source: trunk/www/views/physicalbioassays/index.jsp @ 6314

<%-- $Id: index.jsp 6314 2013-09-02 12:47:53Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2005 Nicklas Nordborg, Gregory Vincic
  Copyright (C) 2006 Jari Häkkinen, 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 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
  @version 2.0
--%>
<%@ page pageEncoding="UTF-8" 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.PhysicalBioAssay"
  import="net.sf.basedb.core.ArraySlide"
  import="net.sf.basedb.core.BioMaterialEvent"
  import="net.sf.basedb.core.BioMaterialEventSource"
  import="net.sf.basedb.core.Extract"
  import="net.sf.basedb.core.Protocol"
  import="net.sf.basedb.core.Hardware"
  import="net.sf.basedb.core.ItemSubtype"
  import="net.sf.basedb.core.DerivedBioAssay"
  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.OwnedItem"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.ItemAlreadyExistsException"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.core.query.Restrictions"
  import="net.sf.basedb.core.query.Expressions"
  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.util.formatter.NameableFormatter"
  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
  import="net.sf.basedb.clients.web.plugins.ItemQueryLoader"
  import="net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter"
  import="net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoaderFromBioAssay"
  import="net.sf.basedb.core.plugin.GuiContext"
  import="net.sf.basedb.util.extensions.ExtensionsInvoker"
  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
  import="net.sf.basedb.clients.web.extensions.JspContext"
  import="net.sf.basedb.clients.web.extensions.edit.EditUtil"
  import="net.sf.basedb.clients.web.extensions.edit.OnSaveRenderer"
  import="net.sf.basedb.clients.web.extensions.list.ListColumnExportRenderer"
  import="net.sf.basedb.clients.web.extensions.list.ListColumnUtil"
  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,itemSubtype,extracts,arraySlide,description");
  private static final Item itemType = Item.PHYSICALBIOASSAY;
  
  private static void registerExportUtils(ItemContext cc)
  {
    // Register formatters
    cc.setObject("export.formatter.&creationEvent.sources(bioMaterial.name)", new BioMaterialEventSourceFormatter());
    cc.setObject("export.formatter.&rootDerivedBioAssays(name)", new NameableFormatter());
    
    // Register dataloaders
    String bioassayParameter = "bioassay";
    cc.setObject("export.dataloader.&creationEvent.sources(bioMaterial.name)", new ParentBioMaterialEventSourceLoaderFromBioAssay());

    ItemQuery<DerivedBioAssay> dbasQuery = DerivedBioAssay.getQuery();
    dbasQuery.include(cc.getInclude());
    dbasQuery.join(Hql.innerJoin("physicalBioAssays", "pba"));
    dbasQuery.restrict(Restrictions.eq(Hql.alias("pba"), Expressions.parameter(bioassayParameter)));
    dbasQuery.restrict(Restrictions.eq(Hql.property("root"), Expressions.bool(true)));
    dbasQuery.order(Orders.asc(Hql.property("name")));
    cc.setObject("export.dataloader.&rootDerivedBioAssays(name)", new ItemQueryLoader(dbasQuery, bioassayParameter));
  }
%>
<%
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_bioassays.jsp?ID="+ID
  +(mode == null ? "" : "&mode="+mode)
  +(callback == null ? "" : "&callback="+callback)
  +(itemId == null ? "" : "&item_id="+itemId);
final String viewPage = "view_bioassay.jsp?ID="+ID;
final String editPage = "edit_bioassay.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();
    PhysicalBioAssay pba = (PhysicalBioAssay)cc.getObject("item");
    BioMaterialEvent creationEvent = null;
    if (pba == null)
    {
      pba = PhysicalBioAssay.getNew(dc);
      creationEvent = pba.getCreationEvent();
      message = "Physical bioassay created";
      dc.saveItem(pba);
    }
    else
    {
      creationEvent = pba.getCreationEvent();
      dc.reattachItem(pba, false);
      dc.reattachItem(creationEvent, false);
      message = "Physical bioassay updated";
    }
    JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.item(Item.PHYSICALBIOASSAY), pba);
    ExtensionsInvoker invoker = EditUtil.useOnSaveExtensions(jspContext);
    try
    {
      pba.setName(Values.getStringOrNull(request.getParameter("name")));
      pba.setDescription(Values.getStringOrNull(request.getParameter("description")));
      pba.setSize(Values.getInt(request.getParameter("size"), 1));

      int subtypeId = Values.getInt(request.getParameter("subtype_id"), -1);
      ItemSubtype subtype = null;
      if (subtypeId >= 0) // < 0 = denied or unchanged
      {
        if (subtypeId > 0) subtype = ItemSubtype.getById(dc, subtypeId);
        pba.setItemSubtype(subtype);
        if (subtype != null) cc.setRecent(subtype, maxRecent);
      }
      
      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);
        pba.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, subtype, maxRecent);
      }
      
      //Hardware
      int hardwareId = Values.getInt(request.getParameter("hardware_id"), -1);
      if (hardwareId >= 0) // < 0 denied or unchanged
      {
        Hardware hw = hardwareId == 0 ? null : Hardware.getById(dc, hardwareId);
        creationEvent.setHardware(hw);
        if (hw != null) cc.setRecent(hw, subtype, maxRecent);
      }
      
      // Extracts
      String[] modifiedExtracts = Values.getString(request.getParameter("+EXTRACT")).split(",");
      for (int i = 0; i < modifiedExtracts.length; ++i)
      {
        int extractId = Values.getInt(modifiedExtracts[i], -1);
        if (extractId != -1) 
        {
          Extract e = Extract.getById(dc, extractId);
          String[] extra = request.getParameter("EXTRACT."+extractId).split(":");
          Float usedQuantity = Values.getFloat(extra[0], null);
          int position = extra.length > 1 ? Values.getInt(extra[1], 1) : 1;
          BioMaterialEventSource evtSrc = creationEvent.addSource(e);
          evtSrc.setUsedQuantity(usedQuantity);
          evtSrc.setPosition(position);
        }
      }
      String[] removedExtracts = Values.getString(request.getParameter("-EXTRACT")).split(",");
      for (int i = 0; i < removedExtracts.length; ++i)
      {
        int extractId = Values.getInt(removedExtracts[i], -1);
        if (extractId != -1) creationEvent.removeSource(Extract.getById(dc, extractId));
      }
      
      // Annotations tab
      Base.updateAnnotations(dc, pba, pba, request);
      
      // OnSave extensions
      invoker.render(OnSaveRenderer.ON_SAVE);
      dc.commit();
      invoker.render(OnSaveRenderer.ON_COMMIT);
    }
    catch (Exception ex)
    {
      invoker.render(OnSaveRenderer.onRollback(ex));
      throw ex;
    }
    finally
    {
      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;
  }
  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;
  }
  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 ("SetOwnerOfItem".equals(cmd))
  {
    // Change owner of items selected on a list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    OwnedItem item = (OwnedItem)itemType.getById(dc, cc.getId());
    cc.setObject("OwnedItems", Collections.singleton(item));
    redirect = "../../common/ownership/ownership.jsp?ID="+ID+"&item_type="+itemType.name();
  }
  else if ("SetOwnerOfItems".equals(cmd))
  {
    // Change owner of items selected on a list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    Set<OwnedItem> items = new HashSet<OwnedItem>();
    for (Integer id : cc.getSelected())
    {
      if (id != null) items.add((OwnedItem)itemType.getById(dc, id));
    }
    dc.close();
    cc.setObject("OwnedItems", items);
    redirect = "../../common/ownership/ownership.jsp?ID="+ID+"&item_type="+itemType.name();
  }
  else if ("ExportItems".equals(cmd))
  {
    // Run an export plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<PhysicalBioAssay> query = PhysicalBioAssay.getQuery();
    dc = sc.newDbControl();
    cc.configureQuery(dc, query, true);
    cc.setQuery(query);
    registerExportUtils(cc);
    JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.list(itemType), null);
    ExtensionsInvoker listInvoker = ListColumnUtil.useExtensions(jspContext);
    listInvoker.render(new ListColumnExportRenderer(cc));
    dc.close();
    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+physical+bioassays";
  }
  else if ("ExportItem".equals(cmd))
  {
    // Run an export plugin in single-item context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    registerExportUtils(cc);
    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+physical+bioassay";
  }
  else if ("ImportItems".equals(cmd))
  {
    // Run an import plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<PhysicalBioAssay> query = PhysicalBioAssay.getQuery();
    dc = sc.newDbControl();
    cc.configureQuery(dc, query, true);
    dc.close();
    cc.setQuery(query);
    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+physical+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+physical+bioassay";
  }
  else if ("RunListPlugin".equals(cmd))
  {
    // Run another plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<PhysicalBioAssay> query = PhysicalBioAssay.getQuery();
    dc = sc.newDbControl();
    cc.configureQuery(dc, query, true);
    dc.close();
    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 if ("NewMergedDerivedBioAssay".equals(cmd))
  {
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    redirect = "../derivedbioassays/index.jsp?ID="+ID+"&cmd=NewItem&useParents=PHYISCALBIOASSAY";
  }
  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)
{
  sc.setSessionSetting("alert-message", message);
  pageContext.forward(forward);
}
else if (redirect != null)
{
  sc.setSessionSetting("alert-message", message);
  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));
}
%>