comment" class="comment dynamic-column">
              <th>Comment</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>
      
      </div>
    </div>
    <div id="right-column">
      <div>
        <div class="info-section" id="histology-info">
          <div>
          <table class="info-table">
          <thead>
            <tr id="histology.name">
              <th>Histology</th>
            </tr>
          </thead>
          <tbody id="histology-details">
            <tr id="histology.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="histology.storageBox" class="dynamic-column">
              <th>Storage box</th>
            </tr>
            <tr id="histology.partitionDate">
              <th>Partition date</th>
            </tr>
            <tr id="histology.usedQuantity">
              <th>Used quantity</th>
            </tr>
            <tr id="histology.embedded" class="subtitle">
              <th>Embedded</th>
            </tr>
            <tr id="histology.paraffinBlock" class="dynamic-column">
              <th>Paraffin block</th>
            </tr>
            <tr id="histology.embedProtocol" class="dynamic-column">
              <th>Protocol</th>
            </tr>
            <tr id="histology.stained" class="subtitle">
              <th>Stained</th>
            </tr>
            <tr id="histology.nofSlides" class="dynamic-column">
              <th>No. slides</th>
            </tr>
            <tr id="histology.heGlass" class="dynamic-column">
              <th>Best slide</th>
            </tr>
            <tr id="histology.stainProtocol" class="dynamic-column">
              <th>Protocol</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>

        <div class="info-section" id="lysate-info">
          <div>
          <table class="info-table dynamic-columns">
          <thead>
            <tr id="lysate.name">
              <th>Lysate</th>
            </tr>
          </thead>
          <tbody id="lysate-details">
            <tr id="lysate.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="lysate.partitionDate">
              <th>Partition date</th>
            </tr>
            <tr id="lysate.usedQuantity">
              <th>Used quantity</th>
            </tr>
            <tr id="lysate.multiplePieces">
              <th>Multiple pieces</th>
            </tr>
            <tr id="lysate.lysisDate" class="subtitle">
              <th>Lysis date</th>
            </tr>
            <tr id="lysate.storageBox" class="dynamic-column">
              <th>Storage box</th>
            </tr>
            <tr id="lysate.lysisProtocol" class="dynamic-column">
              <th>Protocol</th>
            </tr>
            <tr id="lysate.remainingQuantity" class="dynamic-column">
              <th>Remaining quantity</th>
            </tr>
            <tr id="lysate.originalQuantity" class="dynamic-column">
              <th>Original quantity</th>
            </tr>
            <tr id="lysate.comment" class="comment dynamic-column">
              <th>Comment</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>
          
        <div class="info-section" id="rna-info">
          <div>
          <table class="info-table dynamic-columns">
          <thead>
            <tr id="rna.name">
              <th>RNA</th>
            </tr>
          </thead>
          <tbody id="rna-details">
            <tr id="rna.flag" class="dynamic-column">
              <th>Flag</th>
            </tr>
            <tr id="rna.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="rna.storageBox">
              <th>Storage box</th>
            </tr>
            <tr id="rna.extractionDate">
              <th>Extraction date</th>
            </tr>
            <tr id="rna.usedQuantity">
              <th>Used quantity</th>
            </tr>
            <tr id="rna.extractionProtocol">
              <th>Protocol</th>
            </tr>
            <tr id="rna.remainingQuantity">
              <th>Remaining quantity</th>
            </tr>
            <tr id="rna.originalQuantity">
              <th>Original quantity</th>
            </tr>
            <tr id="rna.ndConc">
              <th>ND Conc.</th>
            </tr>
            <tr id="rna.comment" class="comment dynamic-column">
              <th>Comment</th>
            </tr>
            <tr id="rna.qc" class="subtitle">
              <th>QC (last)</th>
            </tr>
            <tr id="rna.nofQc" class="dynamic-column">
              <th>No. QC</th>
            </tr>
            <tr id="rna.qcProtocol" class="dynamic-column">
              <th>Protocol</th>
            </tr>
            <tr id="rna.qcPlate" class="dynamic-column">
              <th>Plate</th>
            </tr>
            <tr id="rna.qcRqs" class="dynamic-column">
              <th>RQS</th>
            </tr>
            <tr id="rna.qcRin" class="dynamic-column">
              <th>RIN</th>
            </tr>
            <tr id="rna.qcComment" class="comment dynamic-column">
              <th>Comment</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>

        <div class="info-section" id="dna-info">
          <div>
          <table class="info-table dynamic-columns">
          <thead>
            <tr id="dna.name">
              <th>DNA</th>
            </tr>
          </thead>
          <tbody id="dna-details">
            <tr id="dna.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="dna.storageBox">
              <th>Storage box</th>
            </tr>
            <tr id="dna.extractionDate">
              <th>Extraction date</th>
            </tr>
            <tr id="dna.extractionProtocol">
              <th>Protocol</th>
            </tr>
            <tr id="dna.remainingQuantity">
              <th>Remaining quantity</th>
            </tr>
            <tr id="dna.originalQuantity">
              <th>Original quantity</th>
            </tr>
            <tr id="dna.ndConc">
              <th>ND Conc.</th>
            </tr>
            <tr id="dna.comment" class="comment dynamic-column">
              <th>Comment</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>

        <div class="info-section" id="ft-info">
          <div>
          <table class="info-table dynamic-columns">
          <thead>
            <tr id="ft.name">
              <th>FlowThrough</th>
            </tr>
          </thead>
          <tbody id="ft-details">
            <tr id="ft.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="ft.storageBox">
              <th>Storage box</th>
            </tr>
            <tr id="ft.extractionDate">
              <th>Extraction date</th>
            </tr>
            <tr id="ft.extractionProtocol">
              <th>Protocol</th>
            </tr>
            <tr id="ft.remainingQuantity">
              <th>Remaining quantity</th>
            </tr>
            <tr id="ft.originalQuantity">
              <th>Original quantity</th>
            </tr>
            <tr id="ft.comment" class="comment dynamic-column">
              <th>Comment</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>
        
        <div class="info-section" id="mrna-info">
          <div>
          <table class="info-table dynamic-columns">
          <thead>
            <tr id="mrna.name">
              <th>mRNA</th>
            </tr>
          </thead>
          <tbody id="mrna-details">
            <tr id="mrna.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="mrna.storageBox">
              <th>Work plate</th>
            </tr>
            <tr id="mrna.result" class="dynamic-column">
              <th>Plate result</th>
            </tr>
            <tr id="mrna.extractionDate">
              <th>Cleanup date</th>
            </tr>
            <tr id="mrna.usedQuantity">
              <th>Used quantity</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>
        
        <div class="info-section" id="cdna-info">
          <div>
          <table class="info-table dynamic-columns">
          <thead>
            <tr id="cdna.name">
              <th>cDNA</th>
            </tr>
          </thead>
          <tbody id="cdna-details">
            <tr id="cdna.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="cdna.storageBox">
              <th>Work plate</th>
            </tr>
            <tr id="cdna.result" class="dynamic-column">
              <th>Plate result</th>
            </tr>
            <tr id="cdna.extractionDate">
              <th>Synthesis date</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>
        
        <div class="info-section" id="lib-info">
          <div>
          <table class="info-table dynamic-columns">
          <thead>
            <tr id="lib.name">
              <th>Library</th>
            </tr>
          </thead>
          <tbody id="lib-details">
            <tr id="lib.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="lib.storageBox">
              <th>Library plate</th>
            </tr>
            <tr id="lib.result" class="dynamic-column">
              <th>Plate result</th>
            </tr>
            <tr id="lib.extractionDate">
              <th>Cleanup date</th>
            </tr>
            <tr id="lib.remainingQuantity">
              <th>Remaining quantity</th>
            </tr>
            <tr id="lib.originalQuantity">
              <th>Original quantity</th>
            </tr>
            <tr id="lib.barcode.name">
              <th>Tag</th>
            </tr>
            <tr id="lib.ca_size">
              <th>CA_Size</th>
            </tr>
            <tr id="lib.ca_molarity">
              <th>CA_Molarity</th>
            </tr>
            <tr id="lib.qubitconc">
              <th>QubitConc</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>
        
        <div class="info-section" id="pooledlib-info">
          <div>
          <table class="info-table dynamic-columns">
          <thead>
            <tr id="pooledlib.name">
              <th>Pooled Library</th>
            </tr>
          </thead>
          <tbody id="pooledlib-details">
            <tr id="pooledlib.registrationDate">
              <th>Registration date</th>
            </tr>
            <tr id="pooledlib.extractionDate">
              <th>Pool date</th>
            </tr>
            <tr id="pooledlib.remainingQuantity">
              <th>Remaining quantity</th>
            </tr>
            <tr id="pooledlib.originalQuantity">
              <th>Original quantity</th>
            </tr>
            <tr id="pooledlib.poolmolarity">
              <th>PoolMolarity</th>
            </tr>
            <tr id="pooledlib.poolconc">
              <th>PoolConc</th>
            </tr>
          </tbody>
          </table>
          </div>
        </div>
        
      </div>
    </div>
  </div>
  </form>
  
  <div class="messagecontainer error" id="errorMessage" style="display: none; width: 950px; margin-left: 20px; margin-bottom: 0px;"></div>

  </div>
  </div>
  <%
  if (popup)
  {
    %>
    <base:buttongroup subclass="dialogbuttons topborder" id="dialogbuttons">
      <base:button onclick="window.close()" title="Close" />
    </base:buttongroup>
    <%
  }
  %>
</base:body>
</base:page>
<%
}
finally
{
  if (dc != null) dc.close();
}
%>