source: trunk/www/biomaterials/wizards/index.jsp @ 5662

<%-- $Id: index.jsp 5662 2011-06-20 11:55:13Z 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 import="net.sf.basedb.core.BioMaterialEventSource"%>
<%@ 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.BioPlateType"
  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.PhysicalBioAssay"
  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.Sample"
  import="net.sf.basedb.core.Extract"
  import="net.sf.basedb.core.Tag"
  import="net.sf.basedb.core.PlateGeometry"
  import="net.sf.basedb.core.InvalidDataException"
  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 if ("CreateChildPlate".equals(cmd))
  {
    dc = sc.newDbControl();
    ItemContext cc = sc.getCurrentContext(Item.BIOPLATEEVENT, BioPlateEventType.CREATE_BIOMATERIAL);
    final int maxRecent = Base.getMaxRecent(sc);
    sc.setUserClientSetting("create-child-plate.show-source-coordinates", 
        Values.getBoolean(request.getParameter("showSourceCoordinates")) ? "1" : "0");

    BioPlate sourcePlate = BioPlate.getById(dc, Values.getInt(request.getParameter("sourceplate_id")));
    Item sourceBioMaterialType = sourcePlate.getBioPlateType().getBioMaterialType();
    Item childBioMaterialType = Item.valueOf(request.getParameter("child_biomaterial_type"));
    boolean isBioAssayEvent = childBioMaterialType == Item.PHYSICALBIOASSAY;
    
    // The event object
    BioPlateEventType createBioMaterial = BioPlateEventType.getById(dc, 
        isBioAssayEvent ? BioPlateEventType.PHYSICAL_BIOASSAY :  BioPlateEventType.CREATE_BIOMATERIAL);
    BioPlateEvent event = BioPlateEvent.getNew(dc, createBioMaterial);
    event.setName(Values.getStringOrNull(request.getParameter("event_name")));
    event.setDescription(Values.getStringOrNull(request.getParameter("event_description")));
    BioPlateEventParticipant sourceParticipant = event.addParticipant(sourcePlate, "source", 1);
    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, sourceBioMaterialType.name(), maxRecent);
    }
    int hardwareId = Values.getInt(request.getParameter("hardware_id"));
    if (hardwareId > 0)
    {
      Hardware hw = Hardware.getById(dc, hardwareId);
      event.setHardware(hw);
      cc.setRecent(hw, sourceBioMaterialType.name(), maxRecent);
    }
    dc.saveItem(event);

    // Child plates & biomaterial
    Hardware freezer = null;
    if (!isBioAssayEvent)
    {
      int freezerId = Values.getInt(request.getParameter("freezer_id"));
      if (freezerId > 0)
      {
        freezer = Hardware.getById(dc, freezerId);
        cc.setRecent(freezer, "freezer", maxRecent);
      }
    }
    int numChildPlates = Values.getInt(request.getParameter("number_of_plates"));
    int size = Values.getInt(request.getParameter("size"));
    PlateGeometry childGeometry = null;
    if (!isBioAssayEvent)
    {
      childGeometry = PlateGeometry.getById(dc, Values.getInt(request.getParameter("plategeometry_id")));
      cc.setRecent(childGeometry, sourceBioMaterialType.name(), maxRecent);
    }
    int rows = isBioAssayEvent ? 1 : childGeometry.getRows();
    int columns = isBioAssayEvent ? size : childGeometry.getColumns();
    int numCreated = 0;
    BioPlateType childPlateType = null;
    if (!isBioAssayEvent)
    {
      childPlateType = BioPlateType.getById(dc, Values.getInt(request.getParameter("bioplatetype_id")));
      cc.setRecent(childPlateType, sourceBioMaterialType.name(), maxRecent);
    }
    Float usedQuantity = Values.getFloat(request.getParameter("used_quantity"));
    Float originalQuantity = Values.getFloat(request.getParameter("original_quantity"));
    for (int plateNo = 0; plateNo < numChildPlates; ++plateNo)
    {
      PhysicalBioAssay pba = null;
      BioMaterialEvent pbaCreationEvent = null;
      BioPlate childPlate = null;
      BioPlateEventParticipant destParticipant = null;
      if (isBioAssayEvent)
      {
        pba = PhysicalBioAssay.getNew(dc, sourceParticipant);
        pba.setName(Values.getStringOrNull(request.getParameter("plate." + plateNo + ".name")));
        pba.setDescription(Values.getStringOrNull(request.getParameter("plate_description")));
        pba.setSize(size);
        dc.saveItem(pba);
        pbaCreationEvent = pba.getCreationEvent();
      }
      else
      {
        childPlate = BioPlate.getNew(dc, childGeometry, childPlateType);
        childPlate.setName(Values.getStringOrNull(request.getParameter("plate." + plateNo + ".name")));
        childPlate.setDescription(Values.getStringOrNull(request.getParameter("plate_description")));
        if (freezer != null) childPlate.setFreezer(freezer);
        childPlate.setBarcode(Values.getStringOrNull(request.getParameter("plate." + plateNo + ".barcode")));
        dc.saveItem(childPlate);
        destParticipant = event.addParticipant(childPlate, "destination", plateNo);
      }
      for (int row = 0; row < rows; ++row)
      {
        for (int column = 0; column < columns; ++column)
        {
          String prefix = "well." + +plateNo + "." + row + "." + column;
          int bioMaterialId = Values.getInt(request.getParameter(prefix));
          if (bioMaterialId > 0)
          {
            MeasuredBioMaterial parent = (MeasuredBioMaterial)sourceBioMaterialType.getById(dc, bioMaterialId);
            if (isBioAssayEvent)
            {
              BioMaterialEventSource evtSrc = pbaCreationEvent.addSource(parent);
              evtSrc.setUsedQuantity(usedQuantity);
              evtSrc.setPosition(column+1);
            }
            else
            {
              BioWell well = childPlate.getBioWell(row, column);
              MeasuredBioMaterial child = null;
              boolean pooled = childBioMaterialType == sourceBioMaterialType;
              if (childBioMaterialType == Item.SAMPLE)
              {
                child = Sample.getNew(dc, destParticipant);
              }
              else if (childBioMaterialType == Item.EXTRACT)
              {
                child = Extract.getNew(dc, destParticipant);
                if (!pooled) ((Extract)child).setSample((Sample)parent).setUsedQuantity(usedQuantity);
              }
              /*
              else if (childBioMaterialType == Item.LABELEDEXTRACT)
              {
                Label label = Label.getById(dc, Values.getInt(request.getParameter("label_id")));
                child = LabeledExtract.getNew(dc, label, destParticipant);
                if (!pooled) ((LabeledExtract)child).setExtract((Extract)parent, usedQuantity);
              }
              */
              else
              {
                throw new InvalidDataException("Can't create child biomaterial of type: " + childBioMaterialType);
              }
              child.setName(Values.getStringOrNull(request.getParameter(prefix + ".name")));
              child.setDescription(Values.getStringOrNull(request.getParameter("child_description")));
              child.setBioWell(well);
              child.setOriginalQuantity(originalQuantity);
              
              if (pooled)
              {
                child.getCreationEvent().addSource(parent).setUsedQuantity(usedQuantity);
              }
              dc.saveItem(child);
            }
            numCreated++;
          }
        }
      }
      
    }

    dc.commit();
    if (isBioAssayEvent)
    {
      message = "Used " + numCreated + " items on " + numChildPlates + " physical bioassay(s)";
    }
    else
    {
      message = "Created " + numCreated + " items on " + numChildPlates + " child plate(s)";
    }
  }
  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));
}
%>