source: trunk/www/views/rawbioassays/rawdata/view_rawdata.jsp @ 5939

<%-- $Id: view_rawdata.jsp 5939 2012-01-30 14:42:18Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006 Johan Enell, Jari Häkkinen, Nicklas Nordborg
  Copyright (C) 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.SessionControl"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.SystemItems"
  import="net.sf.basedb.core.Item"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.ExtendedProperties"
  import="net.sf.basedb.core.ExtendedProperty"
  import="net.sf.basedb.core.RawDataProperty"
  import="net.sf.basedb.core.RawBioAssay"
  import="net.sf.basedb.core.RawDataType"
  import="net.sf.basedb.core.ReporterType"
  import="net.sf.basedb.core.Reporter"
  import="net.sf.basedb.core.Feature"
  import="net.sf.basedb.core.Well"
  import="net.sf.basedb.core.Plate"
  import="net.sf.basedb.core.ArrayDesignBlock"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.PluginDefinition"
  import="net.sf.basedb.core.data.RawData"
  import="net.sf.basedb.core.data.ReporterData"
  import="net.sf.basedb.core.data.FeatureData"
  import="net.sf.basedb.core.plugin.GuiContext"
  import="net.sf.basedb.core.plugin.Plugin"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.util.formatter.Formatter"
  import="net.sf.basedb.util.formatter.WellCoordinateFormatter"
  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
  import="java.util.Date"
  import="java.util.Map"
  import="java.util.Set"
  import="java.util.List"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
<%!
  private static final Item itemType = Item.RAWDATA;
  private static final GuiContext guiContext = new GuiContext(itemType, GuiContext.Type.ITEM);
%>
<%
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final String ID = sc.getId();
final int rawBioAssayId = Values.getInt(request.getParameter("rawbioassay_id"));
final float scale = Base.getScale(sc);
final DbControl dc = sc.newDbControl();
try
{
  final RawBioAssay rawBioAssay = RawBioAssay.getById(dc, rawBioAssayId);
  final RawDataType rawDataType = rawBioAssay.getRawDataType();
  final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, rawDataType.getId(), null, null);
  final int itemId = cc.getId();
  final boolean hasSpotImages = rawBioAssay.hasSpotImages();  
  
  Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);

  final RawData rawData = rawBioAssay.getRawDataById(itemId, true);
  String title = "Raw data of "+HTML.encodeTags(rawBioAssay.getName()) + " at position " + rawData.getPosition();
  
  final ReporterData reporter = rawData.getReporter();
  final FeatureData feature = rawData.getFeature();
  Formatter<Date> dateFormatter = FormatterFactory.getDateTimeFormatter(sc);
  WellCoordinateFormatter rowFormatter = new WellCoordinateFormatter(true);
  WellCoordinateFormatter columnFormatter = new WellCoordinateFormatter(false);
  %>
  <base:page title="<%=title%>" type="popup">
  <base:head scripts="tabcontrol.js" styles="tabcontrol.css">
    <script language="JavaScript">
    function runPlugin(cmd)
    {
      Main.openPopup('index.jsp?ID=<%=ID%>&cmd='+cmd+'&item_id=<%=itemId%>', 'RunPlugin'+cmd, 540, 460);
    }
    </script>
  </base:head>
  <base:body>
    <h1><%=title%></h3>
  
    <t:tabcontrol id="rawdata" 
      subclass="content dialogtabcontrol"
      position="bottom">
    <t:tab id="raw" title="Raw data">
    
      <table class="fullform outlined larger">
      <tbody class="sectionheader">
        <tr>
          <th colspan="4">Common rawdata properties</th>
        </tr>
      </tbody>
      <tbody>
      <tr>
        <th>Position</th>
        <td><%=rawData.getPosition()%></td>
        <th class="leftborder">Block</th>
        <td><%=rawData.getBlock()%></td>
      </tr>
      <tr>
        <th>Row</th>
        <td><%=rawData.getRow()%></td>
        <th class="leftborder">Column</th>
        <td><%=rawData.getColumn()%></td>
      </tr>
      <tr>
        <th>Meta grid X</th>
        <td><%=rawData.getMetaGridX()%></td>
        <th class="leftborder">Meta grid Y</th>
        <td><%=rawData.getMetaGridY()%></td>
      </tr>
      <tr>
        <th>X</th>
        <td><%=rawData.getX()%></td>
        <th class="leftborder">Y</th>
        <td><%=rawData.getY()%></td>
      </tr>
      <tr>
        <th>Reporter</th>
        <td><%=reporter == null ? "<i>- none -</i>" : HTML.encodeTags(reporter.getName())%></td>
        <th class="leftborder">Feature</th>
        <td><%=feature == null ? "<i>- none -</i>" : feature.getId()%></td>
      </tr>
      <tr>
        <th>Spot image</t>
        <td>
          <%
          if (hasSpotImages)
          {
            %>
            <img class="spotimage" src="spotimage/<%=ID%>/<%=rawBioAssay.getId()%>/<%=itemId%>/spot<%=rawData.getPosition()%>.png">
            <%
          }
          else
          {
            %>
            <i>- none -</i>
            <%
          }
          %>
        </td>
        <th class="leftborder"></th>
        <td></td>
      </tr>
      </tbody>
      
      <tbody class="sectionheader">
        <tr>
          <th colspan="4"><%=rawDataType.getName()%> properties</th>
        </tr>
      </tbody>
      
      <tbody>
          <%
          boolean needsTr = true;
          for (RawDataProperty rawProperty : rawDataType.getProperties())
          {
            String name = rawProperty.getName();
            Formatter f = FormatterFactory.getExtendedPropertyFormatter(sc, rawProperty);
            String value = f.format(rawData.getExtended(name));
            title = Values.trimString(rawProperty.getTitle(), 25);
            %>
              <%=needsTr ? "<tr><th>" : "<th class=\"leftborder\"" %>
              <span 
                title="<%=HTML.encodeTags(rawProperty.getDescription())%>"><%=HTML.encodeTags(title)%></span>
              </th>
              <td><%=value%></td>
              <%=needsTr ? "" : "</tr>"%>
            <%
            needsTr = !needsTr;
          }
          %>
          <%=needsTr ? "" : "<th class=\"leftborder\"></th><td></td></tr>"%>
        <tr class="dynamic">
          <th></th>
          <td></td>
          <th class="leftborder"></th>
          <td></td>
        </tr>
      </tbody>      
      </table>
    
    </t:tab>
    
    <%
    if (reporter != null)
    {
      boolean readCurrentReporterType = true;
      ReporterType currentReporterType = null;
      try
      {
        currentReporterType = Reporter.getReporterType(dc, reporter);
      }
      catch (PermissionDeniedException ex)
      {
        readCurrentReporterType = false;
      }
      %>
      <t:tab id="reporter" title="Reporter" >
        <table class="fullform outlined">
        <tbody class="sectionheader">
          <tr>
            <th colspan="4">Common reporter properties</th>
          </tr>
        </tbody>
        <tbody>
        
        <tr>
          <th>Name</th>
          <td><%=HTML.encodeTags(reporter.getName())%></td>
          <th class="leftborder">External ID</th>
          <td><%=HTML.encodeTags(reporter.getExternalId())%></td>
        </tr>
        <tr>
          <th>Gene symbol</td>
          <td><%=HTML.encodeTags(reporter.getSymbol())%></td>
          <th class="leftborder">Type</th>
          <td><%=Base.getEncodedName(currentReporterType, !readCurrentReporterType)%></td>
        </tr>
        <tr>
          <th>Last update</th>
          <td><%=dateFormatter.format(reporter.getLastUpdate())%></td>
          <th class="leftborder">from/by</th>
          <td><%=reporter.getLastSource() %></td>
        </tr>
        <tr>
          <th>Description</th>
          <td colspan="3"><%=HTML.niceFormat(reporter.getDescription())%></td>
        </tr>
        </tbody>
        
        <tbody class="sectionheader">
          <tr>
            <th colspan="4">Extended reporter properties</th>
          </tr>
        </tbody>
        <tbody>
            <%
            List<ExtendedProperty> reporterProperties = ExtendedProperties.getProperties("ReporterData");
            if (reporterProperties != null)
            {
              boolean needsTr = true;
              for (ExtendedProperty ep : reporterProperties)
              {
                String name = ep.getName();
                Formatter f = FormatterFactory.getExtendedPropertyFormatter(sc, ep);
                String value = f.format(reporter.getExtended(name));
                %>
                  <%=needsTr ? "<tr><th>" : "<th class=\"leftborder\">" %>
                  <%=HTML.encodeTags(ep.getTitle())%></th>
                  <td><%=value%></td>
                  <%=needsTr ? "" : "</tr>"%>
                <%
                needsTr = !needsTr;
              }
              %>
              <%=needsTr ? "" : "<th class=\"leftborder\"></th><td></td></tr>"%>
              <%
            }
            %>
          <tr class="dynamic">
            <th></th>
            <td></td>
            <th class="leftborder"></th>
            <td></td>
          </tr>
        </tbody>
        </table>
      </t:tab>
      <%
    }
    %>
    <%
    if (feature != null)
    {
      ArrayDesignBlock block = null;
      boolean readBlock = true;
      try
      {
        block = Feature.getArrayDesignBlock(dc, feature);
      }
      catch (PermissionDeniedException ex)
      {
        readBlock = false;
      }
      
      Well well = null;
      boolean readWell = true;
      try
      {
        well = Feature.getWell(dc, feature);
      }
      catch (PermissionDeniedException ex)
      {
        readWell = false;
      }
      %>
      <t:tab id="feature" title="Feature / well" >
      <table class="fullform outlined">
        <tbody class="sectionheader">
          <tr>
            <th colspan="6">Feature</th>
          </tr>
        </tbody>
        <tbody>
          <tr>
            <th>Position</td>
            <td><%=feature.getPosition()%></td>
            <th class="leftborder">Meta grid X</td>
            <td><%=readBlock ? Integer.toString(block.getMetaGridX()) : "<i>- denied -</i>"%></td>
            <th class="leftborder">Meta grid Y</th>
            <td><%=readBlock ? Integer.toString(block.getMetaGridY()) : "<i>- denied -</i>"%></td>
          </tr>
          <tr>
            <th>Feature ID</th>
            <td><%=feature.getExternalId() %></td>
            <th class="leftborder">Block size X</th>
            <td><%=readBlock ? Integer.toString(block.getBlockSizeX()) : "<i>- denied -</i>"%></td>
            <th class="leftborder">Block size Y</th>
            <td><%=readBlock ? Integer.toString(block.getBlockSizeY()) : "<i>- denied -</i>"%></td>
          </tr>
          <tr>
            <th>Block number</th>
            <td><%=block.getBlockNumber()%></td>
            <th class="leftborder">Origin X</th>
            <td><%=readBlock ? Integer.toString(block.getOriginX()) : "<i>- denied -</i>"%></td>
            <th class="leftborder">Origin Y</th>
            <td><%=readBlock ? Integer.toString(block.getOriginY()) : "<i>- denied -</i>"%></td>
          </tr>
          <tr>
            <th>Row</th>
            <td><%=feature.getRow()%></td>
            <th class="leftborder">Spacing X</th>
            <td><%=readBlock ? Integer.toString(block.getSpacingX()) : "<i>- denied -</i>"%></td>
            <th class="leftborder">Spacing Y</th>
            <td><%=readBlock ? Integer.toString(block.getSpacingY()) : "<i>- denied -</i>"%></td>
          </tr>
          <tr>
            <th>Column</th>
            <td><%=feature.getColumn()%></td>
            <th class="leftborder"></th>
            <td></td>
            <th class="leftborder"></th>
            <td></td>
          </tr>
        </tbody>
        
        <tbody class="sectionheader">
          <tr>
            <th colspan="6">Plate position</th>
          </tr>
        </tbody>
        
        <tbody>
          <%
          if (!readWell)
          {
            %>
            <tr>
              <th>Plate</th>
              <td colspan="5"><i>- denied -</i></td>
            </tr>
            <%
          }
          else if (well == null)
          {
            %>
            <tr>
              <th>Plate</th>
              <td colspan="5"><i>- none -</i></td>
            </tr>
            <%
          }
          else
          {
            Plate plate = well.getPlate();
            %>
            <tr>
              <th>Plate</th>
              <td colspan="5"><%=HTML.encodeTags(plate.getName())%></td>
            </tr>
            <tr>
              <th>Well</th>
              <td colspan="5"><%=rowFormatter.format(well.getRow())%><%=columnFormatter.format(well.getColumn())%></td>
            </tr>
            <%
          }
          %>
          <tr class="dynamic">
            <th></th>
            <td colspan="5"></td>
          </tr>
        </tbody>
      </table>
      </t:tab>
      <%
    }
    %>
    </t:tabcontrol>

    <base:buttongroup subclass="dialogbuttons">
      <base:button onclick="window.close()" title="Close" />
    </base:buttongroup>
    
  </base:body>
  </base:page>
  <%
}
finally
{
  if (dc != null) dc.close();
}

%>