source: trunk/www/plugins/net/sf/basedb/plugins/jep_intensity_transformer.jsp @ 2993

<%-- $Id: jep_intensity_transformer.jsp 2993 2006-12-01 14:34:35Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) Authors contributing to this file.

  This file is part of BASE - BioArray Software Environment.
  Available at http://base.thep.lu.se/

  BASE is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 2
  of the License, or (at your option) any later version.

  BASE is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place - Suite 330,
  Boston, MA  02111-1307, USA.
  ------------------------------------------------------------------

  @author Nicklas
  @version 2.0
--%>
<%@ page session="false"
  import="net.sf.basedb.core.SessionControl"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.Item"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.RawDataType"
  import="net.sf.basedb.core.BioAssaySet"
  import="net.sf.basedb.core.Formula"
  import="net.sf.basedb.core.Job"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.ItemResultList"
  import="net.sf.basedb.core.Include"
  import="net.sf.basedb.core.PluginConfigurationRequest"
  import="net.sf.basedb.core.RequestInformation"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.WebException"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.util.Values"
  import="java.util.List"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
<%
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final String ID = sc.getId();
final ItemContext cc = sc.getCurrentContext(Item.BIOASSAYSET);
DbControl dc = null;
try
{
  String errorMessage = (String)sc.getSessionSetting("plugin.configure.errors.message");
  List<Throwable> errors = (List<Throwable>)sc.getSessionSetting("plugin.configure.errors.list");
  
  PluginConfigurationRequest pcRequest = (PluginConfigurationRequest)sc.getSessionSetting("plugin.configure.request");
  RequestInformation info = pcRequest.getRequestInformation();
  
  dc = sc.newDbControl();
  Job job = (Job)sc.getSessionSetting("plugin.configure.job");
  dc.reattachItem(job);
  BioAssaySet source = null;
  source = (BioAssaySet)job.getParameterValue("source");
  if (source == null && cc.getId() != 0) source = BioAssaySet.getById(dc, cc.getId());
  if (source == null) throw new WebException("popup", "No current bioassay set", 
    "Could not find any current bioassay set. Please select a bioassay set before trying again");
  int maxRawMappings = source.getMaxRawMappingsForSpot();

  RawDataType rdt = source.getRawDataType();
  
  // Current parameter values
  String childName = Values.getString((String)job.getParameterValue("childName"), source.getName());
  String childDescription = (String)job.getParameterValue("childDescription");
  String transformationName = (String)job.getParameterValue("transformationName");
  
  // Predefined formulas
  ItemQuery<Formula> formulaQuery = Formula.getQuery(Formula.Type.INTENSITY_TRANSFORMATION, rdt);
  formulaQuery.order(Orders.asc(Hql.property("name")));
  formulaQuery.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
  ItemResultList<Formula> formulas = formulaQuery.list(dc);
  %>
  <base:page type="popup" title="Transform intensities">
  <base:head styles="parameters.css">
    <script language="JavaScript">
    function hideErrorList()
    {
      Main.hide('errorlist');
      Main.show('showerrorlist');
    }
    function showErrorList()
    {
      Main.show('errorlist');
      Main.hide('showerrorlist');
    }
    function presetOnChange()
    {
      var frm = document.forms['transformation'];
      var formulaId = frm.presets[frm.presets.selectedIndex].value;
      frm['parameter:transformationName'].value = frm.presets[frm.presets.selectedIndex].text;
      for (var ch = 1; ch <= <%=rdt.getChannels()%>; ch++)
      {
        frm['parameter:ch'+ch+'.expression'].value = formulas[formulaId+'.'+ch];
      }
      frm.presets.selectedIndex = 0;
    }
    function openExpressionBuilder(title, inputName)
    {
      Main.expressionBuilder('<%=ID%>', title, 'transformation', inputName, 'INTENSITY_TRANSFORMATION', '<%=rdt.getId()%>', <%=rdt.getChannels()%>, false, '<%=source.getId()%>');
    }
    function validate()
    {
      var frm = document.forms['transformation'];
      for (var ch = 1; ch <= <%=rdt.getChannels()%>; ch++)
      {
        var inputName = 'parameter:ch'+ch+'.expression';
        if (Main.trimString(frm[inputName].value) == '')
        {
          alert('You must enter an expression for channel ' + ch);
          frm[inputName].focus();
          return false;
        }
        else if (<%=maxRawMappings != 1 ? "true" : "false"%> && frm[inputName].value.search(/raw\(/) != -1)
        {
          alert('Can\'t use function raw() for bioassaysets with multiple mappings to raw data');
          frm[inputName].focus();
          return false;
        }
      }
      return true;
    }
    function doNext()
    {
      if (validate())
      {
        var frm = document.forms['transformation'];
        frm.submit();
      }
    }
    
    var formulas = new Array();
    function init()
    {
      <%
      for (Formula f : formulas)
      {
        for (int ch = 1; ch <= rdt.getChannels(); ++ch)
        {
          String formula = f.getFormula(ch-1);
          %>
          formulas['<%=f.getId()%>.<%=ch%>'] = '<%=HTML.javaScriptEncode(formula)%>';
          <%
        }
      }
      %>
    }
    </script>
  </base:head>
  <base:body onload="init()">
    <form name="transformation" action="index.jsp" method="get" onsubmit="return false;">
    <input type="hidden" name="ID" value="<%=ID%>">
    <input type="hidden" name="cmd" value="SetParameters">
    <input type="hidden" name="parameter:source" value="<%=source.getId()%>">
    
    <h3 class="docked">Transform intensities <base:help helpid="jepintensitytransformer.options"/></h3>
    <div class="boxed">
    <%
    if (errorMessage != null || (errors != null && errors.size() > 0))
    {
      %>
      <div id="errors" style="margin-bottom: 12px;" class="parameterhelp">
        <div class="error" style="margin: 0px;">
        <%=errorMessage %>
        </div>
        <%
        if (errors != null && errors.size() > 0)
        {
          %>
          <div id="showerrorlist" style="display: none;">
            <base:icon image="bullet.gif" /><a href="javascript:showErrorList()">Show details</a>
          </div>
          <div id="errorlist">
          <ol>
          <%
          for (Throwable t : errors)
          {
            %>
            <li><%=t.getMessage()%><br>
            <%
          }
          %>
          </ol>
          <base:icon image="bullet.gif" /><a href="javascript:hideErrorList()">Hide details</a>
          </div>
          <%
        }
        %>
      </div>
      <%
    }
    %>

      <table class="form" width="100%">
      <tr valign="top">
        <td class="prompt">Source bioassay set</td>
        <td><%=HTML.encodeTags(source.getName())%></td>
      </tr>     
      <tr>
        <td class="prompt" colspan="2">Child bioassay set</td>
      </tr>
      <tr>
        <td style="text-align: right">Name</td>
        <td>
          <input type="text" class="text required" size="50" maxlength="255" name="parameter:childName" 
            value="<%=HTML.encodeTags(childName)%>"></td>
      </tr>
      <tr valign="top">
        <td style="text-align: right">Description</td>
        <td nowrap>
          <textarea class="text" rows="4" cols="50" name="parameter:childDescription" wrap="virtual"
            ><%=HTML.encodeTags(childDescription)%></textarea>
          <a href="javascript:Main.zoom('Description', 'transformation', 'parameter:childDescription')"
            title="Edit in larger window"><base:icon image="zoom.gif" /></a>
        </td>
      </tr>
      <tr>
        <td class="prompt">Transformation</td>
        <td>
        <%
        if (formulas.size() > 0)
        {
          %>
          <select name="presets" style="width: 32em;"
            onchange="presetOnChange()" 
            >
            <option value="">- select from list or enter formula below -
            <%
            for (Formula f : formulas)
            {
              boolean ok = true;
              if (maxRawMappings != 1)
              {
                for (String formula : f.getFormulas())
                {
                  ok &= !formula.contains("raw(");
                }
              }
              if (ok)
              {
                %>
                <option value="<%=f.getId()%>" title="<%=HTML.encodeTags(f.getDescription())%>"
                  ><%=HTML.encodeTags(f.getName())%>
                <%
              }
            }
            %>
          </select>
          <%
        }
        %>
        </td>
      </tr>
      <tr>
        <td style="text-align: right">Name</td>
        <td>
          <input type="text" class="text" size="50" maxlength="255" name="parameter:transformationName" 
            value="<%=HTML.encodeTags(transformationName)%>"></td>
      </tr>
      
      <%
      for (int ch = 1; ch <= rdt.getChannels(); ++ch)
      {
        String inputName = "parameter:ch" + ch + ".expression";
        String value = (String)job.getParameterValue("ch"+ch+".expression");
        if (value == null) value = (String)info.getParameter("ch"+ch+".expression").getParameterType().getDefaultValue();
        %>
        <tr valign="top">
          <td style="text-align: right">Ch <%=ch%></td>
          <td>
            <table border="0" cellspacing="0" cellpadding="0">
            <tr valign="top">
            <td>
              <input type="text" class="text required" name="<%=inputName%>"
                size="50" 
                value="<%=HTML.encodeTags(value)%>">&nbsp;
            </td>
            <td><base:button onclick="<%="openExpressionBuilder('Ch "+ch+" expression', '"+inputName+"')"%>" 
              title=""
              image="expression_builder.gif"
              tooltip="A simple utility for building expressions" />
            </td>
            </tr>
            </table>
          </td>
        </tr>
        <%
      }
      %>
      </table>
    </div>
    </form>
  
    <table align="center">
    <tr>
      <td width="50%"><base:button onclick="doNext();" title="Next" /></td>
      <td width="50%"><base:button onclick="window.close();" title="Cancel" /></td>
    </tr>
    </table>
  </base:body>
  </base:page>
  <%
}
finally
{
  if (dc != null) dc.close();
}%>