source: trunk/www/common/expression_builder.jsp @ 6314

<%-- $Id: expression_builder.jsp 6314 2013-09-02 12:47:53Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006, 2007 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 3 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 BASE. If not, see <http://www.gnu.org/licenses/>.
  ------------------------------------------------------------------

  @author Nicklas
  @version 2.0
--%>
<%@ page pageEncoding="UTF-8" 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.VirtualDb"
  import="net.sf.basedb.core.ReporterCloneTemplate"
  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.IntensityTransform"
  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 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);
    VirtualDb vdb = bas != null ? bas.getExperiment().getVirtualDb() : null;
    ReporterCloneTemplate template = vdb != null && vdb.hasClonedReporters() ? vdb.getReporterCloneTemplate() : null;
        
    IntensityTransform transform = bas == null ? null : bas.getIntensityTransform();
    int maxRawMappings = bas == null ? 1 : bas.getMaxRawMappingsForSpot();

    List<TableColumn> spotProperties = new LinkedList<TableColumn>();
    DynamicUtil.addSpotColumns(spotProperties, dc, channels, transform);
    List<TableColumn> rawProperties = new LinkedList<TableColumn>();
    if (rawDataType != null)
    {
      DynamicUtil.addFormulaColumns(spotProperties, dc, rawDataType, 
        Formula.Type.COLUMN_EXPRESSION, transform, "", "", 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, template, "", "", "");
    
    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,~expression_builder.js" styles="toolbar.css" />
  <base:body>
    <h1>Expression builder <base:help helpid="expressionbuilder" /></h1>
    <div id="page-data" class="datacontainer"
      data-textarea="<%=textarea%>"
      data-formula-type="<%=formulaType.name() %>"
      data-raw-data-type="<%=rawDataType == null ? "" : rawDataType.getId()%>"
      data-channels="<%=channels%>"
    ></div>
  
    <form name="expression">
    <div class="content">
      <table class="fullform input100 bottomborder">
      <tr>
        <td class="filled">
        <tbl:toolbar subclass="bottomborder">
          <tbl:label
            style="width: 100px;"
            title="Operators:"
          />
          <tbl:button 
            title="AND"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=" &amp;&amp; "
            data-suffix=""
            tooltip="BOOLEAN AND: expr1 &amp;&amp; expr2"
          />
          <tbl:button 
            title="OR"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=" || "
            data-suffix=""
            tooltip="BOOLEAN OR: expr1 || expr2"
          />
          <tbl:button 
            title="NOT"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix="!"
            data-suffix=""
            tooltip="BOOLEAN NOT: !expr1"
          />
          <tbl:button 
            title="=="
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=" == "
            data-suffix=""
            tooltip="EQUAL: expr1 == expr2"
          />
          <tbl:button 
            title="!="
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=" != "
            data-suffix=""
            tooltip="INEQUAL: expr1 != expr2"
          />
          <tbl:button 
            title="&lt;"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=" &lt; "
            data-suffix=""
            tooltip="LESS: expr1 &lt; expr2"
          />
          <tbl:button 
            title="&lt;="
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=" &lt;= "
            data-suffix=""
            tooltip="LESS OR EQUAL: expr1 &lt;= expr2"
          />
          <tbl:button 
            title="&gt;="
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=" &gt;= "
            data-suffix=""
            tooltip="MORE OR EQUAL: expr1 &gt;= expr2"
            visible="<%=restrictions%>"
          />
          <tbl:button 
            title="&gt;"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=" &gt; "
            data-suffix=""
            tooltip="MORE: expr1 &gt; expr2"
          />
          <tbl:button 
            title="+"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=" + "
            data-suffix=""
            tooltip="ADD: expr1 + expr2"
          />
          <tbl:button 
            title="-"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=" - "
            data-suffix=""
            tooltip="SUBTRACT: expr1 - expr2"
          />
          <tbl:button 
            title="*"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=" * "
            data-suffix=""
            tooltip="MULTIPLY: expr1 * expr2"
          />
          <tbl:button 
            title="/"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=" / "
            data-suffix=""
            tooltip="DIVIDE: expr1 / expr2"
          />
          <tbl:button 
            title="( )"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix="("
            data-suffix=")"
            tooltip="PARENTHESIS: (expr1)"
          />
        </tbl:toolbar>
        <tbl:toolbar subclass="bottomborder">
          <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%>"
              subclass="auto-init"
              data-auto-init="enclose-selection"
              data-prefix="<%=function+"(" %>"
              data-suffix=")"
              tooltip="<%=functions.getValue(i)%>"
            />
            <%
          }
          %>
          <tbl:label
            title="Constants:"
            style="width: 100px;"
          />
          <tbl:button 
            title="null"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=""
            data-suffix="null"
            tooltip="The null (unknown) value"
          />
          <tbl:button 
            title="pi"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=""
            data-suffix="<%=Math.PI%>"
            tooltip="<%="The pi value: " + Math.PI %>"
          />
          <tbl:button 
            title="e"
            subclass="auto-init"
            data-auto-init="enclose-selection"
            data-prefix=""
            data-suffix="<%=Math.E %>"
            tooltip="<%="The base of the natural logarithm: " + Math.E%>"
          />
        </tbl:toolbar>
        <tbl:toolbar subclass="bottomborder">
          <%
          if (formulaType != Formula.Type.INTENSITY_EXPRESSION)
          {
            %>
            <td class="label">Spot:
              <select name="spot" id="spot" style="width: 12em;">
              <option value="">- select -
              <%
              for (TableColumn tc : spotProperties)
              {
                if (tc.getJepExpression() != null)
                {
                  %>
                  <option data-prefix="<%=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" id="rawdata" style="width: 12em;">
              <option value="">- select -
              <%
              for (TableColumn tc : rawProperties)
              {
                %>
                <option data-prefix="<%=tc.getJepExpression()%>" 
                  title="<%=HTML.encodeTags(tc.getDescription())%>"><%=HTML.encodeTags(tc.getTitle())%>
                <%
              }
              %>
              </select>
            </td>
            <%
          }
          %>
          
          <td class="label">Reporter:
            <select name="reporter" id="reporter" style="width: 12em;">
            <option value="">- select -
              <%
              for (TableColumn tc : reporterProperties)
              {
                %>
                <option data-prefix="<%=tc.getJepExpression()%>" 
                  title="<%=HTML.encodeTags(tc.getDescription())%>"><%=HTML.encodeTags(tc.getTitle())%>
                <%
              }
              %>
            </select>
        </tbl:toolbar>
        <tbl:toolbar subclass="bottomborder"
          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" id="reporterList">
            <option value="">- select -
              <%
              for (ReporterList list : reporterLists)
              {
                %>
                <option value="<%=list.getId()%>" 
                  title="<%=HTML.encodeTags(list.getDescription())%>"><%=HTML.encodeTags(list.getName())%>
                <%
              }
              %>
            </select>
          </td>
        </tbl:toolbar>
        </td>
      </tr>
      <tr class="dynamic">
        <td class="filled">
        <textarea class="autohight" name="expression" rows="16"></textarea>
        </td>
      </tr>
      </table>

      </div>
    </form>

    <base:buttongroup subclass="dialogbuttons">
      <base:button 
        id="btnValidate"
        title="Validate&hellip;" 
        image="validate_formula.png"
        tooltip="Validate the expression. EXPERIMENTAL!!" />
      <base:button id="btnSave" title="Ok" />
      <base:button id="close" title="Cancel" />
    </base:buttongroup>
  </base:body>
  </base:page>
  <%
  }
finally
{
  if (dc != null) dc.close();
}
%>