source: extensions/net.sf.basedb.reggie/trunk/resources/libprep/sequencing_started.jsp @ 2237

<%@ page
  pageEncoding="UTF-8"
  session="false"
  import="net.sf.basedb.core.User"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.SessionControl"
  import="net.sf.basedb.core.Application"
  import="net.sf.basedb.clients.web.Base" 
  import="net.sf.basedb.clients.web.util.HTML"  
  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
%>
<%@ 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());
%>
<base:page type="default" >
<base:head scripts="ajax.js" styles="path.css">
  <link rel="stylesheet" type="text/css" href="../css/reggie.css">
  <script language="JavaScript" src="../reggie.js" type="text/javascript" charset="UTF-8"></script>

<script language="JavaScript">

var debug = 1;
var currentStep = 1;
var runParametersIsValid = false;

var runParameters;
var flowCell;

function goNextAuto()
{
  goNext(false);
}

function goNext(manual)
{
  setInnerHTML('gonext.message', '');
  if (currentStep == 1)
  {
    if (step1IsValid()) gotoStep2();
  }
}


function step1IsValid()
{
  return runParametersIsValid;
}


function init()
{
  var frm = document.forms['reggie'];
  
  // Load sequencing protocols
  var sequencingProtocols = getProtocols('SEQUENCING_PROTOCOL');
  for (var i = 0; i < sequencingProtocols.length; i++)
  {
    var protocol = sequencingProtocols[i];
    frm.sequencingProtocol[frm.sequencingProtocol.length] = new Option(protocol.name, protocol.id, protocol.isDefault);
    setInputStatus('sequencingProtocol', '', 'valid');
  }
  if (frm.sequencingProtocol.length == 0)
  {
    frm.sequencingProtocol[0] = new Option('- none -', '');
  }
  
  // Load sequencing machines
  var sequencers = getHardware('SEQUENCER');
  for (var i = 0; i < sequencers.length; i++)
  {
    var sequencer = sequencers[i];
    frm.sequencer[frm.sequencer.length] = new Option(sequencer.name, sequencer.id, sequencer.isDefault);
    setInputStatus('sequencer', '', 'valid');
  }
  if (frm.sequencer.length == 0)
  {
    frm.sequencer[0] = new Option('- none -', '');
  }
}

function getProtocols(subtype)
{
  var request = Ajax.getXmlHttpRequest();
  try
  {
    showLoadingAnimation('Loading ' + subtype + ' protocols...');
    var url = '../Protocol.servlet?ID=<%=ID%>&cmd=GetProtocols&subtype='+subtype;   
    request.open("GET", url, false);  
    request.send(null);
  }
  finally
  {
    hideLoadingAnimation();
  }

  if (debug) Main.debug(request.responseText);
  var response = JSON.parse(request.responseText);  
  if (response.status != 'ok')
  {
    setFatalError(response.message);
    return false;
  }
  return response.protocols;
}

function getHardware(subtype)
{
  var request = Ajax.getXmlHttpRequest();
  try
  {
    showLoadingAnimation('Loading ' + subtype + ' hardware...');
    var url = '../Hardware.servlet?ID=<%=ID%>&cmd=GetHardware&subtype='+subtype;    
    request.open("GET", url, false);  
    request.send(null);
  }
  finally
  {
    hideLoadingAnimation();
  }

  if (debug) Main.debug(request.responseText);
  var response = JSON.parse(request.responseText);  
  if (response.status != 'ok')
  {
    setFatalError(response.message);
    return false;
  }
  return response.hardware;
}


function runParametersXmlFileOnChange(event)
{
  var frm = document.forms['reggie'];
  var file = event.target.files[0];
  
  // Clear information
  setInnerHTML('experimentName', '');
  setInnerHTML('externalId', '');
  setInnerHTML('runId', '');
  setInnerHTML('position', '');
  setInnerHTML('runNumber', '');
  setInnerHTML('startDate', '');
  setInnerHTML('sequencingCycles', '');
  setInnerHTML('flowCellName', 'Flow cell information');
  setInnerHTML('pools', '');
  setInnerHTML('libPlate', '');
  Main.hide('existing-sequencing-runs');
  setInnerHTML('existing-sequencing-runs', '');
  
  var reader = new FileReader();
  reader.onload = runParametersXmlFileLoaded;
  reader.readAsText(file);
}

function runParametersXmlFileLoaded(event)
{
  parseRunParametersXmlFile(event.target.result);
  var frm = document.forms['reggie'];
  frm.comments.focus();
}


function parseRunParametersXmlFile(data)
{
  var frm = document.forms['reggie'];
  runParametersIsValid = false;
  setInputStatus('runParametersXml', '', '');
  
  var doc;
  try
  {
    var parser = new DOMParser();
    doc = parser.parseFromString(data, "application/xml");
  
    if (doc.documentElement.tagName == 'parsererror')
    {
      setInputStatus('runParametersXml', doc.documentElement.firstChild.textContent.split(/\n/)[0], 'invalid');
      return;
    }
  }
  catch (err)
  {
    setInputStatus('runParametersXml', err, 'invalid');
    return;
  }
  
  var info = {};
  try
  {
    info.ExperimentName = getTextValue(doc, 'ExperimentName');
    info.RunID = getTextValue(doc, 'RunID');
    info.HiSeqPosition = getTextValue(doc, 'FCPosition');
    info.ScannerID = getTextValue(doc, 'ScannerID');
    info.ScanNumber = parseInt(getTextValue(doc, 'ScanNumber'));
    info.FlowCellID = getTextValue(doc, 'Barcode');
    info.SequencingCycles = getTextValue(doc, 'Read1') + '-' + getTextValue(doc, 'IndexRead1') + '-' + getTextValue(doc, 'Read2');
    info.SequencingStart = '20'+getTextValue(doc, 'RunStartDate');

    validateAndCopyRunParameters(info);
  }
  catch (msg)
  {
    setInputStatus('runParametersXml', msg, 'invalid');
    if (debug) Main.debug(JSON.stringify(info));
    return;
  }
  
  runParametersIsValid = true;
  runParameters = info;
  setInputStatus('runParametersXml', '', 'valid');

  if (debug) Main.debug(JSON.stringify(info));
}


function getTextValue(doc, selector)
{
  var el = doc.querySelector(selector);
  if (el == null)
  {
    throw "Can't find tag &lt;"+selector+"&gt;";
  }
  return el.textContent;
}

function validateAndCopyRunParameters(info)
{
  var frm = document.forms['reggie'];

  setInnerHTML('experimentName', info.ExperimentName);
  setInnerHTML('externalId', info.FlowCellID);
  setInnerHTML('runId', info.RunID);
  setInnerHTML('position', info.HiSeqPosition);
  setInnerHTML('runNumber', info.ScanNumber);
  setInnerHTML('startDate', formatDate(info.SequencingStart));
  setInnerHTML('sequencingCycles', info.SequencingCycles);

  flowCell = getFlowCellInfoByBarcode(info.FlowCellID);
  if (flowCell == null)
  {
    setInnerHTML('flowCellName', 'Can\'t find flow cell ' + info.FlowCellID);
    throw 'Flow cell with ID='+info.FlowCellID+' not found.';
  }
  
  setInnerHTML('flowCellName', Main.encodeTags(flowCell.name));

  var pools = flowCell.pools;
  var html = '';
  var libPlateHtml = '';
  for (var poolNo = 0; poolNo < pools.length; poolNo++)
  {
    var pool = pools[poolNo];
    if (poolNo > 0) html += ', ';
    html += Main.encodeTags(pool.name);
    if (pool.LibPlate && libPlateHtml.indexOf(pool.LibPlate.name) == -1)
    {
      if (libPlateHtml.length > 0) libPlateHtml += ', ';
      libPlateHtml += Main.encodeTags(pool.LibPlate.name);
    }
  }
  setInnerHTML('pools', html);
  setInnerHTML('libPlate', libPlateHtml || 'n/a');

  var html = '';
  html += '<tr valign="top" class="fc-info">';
  html += '<td class="prompt" colspan="2">Existing sequencing runs</td>';
  html += '';
  html += '<td class="status"></td>';
  html += '<td class="help">Start and end date is shown for other registered sequencing runs.</td>';
  html += '</tr>';

  var seqRuns = getSequencingRunsForFlowCell(flowCell);
  var runExists = null;
  if (seqRuns.length > 0)
  {
    for (var seqNo = 0; seqNo < seqRuns.length; seqNo++)
    {
      var seqRun = seqRuns[seqNo];
      html += '<tr valign="top" class="fc-info">';
      html += '<td class="subprompt">'+seqRun.name+'</td>';
      html += '<td class="input" colspan="2">';
      html += formatDate(seqRun.SequencingStart, '(no start date)') + ' -- ' + formatDate(seqRun.SequencingEnd, '(no end date)');
      if (seqRun.SequencingResult)
      {
        html += ': ' + seqRun.SequencingResult;
      }
      html += '</td>';
      html += '<td class="help"></td>';
      html += '</tr>';
      if (seqRun.DataFilesFolder == info.RunID)
      {
        runExists = seqRun;
      }
    }
  }
  else
  {
    html += '<tr valign="top" class="fc-info">';
    html += '<td class="subprompt"></td>';
    html += '<td class="input" colspan="2">';
    html += 'none';
    html += '</td>';
    html += '<td class="help"></td>';
    html += '</tr>';
    
  }
  Main.show('existing-sequencing-runs');
  setInnerHTML('existing-sequencing-runs', html);
  if (runExists != null)
  {
    throw 'This sequencing run has already been registered: ' + runExists.name;
  }
  
}

function getFlowCellInfoByBarcode(barcode)
{
  var url = '../FlowCell.servlet?ID=<%=ID%>&cmd=GetFlowCellByBarcode';
  url += '&barcode='+encodeURIComponent(barcode);
  
  var request = Ajax.getXmlHttpRequest();
  try
  {
    showLoadingAnimation('Checking flow cell id...');
    request.open("GET", url, false);
    request.send(null);
  }
  finally
  {
    hideLoadingAnimation();
  }
  
  if (debug) Main.debug(request.responseText);
  var response = JSON.parse(request.responseText);

  if (response.status != 'ok')
  {
    throw response.message;
  }

  return response.flowCell;
}

function getSequencingRunsForFlowCell(flowCell)
{
  var url = '../SequencingRun.servlet?ID=<%=ID%>&cmd=GetSequencingRunsForFlowCell';
  url += '&flowCell='+flowCell.id;
  
  var request = Ajax.getXmlHttpRequest();
  try
  {
    showLoadingAnimation('Loading sequencing runs...');
    request.open("GET", url, false);
    request.send(null);
  }
  finally
  {
    hideLoadingAnimation();
  }
  
  if (debug) Main.debug(request.responseText);
  var response = JSON.parse(request.responseText);

  if (response.status != 'ok')
  {
    throw response.message;
  }

  return response.sequencingRuns;
}

function formatDate(value, defaultValue)
{
  if (!value) return defaultValue || '';
  if (value.length == 8)
  {
    // YYYYMMDD
    value = value.substr(0, 4) + '-' + value.substr(4, 2) + '-' + value.substr(6, 2);
  }
  else if (value.length == 13)
  {
    // YYYYMMDD HHMM
    value = value.substr(0, 4) + '-' + value.substr(4, 2) + '-' + value.substr(6, 2) + ' ' + value.substr(9, 2) + ':' + value.substr(11, 2);
  }
  return value;
}


function goRegister()
{
  if (!step1IsValid()) return;
  var frm = document.forms['reggie'];

  frm.sequencingOperator.disabled = true;
  frm.sequencer.disabled = true;
  frm.sequencingProtocol.disabled = true;
  frm.comments.disabled = true;
  
  Main.hide('goregister');
  Main.hide('gocancel');
  Main.hide('gonext.message');
  
  var submitInfo = {};
  submitInfo.flowCell = flowCell;
  submitInfo.runParameters = runParameters;
  
  var sequencingRun = {};
  sequencingRun.operator = frm.sequencingOperator.value;
  sequencingRun.sequencer = parseInt(frm.sequencer.value);
  sequencingRun.protocol = parseInt(frm.sequencingProtocol.value);
  sequencingRun.comments = frm.comments.value;
  submitInfo.sequencingRun = sequencingRun;
  
  if (debug) Main.debug(JSON.stringify(submitInfo));
  var url = '../SequencingRun.servlet?ID=<%=ID%>&cmd=RegisterSequencingStarted';
  var request = Ajax.getXmlHttpRequest();
  
  try
  {
    showLoadingAnimation('Performing registration...');
    request.open("POST", url, false);
    request.send(JSON.stringify(submitInfo));
  }
  finally
  {
    hideLoadingAnimation();
  }
  
  if (debug) Main.debug(request.responseText);
  var response = JSON.parse(request.responseText);
  
  if (response.messages && response.messages.length > 0)
  {
    var msg = '<ul>';
    for (var i = 0; i < response.messages.length; i++)
    {
      var msgLine = response.messages[i];
      if (msgLine.indexOf('[Warning]') >= 0)
      {
        msg += '<li class="warning">' + msgLine.replace('[Warning]', '');
      }
      else
      {
        msg += '<li>' + msgLine;
      }
    }
    msg += '</ul>';
    setInnerHTML('messages', msg);
    Main.show('messages');
  }
  
  if (response.status != 'ok')
  {
    Main.addClass(document.getElementById('messages'), 'failure');
    setFatalError(response.message);
    return false;
  }

  Main.show('gorestart'); 
}

</script>
<style>

.fc-info
{
  background-color: #F4F4F4;
}

.fc-info .subprompt
{
  font-weight: normal;
  padding-left: 2em;
  text-align: left;
}

.fc-info .input
{
  font-style: italic;
}

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

  <p:path><p:pathelement 
    title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
    /><p:pathelement title="Register sequencing started" 
    /></p:path>

  <div class="content">
  <%
  if (sc.getActiveProjectId() == 0)
  {
    %>
    <div class="messagecontainer note" style="width: 950px; margin-left: 20px; margin-bottom: 20px; margin-right: 0px; font-weight: bold; color: #cc0000;">
      No project has been selected. You may proceed with the registration but 
      created items will not be shared.
    </div>
    <%
  }
  %>

  <form name="reggie" onsubmit="return false;">
  <div id="step.1.section">
  <table class="stepform">
  <tr>
    <td rowspan="3" class="stepno">1</td>
    <td class="steptitle">Sequencing startup information</td>
  </tr>
  <tr>
    <td class="stepfields">
      <table style="border-collapse: collapse;">
      <tr valign="top">
        <td class="prompt">Operator</td>
        <td class="input">
          <input type="text" name="sequencingOperator" value="<%=HTML.encodeTags(user.getName()) %>" 
            style="width: 90%;" maxlength="255" onkeypress="focusOnEnter(event, 'sequencer')">
        </td>
        <td class="status" id="sequencingOperator.status"></td>
        <td class="help">
          <span id="sequencingOperator.message" class="message" style="display: none;"></span>
        </td>
      </tr>
      <tr valign="top">
        <td class="prompt">Sequencing machine</td>
        <td class="input"><select style="width:90%" name="sequencer" id="sequencer" 
          onkeypress="focusOnEnter(event, 'sequencingProtocol')"></select></td>
        <td class="status" id="sequencer.status"></td>
        <td class="help"><span id="sequencer.message" class="message" style="display: none;"></span>
          Select the HiSeq machine which is used for sequencing.
        </td>
      </tr>
      <tr valign="top">
        <td class="prompt">Protocol</td>
        <td class="input"><select style="width:90%" name="sequencingProtocol" id="sequencingProtocol" 
          onkeypress="focusOnEnter(event, 'fc-0.externalId')"></select></td>
        <td class="status" id="sequencingProtocol.status"></td>
        <td class="help"><span id="sequencingProtocol.message" class="message" style="display: none;"></span>
          Select the protocol which was used in the clustering.
        </td>
      </tr>
      <tr valign="baseline">
        <td class="prompt">runParameters.xml</td>
        <td class="input">
          <input type="file" multiple class="required" name="runParametersXml" onchange="runParametersXmlFileOnChange(event)" style="width: 90%;">
        </td>
        <td class="status" id="runParametersXml.status"></td>
        <td class="help" rowspan="12"><span id="runParametersXml.message" class="message" style="display:none;"></span>
          Select the <b>runParameters.xml</b> file that was created by the HiSeq. Typically found in
          <b>D:\Illumina\HiSeqTemp\&lt;run-folder&gt;</b> subfolder.
        </td>
      </tr>
      <tr valign="top" class="fc-info" style="border-top: 1em solid transparent;">
        <td class="prompt" colspan="2">Sequencing information</td>
        <td class="status"></td>
      </tr>
      <tr valign="top" class="fc-info">
        <td class="subprompt">Experiment</td>
        <td class="input" id="experimentName"></td>
        <td class="status"></td>
      </tr>
      <tr valign="top" class="fc-info">
        <td class="subprompt">RunID</td>
        <td class="input" id="runId"></td>
        <td class="status"></td>
      </tr>
      <tr valign="top" class="fc-info">
        <td class="subprompt">Barcode</td>
        <td class="input" id="externalId"></td>
        <td class="status"></td>
      </tr>
      <tr valign="top" class="fc-info">
        <td class="subprompt">HiSeq position</td>
        <td class="input" id="position"></td>
        <td class="status"></td>
      </tr>
      <tr valign="top" class="fc-info">
        <td class="subprompt">Run number</td>
        <td class="input" id="runNumber"></td>
        <td class="status"></td>
      </tr>
      <tr valign="top" class="fc-info">
        <td class="subprompt">Start date</td>
        <td class="input" id="startDate"></td>
        <td class="status"></td>
      </tr>
      <tr valign="top" class="fc-info">
        <td class="subprompt">Sequencing cycles</td>
        <td class="input" id="sequencingCycles"></td>
        <td class="status"></td>
      </tr>
      <tr valign="top" class="fc-info">
        <td class="prompt" colspan="2" id="flowCellName">Flow cell information</td>
        <td class="status"></td>
      </tr>
      <tr valign="top" class="fc-info">
        <td class="subprompt">Pools</td>
        <td class="input" id="pools"></td>
        <td class="status"></td>
      </tr>
      <tr valign="top" class="fc-info">
        <td class="subprompt">LibPlate</td>
        <td class="input" id="libPlate"></td>
        <td class="status"></td>
      </tr>
      <tbody id="existing-sequencing-runs" style="border-bottom: 1em solid transparent;">
      <tr valign="top" class="fc-info">
        <td class="subprompt"></td>
        <td class="input"></td>
        <td class="status"></td>
        <td class="help"></td>
      </tr>
      </tbody>
      <tr valign="top">
        <td class="prompt">Comments</td>
        <td class="input"><textarea rows="6" cols="50" style="width: 95%;" name="comments"></textarea></td>
        <td class="status" id="comments.status"></td>
        <td class="help"><span id="comments.message" class="message" style="display: none;"></span>
          Comments about the sequencing startup.
        </td>
      </tr>
      </table>
    </td>
  </tr>
  </table>
  </div>
  
  
  <div class="loading" id="loading" style="display: none;"><table><tr><td><img src="../images/loading.gif"></td><td id="loading.msg">Please wait...</td></tr></table></div>
  
  <div class="messagecontainer error" id="errorMessage" style="display: none; width: 950px; margin-left: 20px; margin-bottom: 0px;"></div>
  
  <div id="messages" class="success" style="display: none; width: 950px; margin-left: 20px; margin-top: 20px;"></div>
  
  <table style="margin-left: 20px; margin-top: 10px;" class="navigation">
    <tr>
      <td><base:button id="gocancel" title="Cancel" onclick="goRestart(false)" style="display: none;"/></td>
      <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" onclick="goNext(true)" style="display: none;"/></td>
      <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>" onclick="goRegister()" /></td>
      <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" onclick="goRestart(true)" style="display: none;"/></td>
      <td id="gonext.message" class="message"></td>
    </tr>
  </table>
  
  </form>
  </div>
  
</base:body>
</base:page>
<%
}
finally
{
  if (dc != null) dc.close();
}
%>