source: trunk/www/views/hybridizations/index.jsp @ 4133

<%-- $Id: index.jsp 4133 2008-02-08 10:54:05Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2005 Nicklas Nordborg, Gregory Vincic
  Copyright (C) 2006 Jari Hakkinen, Nicklas Nordborg, Martin Svensson

  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.Include"
  import="net.sf.basedb.core.Hybridization"
  import="net.sf.basedb.core.ArraySlide"
  import="net.sf.basedb.core.BioMaterialEvent"
  import="net.sf.basedb.core.LabeledExtract"
  import="net.sf.basedb.core.Protocol"
  import="net.sf.basedb.core.Hardware"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.ItemResultIterator"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.MultiPermissions"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.ItemAlreadyExistsException"
  import="net.sf.basedb.util.RemovableUtil"
  import="net.sf.basedb.util.ShareableUtil"
  import="net.sf.basedb.util.OwnableUtil"
  import="net.sf.basedb.clients.web.Base"
  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.util.formatter.Formatter"
  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
  import="java.util.Enumeration"
  import="java.util.Set"
  import="java.util.HashSet"
  import="java.util.List"
  import="java.util.ArrayList"
  import="java.util.Collections"
  import="java.util.Date"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%!
  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,labeledExtracts,arraySlide,scans,description");
  private static final Item itemType = Item.HYBRIDIZATION;
%>
<%
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");
final String itemId = request.getParameter("item_id");
final String listPage = "list_hybridizations.jsp?ID="+ID
  +(mode == null ? "" : "&mode="+mode)
  +(callback == null ? "" : "&callback="+callback)
  +(itemId == null ? "" : "&item_id="+itemId);
final String viewPage = "view_hybridization.jsp?ID="+ID;
final String editPage = "edit_hybridization.jsp?ID="+ID;

String forward = null;
String redirect = null;
String message = null;
DbControl dc = null;

try
{
  if (cmd == null || "List".equals(cmd))
  {
    // Display the list page without updatinging the current context
    Base.getAndSetCurrentContext(sc, itemType, null, defaultContext, true);
    redirect = listPage;
  }
  else if ("UpdateContext".equals(cmd))
  {
    // Display the list page after updating the current context from the request parameters
    Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = listPage;
  }
  else if ("LoadContext".equals(cmd))
  {
    // Display the list page after loading a saved context
    int contextId = Values.getInt(request.getParameter("context"));
    Base.loadContext(sc, contextId, defaultContext);
    redirect = listPage;
  }

  else if ("ViewItem".equals(cmd))
  {
    // Display the view page for a single item 
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    forward = viewPage;
  }
  else if ("EditItem".equals(cmd))
  {
    // Display the edit page for a single item (should be opened in a popup)
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = editPage;
  }
  else if ("NewItem".equals(cmd))
  {
    // Display the edit page for a new item (should be opened in a popup)
    if (!sc.hasPermission(Permission.CREATE, itemType))
    {
      throw new PermissionDeniedException(Permission.CREATE, itemType.toString());
    }
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    cc.setId(0);
    forward = editPage;
  }
  else if ("UpdateItem".equals(cmd))
  {
    // Update the properties on an item (will close the popup)
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, defaultContext);
    final int maxRecent = Base.getMaxRecent(sc);
    dc = sc.newDbControl();
    Hybridization hyb = (Hybridization)cc.getObject("item");
    BioMaterialEvent creationEvent = null;
    if (hyb == null)
    {
      hyb = Hybridization.getNew(dc);
      creationEvent = hyb.getCreationEvent();
      message = "Hybridization created";
      dc.saveItem(hyb);
    }
    else
    {
      creationEvent = hyb.getCreationEvent();
      dc.reattachItem(hyb);
      dc.reattachItem(creationEvent);
      message = "Hybridization updated";
    }
    hyb.setName(Values.getStringOrNull(request.getParameter("name")));
    hyb.setDescription(Values.getStringOrNull(request.getParameter("description")));
    hyb.setNumArrays(Values.getInt(request.getParameter("numArrays"), 1));
    
    int arraySlideId = Values.getInt(request.getParameter("arrayslide_id"), -1);
    if (arraySlideId >= 0) // < 0 = denied or unchanged
    {
      ArraySlide slide = arraySlideId == 0 ? null : ArraySlide.getById(dc, arraySlideId);
      hyb.setArraySlide(slide);
    }
    Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
    creationEvent.setEventDate(dateFormatter.parseString(Values.getStringOrNull(request.getParameter("event_date"))));
    int protocolId = Values.getInt(request.getParameter("protocol_id"), -1);
    if (protocolId >= 0) // < 0 = denied or unchanged
    {
      Protocol pt = protocolId == 0 ? null : Protocol.getById(dc, protocolId);
      creationEvent.setProtocol(pt);
      if (pt != null) cc.setRecent(pt, maxRecent);
    }
    
    //Hybridization station
    int hybStationId = Values.getInt(request.getParameter("hardware_id"), -1);
    if (hybStationId >= 0) // < 0 denied or unchanged
    {
      Hardware hw = hybStationId == 0 ? null : Hardware.getById(dc, hybStationId);
      creationEvent.setHardware(hw);
      if (hw != null) cc.setRecent(hw, maxRecent);
    }
    
    // Labeled extracts
    String[] modifiedLabeledExtracts = Values.getString(request.getParameter("modifiedLabeledExtracts")).split(",");
    for (int i = 0; i < modifiedLabeledExtracts.length; ++i)
    {
      int leId = Values.getInt(modifiedLabeledExtracts[i], -1);
      if (leId != -1) 
      {
        LabeledExtract le = LabeledExtract.getById(dc, leId);
        String[] extra = request.getParameter("L"+leId).split(":");
        Float usedQuantity = Values.getFloat(extra[0], null);
        int arrayIndex = extra.length > 1 ? Values.getInt(extra[1], 1) : 1;
        creationEvent.addSource(le, usedQuantity);
        creationEvent.setSourceGroup(le, arrayIndex);
      }
    }
    String[] removedLabeledExtracts = Values.getString(request.getParameter("removedLabeledExtracts")).split(",");
    for (int i = 0; i < removedLabeledExtracts.length; ++i)
    {
      int leId = Values.getInt(removedLabeledExtracts[i], -1);
      if (leId != -1) creationEvent.removeSource(LabeledExtract.getById(dc, leId));
    }
    
    // Annotations tab
    Base.updateAnnotations(dc, hyb, hyb, request);
    dc.commit();
    cc.removeObject("item");
  }
  else if ("DeleteItem".equals(cmd))
  {
    // Delete a single item and then return to the view page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    RemovableUtil.setRemoved(dc, itemType, Collections.singleton(cc.getId()), true);
    dc.commit();
    redirect = viewPage;
  }
  else if ("DeleteItems".equals(cmd))
  {
    // Delete all selected items on the list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    int numTotal = cc.getSelected().size();
    int numRemoved = RemovableUtil.setRemoved(dc, itemType, cc.getSelected(), true);
    dc.commit();
    if (numTotal != numRemoved)
    {
      message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be deleted, because you have no DELETE permission";
    }
    redirect = listPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
  }
  else if ("RestoreItem".equals(cmd))
  {
    // Restore a single item and then return to the view page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    RemovableUtil.setRemoved(dc, itemType, Collections.singleton(cc.getId()), false);
    dc.commit();
    redirect = viewPage;
  }
  else if ("RestoreItems".equals(cmd))
  {
    // Restore all selected items on the list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    int numTotal = cc.getSelected().size();
    int numRemoved = RemovableUtil.setRemoved(dc, itemType, cc.getSelected(), false);
    dc.commit();
    if (numTotal != numRemoved)
    {
      message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be restored, because you have no WRITE permission";
    }
    redirect = listPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
  }
  else if ("ShareItem".equals(cmd))
  {
    // Display a popup window for sharing a single item
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    MultiPermissions permissions = ShareableUtil.getMultiPermissions(dc, itemType, Collections.singleton(cc.getId()));
    dc.close();
    cc.setObject("MultiPermissions", permissions);
    redirect = "../../common/share/share.jsp?ID="+ID+"&item_type="+itemType.name();
  }
  else if ("ShareItems".equals(cmd))
  {
    // Display a popup window for sharing all selected items on the list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    MultiPermissions permissions = ShareableUtil.getMultiPermissions(dc, itemType, cc.getSelected());
    dc.close();
    cc.setObject("MultiPermissions", permissions);
    redirect = "../../common/share/share.jsp?ID="+ID+"&item_type="+itemType.name();
  }
  else if ("TakeOwnershipOfItem".equals(cmd))
  {
    // Take ownership a single item and then return to the view page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    OwnableUtil.setOwner(dc, itemType, Collections.singleton(cc.getId()), null);
    dc.commit();
    redirect = viewPage;
  }
  else if ("TakeOwnershipOfItems".equals(cmd))
  {
    // Take ownership all selected items on the list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    int numTotal = cc.getSelected().size();
    int numOwned = OwnableUtil.setOwner(dc, itemType, cc.getSelected(), null);
    dc.commit();
    if (numTotal != numOwned)
    {
      message = (numOwned == 0 ? "No" : "Only "+numOwned+" of "+numTotal) + " items could be taken, because you have no SET_OWNER permission";
    }
    redirect = listPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
  }
  else if ("ExportItems".equals(cmd))
  {
    // Run an export plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<Hybridization> query = Hybridization.getQuery();
    cc.configureQuery(query, true);
    cc.setQuery(query);
    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+hybridizations";
  }
  else if ("ExportItem".equals(cmd))
  {
    // Run an export plugin in single-item context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+hybridization";
  }
  else if ("ImportItems".equals(cmd))
  {
    // Run an import plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<Hybridization> query = Hybridization.getQuery();
    cc.configureQuery(query, true);
    cc.setQuery(query);
    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+hybrydizations";
  }
  else if ("ImportItem".equals(cmd))
  {
    // Run an import plugin in single-item context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+hybridization";
  }
  else if ("RunListPlugin".equals(cmd))
  {
    // Run another plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<Hybridization> query = Hybridization.getQuery();
    cc.configureQuery(query, true);
    cc.setQuery(query);
    redirect = "../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&main_type=OTHER&title=Run+plugin";
  }
  else if ("RunPlugin".equals(cmd))
  {
    // Run another plugin in single-item context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = "../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&main_type=OTHER&title=Run+plugin";
  }
  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));
}
%>