source: trunk/www/views/experiments/explorer/search/list.jsp @ 4306

<%-- $Id: list.jsp 4306 2008-05-21 13:39:59Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006 Johan Enell, Nicklas Nordborg
  Copyright (C) 2007 Johan Enell

  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.Permission"
  import="net.sf.basedb.core.BioAssaySet"
  import="net.sf.basedb.core.Experiment"
  import="net.sf.basedb.core.RawDataType"
  import="net.sf.basedb.core.ExtendedProperties"
  import="net.sf.basedb.core.ExtendedProperty"
  import="net.sf.basedb.core.DynamicSpotQuery"
  import="net.sf.basedb.core.DynamicResultIterator"
  import="net.sf.basedb.core.VirtualColumn"
  import="net.sf.basedb.core.data.ReporterData"
  import="net.sf.basedb.core.query.Restrictions"
  import="net.sf.basedb.core.query.Expressions"
  import="net.sf.basedb.core.query.Dynamic"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.core.query.Selects"
  import="net.sf.basedb.core.query.Aggregations"
  import="net.sf.basedb.core.query.JoinType"
  import="net.sf.basedb.core.query.SqlResult"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.DynamicUtil"
  import="net.sf.basedb.clients.web.ExperimentExplorer"
  import="net.sf.basedb.clients.web.WebException"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.clients.web.taglib.table.TableColumn"
  import="java.util.Date"
  import="java.util.Map"
  import="java.util.HashMap"
  import="java.util.List"
  import="java.util.LinkedList"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
<%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
<%!
  private static final Item itemType = Item.REPORTER;
%>

<%
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final String ID = sc.getId();
final float scale = Base.getScale(sc);
final String root = request.getContextPath();

final int bioAssaySetId = Values.getInt(request.getParameter("bioassayset_id"));
final DbControl dc = sc.newDbControl();
DynamicResultIterator reporters = null;
try
{
  String title = null;
  final BioAssaySet bioAssaySet = BioAssaySet.getById(dc, bioAssaySetId);
  final Experiment experiment = bioAssaySet.getExperiment();
  final RawDataType rawDataType = experiment.getRawDataType();
  
  final ExperimentExplorer explorer = ExperimentExplorer.getExplorer(bioAssaySet);
  final ItemContext cc = explorer.getAndSetReporterContext(sc, null);
  final String subContext = cc.getSubContext();

  List<TableColumn> columns = new LinkedList<TableColumn>();
  DynamicUtil.addReporterColumns(columns, dc, "", "@", "");
  
  DynamicUtil.SelectedInfo selected = DynamicUtil.getSelectedColumns(cc, columns, false);
  Map<String, Integer> selectedIndex = new HashMap<String, Integer>();
  for (int i = 0; i < selected.selectedIds.size(); ++i)
  {
    selectedIndex.put(selected.selectedIds.get(i), i+2);
  }
  
  try
  {
    DynamicSpotQuery reporterQuery = explorer.getReporterQuery(dc, selected.selectedProperties);
    reporters = reporterQuery.iterate(dc);
  }
  catch (Throwable t)
  {
    cc.setMessage(t.getMessage());
  }
  int numListed = 0;
  %>

  <base:page title="<%=title%>">
  <base:head scripts="table.js,tabcontrol.js,newjoust.js" styles="table.css,toolbar.css,headertabcontrol.css,path.css,newjoust.css">
  <script language="JavaScript">
    var submitPage = 'index.jsp';
    var formId = 'reporters';
    function editItem(itemId)
    {
      Main.viewOrEditItem('<%=ID%>', '<%=itemType.name()%>', itemId, true);
    }
    function viewItem(itemId)
    {
      Main.viewOrEditItem('<%=ID%>', '<%=itemType.name()%>', itemId, false);
    }
    function itemOnClick(evt, itemId)
    {
      Table.itemOnClick(formId, evt, itemId, 'DEFAULT', viewItem, editItem, null);
    }   
    function configureColumns()
    {
      Table.configureColumns('<%=ID%>', formId, '<%=itemType.name()%>', '<%=(String)cc.getObject("defaultColumns")%>', '<%=subContext%>');
    }
    function presetOnChange()
    {
      Table.presetOnChange('<%=ID%>', formId, '<%=itemType.name()%>', '<%=(String)cc.getObject("defaultColumns")%>', '<%=subContext%>');
    }
    function viewReporter(index)
    {
      var url = '../view/index.jsp?ID=<%=ID%>&bioassayset_id=<%=bioAssaySetId%>';
      if (index >= 0)
      {
        url += '&cmd=SetReporterIndex&reporterIndex='+index;
      }
      location.href = url;
    }

    function switchTab(tabControlId, tabId)
    {
      if (tabId == 'view')
      {
        viewReporter(-1);
      }
      else
      {
        TabControl.setActiveTab(tabControlId, tabId);
      }
    }
    function newReporterList()
    {
      Table.submitToPopup(formId, 'CreateReporterList', 540, 400);
    }
  </script>
  </base:head>
  <base:body>
    <p>
    <p:path>
      <p:pathelement title="Experiments" href="<%="../../index.jsp?ID="+ID%>" />
      <p:pathelement title="<%=HTML.encodeTags(experiment.getName())%>" 
        href="<%="../../bioassaysets/index.jsp?ID="+ID+"&experiment_id="+experiment.getId()%>" />
      <p:pathelement title="<%=HTML.encodeTags(bioAssaySet.getName())%>" 
        href="<%="../../bioassaysets/index.jsp?ID="+ID+"&cmd=ViewItem&item_id="+bioAssaySetId%>" />
      <p:pathelement title="Explorer" />
    </p:path>
    
    <t:tabcontrol id="explorer" switch="switchTab" remember="false" active="search">
    <t:tab id="search" title="Reporter search">
    <%
    if (cc.getMessage() != null)
    {
      %>
      <div class="error"><%=cc.getMessage()%></div>
      <%
      cc.setMessage(null);
    }
    %>
    <tbl:table 
      id="reporters" 
      clazz="itemlist" 
      columns="<%=cc.getSetting("columns")%>"
      sortby="<%=cc.getSortProperty()%>" 
      direction="<%=cc.getSortDirection()%>"
      title="<%=title%>"
      action="index.jsp"
      sc="<%=sc%>"
      item="<%=itemType%>"
      subcontext="<%=subContext%>"
      >
      <tbl:hidden 
        name="bioassayset_id" 
        value="<%=String.valueOf(bioAssaySetId)%>" 
      />
      <tbl:columndef 
        id="reporterList"
        property="£reporterList"
        datatype="int"
        title="Reporter list"
        filterable="true"
        enumeration="<%=Base.getReporterListsEnum(dc)%>"
        multiple="false"
      />      
      <%
      for (TableColumn tc : columns)
      {
        %>
        <tbl:columndef
          id="<%=tc.getId()%>"
          property="<%=tc.getProperty()%>"
          datatype="<%=tc.getDatatype().getStringValue()%>"
          title="<%=tc.getTitle()%>"
          sortable="<%=tc.getSortable()%>"
          filterable="<%=tc.getFilterable()%>"
          exportable="<%=tc.getExportable()%>"
          show="<%=tc.getShow()%>"
          formatter="<%=tc.getFormatter()%>"
        />
        <%
      }
      %>
        
      <tbl:toolbar>
        <tbl:button 
          image="columns.gif" 
          onclick="configureColumns()" 
          title="Columns&hellip;" 
          tooltip="Show, hide and re-order columns" 
        />
        <tbl:button
          image="add.png"
          onclick="newReporterList()"
          title="New reporter list&hellip;"
          tooltip="Create a new reporter list from matching reporters"
          visible="<%=sc.hasPermission(Permission.CREATE, Item.REPORTERLIST)%>"
        />
      </tbl:toolbar>
      <tbl:navigator
        page="<%=cc.getPage()%>" 
        rowsperpage="<%=cc.getRowsPerPage()%>" 
        totalrows="<%=reporters == null ? 0 : reporters.getTotalCount()%>" 
      />
      <tbl:data>
        <tbl:columns>
        <tbl:presetselector 
          clazz="columnheader"
          colspan="1"
          onchange="presetOnChange()"
        />
        </tbl:columns>
        <tr>
          <tbl:header 
            clazz="icons"
            >&nbsp;</tbl:header>
          <tbl:propertyfilter />
        </tr>
        <tbl:rows>
        
      <%
      int index = cc.getPage()*cc.getRowsPerPage();
      if (reporters != null)
      {
        while (reporters.hasNext())
        {
          SqlResult item = reporters.next();
          int itemId = item.getInt(1);
          index++;
          numListed++;
          %>
          <tbl:row>
            <tbl:header 
              clazz="icons"
              ><a href="javascript:viewReporter(<%=index-1%>)"><%=index%></a></tbl:header>
            <tbl:cell column="name"><div class="link" onclick="itemOnClick(event, <%=itemId%>)" 
              title="View this item (use CTRL, ALT or SHIFT to edit)"><%=HTML.encodeTags(item.getString(selectedIndex.get("name")))%></div></tbl:cell>
            <tbl:cell column="externalId"><tbl:cellvalue value="<%=item.getString(selectedIndex.get("externalId"))%>"/></tbl:cell>
            <tbl:cell column="symbol"><tbl:cellvalue value="<%=item.getString(selectedIndex.get("symbol"))%>"/></tbl:cell>
            <tbl:cell column="description"><tbl:cellvalue value="<%=item.getString(selectedIndex.get("description"))%>"/></tbl:cell>
            <tbl:cell column="lastUpdate"><tbl:cellvalue value="<%=item.getObject(selectedIndex.get("lastUpdate"))%>"/></tbl:cell>
            <%
            List<ExtendedProperty> reporterProperties = ExtendedProperties.getProperties("ReporterData");
            if (reporterProperties != null)
            {
              for (ExtendedProperty ep : reporterProperties)
              {
                String name = ep.getName();
                %>
                <tbl:cell column="<%=name%>"><tbl:cellvalue value="<%=item.getObject(selectedIndex.get(name))%>" /></tbl:cell>
              <%
              }
            }
            %>
          </tbl:row>
          <%
        }
      }
      %>
      </tbl:rows>
      </tbl:data>
      <%
      if (numListed == 0)
      {
        %>
        <tbl:panel><%=reporters == null || reporters.getTotalCount() == 0 ? "No reporters were found" : "No reporters on this page. Please select another page!" %></tbl:panel>
        <%
      }
      else
      {
        %>
        <tbl:navigator
          page="<%=cc.getPage()%>" 
          rowsperpage="<%=cc.getRowsPerPage()%>" 
          totalrows="<%=reporters == null ? 0 : reporters.getTotalCount()%>"
          locked="true"
        />
        <%
      }
      %>
      </tbl:table>
    </t:tab>

    <t:tab id="view" title="Reporter view" />
    </t:tabcontrol>

  </base:body>
  </base:page>
  <%
}
finally
{
  if (reporters != null) reporters.close();
  if (dc != null) dc.close();
}

%>