source: extensions/net.sf.basedb.reggie/branches/ticket-422/resources/index.jsp @ 1745

<%@ 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;
  boolean hasCreateSamplePermission = sc.hasPermission(Permission.CREATE, Item.SAMPLE);
  boolean hasCreateExtractPermission = sc.hasPermission(Permission.CREATE, Item.EXTRACT);
  boolean hasCreateBioPlatePermission = sc.hasPermission(Permission.CREATE, Item.BIOPLATE);
  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">
  <link rel="stylesheet" type="text/css" href="css/reggie.css">
<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;
}
ul
{
  margin-top: 0px;
  margin-bottom: 0px;
}
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;
}
</style>
</base:head>
<base:body>

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

  <div class="content">
    <div class="absolutefull" style="width: 50%;">
      <div class="absolutefull" style="left: 1em; right: 0.5em; ">
        
        <%
        if (isAdmin)
        {
          %>
          <h3>Server administrator wizards</h3>
          <dl class="leftborder rightborder bottomborder">
          <dt>
            <base:icon image="<%=home + "/images/install.png" %>" />
            <a href="install.jsp?ID=<%=ID%>">Installation wizard</a>
          </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" %>"/>
            <a href="persinfo.jsp?ID=<%=ID%>">Pathology referral form registration</a>
          </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" %>"/>
            <a href="bloodform.jsp?ID=<%=ID%>">Blood referral form registration</a>
          </dt>
          <dd>
            <ul>
            <li>Register new blood referral forms and patients.
            <li>Update information for existing blood referral forms.
            </ul>
          </dd>
          
          <dt>
            <base:icon image="<%=home+"/images/consent.png" %>"/>
            <a href="consentform.jsp?ID=<%=ID%>">Consent form registration</a>
          </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><a href="export_monthly_oplist.jsp?ID=<%=ID%>">Export monthly operation list</a>
            </ul>
          </dd>
          </dl>
          <%
        }
        %>
        
        <h3>Laboratory wizards</h3>
        <dl class="leftborder rightborder bottomborder">
        <%
        if (hasCreateSamplePermission)
        {
          %>
          <dt>
            <base:icon image="<%=home+"/images/specimen.png" %>" />
            <a href="specimentube.jsp?ID=<%=ID%>">Specimen tube registration</a>
          </dt>
          <dd>
            <ul>
            <li>Register new specimen tubes.
            <li>Update existing specimen tubes.
            </ul>
          </dd>
          <%
        }
        if (hasCreateSamplePermission && hasCreateExtractPermission)
        {
          %>
          <dt>
            <base:icon image="<%=home+"/images/partition.png" %>" />
            <a href="partitionform.jsp?ID=<%=ID%>">Partition wizard</a>
          </dt>
          <dd>
            <ul>
            <li>Register new partitions of existing specimens.
            </ul>
          </dd>
          <%
        }
        if (hasCreateSamplePermission && hasCreateBioPlatePermission)
        {
          %>
          <dt>
            <base:icon image="<%=home+"/images/microscope.png" %>" />
            Histology wizards
          </dt>
          <dd>
            <ul>
            <li><a href="histology_protocol.jsp?ID=<%=ID%>">Lab tracking protocol for FFPE/HE</a>
            <li><a href="histology_block.jsp?ID=<%=ID%>">Register paraffin blocks</a>
            <li><a href="histology_glass.jsp?ID=<%=ID%>">Register histology HE glass information</a>
            </ul>
          </dd>
          <%
        }
        if (hasCreateExtractPermission)
        {
          %>
          <dt>
            <base:icon image="<%=home+"/images/extraction.png" %>" />
            DNA/RNA extraction wizards
          </dt>
          <dd>
            <ul>
            <li><a href="allprep_protocol.jsp?ID=<%=ID%>">Lab tracking protocol for Allprep isolation</a>
            <li><a href="extraction_registration.jsp?ID=<%=ID%>">DNA/RNA/FlowThrough registration</a>
            </ul>
          </dd>
          <dt>
            <base:icon image="<%=home+"/images/rnaqc.png" %>" />
            RNA quality control wizards
          </dt>
          <dd>
            <ul>
            <li><a href="rnaqc_aliquot.jsp?ID=<%=ID%>">Create aliquots on Bioanalyzer/Caliper plates</a>
            <li><a href="rnaqc_plate_export.jsp?ID=<%=ID%>">Export Caliper sample names and run parameters</a>
            <li><a href="rnaqc_plate_import.jsp?ID=<%=ID%>">Import RQS scores from Caliper well table file</a>
            </ul>
          </dd>
          <%
        }
        %>        
        </dl>
      </div>
    </div>
    
    <div class="absolutefull" style="width: 50%; left: auto;">
      <div class="absolutefull" style="left: 0.5em; right: 1em;">
        <h3>Reggie reports</h3>
        <dl class="leftborder rightborder bottomborder">
          <dt>
            <base:icon image="<%=home+"/images/report.png" %>" />
            <a href="samplereportgenerator.jsp?ID=<%=ID%>">Report generator</a>
          </dt>       
          <dd>        
            <ul>
            <li>Sample count report</li> 
            <li>Consent count report</li> 
            </ul>
          </dd>
        </dl>
      
      
        <h3>Library preparation wizards</h3>
        <dl class="leftborder rightborder bottomborder">
        <%
        if (hasCreateExtractPermission && hasCreateBioPlatePermission)
        {
          %>
          <dt>
            <base:icon image="<%=home+"/images/pipette.png" %>" />
            RNA to cDNA wizards
          </dt>
          <dd>
            <ul>
            <li><a href="libprep/select_rna.jsp?ID=<%=ID%>">Create new mRNA plate</a>
            <li><a href="libprep/mrna_protocol.jsp?ID=<%=ID%>">Lab tracking protocol for mRNA and cDNA preparation</a>
            <li><a href="?ID=<%=ID%>">Export files for mRNA quality control</a>
            <li><a href="?ID=<%=ID%>">Import mRNA quality control results</a>
            <li><a href="?ID=<%=ID%>">cDNA registration</a>
            </ul>
          </dd>
          <%
        }
        %>
        </dl>
      
      </div>
    </div>

  </div>
  
</base:body>
</base:page>
<%
}
finally
{
  if (dc != null) dc.close();
}
%>