source: trunk/www/biomaterials/wizards/index.jsp @ 5541

<%-- $Id: index.jsp 5541 2011-01-17 10:00:42Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2010 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
--%>
<%@ page pageEncoding="UTF-8" session="false"
  import="net.sf.basedb.core.SessionControl"
  import="net.sf.basedb.core.BioMaterial"
  import="net.sf.basedb.core.BioMaterialEvent"
  import="net.sf.basedb.core.BioPlate"
  import="net.sf.basedb.core.BioPlateEvent"
  import="net.sf.basedb.core.BioPlateEventType"
  import="net.sf.basedb.core.BioPlateEventParticipant"
  import="net.sf.basedb.core.BioWell"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.Item"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.MeasuredBioMaterial"
  import="net.sf.basedb.core.Hardware"
  import="net.sf.basedb.core.Protocol"
  import="net.sf.basedb.core.PlateGeometry"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.WebException"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.util.formatter.Formatter"
  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
  import="net.sf.basedb.clients.web.formatter.FormatterSettings"
  import="net.sf.basedb.clients.web.util.HTML"
  import="java.util.Set"
  import="java.util.Date"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%
final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
final String ID = sc.getId();
final String cmd = request.getParameter("cmd");
final String root = request.getContextPath()+"/";
final String mode = request.getParameter("mode");
final String callback = request.getParameter("callback");
String forward = null;
String redirect = null;
String message = null;
DbControl dc = null;

try
{
  if ("PlaceOnPlate".equals(cmd))
  {
    dc = sc.newDbControl();
    Item bioMaterialType = Item.valueOf(request.getParameter("itemType"));
    String subContext = Values.getString(request.getParameter("subcontext"), "");
    ItemContext cc = sc.getCurrentContext(Item.BIOPLATEEVENT, BioPlateEventType.PLACE_ON_PLATE);
    final int maxRecent = Base.getMaxRecent(sc);

    sc.setUserClientSetting("place-on-plate.auto-select-unmapped-item", 
        Values.getBoolean(request.getParameter("autoSelectUnmappedItem")) ? "1" : "0");
    BioPlate plate = BioPlate.getById(dc, Values.getInt(request.getParameter("plate_id")));
    int rows = Values.getInt(request.getParameter("rows"));
    int columns = Values.getInt(request.getParameter("columns"));
    
    BioPlateEventType placeOnPlate = BioPlateEventType.getById(dc, BioPlateEventType.PLACE_ON_PLATE);
    BioPlateEvent event = BioPlateEvent.getNew(dc, placeOnPlate);
    BioPlateEventParticipant destination = event.addParticipant(plate, "destination", 1);
    
    event.setName(Values.getStringOrNull(request.getParameter("name")));
    event.setDescription(Values.getStringOrNull(request.getParameter("description")));
    Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
    event.setEventDate(dateFormatter.parseString(Values.getStringOrNull(request.getParameter("event_date"))));
    int protocolId = Values.getInt(request.getParameter("protocol_id"));
    if (protocolId > 0) 
    {
      Protocol pt = Protocol.getById(dc, protocolId);
      event.setProtocol(pt);
      cc.setRecent(pt, maxRecent);
    }
    int hardwareId = Values.getInt(request.getParameter("hardware_id"));
    if (hardwareId > 0)
    {
      Hardware hw = Hardware.getById(dc, hardwareId);
      event.setHardware(hw);
      cc.setRecent(hw, maxRecent);
    }
    dc.saveItem(event);
    
    int numPlaced = 0;
    for (int row = 0; row < rows; ++row)
    {
      for (int column = 0; column < columns; ++column)
      {
        int bioMaterialId = Values.getInt(request.getParameter("well." + row + "." + column));
        if (bioMaterialId > 0)
        {
          MeasuredBioMaterial bioMaterial = (MeasuredBioMaterial)bioMaterialType.getById(dc, bioMaterialId);
          BioWell well = plate.getBioWell(row, column);
          bioMaterial.setBioWell(well);
          BioMaterialEvent bmEvent = bioMaterial.newEvent(destination);
          bmEvent.setComment("Well: " + well.getCoordinate());
          dc.saveItem(bmEvent);
          numPlaced++;
        }
      }
    }
    
    dc.commit();
    message = "Placed " + numPlaced + " items on plate " + plate.getName();
  }
  else if ("MoveBioMaterial".equals(cmd))
  {
    dc = sc.newDbControl();
    ItemContext cc = sc.getCurrentContext(Item.BIOPLATEEVENT, BioPlateEventType.MOVE);
    final int maxRecent = Base.getMaxRecent(sc);
    sc.setUserClientSetting("move-biomaterial.show-source-coordinates", 
        Values.getBoolean(request.getParameter("showSourceCoordinates")) ? "1" : "0");

    BioPlate sourcePlate = BioPlate.getById(dc, Values.getInt(request.getParameter("sourceplate_id")));
    BioPlate destPlate = BioPlate.getById(dc, Values.getInt(request.getParameter("destplate_id")));
    int rows = Values.getInt(request.getParameter("rows"));
    int columns = Values.getInt(request.getParameter("columns"));
    
    BioPlateEventType moveBioMaterial = BioPlateEventType.getById(dc, BioPlateEventType.MOVE);
    BioPlateEvent event = BioPlateEvent.getNew(dc, moveBioMaterial);
    BioPlateEventParticipant destination = event.addParticipant(destPlate, "destination", 1);
    BioPlateEventParticipant source = event.addParticipant(sourcePlate, "source", 1);
    
    event.setName(Values.getStringOrNull(request.getParameter("name")));
    event.setDescription(Values.getStringOrNull(request.getParameter("description")));
    Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
    event.setEventDate(dateFormatter.parseString(Values.getStringOrNull(request.getParameter("event_date"))));
    int protocolId = Values.getInt(request.getParameter("protocol_id"));
    if (protocolId > 0) 
    {
      Protocol pt = Protocol.getById(dc, protocolId);
      event.setProtocol(pt);
      cc.setRecent(pt, maxRecent);
    }
    int hardwareId = Values.getInt(request.getParameter("hardware_id"));
    if (hardwareId > 0)
    {
      Hardware hw = Hardware.getById(dc, hardwareId);
      event.setHardware(hw);
      cc.setRecent(hw, maxRecent);
    }
    dc.saveItem(event);
    
    int numMoved = 0;
    for (int row = 0; row < rows; ++row)
    {
      for (int column = 0; column < columns; ++column)
      {
        int bioMaterialId = Values.getInt(request.getParameter("well." + row + "." + column));
        if (bioMaterialId > 0)
        {
          MeasuredBioMaterial bioMaterial = (MeasuredBioMaterial)BioMaterial.getById(dc, bioMaterialId);
          BioWell well = destPlate.getBioWell(row, column);
          bioMaterial.setBioWell(well);
          BioMaterialEvent bmEvent = bioMaterial.newEvent(destination);
          bmEvent.setComment("Well: " + well.getCoordinate());
          dc.saveItem(bmEvent);
          numMoved++;
        }
      }
    }
    
    dc.commit();
    message = "Moved " + numMoved + " items to plate " + destPlate.getName();
  }
  else
  {
    throw new WebException("popup", "Invalid command", "The command {1} is not recognised as a valid command.", cmd);
  }
}
finally
{
  if (dc != null) dc.close();
}

if (forward != null)
{
  pageContext.forward(forward);
}
else if (redirect != null)
{
  response.sendRedirect(redirect);
}
else if (message == null)
{
  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&wait=0");
}
else
{
  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&message="+HTML.urlEncode(message));
}
%>