source: trunk/www/views/experiments/index.jsp @ 3005

<%-- $Id: index.jsp 3005 2006-12-07 08:25:06Z martin $
  ------------------------------------------------------------------
  Copyright (C) Authors contributing to this file.

  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.Experiment"
  import="net.sf.basedb.core.RawBioAssay"
  import="net.sf.basedb.core.AnnotationType"
  import="net.sf.basedb.core.RawDataType"
  import="net.sf.basedb.core.RawDataTypes"
  import="net.sf.basedb.core.User"
  import="net.sf.basedb.core.Directory"
  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,rawDataType,description,actions");
  private static final Item itemType = Item.EXPERIMENT;
%>
<%
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_experiments.jsp?ID="+ID
  +(mode == null ? "" : "&mode="+mode)
  +(callback == null ? "" : "&callback="+callback)
  +(itemId == null ? "" : "&item_id="+itemId);
final String viewPage = "view_experiment.jsp?ID="+ID;
final String editPage = "edit_experiment.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();
    
    Experiment experiment = (Experiment)cc.getObject("item");
    if (experiment == null)
    {
      RawDataType rdt = RawDataTypes.getRawDataType(Values.getStringOrNull(request.getParameter("rawdatatype")));
      if (rdt != null) cc.setRecent("RawDataType", rdt.getId(), maxRecent);
      experiment = Experiment.getNew(dc, rdt);
      message = "Experiment created";
      dc.saveItem(experiment);
    }
    else
    {
      dc.reattachItem(experiment);
      message = "Experiment updated";
    }

    Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
    experiment.setName(Values.getStringOrNull(request.getParameter("name")));
    experiment.setTitle(Values.getStringOrNull(request.getParameter("title")));
    experiment.setAbstract(Values.getStringOrNull(request.getParameter("abstract")));
    experiment.setAffiliations(Values.getStringOrNull(request.getParameter("affiliations")));
    experiment.setAuthors(Values.getStringOrNull(request.getParameter("authors")));
    experiment.setExperimentDesign(Values.getStringOrNull(request.getParameter("experimentDesign")));
    experiment.setExperimentType(Values.getStringOrNull(request.getParameter("experimentType")));
    experiment.setPublication(Values.getStringOrNull(request.getParameter("publication")));
    experiment.setPublicationDate(dateFormatter.parseString(Values.getStringOrNull(request.getParameter("publicationDate"))));
    experiment.setPubMedId(Values.getStringOrNull(request.getParameter("pubMedId")));
    experiment.setDescription(Values.getStringOrNull(request.getParameter("description")));

    int directoryId = Values.getInt(request.getParameter("directory_id"), -1);
    if (directoryId >= 0) // < 0 = denied or unchanged
    {
      Directory dir = directoryId == 0 ? null : Directory.getById(dc, directoryId);
      experiment.setDirectory(dir);
      if (dir != null) cc.setRecent(dir, maxRecent);
    }

    String[] removeRawBioAssays = Values.getString(request.getParameter("removedRawBioAssays")).split(",");
    for (int i = 0; i < removeRawBioAssays.length; ++i)
    {
      int rawBioAssayId = Values.getInt(removeRawBioAssays[i], -1);
      if (rawBioAssayId != -1) experiment.removeRawBioAssay(RawBioAssay.getById(dc, rawBioAssayId));
    }
    
    String[] addRawBioAssays = Values.getString(request.getParameter("addedRawBioAssays")).split(",");
    for (int i = 0; i < addRawBioAssays.length; ++i)
    {
      int rawBioAssayId = Values.getInt(addRawBioAssays[i], -1);
      if (rawBioAssayId != -1) experiment.addRawBioAssay(RawBioAssay.getById(dc, rawBioAssayId));
    }
    
    String[] removeAnnotationTypes = Values.getString(request.getParameter("removedAnnotationTypes")).split(",");
    for (int i = 0; i < removeAnnotationTypes.length; ++i)
    {
      int annotationTypeId = Values.getInt(removeAnnotationTypes[i], -1);
      if (annotationTypeId != -1) experiment.removeExperimentalFactor(AnnotationType.getById(dc, annotationTypeId));
    }
    
    String[] addAnnotationTypes = Values.getString(request.getParameter("addedAnnotationTypes")).split(",");
    for (int i = 0; i < addAnnotationTypes.length; ++i)
    {
      int annotationTypeId = Values.getInt(addAnnotationTypes[i], -1);
      if (annotationTypeId != -1) experiment.addExperimentalFactor(AnnotationType.getById(dc, annotationTypeId));
    }

    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);
    int numTotal = cc.getSelected().size();
    int[] numRemoved = RemovableUtil.removeRecursively(dc, itemType, cc.getSelected(), true);
    numTotal += numRemoved[1];
    dc.commit();
    if (numTotal != numRemoved[0])
    {
      message = (numRemoved[0] == 0 ? "No" : "Only "+numRemoved[0]+" 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.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);
    int numTotal = cc.getSelected().size();
    int[] numRemoved = RemovableUtil.removeRecursively(dc, itemType, cc.getSelected(), false);
    numTotal += numRemoved[1];
    dc.commit();
    if (numTotal != numRemoved[0])
    {
      message = (numRemoved[0] == 0 ? "No" : "Only "+numRemoved[0]+" 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<Experiment> query = Experiment.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+raw+bioassays";
  }
  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+raw+bioassay";
  }
  else if ("ImportItems".equals(cmd))
  {
    // Run an import plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<Experiment> query = Experiment.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+raw+bioassays";
  }
  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+raw+bioassay";
  }
  else if ("RunListPlugin".equals(cmd))
  {
    // Run another plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<Experiment> query = Experiment.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));
}
%>