source: extensions/net.sf.basedb.reggie/branches/2.15-stable/resources/index.jsp @ 2322

<%@ 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.Item"
  import="net.sf.basedb.core.Permission"
  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)
  {}
%>
<base:page type="default" >
<base:head styles="path.css" scripts="ajax.js">
  <script language="JavaScript" src="reggie.js" type="text/javascript" charset="UTF-8"></script>
  <link rel="stylesheet" type="text/css" href="css/reggie.css">
  <script language="JavaScript">
  
  var debug = false;
  var myPermissions = {};
  
  function init()
  {
    // Get permission information
    var url = 'Install.servlet?ID=<%=ID%>&cmd=GetPermissions';
    var request = Ajax.getXmlHttpRequest();
    request.open("GET", url, false);
    Ajax.setReadyStateHandler(request, onPermissions, onPermissions);
    request.send(null);
  }
  
  // Callback when permission information is ready
  function onPermissions(request)
  {
    if (debug) Main.debug(Main.encodeTags(request.responseText));
    var response;
    var error = false;
    try
    {
      response = JSON.parse(request.responseText);
      if (response.status != 'ok')
      {
        error = response.message || response.stacktrace || 'Unexpected error';
      }
    }
    catch (ex)
    {
      error = ex;
    }
    
    if (error)
    {
      alert(error);
      return;
    }
    
    myPermissions = response.permissions;
    var isAdmin = myPermissions['Administrator'] == 1;
    
    // Enable links based on the permission
    var wizards = document.getElementsByClassName('require-permission');
    // NOTE! Loop backwards since changing the classname 
    // of an element so that 'require-permission' no longer is included
    // removes the element from the 'wizards' list
    for (var wizardNo = wizards.length-1; wizardNo >= 0; wizardNo--)
    {
      var wizard = wizards[wizardNo];
      if (wizard.className.indexOf('not-implemented') == -1)
      {
        var role = wizard.getAttribute('data-role');
        if (myPermissions[role] == 1 || isAdmin)
        {
          wizard.className = 'link';
          wizard.addEventListener('click', goWizard);
        }
        else
        {
          wizard.title = 'You do not have permission to user this wizard';
        }
      }
    }
    
    // Start couting queued items
    startCounting('specimen');
  }
  
  function caseSummary()
  {
    var frm = document.forms['reggie'];
    
    var caseName = frm.caseName.value;
    if (!caseName)
    {
      alert('Please enter a 7-digit case id');
      return;
    }
    location.href = 'reports/case_summary.jsp?ID=<%=ID%>&caseName='+encodeURIComponent(caseName);
  }
  
  var currentCount;
  function startCounting(what)
  {
    var url;
    currentCount = what;
    if (what == 'specimen')
    {
      url = 'PartitionRegistration.servlet?ID=<%=ID%>&cmd=CountSpecimenTubes';
    }
    else if (what == 'histology-lists')
    {
      url = 'Histology.servlet?ID=<%=ID%>&cmd=CountHistologyWorkLists';
    }
    else if (what == 'paraffin-blocks')
    {
      url = 'Histology.servlet?ID=<%=ID%>&cmd=CountParaffinBlocks';
    }
    else if (what == 'paraffin-blocks-without-heglass')
    {
      url = 'Histology.servlet?ID=<%=ID%>&cmd=CountParaffinBlocksWithoutHeGlass';
    }
    else if (what == 'unscored-heglass')
    {
      url = 'Histology.servlet?ID=<%=ID%>&cmd=CountUnscoredHeGlass';
    }
    else if (what == 'lysate')
    {
      url = 'Extraction.servlet?ID=<%=ID%>&cmd=CountUnprocessedLysates';
    }
    else if (what == 'rnaqc')
    {
      url = 'RnaQc.servlet?ID=<%=ID%>&cmd=CountRnaExtractsWithoutQc';
    }
    else if (what == 'caliper-plates')
    {
      url = 'RnaQc.servlet?ID=<%=ID%>&cmd=CountActiveRnaQcBioPlates';
    }
    else if (what == 'rna-without-mrna')
    {
      url = 'MRna.servlet?ID=<%=ID%>&cmd=CountRnaWithoutMRna';
    }
    else if (what == 'mrna-plates')
    {
      url = 'MRna.servlet?ID=<%=ID%>&cmd=CountUnprocessedPlates&plateType=MRNA';
    }
    else if (what == 'cdna-plates')
    {
      url = 'MRna.servlet?ID=<%=ID%>&cmd=CountUnprocessedPlates&plateType=CDNA';
    }
    else if (what == 'cdna-plates-for-barcoding')
    {
      url = 'LibPrep.servlet?ID=<%=ID%>&cmd=CountCDNAPlatesForBarcoding';
    }
    else if (what == 'lib-plates')
    {
      url = 'LibPrep.servlet?ID=<%=ID%>&cmd=CountLibPlatesForLibPrep';
    }
    else if (what == 'lib-plates-for-pooling')
    {
      url = 'Pool.servlet?ID=<%=ID%>&cmd=CountLibraryPlatesForPooling';
    }
    else if (what == 'unregistered-pools')
    {
      url = 'Pool.servlet?ID=<%=ID%>&cmd=CountUnprocessedPools';
    }
    else if (what == 'unused-pools')
    {
      url = 'FlowCell.servlet?ID=<%=ID%>&cmd=CountUnusedPools';
    }
    else if (what == 'unregistered-flow-cells')
    {
      url = 'FlowCell.servlet?ID=<%=ID%>&cmd=CountUnprocessedFlowCells';
    }
    else if (what == 'clustered-flow-cells')
    {
      url = 'FlowCell.servlet?ID=<%=ID%>&cmd=CountClusteredFlowCells';
    }
    else if (what == 'active-sequencing-runs')
    {
      url = 'SequencingRun.servlet?ID=<%=ID%>&cmd=CountActiveSequencingRuns';
    }
    else if (what == 'unconfirmed-sequencing-runs')
    {
      url = 'SequencingRun.servlet?ID=<%=ID%>&cmd=CountUncomfirmedSequencingRuns';
    }
    
    if (url)
    {
      var request = Ajax.getXmlHttpRequest();
      request.open("GET", url, true);
      Ajax.setReadyStateHandler(request, onCounted, onCounted);
      request.send(null);
    }
  }
  
  function onCounted(request)
  {
    if (debug) Main.debug(currentCount +': ' + Main.encodeTags(request.responseText));
    var response;
    var error = false;
    try
    {
      response = JSON.parse(request.responseText);
      if (response.status != 'ok')
      {
        error = response.message || response.stacktrace || 'Unexpected error';
      }
    }
    catch (ex)
    {
      error = ex;
    }
    
    if (currentCount == 'specimen')
    {
      var msg = error || 'Number of unpartitioned specimen';
      var count = error ? -1 : response.count;
      setCount('count.specimen', count, 'specimens', msg);
      startCounting('histology-lists');
    }
    else if (currentCount == 'histology-lists')
    {
      var msg = error || 'Number of active histology work lists';
      var count = error ? -1 : response.count;
      setCount('count.histology-lists', count, 'work lists', msg);
      startCounting('paraffin-blocks');
    }
    else if (currentCount == 'paraffin-blocks')
    {
      var msg = error || 'Number of paraffin blocks waiting for registration';
      var count = error ? -1 : response.count;
      setCount('count.paraffin-blocks', count, 'paraffin blocks', msg);
      startCounting('paraffin-blocks-without-heglass');
    }
    else if (currentCount == 'paraffin-blocks-without-heglass')
    {
      var msg = error || 'Number of paraffin blocks without HE glass';
      var count = error ? -1 : response.count;
      setCount('count.paraffin-blocks-without-heglass', count, 'paraffin blocks', msg);
      startCounting('unscored-heglass');
    }
    else if (currentCount == 'unscored-heglass')
    {
      var msg = error || 'Number of unscored HE glass';
      var count = error ? -1 : response.count;
      setCount('count.unscored-heglass', count, 'HE glass', msg);
      startCounting('lysate');
    }
    else if (currentCount == 'lysate')
    {
      var msg = error || 'Number of unprocessed lysates';
      var count = error ? -1 : response.count;
      setCount('count.lysate.1', count, 'lysates', msg);
      setCount('count.lysate.2', count, 'lysates', msg);
      startCounting('rnaqc');
    }
    else if (currentCount == 'rnaqc')
    {
      var msg = error || 'Number of RNA waiting for QC';
      var count = error ? -1 : response.count;
      setCount('count.rnaqc', count, 'RNA', msg);
      startCounting('caliper-plates');
    }
    else if (currentCount == 'caliper-plates')
    {
      var msg = error || 'Number of active Caliper plates';
      var count = error ? -1 : response.count;
      setCount('count.caliper-plates.1', count, 'Caliper plates', msg);
      setCount('count.caliper-plates.2', count, 'Caliper plates', msg);
      startCounting('rna-without-mrna');
    }
    else if (currentCount == 'rna-without-mrna')
    {
      var msg = error || 'Number of RNA with no mRNA';
      var count = error ? -1 : response.count;
      setCount('count.rna-without-mrna', count, 'RNA', msg);
      startCounting('mrna-plates');
    }
    else if (currentCount == 'mrna-plates')
    {
      var msg = error || 'Number of mRNA plates waiting for registration';
      var count = error ? -1 : response.count;
      setCount('count.mrna-plates.1', count, 'mRNA plates', msg);
      setCount('count.mrna-plates.2', count, 'mRNA plates', msg);
      startCounting('cdna-plates');
    }
    else if (currentCount == 'cdna-plates')
    {
      var msg = error || 'Number of cDNA plates waiting for registration';
      var count = error ? -1 : response.count;
      setCount('count.cdna-plates.1', count, 'cDNA plates', msg);
      startCounting('cdna-plates-for-barcoding');
    }
    else if (currentCount == 'cdna-plates-for-barcoding')
    {
      var msg = error || 'Number of cDNA plates waiting for barcode layout';
      var count = error ? -1 : response.count;
      setCount('count.cdna-plates-for-barcoding', count, 'cDNA plates', msg);
      startCounting('lib-plates')
    }
    else if (currentCount == 'lib-plates')
    {
      var msg = error || 'Number of Lib plates waiting for registration';
      var count = error ? -1 : response.count;
      setCount('count.lib-plates.1', count, 'Lib plates', msg);
      setCount('count.lib-plates.2', count, 'Lib plates', msg);
      setCount('count.lib-plates.3', count, 'Lib plates', msg);
      startCounting('lib-plates-for-pooling');
    }
    else if (currentCount == 'lib-plates-for-pooling')
    {
      var msg = error || 'Number of Lib plates waiting for pooling';
      var count = error ? -1 : response.count;
      setCount('count.lib-plates-for-pooling', count, 'Lib plates', msg);
      startCounting('unregistered-pools');
    }
    else if (currentCount == 'unregistered-pools')
    {
      var msg = error || 'Number of pools waiting for registration';
      var count = error ? -1 : response.count;
      setCount('count.pools.1', count, 'pools', msg);
      setCount('count.pools.2', count, 'pools', msg);
      startCounting('unused-pools');
    }
    else if (currentCount == 'unused-pools')
    {
      var msg = error || 'Number of pools waiting for sequencing';
      var count = error ? -1 : response.count;
      setCount('count.pools.3', count, 'pools', msg);
      startCounting('unregistered-flow-cells');
    }
    else if (currentCount == 'unregistered-flow-cells')
    {
      var msg = error || 'Number of flow cells waiting for clustering';
      var count = error ? -1 : response.count;
      setCount('count.flow-cells.1', count, 'flow cells', msg);
      setCount('count.flow-cells.2', count, 'flow cells', msg);
      startCounting('clustered-flow-cells');
    }
    else if (currentCount == 'clustered-flow-cells')
    {
      var msg = error || 'Number of flow cells waiting for sequencing';
      var count = error ? -1 : response.count;
      setCount('count.flow-cells.3', count, 'flow cells', msg);
      startCounting('active-sequencing-runs');
    }
    else if (currentCount == 'active-sequencing-runs')
    {
      var msg = error || 'Number of active sequencing runs';
      var count = error ? -1 : response.count;
      setCount('count.sequencing-run', count, 'sequencing runs', msg);
      startCounting('unconfirmed-sequencing-runs');
    }
    else if (currentCount == 'unconfirmed-sequencing-runs')
    {
      var msg = error || 'Number of ended but not confirmed sequencing runs';
      var count = error ? -1 : response.count;
      setCount('count.unconfirmed-sequencing-run', count, 'sequencing runs', msg);
    }
    
  }
  
  function setCount(id, count, unit, msg)
  {
    var div = document.getElementById(id);
    div.title = msg;
    if (count == -1)
    {
      div.innerHTML = '(-)';
    }
    else
    {
      div.innerHTML = '(' + count + ')';
    }
  }
  
  function goWizard(event)
  {
    var role = event.currentTarget.getAttribute('data-role');
    var isAdmin = myPermissions['Administrator'] == 1;
    if (isAdmin || myPermissions[role] == 1)
    {
      var link = event.currentTarget.getAttribute('data-link');
      location.href = link;
    }
    else
    {
      alert('You do not have permission to use this wizard!');
    }
  }
  
  </script>
<style>
dl
{
  margin-top: 0px;
  padding: 3px;
}
dt
{
  margin-top: 0.5em;
  margin-left: 0.5em;
}
dd
{
  margin-left: 0.5em;
  margin-bottom: 0.5em;
  padding-left: 3em;
}
ul
{
  margin-top: 0px;
  margin-bottom: 0px;
  margin-left: 0em;
  padding-left: 0em;
}
li
{
  margin-left: 0em;
}
img
{
  vertical-align: text-bottom;
}
h3
{
  color: #333377;
  background: #E8E8E8;
  font-weight: bold;
  margin-bottom: 0em;
  padding: 1px 4px 1px 4px;
  border: 1px solid #A0A0A0;
  font-size: 1em;
}
.not-implemented
{
  filter: url(css/filters.svg#grayscale); /* Firfox, etc */
  filter: gray; /* IE */
  opacity: 0.75;
  pointer-events: none;
}

.not-implemented:after
{
  content: ' -- coming soon';
}
.counter
{
  color: #999999;
  font-style: italic;
}

.require-permission
{
  color: #999999;
  font-style: italic;
}

</style>
</base:head>
<base:body onload="init()">

  <p:path><p:pathelement title="Reggie" /></p:path>

  <div class="content">
    <form name="reggie" onsubmit="return false;">
    <div class="absolutefull" style="width: 33%;">
      <div class="absolutefull" style="left: 1em; right: 0.5em; ">
      
        <h3>Sample processing wizards</h3>
        <dl class="leftborder rightborder bottomborder has-lib-prep">

        <dt>
          <base:icon image="<%=home+"/images/specimen.png" %>" />
          <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/specimentube.jsp?ID=<%=ID%>"
            >Specimen tube registration</span>
        </dt>
        <dd>
          <ul>
          <li>Register new specimen tubes.
          <li>Update existing specimen tubes.
          </ul>
        </dd>

        <dt>
          <base:icon image="<%=home+"/images/partition.png" %>" />
          <span class="require-permission" data-role="SamplePrep" data-link="sampleproc/partitionform.jsp?ID=<%=ID%>"
            >Partition wizard</span>
        </dt>
        <dd>
          <ul>
          <li>Register new partitions of existing specimens <span class="counter" id="count.specimen" title="Counting..."><img src="images/loading-small.gif"></span>
          </ul>
        </dd>
          
        <dt>
          <base:icon image="<%=home+"/images/extraction.png" %>" />
          DNA/RNA extraction wizards
        </dt>
        <dd>
          <ul>
          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/allprep_protocol.jsp?ID=<%=ID%>"
            >Lab tracking protocol for Allprep isolation</span> <span class="counter" id="count.lysate.1" title="Counting..."><img src="images/loading-small.gif"></span>

          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/extraction_registration.jsp?ID=<%=ID%>"
            >DNA/RNA/FlowThrough registration</span> <span class="counter" id="count.lysate.2" title="Counting..."><img src="images/loading-small.gif"></span>
          </ul>
        </dd>
        <dt>
          <base:icon image="<%=home+"/images/rnaqc.png" %>" />
          RNA quality control wizards
        </dt>
        <dd>
          <ul>
          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_aliquot.jsp?ID=<%=ID%>"
            >Create aliquots on Bioanalyzer/Caliper plates</span> <span class="counter" id="count.rnaqc" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_plate_export.jsp?ID=<%=ID%>"
            >Export Caliper sample names and run parameters</span> <span class="counter" id="count.caliper-plates.1" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="SamplePrep" data-link="sampleproc/rnaqc_plate_import.jsp?ID=<%=ID%>"
            >Import RQS scores from Caliper well table file</span> <span class="counter" id="count.caliper-plates.2" title="Counting..."><img src="images/loading-small.gif"></span>
          </ul>
        </dd>     
        </dl>
      
        <h3>Histology wizards</h3>
        <dl class="leftborder rightborder bottomborder">      
        <dt>
          <base:icon image="<%=home+"/images/histology.png" %>" />
          Embedding and staining wizards
        </dt>
        <dd>
          <ul>
          <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_protocol.jsp?ID=<%=ID%>"
            >Lab tracking protocol for FFPE/HE</span> <span class="counter" id="count.histology-lists" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_block.jsp?ID=<%=ID%>"
            >Register paraffin blocks</span> <span class="counter" id="count.paraffin-blocks" title="Counting..."><img src="images/loading-small.gif"></span>

          <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_labels.jsp?ID=<%=ID%>"
            >Download HE glass labels</span>
          
          <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_glass.jsp?ID=<%=ID%>"
            >Register HE glass</span> <span class="counter" id="count.paraffin-blocks-without-heglass" title="Counting..."><img src="images/loading-small.gif"></span>
        </dd>
        
        <dt>
          <base:icon image="<%=home+"/images/microscope.png" %>" />
          Scoring wizard
        </dt>
        <dd>
          <li><span class="require-permission" data-role="Histology" data-link="sampleproc/histology_score.jsp?ID=<%=ID%>"
            >Score HE glass</span> <span class="counter" id="count.unscored-heglass" title="Counting..."><img src="images/loading-small.gif"></span>
          </ul>
        </dd>
        </dl>
      
      
        <h3>Library preparation wizards</h3>
        <dl class="leftborder rightborder bottomborder">
      
        <dt>
          <base:icon image="<%=home+"/images/pipette.png" %>" />
          RNA to cDNA wizards
        </dt>
        <dd>
          <ul>
          <li><span class="require-permission" data-role="LibraryPlateDesigner" data-link="libprep/select_rna.jsp?ID=<%=ID%>"
            >Create new mRNA plate</span> <span class="counter" id="count.rna-without-mrna" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/mrna_protocol.jsp?ID=<%=ID%>"
            >Lab protocols for mRNA and cDNA preparation</span> <span class="counter" id="count.mrna-plates.1" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/mrna_registration.jsp?ID=<%=ID%>"
            >mRNA registration and quality control results</span> <span class="counter" id="count.mrna-plates.2" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/cdna_registration.jsp?ID=<%=ID%>"
            >cDNA registration</span> <span class="counter" id="count.cdna-plates.1" title="Counting..."><img src="images/loading-small.gif"></span>
          </ul>
        </dd>
        
        <dt>
          <base:icon image="<%=home+"/images/libprep.png" %>" />
          Library preparation wizards
        </dt>
        <dd>
          <ul>
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/assign_barcode.jsp?ID=<%=ID%>"
            >Assign barcodes to cDNA plate</span> <span class="counter" id="count.cdna-plates-for-barcoding" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/libprep_protocol.jsp?ID=<%=ID%>"
            >Lab protocols and files for library preparation</span> <span class="counter" id="count.lib-plates.1" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/libqc_registration.jsp?ID=<%=ID%>"
            >Register quality control results</span> <span class="counter" id="count.lib-plates.2" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/lib_registration.jsp?ID=<%=ID%>"
            >Library registration</span> <span class="counter" id="count.lib-plates.3" title="Counting..."><img src="images/loading-small.gif"></span>
          </ul>
        </dd>
        <dt>
          <base:icon image="<%=home+"/images/pool.png" %>" />
          Pooling wizards
        </dt>
        <dd>
          <ul>
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/create_pools.jsp?ID=<%=ID%>"
            >Create pooled libraries</span> <span class="counter" id="count.lib-plates-for-pooling" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/pool_protocol.jsp?ID=<%=ID%>"
            >Lab protocols for pooling</span> <span class="counter" id="count.pools.1" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/pool_registration.jsp?ID=<%=ID%>"
            >Register pooled libraries</span> <span class="counter" id="count.pools.2" title="Counting..."><img src="images/loading-small.gif"></span>
          </ul>
        </dd>
        
        <dt>
          <base:icon image="<%=home+"/images/flowcell.png" %>" />
          Clustering and sequencing wizards
        </dt>
        <dd>
          <ul>
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/create_flowcells.jsp?ID=<%=ID%>"
            >Create flow cells</span> <span class="counter" id="count.pools.3" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/flowcell_protocol.jsp?ID=<%=ID%>"
            >Lab protocol for clustering and sequencing</span> <span class="counter" id="count.flow-cells.1" title="Counting..."><img src="images/loading-small.gif"></span>
          
          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/flowcell_registration.jsp?ID=<%=ID%>"
            >Register clustering</span> <span class="counter" id="count.flow-cells.2" title="Counting..."><img src="images/loading-small.gif"></span>

          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/sequencing_started.jsp?ID=<%=ID%>"
            >Register sequencing started</span> <span class="counter" id="count.flow-cells.3" title="Counting..."><img src="images/loading-small.gif"></span>

          <li><span class="require-permission" data-role="LibraryPrep" data-link="libprep/sequencing_ended.jsp?ID=<%=ID%>"
            >Register sequencing ended</span> <span class="counter" id="count.sequencing-run" title="Counting..."><img src="images/loading-small.gif"></span>
          </ul>
        </dd>
        
        </dl>
      </div>
    </div>
    
    <div class="absolutefull" style="width: 34%; left: 33%; right: auto;">
      <div class="absolutefull" style="left: 0.5em; right: 0.5em;">
        <h3>Secondary analysis wizards</h3>
        <dl class="leftborder rightborder bottomborder">
          <dt>
            <base:icon image="<%=home+"/images/server.png" %>" />
            Demux and merge wizards
          </dt>
          <dd>
            <ul>
            <li><span class="require-permission" data-role="SecondaryAnalysis" data-link="analysis/sequencing_confirm.jsp?ID=<%=ID%>"
              >Confirm sequencing completed</span> <span class="counter" id="count.unconfirmed-sequencing-run" title="Counting..."><img src="images/loading-small.gif"></span>
            
            <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/demux_start.jsp?ID=<%=ID%>"
              >Start demux and merge</span> 
            <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/demux_end.jsp?ID=<%=ID%>"
              >Register demux and merge completed</span> 
            </ul>
          </dd>
          
          <dt>
            <base:icon image="<%=home+"/images/align.png" %>" />
            Filter and alignment wizards
          </dt>
          <dd>
            <ul>
            <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/filter_start.jsp?ID=<%=ID%>"
              >Start filter and alignment</span> 
            <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/align_end.jsp?ID=<%=ID%>"
              >Register filter and alignment completed</span> 
            </ul>
          </dd>
          <dt>
          
            <base:icon image="<%=home+"/images/wizard.png" %>" />
            Feature extraction wizards
          </dt>
          <dd>
            <ul>
            <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/feature_start.jsp?ID=<%=ID%>"
              >Start feature extraction</span> 
            <li><span class="require-permission not-implemented" data-role="SecondaryAnalysis" data-link="analysis/feature_end.jsp?ID=<%=ID%>"
              >Register feature extraction completed</span> 
            </ul>
          </dd>
        </dl>
      </div>
    </div>
    
    <div class="absolutefull" style="width: 33%; left: auto;">
      <div class="absolutefull" style="left: 0.5em; right: 1em;">
        <%
        if (isAdmin)
        {
          %>
          <h3>Server administrator wizards</h3>
          <dl class="leftborder rightborder bottomborder">
          <dt>
            <base:icon image="<%=home + "/images/install.png" %>" />
            <span class="require-permission" data-role="Administrator" data-link="admin/install.jsp?ID=<%=ID%>">Installation wizard</span>
          </dt>
          <dd>
            <ul>
            <li>Check that annotation types and other items used by Reggie exists in BASE.
            <li>Create missing items.
            </ul>
          </dd>
          </dl>
          <%
        }
        if (isPatientCurator || isAdmin)
        {
          %>
          <h3>Personal information wizards</h3>
          <dl class="leftborder rightborder bottomborder">
          <dt>
            <base:icon image="<%=home + "/images/personal.png" %>"/>
            <span class="require-permission" data-role="PatientCurator" data-link="personal/persinfo.jsp?ID=<%=ID%>"
              >Pathology referral form registration</span>
          </dt>
          <dd>
            <ul>
            <li>Register new cases and patients.
            <li>Update existing cases and specimen tubes.
            </ul>
          </dd>
          
          <dt>
            <base:icon image="<%=home + "/images/blood.png" %>"/>
            Blood referral form registration
          </dt>
          <dd>
            <ul>
            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/bloodform.jsp?ID=<%=ID%>"
              >Register new/updated blood referral forms and patients</span>
              
            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/bloodfollowupform.jsp?ID=<%=ID%>"
              >Register new/updated follow-up blood referral forms</span>
            </ul>
          </dd>
          
          <dt>
            <base:icon image="<%=home+"/images/consent.png" %>"/>
            <span class="require-permission" data-role="PatientCurator" data-link="personal/consentform.jsp?ID=<%=ID%>"
              >Consent form registration</span>
          </dt>
          <dd>
            <ul>
            <li>Register consent forms.
            </ul>
          </dd>
          
          <dt>
            <base:icon image="<%=home+"/images/export_import.png" %>" />
            Export/import information to/from external registers.
          </dt>
          <dd>
            <ul>
            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_monthly_oplist.jsp?ID=<%=ID%>"
              >Export monthly operation list</span>
              
            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_inca.jsp?ID=<%=ID%>"
              >INCA export</span>

            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_missing_data_sample_list.jsp?ID=<%=ID%>"
              >Export missing data sample list</span>

            <li><span class="require-permission" data-role="PatientCurator" data-link="personal/export_missing_consent_data_sample_list.jsp?ID=<%=ID%>"
              >Export missing consent data sample list</span>
            </ul>
          </dd>
          </dl>
          <%
        }
        %>
        
        <h3>Statistics and reporting wizards</h3>
        <dl class="leftborder rightborder bottomborder">
          <dt>
            <base:icon image="<%=home+"/images/case_summary.png" %>" />
            Case summary
          </dt>
          <dd>
            <table>
            <tr>
              <td><input type="text" class="text" 
                name="caseName" title="Please enter a 7-digit case id" 
                style="width: 25em;"
                onkeypress="if (event.keyCode==13 && this.value) caseSummary()"></td>
              <td><base:button title="Go" image="<%=home+"/images/gonext.png"%>" onclick="caseSummary()"/></td>
            </tr>
            </table>
          </dd>
        
          <dt>
            <base:icon image="<%=home+"/images/report.png" %>" />
            <a href="reports/samplereportgenerator.jsp?ID=<%=ID%>">Sample source report</a>
          </dt>       
          <dd>        
            <ul>
            <li>Sample count report</li> 
            <li>Consent count report</li> 
            <li>Patient count report</li> 
            <li>Overview report</li> 
            <li>Missing sample data report</li> 
            </ul>
          </dd>
          <dt>
            <base:icon image="<%=home+"/images/chart_bar.png" %>" />
            <a href="reports/scanbquartermonthreportgenerator.jsp?ID=<%=ID%>">Sample processing statistics</a>
          </dt>       
          <dd>        
            <ul>
            <li>SCAN-B quarter/month report</li> 
            </ul>
          </dd>
        </dl>
      </div>
    </div>
    </form>
  </div>
  
</base:body>
</base:page>
<%
}
finally
{
  if (dc != null) dc.close();
}
%>