source: trunk/www/common/expression_builder.jsp @ 2993

<%-- $Id: expression_builder.jsp 2993 2006-12-01 14:34:35Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006 Nicklas Nordborg

  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.DbControl"
  import="net.sf.basedb.core.SessionControl"
  import="net.sf.basedb.core.Item"
  import="net.sf.basedb.core.BioAssaySet"
  import="net.sf.basedb.core.RawDataType"
  import="net.sf.basedb.core.RawDataTypes"
  import="net.sf.basedb.core.RawDataProperty"
  import="net.sf.basedb.core.ExtendedProperty"
  import="net.sf.basedb.core.ExtendedProperties"
  import="net.sf.basedb.core.Formula"
  import="net.sf.basedb.core.ReporterList"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.Include"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.util.Enumeration"
  import="net.sf.basedb.util.jep.Jep"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.clients.web.DynamicUtil"
  import="net.sf.basedb.clients.web.taglib.table.TableColumn"
  import="java.util.List"
  import="java.util.LinkedList"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
<%
  String title = request.getParameter("title");
  String form = request.getParameter("form");
  String textarea = request.getParameter("textarea");
  Formula.Type formulaType = Formula.Type.valueOf(request.getParameter("formulatype"));
  RawDataType rawDataType = RawDataTypes.getRawDataType(request.getParameter("rawdatatype"));
  int bioAssaySetId = Values.getInt(request.getParameter("bioassayset_id"), -1);
  boolean restrictions = Values.getBoolean(request.getParameter("restrictions"));
  int channels = Values.getInt(request.getParameter("channels"));
  final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
  
  DbControl dc = sc.newDbControl();
  try
  {
    BioAssaySet bas = bioAssaySetId == -1 ? null : BioAssaySet.getById(dc, bioAssaySetId);
    int maxRawMappings = bas == null ? 1 : bas.getMaxRawMappingsForSpot();

    List<TableColumn> spotProperties = new LinkedList<TableColumn>();
    DynamicUtil.addSpotColumns(spotProperties, dc, channels);
    List<TableColumn> rawProperties = new LinkedList<TableColumn>();
    if (rawDataType != null)
    {
      DynamicUtil.addFormulaColumns(spotProperties, dc, rawDataType, Formula.Type.COLUMN_EXPRESSION, "", "", maxRawMappings == 1);
      if (bas != null) DynamicUtil.addExtraColumns(spotProperties, dc, bas, "", "", "[Xtra] ");
      if (maxRawMappings == 1) DynamicUtil.addRawDataColumns(rawProperties, dc, rawDataType, "", "", "");
    }
    List<TableColumn> reporterProperties = new LinkedList<TableColumn>();
    DynamicUtil.addReporterColumns(reporterProperties, dc, "", "", "");
    
    ItemQuery<ReporterList> reporterListQuery = ReporterList.getQuery();
    reporterListQuery.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
    reporterListQuery.order(Orders.asc(Hql.property("name")));
    List<ReporterList> reporterLists = reporterListQuery.list(dc);
    
  %>
  <base:page type="popup" title="<%=title%>">
  <base:head scripts="table.js" styles="toolbar.css">
    <script language="JavaScript">
    function getText()
    {
      document.forms['expression'].expression.value = window.opener.document.forms['<%=form%>'].elements['<%=textarea%>'].value;
    }
    function setExpressionAndClose()
    {
      var textElement = window.opener.document.forms['<%=form%>'].elements['<%=textarea%>'];
      var value = document.forms['expression'].expression.value;
      if (textElement.type == 'text') value = value.replace(/\n/g, '');
      textElement.value = value;
      window.close();
    }
    function insertSelected(list, prefix, suffix)
    {
      var value = list[list.selectedIndex].value;
      if (value != '')
      {
        if (prefix) value = prefix + value;
        if (!suffix) suffix = ''; 
        encloseSelection(value, suffix);
      }
      list.selectedIndex = 0;
    }
    function insertReporterListFunction()
    {
      var frm = document.forms['expression'];
      var listFunction = frm.listFunction[frm.listFunction.selectedIndex].value;
      var listId = frm.reporterList[frm.reporterList.selectedIndex].value;
      encloseSelection(listFunction+'(' + listId + ')', '');
      frm.reporterList.selectedIndex = 0;
    }
  
    /*
      Enclose the selected text with prefix and suffix. Code taken
      from Trac: http://projects.edgewall.com/trac/
    */
    function encloseSelection(prefix, suffix) 
    {
      var frm = document.forms['expression'];
      var textarea = frm.expression;
      textarea.focus();
        var start, end, sel, scrollPos, subst;
        if (typeof(document["selection"]) != "undefined") 
        {
          sel = document.selection.createRange().text;
        } 
        else if (typeof(textarea["setSelectionRange"]) != "undefined") 
        {
          start = textarea.selectionStart;
          end = textarea.selectionEnd;
          scrollPos = textarea.scrollTop;
          sel = textarea.value.substring(start, end);
        }
        if (sel.match(/ $/)) 
        { 
          // exclude ending space char, if any
            sel = sel.substring(0, sel.length - 1);
            suffix = suffix + " ";
        }
        subst = prefix + sel + suffix;
        if (typeof(document["selection"]) != "undefined") 
        {
          var range = document.selection.createRange().text = subst;
          textarea.caretPos -= suffix.length;
        } 
        else if (typeof(textarea["setSelectionRange"]) != "undefined") 
        {
          textarea.value = textarea.value.substring(0, start) + subst +
                           textarea.value.substring(end);
          if (sel) 
          {
            textarea.setSelectionRange(start + subst.length, start + subst.length);
          } 
          else 
          {
            textarea.setSelectionRange(start + prefix.length, start + prefix.length);
          }
          textarea.scrollTop = scrollPos;
        }
      }
    
    var properties = new Array();
    <%
    for (TableColumn tc : rawProperties)
    {
      %>
      properties['raw.<%=tc.getProperty()%>'] = 1;
      <%
    }
    for (TableColumn tc : reporterProperties)
    {
      %>
      properties['reporter.<%=tc.getProperty()%>'] = 1;
      <%
    }
    %>
      
    function validateOnClick()
    {
      var frm = document.forms['expression'];
      if (frm.expression.value != '')
      {
        try
        {
          var result = eval(frm.expression.value);
          alert('The expressions seems to be ok.\nNote! This feature is experimental and may not be 100% correct.');
        }
        catch (er)
        {
          alert(er + '\nNote! This feature is experimental and may not be 100% correct.');
        }
      }
    }
    
    function raw(property)
    {
      <%
      if (maxRawMappings != 1)
      {
        %>
        throw 'Cannot use function raw() for bioassayset that has multiple mappings to raw data';
        <%
      }
      %>
      var rdt = '<%=rawDataType == null ? "" : rawDataType.getId()%>';
      if (!property) throw 'Property must be specified for function raw()';
      if (rdt == '') throw 'Cannot use function raw(). No raw data type selected';
      if (!properties['raw.'+property]) throw 'Property '+property+' not found for raw data type ' + rdt;
      return Math.random() * 100;
    }
    
    function mean(property)
    {
      var rdt = '<%=rawDataType == null ? "" : rawDataType.getId()%>';
      if (!property) throw 'Property must be specified for function mean()';
      if (rdt == '') throw 'Cannot use function mean(). No raw data type selected';
      if (!properties['property.'+property]) throw 'Property '+property+' not found for raw data type ' + rdt;
      return Math.random() * 100;
    }
  
    function ch(channel)
    {
      var type = '<%=formulaType.name()%>';
      if (type == '<%=Formula.Type.INTENSITY_EXPRESSION.name()%>')
      {
        // Channel function not available
        throw 'Function ch() is not available for ' + type;
      }
  
      var channels = <%=channels%>;
      if (!channel || channel <= 0 || channel > channels) throw 'Invalid channel: ' + channel + '; must be between 1 and '+ channels;
      return channel;
    }
    
    function rep(property)
    {
      if (!property) throw 'Property must be specified for function rep()';
      if (!properties['reporter.'+property]) throw 'Property '+property+' not found for reporter';
      return Math.random() * 100;
    }
    
    function xtra(arg)
    {
      if (!arg) throw 'One argument is required for function xtra()';
      return Math.random() * 100;
    }
    
    function log(value)
    {
      return Math.log(value);
    }
    function log2(value)
    {
      return Math.log(value);
    }
    function ln(value)
    {
      return Math.log(value);
    }
    function sqrt(value)
    {
      return Math.sqrt(value);
    }
    function abs(value)
    {
      return Math.abs(value);
    }
    function exp(value)
    {
      return Math.exp(value);
    }
    function score(reporterListId)
    {
      return Math.random() * 100;
    }
    </script>
  </base:head>
  <base:body onload="getText()">
  
    <form name="expression" onsubmit="return false;">
  
        <h3 class="docked">Expression builder <base:help helpid="expressionbuilder" /></h3>
        
        <tbl:toolbar>
          <tbl:label
            style="width: 100px;"
            title="Operators:"
          />
          <tbl:button 
            title="AND"
            tooltip="BOOLEAN AND: expr1 &amp;&amp; expr2"
            onclick="encloseSelection(' &amp;&amp; ', '')"
            visible="<%=restrictions%>"
          />
          <tbl:button 
            title="OR"
            tooltip="BOOLEAN OR: expr1 || expr2"
            onclick="encloseSelection(' || ', '')"
            visible="<%=restrictions%>"
          />
          <tbl:button 
            title="NOT"
            tooltip="BOOLEAN NOT: !expr1"
            onclick="encloseSelection('!', '')"
            visible="<%=restrictions%>"
          />
          <tbl:button 
            title="=="
            tooltip="EQUAL: expr1 == expr2"
            onclick="encloseSelection(' == ', '')"
            visible="<%=restrictions%>"
          />
          <tbl:button 
            title="!="
            tooltip="INEQUAL: expr1 != expr2"
            onclick="encloseSelection(' != ', '')"
            visible="<%=restrictions%>"
          />
          <tbl:button 
            title="&lt;"
            tooltip="LESS: expr1 &lt; expr2"
            onclick="encloseSelection(' &lt; ', '')"
            visible="<%=restrictions%>"
          />
          <tbl:button 
            title="&lt;="
            tooltip="LESS OR EQUAL: expr1 &lt;= expr2"
            onclick="encloseSelection(' &lt;= ', '')"
            visible="<%=restrictions%>"
          />
          <tbl:button 
            title="&gt;="
            tooltip="MORE OR EQUAL: expr1 &gt;= expr2"
            onclick="encloseSelection(' &gt;= ', '')"
            visible="<%=restrictions%>"
          />
          <tbl:button 
            title="&gt;"
            tooltip="MORE: expr1 &gt; expr2"
            onclick="encloseSelection(' &gt; ', '')"
            visible="<%=restrictions%>"
          />
          <tbl:button 
            title="+"
            tooltip="ADD: expr1 + expr2"
            onclick="encloseSelection(' + ', '')"
          />
          <tbl:button 
            title="-"
            tooltip="SUBTRACT: expr1 - expr2"
            onclick="encloseSelection(' - ', '')"
          />
          <tbl:button 
            title="*"
            tooltip="MULTIPLY: expr1 * expr2"
            onclick="encloseSelection(' * ', '')"
          />
          <tbl:button 
            title="/"
            tooltip="DIVIDE: expr1 / expr2"
            onclick="encloseSelection(' / ', '')"
          />
          <tbl:button 
            title="( )"
            tooltip="PARENTHESIS: (expr1)"
            onclick="encloseSelection('(', ')')"
          />
        </tbl:toolbar>
        <tbl:toolbar
          style="border-top: 0px;"
          >
          <tbl:label
            title="Functions:"
            style="width: 100px;"
          />
          <%
          Enumeration<String, String> functions = Jep.getFunctions();
          for (int i = 0; i < functions.size(); ++i)
          {
            String function = functions.getKey(i);
            %>
            <tbl:button 
              title="<%=function%>"
              tooltip="<%=functions.getValue(i)%>"
              onclick="<%="encloseSelection('" + function +"(', ')')"%>"
            />
            <%
          }
          %>
        </tbl:toolbar>
        <tbl:toolbar
          style="border-top: 0px;">
          <td class="label">Spot:
            <select name="spot" onchange="insertSelected(this)" >
            <option value="">- select -
            <%
            for (TableColumn tc : spotProperties)
            {
              if (tc.getJepExpression() != null)
              {
                %>
                <option value="<%=tc.getJepExpression()%>" 
                  title="<%=HTML.encodeTags(tc.getDescription())%>"><%=HTML.encodeTags(tc.getTitle())%>
                <%
              }
            }
            %>
            </select>   
          </td>
          <%
          if (rawDataType != null && rawDataType.isStoredInDb() && rawProperties.size() > 0)
          {
            %>
            <td class="label">Raw data:
              <select name="rawdata" onchange="insertSelected(this)" >
              <option value="">- select -
              <%
              for (TableColumn tc : rawProperties)
              {
                %>
                <option value="<%=tc.getJepExpression()%>" 
                  title="<%=HTML.encodeTags(tc.getDescription())%>"><%=HTML.encodeTags(tc.getTitle())%>
                <%
              }
              %>
              </select>
            </td>
            <%
          }
          %>
          
          <td class="label">Reporter:
            <select name="reporter" onchange="insertSelected(this)">
            <option value="">- select -
              <%
              for (TableColumn tc : reporterProperties)
              {
                %>
                <option value="<%=tc.getJepExpression()%>" 
                  title="<%=HTML.encodeTags(tc.getDescription())%>"><%=HTML.encodeTags(tc.getTitle())%>
                <%
              }
              %>
            </select>
        </tbl:toolbar>
        <tbl:toolbar
          style="border-top: 0px;"
          visible="<%=reporterLists.size() > 0%>">
          <td class="label">
            Reporter lists: 
            
            <select name="listFunction" >
            <option value="score">score
            <%
            if (restrictions)
            {
              %>
              <option value="inList">in
              <option value="notInList">not in
              <%
            }
            %>
            </select>
            
            <select name="reporterList" onchange="insertReporterListFunction()">
            <option value="">- select -
              <%
              for (ReporterList list : reporterLists)
              {
                %>
                <option value="<%=list.getId()%>" 
                  title="<%=HTML.encodeTags(list.getDescription())%>"><%=HTML.encodeTags(list.getName())%>
                <%
              }
              %>
            </select>
          </td>
        </tbl:toolbar>
        <br>
        <b>Expression</b><br>
        <textarea name="expression" rows="16" cols="80" wrap="soft" style="width: 100%;"></textarea>

        <br><br>
        <table align="center">
        <tr>
          <td width="33%"><base:button 
            onclick="validateOnClick()" title="Validate&hellip;" 
            image="validate_formula.gif"
            tooltip="Validate the expression. EXPERIMENTAL!!" /></td>
          <td width="33%"><base:button onclick="setExpressionAndClose()" title="Ok" /></td>
          <td width="33%"><base:button onclick="window.close()" title="Cancel" /></td>
          
        </tr>
        </table>
  
    </form>
  </base:body>
  </base:page>
  <%
  }
finally
{
  if (dc != null) dc.close();
}
%>