source: trunk/www/views/experiments/bioassaysets/index.jsp @ 2993

<%-- $Id: index.jsp 2993 2006-12-01 14:34:35Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006 Nicklas Nordborg

  This file is part of BASE - BioArray Software Environment.
  Available at http://base.thep.lu.se/

  This file is part of BASE.

  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.Experiment"
  import="net.sf.basedb.core.BioAssaySet"
  import="net.sf.basedb.core.Job"
  import="net.sf.basedb.core.RawBioAssay"
  import="net.sf.basedb.core.StringParameterType"
  import="net.sf.basedb.core.IntegerParameterType"
  import="net.sf.basedb.core.ItemParameterType"
  import="net.sf.basedb.core.User"
  import="net.sf.basedb.core.Path"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.ItemResultIterator"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.PluginDefinition"
  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.core.query.Restriction"
  import="net.sf.basedb.util.RemovableUtil"
  import="net.sf.basedb.util.ShareableUtil"
  import="net.sf.basedb.util.BioAssaySetUtil"
  import="net.sf.basedb.util.DynamicFilter"
  import="net.sf.basedb.util.IncludeExcludeFilter"
  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="java.util.Enumeration"
  import="java.util.Set"
  import="java.util.HashSet"
  import="java.util.List"
  import="java.util.LinkedList"
  import="java.util.Collections"
  import="java.util.Arrays"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%!
  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,spots,reporters,date,tools");
  private static final Item itemType = Item.BIOASSAYSET;
  
  
  private void setClosed(HttpServletRequest request, ItemContext cc)
  {
    String closed = request.getParameter("closed");
    if (closed != null)
    {
      cc.setObject("closed", new HashSet<String>(Arrays.asList(closed.split(","))));
    }
  }
%>
<%
final int experimentId = Values.getInt(request.getParameter("experiment_id"));
final String transformationId = request.getParameter("transformation_id");
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_bioassaysets.jsp?ID="+ID+"&experiment_id="+experimentId
  +(mode == null ? "" : "&mode="+mode)
  +(callback == null ? "" : "&callback="+callback)
  +(itemId == null ? "" : "&item_id="+itemId);
final String viewPage = "view_bioassayset.jsp?ID="+ID+"&experiment_id="+experimentId;
final String editPage = "edit_bioassayset.jsp?ID="+ID+"&experiment_id="+experimentId;
final String viewTransformationPage = "../transformations/view_transformation.jsp?ID="+ID+
  "&experiment_id="+experimentId;
final String newPage = "../../../common/plugin/index.jsp?ID="+ID
  +"&cmd=SelectPlugin&main_type=INTENSITY&item_type=BIOASSAYSET&context_type=LIST&title=Create+root+bioassay+set";

if (experimentId != 0) sc.getCurrentContext(Item.EXPERIMENT).setId(experimentId);

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
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, defaultContext, true);
    if (transformationId != null)
    {
      forward = viewTransformationPage;
    }
    else if (itemId != null)
    {
      forward = viewPage;
    }
    else
    {
      redirect = listPage;
    }
  }
  else if ("UpdateContext".equals(cmd))
  {
    // Display the list page after updating the current context from the request parameters
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    setClosed(request, cc);
    if (transformationId != null)
    {
      forward = viewTransformationPage;
    }
    else if (itemId != null)
    {
      forward = viewPage;
    }
    else
    {
      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);
    if (transformationId != null)
    {
      forward = viewTransformationPage;
    }
    else if (itemId != null)
    {
      forward = viewPage;
    }
    else
    {
      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)
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    cc.setId(0);
    redirect = newPage;
  }
  else if ("UpdateItem".equals(cmd))
  {
    // Update the properties on an item (will close the popup)
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, defaultContext);
    dc = sc.newDbControl();
    
    BioAssaySet bas = (BioAssaySet)cc.getObject("item");
    if (bas != null)
    {
      dc.reattachItem(bas);
      message = "Bioassay set updated";
      bas.setName(Values.getStringOrNull(request.getParameter("name")));
      bas.setDescription(Values.getStringOrNull(request.getParameter("description")));

      // Annotations tab
      Base.updateAnnotations(dc, bas, bas, 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.removeRecursively(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);
    ItemContext tc = sc.getCurrentContext(Item.TRANSFORMATION);
    ItemContext xc = sc.getCurrentContext(Item.EXTRAVALUE);
    setClosed(request, cc);

    int numTotal = cc.getSelected().size()+tc.getSelected().size();
    int numRemoved = 0;
    int[] numTransformationRemoved = RemovableUtil.removeRecursively(dc, Item.TRANSFORMATION, tc.getSelected(), true);
    int[] numBioAssaySetRemoved = RemovableUtil.removeRecursively(dc, itemType, cc.getSelected(), true);
    int numXV = RemovableUtil.delete(dc, Item.EXTRAVALUE, xc.getSelected());
    numTotal += numTransformationRemoved[1] + numBioAssaySetRemoved[1];
    numRemoved += numTransformationRemoved[0] + numBioAssaySetRemoved[0];

    dc.commit();
    if (numTotal != numRemoved)
    {
      message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be deleted, because you have no DELETE permission";
    }
    if (transformationId != null)
    {
      forward = viewTransformationPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
    }
    else if (itemId != null)
    {
      forward = viewPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
    }
    else
    {
      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.removeRecursively(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);
    ItemContext tc = sc.getCurrentContext(Item.TRANSFORMATION);
    setClosed(request, cc);

    int numTotal = cc.getSelected().size()+tc.getSelected().size();
    int numRemoved = 0;
    int[] numTransformationRemoved = RemovableUtil.removeRecursively(dc, Item.TRANSFORMATION, tc.getSelected(), false);
    int[] numBioAssaySetRemoved = RemovableUtil.removeRecursively(dc, itemType, cc.getSelected(), false);
    numTotal += numTransformationRemoved[1] + numBioAssaySetRemoved[1];
    numRemoved += numTransformationRemoved[0] + numBioAssaySetRemoved[0];
    
    dc.commit();
    if (numTotal != numRemoved)
    {
      message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be restored, because you have no WRITE permission";
    }
    if (transformationId != null)
    {
      forward = viewTransformationPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
    }
    else if (itemId != null)
    {
      forward = viewPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
    }
    else
    {
      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);
    setClosed(request, cc);
    dc = sc.newDbControl();
    final Experiment experiment = Experiment.getById(dc, experimentId);
    dc.close();
    final ItemQuery<BioAssaySet> query = experiment.getBioAssaySets();
    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+bioassay+sets";
  }
  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+bioassay+set";
  }
  else if ("ImportItems".equals(cmd))
  {
    // Run an import plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    setClosed(request, cc);
    dc = sc.newDbControl();
    final Experiment experiment = Experiment.getById(dc, experimentId);
    dc.close();
    final ItemQuery<BioAssaySet> query = experiment.getBioAssaySets();
    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+bioassay+sets";
  }
  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+bioassay+set";
  }
  else if ("RunListPlugin".equals(cmd))
  {
    // Run another plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    setClosed(request, cc);
    dc = sc.newDbControl();
    final Experiment experiment = Experiment.getById(dc, experimentId);
    dc.close();
    final ItemQuery<BioAssaySet> query = experiment.getBioAssaySets();
    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 a 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 if ("RunAnalysisPlugin".equals(cmd))
  {
    // Run an analysis 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=ANALYZE&title=Run+analysis+plugin";
  }
  else if ("NewFilteredBioAssaySet".equals(cmd))
  {
    // Display the edit page for for filtering a bioassay set (should be opened in a popup)
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = "../../../common/plugin/index.jsp?ID="+ID+"&cmd=NewJob&item_type="+itemType.name()+"&context_type=ITEM&main_type=ANALYZE&title=Filter+bioassay+set&plugin_class=net.sf.basedb.plugins.FormulaFilter";
  }
  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));
}
%>