source: extensions/net.sf.basedb.reggie/trunk/resources/batch/import-external-specimen.jsp @ 6211

<%@ page
  pageEncoding="UTF-8"
  session="false"
  import="net.sf.basedb.core.Application"
  import="net.sf.basedb.core.User"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.SessionControl"
  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"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
<%
final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
final String ID = sc.getId();
final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
DbControl dc = null;
try
{
  dc = sc.newDbControl();
  final User user = User.getById(dc, sc.getLoggedInUserId());
%>
<base:page type="default" >
<base:head 
  scripts="~../reggie-2.js,~import-external-specimen.js" 
  styles="path.css,~../css/reggie-2.css"
>
<style>


#importItemsTable
{
  width: 100%; 
  border-collapse: collapse;
}

#importItemsTable tr.highlight
{
  border-top-width: 1px;
  border-top-style: dotted;
}

#importItemsTable thead
{
  border-bottom-width: 1px;
  border-top-width: 1px;
}

#importItemsTable td
{
  text-align: center;
  min-width: 4.5em;
}

#importItemsTable tbody td
{
  padding: 1px 2px;
}

#importItemsTable td.icon
{
  width: 20px;
  min-width: 20px;
}

#importItemsTable td.valid
{
  text-align: left;
}

</style>
</base:head>
<base:body>

  <p:path><p:pathelement 
    title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
    /><p:pathelement title="Import externally processed samples" 
    /></p:path>

  <div class="content">
  <form name="reggie" id="wizard" class="wizard">
  
    <div class="step" id="step-1">
      <div class="step-no">1</div>
      <div class="step-content">
  
        <div id="itemTable"></div>
        
      </div>
    </div>
  
    <div class="step" id="step-2">
      <div class="step-no">2</div>
      <div class="step-title">FASTQ import options</div>
      <div class="step-content">
  
        <table class="step-form">
        <tbody>
          <tr>
            <td class="subprompt">Auto-analyze</td>
            <td class="input">
              <label><input type="radio" name="autoAnalyze" id="autoAnalyzeYes" disabled>Yes</label>
              <label><input type="radio" name="autoAnalyze" id="autoAnalyzeNo" disabled>No</label>
            </td>
            <td class="status" id="autoAnalyze.status"></td>
            <td class="help">
              <span id="autoAnalyze.message" class="message"></span>
              If the auto-analyze option is enabled, Reggie will automatically start
              importing the FASTQ files after a successful JSON import.
            </td>
          </tr>
          <tr>
            <td class="subprompt">Protocol</td>
            <td class="input">
              <select name="mergeProtocol" id="mergeProtocol" disabled></select>
            </td>
            <td class="status" id="mergeProtocol.status"></td>
            <td class="help">
              <span id="mergeProtocol.message" class="message"></span>
              Select the protocol used for merging.
            </td>
          </tr>
          <tr>
            <td class="subprompt">Software</td>
            <td class="input">
              <select name="mergeSoftware" id="mergeSoftware" disabled></select>
            </td>
            <td class="status" id="mergeSoftware.status"></td>
            <td class="help">
              <span id="mergeSoftware.message" class="message"></span>
              Select the software to use for merging the FASTQ files.
            </td>
          </tr>
        </tbody>
        <tbody>
          <tr class="section-header">
            <td colspan="4">Open Grid Scheduler</td>
          </tr>
          <tr>
            <td class="subprompt">Open Grid Cluster</td>
            <td class="input">
              <select name="clusters" id="clusters" class="required" disabled></select>
            </td>
            <td class="status" id="clusters.status"></td>
            <td class="help">
              <span id="clusters.message" class="message"></span>
              Select the cluster to use for running the analysis.
            </td>
          </tr>
          <tr>
            <td class="subprompt">Job priority</td>
            <td class="input">
              <select name="priority" id="priority" disabled></select>
            </td>
            <td class="status" id="priority.status"></td>
            <td class="help">
              <span id="priority.message" class="message"></span>
              Select the priority of the analysis jobs.
            </td>
          </tr>
          <tr>
            <td class="subprompt">Auto-confirm</td>
            <td class="input"><input type="checkbox" name="autoConfirm" checked disabled></td>
            <td class="status" id="autoConfirm.status"></td>
            <td class="help">
              <span id="autoConfirm.message" class="message"></span>
              If the FASTQ analysis is successful, with at least 10M reads 
              after trimmomatic and valid fragment size values, it is
              automatically confirmed and alignment is started.
            </td>
          </tr>
          <tr>
            <td class="subprompt">Debug</td>
            <td class="input"><input type="checkbox" name="debug" disabled></td>
            <td class="status" id="debug.status"></td>
            <td class="help">
              <span id="debug.message" class="message"></span>
              When running in debug mode only part of the sequenced data is used and
              temporary files are not removed from the cluster nodes.
            </td>
          </tr>
        </tbody>
        </table>
      </div>
    </div>
  
    <div id="wizard-status"></div>
    <div id="wizard-progress"></div>

    <table class="navigation" id="navigation">
    <tr>
      <td><base:button id="gocancel" title="Cancel" /></td>
      <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
      <td><base:button id="goregister" title="Register" image="<%=home+"/images/gonext.png"%>" /></td>
      <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
      <td id="gonext-message" class="message"></td>
    </tr>
    </table>
  </form>
  </div>
  
</base:body>
</base:page>
<%
}
finally
{
  if (dc != null) dc.close();
}
%>