source: extensions/net.sf.basedb.reggie/trunk/resources/libprep/mrna_registration.jsp @ 2073

<%@ 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 MRNA_QC_FILES_PATH = '/home/SCANB/MRnaPlateQC';
var firstBrowse = true;
var subtypeBioAnalyzerPdf;

var debug = false;
var currentStep = 1;

var dateIsValid = [];

var pdfIsValid = false;
var commentsIsValid = false;

function init()
{
  var frm = document.forms['reggie'];
  var bioplates = getMRnaBioPlates();
  
  // Load existing mRNA plates not yet registered
  var plates = frm.bioplate;
  if (bioplates != null && bioplates.length > 0)
  {
    for (var i=0; i < bioplates.length; i++)
    {
      var bioplate = bioplates[i];
      var option = new Option(bioplate.name, bioplate.id);
      option.comments = bioplate.comments;
      plates.options[plates.length] = option;
    }
    bioplateIsValid = true;
    setInputStatus('bioplate', '', 'valid');
    bioPlateOnChange();
    outcomeOnChange();
  }
  else
  {
    var msg = 'No mRNA bioplates available for processing.';
    setFatalError(msg);
    return;
  }

  // All is ok
  frm.bioplate.focus();
}


function goNextAuto()
{
  goNext(false);
}

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



function getMRnaBioPlates()
{
  var frm = document.forms['reggie']; 
  
  var request = Ajax.getXmlHttpRequest();
  try
  {
    showLoadingAnimation('Loading histology work lists...');
    var url = '../MRna.servlet?ID=<%=ID%>&cmd=GetUnprocessedPlates&plateType=MRNA';   
    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.bioplates;
}

function gotoStep2()
{
  var frm = document.forms['reggie']; 
  frm.bioplate.disabled = true;
  frm.outcome[0].disabled = true;
  frm.outcome[1].disabled = true;

  
  currentStep = 2;
  Main.show('step.2.section');
  Main.addClass(document.getElementById('step.1.section'), 'disabled');
  Main.hide('gonext');
  Main.show('gocancel');
  Main.show('goregister');
  
  // Load mRNA protocols
  var mrnaProtocols = getProtocols('MRNA_PROTOCOL');
  for (var i = 0; i < mrnaProtocols.length; i++)
  {
    var protocol = mrnaProtocols[i];
    frm.mrnaProtocol[frm.mrnaProtocol.length] = new Option(protocol.name, protocol.id, protocol.isDefault);
    setInputStatus('mrnaProtocol', '', 'valid');
  }
  if (frm.mrnaProtocol.length == 0)
  {
    frm.mrnaProtocol[0] = new Option('- none -', '');
  }

  if (document.getElementById('outcomeFailed').checked)
  {
    setInnerHTML('gonext.message', '<input type="checkbox" name="verifyFailure" onclick="verifyFailureOnClick()"> Check to verify registration of failure');
    Main.addClass(document.getElementById('goregister'), 'disabled');
  }
  
  frm.dilutionDate.focus();
}

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 bioPlateOnChange()
{
  var frm = document.forms['reggie'];
  frm.comments.value = frm.bioplate[frm.bioplate.selectedIndex].comments;
  commentsOnChange();
}

function outcomeOnChange()
{
  var frm = document.forms['reggie'];
  Main.addOrRemoveClass(frm['pdf.path'], 'required', document.getElementById('outcomeSuccess').checked);
  Main.addOrRemoveClass(frm['comments'], 'required', document.getElementById('outcomeFailed').checked);
  pdfFileOnChange();
  commentsOnChange();
}

function browseOnClick(extension)
{
  var frm = document.forms['reggie'];
  if (frm[extension+'.path'].disabled) return;
  if (firstBrowse)
  {
    firstBrowse = false;
    setCurrentDirectory('<%=ID%>', MRNA_QC_FILES_PATH, debug, '../');
    subtypeBioAnalyzerPdf = getSubtypeInfo('<%=ID%>', 'BIOANALYZER_PDF', debug, '../');
  }
  var url = getRoot() + 'filemanager/index.jsp?ID=<%=ID%>&cmd=SelectOne&callback=setFileCallback';
  url += '&resetTemporary=1&tmpfilter:STRING:name='+escape('%.' + extension.substr(0, 3));
  if (subtypeBioAnalyzerPdf)
  {
    url += '&tmpfilter:INT:itemSubtype='+subtypeBioAnalyzerPdf.id;
  }
  lastExtension = extension;
  Main.openPopup(url, 'SelectFile', 1000, 700);
}

function setFileCallback(id, path)
{
  var frm = document.forms['reggie'];
  frm[lastExtension+'.id'].value = id;
  frm[lastExtension+'.path'].value = path;
  setInputStatus(lastExtension, '', 'valid');
  if (lastExtension == 'pdf')
  {
    pdfIsValid = true;
  }
}

function pdfFileOnChange()
{
  var frm = document.forms['reggie'];
  if (!frm['pdf.id'].value)
  {
    var outcomeSuccess = document.getElementById('outcomeSuccess');
    pdfIsValid = false;
    // A PDF is reuired for successful registration, optional after a failure
    var status = outcomeSuccess.checked ? 'invalid' : 'warning';
    if (!frm['pdf.path'].value)
    {
      setInputStatus('pdf', 'Missing', status);
      pdfIsValid = !outcomeSuccess.checked;
    }
    else
    {
      setInputStatus('pdf', 'Use the Browse button to select a file', 'invalid');
    }
  }
}

function dateOnChange(dateField)
{
  var frm = document.forms['reggie'];

  setInputStatus(dateField, '', '');
  dateIsValid[dateField] = true;
  var date = frm[dateField].value;

  if (date == '')
  {
    setInputStatus(dateField, 'Missing date', 'warning');
    return;
  }

  // Auto-fill the date if it's only given with 4(MMdd) or 6(yyMMdd) digits.    
  date = autoFillDate(date);
  frm[dateField].value = date;
  if (!Dates.isDate(date, 'yyyyMMdd'))
  {
    setInputStatus(dateField, 'Not a valid date', 'invalid');
    dateIsValid[dateField] = false;
    return;
  }
  
  setInputStatus(dateField, '', 'valid');
}

function setDate(frmName, dateField, date)
{
  var frm = document.forms['reggie'];
  frm[dateField].value = date;
  dateOnChange(dateField);
  frm[dateField].focus();
}

function commentsOnChange()
{
  var frm = document.forms['reggie'];
  commentsIsValid = false;
  setInputStatus('comments', '', '');
  
  var comments = frm.comments.value;
  
  if (comments == '' && document.getElementById('outcomeFailed').checked)
  {
    setInputStatus('comments', 'Missing', 'invalid');
    return;
  }

  setInputStatus('comments', '', 'valid');
  commentsIsValid = true;
}

function step2IsValid()
{
  var frm = document.forms['reggie'];
  if (!pdfIsValid || !commentsIsValid) return false;
  
  if (dateIsValid['dilutionDate'] == false) return false;
  if (dateIsValid['purificationDate'] == false) return false;
  if (dateIsValid['fragmentationDate'] == false) return false;
  if (dateIsValid['cleanupDate'] == false) return false;
  
  if (document.getElementById('outcomeFailed').checked && !frm.verifyFailure.checked) return false;
  
  return true;
}

function verifyFailureOnClick()
{
  var frm = document.forms['reggie'];
  var checked = frm.verifyFailure.checked;
  Main.addOrRemoveClass(document.getElementById('goregister'), 'disabled', !checked);
}

function goRegister()
{
  if (!step2IsValid()) return;

  var frm = document.forms['reggie'];
  var pdfId = parseInt(frm['pdf.id'].value, 10);
  
  Main.hide('goregister');
  Main.hide('gocancel');
  Main.hide('gonext.message');
  Main.addClass(document.getElementById('step.2.section'), 'disabled');

  frm['pdf.path'].disabled = true;
  Main.addClass(document.getElementById('btnPdf'), 'disabled');
  frm.dilutionDate.disabled = true;
  frm.dilutionOperator.disabled = true;
  frm.purificationDate.disabled = true;
  frm.purificationOperator.disabled = true;
  frm.fragmentationDate.disabled = true;
  frm.fragmentationOperator.disabled = true;
  frm.cleanupDate.disabled = true;
  frm.cleanupOperator.disabled = true;
  frm.mrnaProtocol.disabled = true;
  frm.comments.disabled = true;
  
  var submitInfo = {};
  submitInfo.bioplate = parseInt(frm.bioplate.value, 10);
  submitInfo.mrnaProtocol = parseInt(frm.mrnaProtocol.value, 10);
  submitInfo.failed = document.getElementById('outcomeSuccess').checked ? false : true;
  submitInfo.pdf = pdfId;
  submitInfo.dilutionDate = frm.dilutionDate.value;
  submitInfo.dilutionOperator = frm.dilutionOperator.value;
  submitInfo.purificationDate = frm.purificationDate.value;
  submitInfo.purificationOperator = frm.purificationOperator.value;
  submitInfo.fragmentationDate = frm.fragmentationDate.value;
  submitInfo.fragmentationOperator = frm.fragmentationOperator.value;
  submitInfo.cleanupDate = frm.cleanupDate.value;
  submitInfo.cleanupOperator = frm.cleanupOperator.value;
  submitInfo.comments = frm.comments.value;
  
  if (debug) Main.debug(JSON.stringify(submitInfo));
  var url = '../MRna.servlet?ID=<%=ID%>&cmd=ImportMRnaQCResults';
  
  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>

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

  <p:path><p:pathelement 
    title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
    /><p:pathelement title="mRNA registration and quality control results" 
    /></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;">
    <input type="hidden" name="pdf.id" value="">
  
  <div id="step.1.section">
  <table class="stepform">
  <tr>
    <td rowspan="3" class="stepno">1</td>
    <td class="steptitle">Select mRNA bioplate</td>
  </tr>
  <tr>
    <td class="stepfields">
      <table>
      <tr valign="top">
        <td class="prompt">mRNA bioplate</td>
        <td class="input"><select class="required" style="width:90%;" 
            name="bioplate" id="bioplate" onchange="bioPlateOnChange()"></select>
        </td>
        <td class="status" id="bioplate.status"></td>
        <td class="help"><span id="bioplate.message" class="message" style="display: none;"></span>
          Select an existing mRNA bioplate. The list contain all mRNA bioplates that
          has not yet been processed (determined by the absence of a 'creation' date).
        </td>
      </tr>
      <tr valign="top">
        <td class="prompt">Outcome</td>
        <td class="input">
          <input type="radio" name="outcome" id="outcomeSuccess" 
            onchange="outcomeOnChange()" checked><label for="outcomeSuccess">Success</label> - continue processing to cDNA<br>
          <input type="radio" name="outcome" id="outcomeFailed" 
            onchange="outcomeOnChange()"><label for="outcomeFailed">Failure</label> - no further processing to cDNA
        </td>
        <td class="status"></td>
        <td class="help">
          Select the <b>Failure</b> option if further processing to cDNA is not possible.
          No child cDNA plate will be created and existing RNA will be flagged and added
          to the <b>Flagged RNA</b> list.
        </td>
      </tr>
      </table>
    </td>
  </tr>
  </table>
  </div>
  
  <div id="step.2.section" style="display: none;">
  <table class="stepform">
  <tr>
    <td rowspan="3" class="stepno">2</td>
    <td class="steptitle">mRNA preparation information</td>
  </tr>
  <tr>
    <td class="stepfields">
      <table>
      <tr valign="top">
        <td class="prompt">Step</td>
        <td style="width: 11em;"><b>Date</b></td>
        <td><b>Operator</b></td>
        <td class="status"></td>
        <td class="help" rowspan="5">
          <span id="mrnaDate.message" class="message" style="display: none;"></span>
          Enter date and operator for each step in the mRNA preparation.
          (YYYYMMDD or MMDD)
        </td>
      </tr>
      <tr>
        <td class="subprompt">Dilution</td>
        <td>
          <input type="text" name="dilutionDate" maxlength="10" style="width: 8em;"
            onblur="dateOnChange('dilutionDate')" onkeypress="focusOnEnter(event, 'dilutionOperator')">
            <base:icon 
              onclick="Dates.selectDate('Dilution date', 'reggie', 'dilutionDate', 'setDate', 'yyyyMMdd')"
              image="calendar.png" 
              tooltip="Select a date from a calendar" 
              tabindex="-1"
            />
        </td>
        <td>
          <input type="text" name="dilutionOperator" value="<%=HTML.encodeTags(user.getName()) %>" 
            style="width: 95%;" maxlength="255" onkeypress="focusOnEnter(event, 'purificationDate')">
        </td>
        <td class="status" id="dilutionDate.status"></td>
      </tr>
      <tr>
        <td class="subprompt">Purification</td>
        <td>
          <input type="text" name="purificationDate" maxlength="10" style="width: 8em;"
            onblur="dateOnChange('purificationDate')" onkeypress="focusOnEnter(event, 'purificationOperator')">
            <base:icon 
              onclick="Dates.selectDate('Purification date', 'reggie', 'purificationDate', 'setDate', 'yyyyMMdd')"
              image="calendar.png" 
              tooltip="Select a date from a calendar" 
              tabindex="-1"
            />
        </td>
        <td>
          <input type="text" name="purificationOperator" value="<%=HTML.encodeTags(user.getName()) %>" 
            style="width: 95%;" maxlength="255" onkeypress="focusOnEnter(event, 'fragmentationDate')">
        </td>
        <td class="status" id="purificationDate.status"></td>
      </tr>
      <tr>
        <td class="subprompt">Fragmentation</td>
        <td>
          <input type="text" name="fragmentationDate" maxlength="10" style="width: 8em;"
            onblur="dateOnChange('fragmentationDate')" onkeypress="focusOnEnter(event, 'fragmentationOperator')">
            <base:icon 
              onclick="Dates.selectDate('Fragmentation date', 'reggie', 'fragmentationDate', 'setDate', 'yyyyMMdd')"
              image="calendar.png" 
              tooltip="Select a date from a calendar" 
              tabindex="-1"
            />
        </td>
        <td>
          <input type="text" name="fragmentationOperator" value="<%=HTML.encodeTags(user.getName()) %>" 
            style="width: 95%;" maxlength="255" onkeypress="focusOnEnter(event, 'cleanupDate')">
        </td>
        <td class="status" id="fragmentationDate.status"></td>
      </tr>
      <tr>
        <td class="subprompt">Cleanup</td>
        <td>
          <input type="text" name="cleanupDate" maxlength="10" style="width: 8em;"
            onblur="dateOnChange('cleanupDate')" onkeypress="focusOnEnter(event, 'cleanupOperator')">
            <base:icon 
              onclick="Dates.selectDate('Cleanup date', 'reggie', 'cleanupDate', 'setDate', 'yyyyMMdd')"
              image="calendar.png" 
              tooltip="Select a date from a calendar" 
              tabindex="-1"
            />
        </td>
        <td>
          <input type="text" name="cleanupOperator" value="<%=HTML.encodeTags(user.getName()) %>" 
            style="width: 95%;" maxlength="255" onkeypress="focusOnEnter(event, 'pdf.path')">
        </td>
        <td class="status" id="cleanupDate.status"></td>
      </tr>
      <tr valign="top">
        <td class="prompt">BA PDF file</td>
        <td class="input" colspan="2">
          <table>
          <tr>
          <td><input class="text required" type="text" 
            name="pdf.path" value=""
            size="50" onkeypress="doOnEnter(event, function(){document.getElementById('btnPdf').click()})"
            onblur="pdfFileOnChange()"
            ></td>
          <td style="padding-left: 4px;"><base:button 
              title="Browse&hellip;"
              onclick="browseOnClick('pdf')"
              id="btnPdf"
              />
          </td>
          </tr>
          </table>
        </td>
        <td class="status" id="pdf.status"></td>
        <td class="help"><span id="pdf.message" class="message" style="display: none;"></span>
          Select the <b>BioAnalyzer PDF file</b> that contains a printout with diagrams and other
          useful documentation.
        </td>
      </tr>
      <tr valign="top">
        <td class="prompt">Protocol</td>
        <td class="input" colspan="2"><select style="width:90%" name="mrnaProtocol" id="mrnaProtocol" 
          onkeypress="focusOnEnter(event, 'mrnaOperator')"></select></td>
        <td class="status" id="mrnaProtocol.status"></td>
        <td class="help"><span id="mrnaProtocol.message" class="message" style="display: none;"></span>
          Select the protocol which was used in the mRNA preparation.
        </td>
      </tr>
      <tr valign="top">
        <td class="prompt">Comments</td>
        <td class="input" colspan="2"><textarea rows="4" cols="50" style="width: 90%;" name="comments" value="" onblur="commentsOnChange()"></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 mRNA processing.</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)"/></td>
      <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>" onclick="goRegister()" style="display: none;"/></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();
}
%>