source: trunk/www/views/derivedbioassays/index.jsp @ 6695

<%-- $Id $
  ------------------------------------------------------------------
  Copyright (C) 2011 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 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/>.
  ------------------------------------------------------------------

--%>
<%@ page pageEncoding="UTF-8" session="false"
  import="net.sf.basedb.core.SessionControl"
  import="net.sf.basedb.core.DbControl"
  import="net.sf.basedb.core.DerivedBioAssay"
  import="net.sf.basedb.core.PhysicalBioAssay"
  import="net.sf.basedb.core.RawBioAssay"
  import="net.sf.basedb.core.ItemSubtype"
  import="net.sf.basedb.core.Extract"
  import="net.sf.basedb.core.Protocol"
  import="net.sf.basedb.core.Software"
  import="net.sf.basedb.core.Hardware"
  import="net.sf.basedb.core.Item"
  import="net.sf.basedb.core.Include"
  import="net.sf.basedb.core.User"
  import="net.sf.basedb.core.OwnedItem"
  import="net.sf.basedb.core.AnnotatedItem"
  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.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.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="net.sf.basedb.core.plugin.GuiContext"
  import="net.sf.basedb.util.extensions.ExtensionsInvoker"
  import="net.sf.basedb.util.formatter.NameableFormatter"
  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="net.sf.basedb.clients.web.plugins.ItemQueryLoader"
  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,itemSubtype,physicalBioAssay,extract,parent,description");
  private static final Item itemType = Item.DERIVEDBIOASSAY;
  
  private static void registerExportUtils(ItemContext cc)
  {
    // Register formatters
    cc.setObject("export.formatter.&physicalBioAssays(name)", new NameableFormatter());
    cc.setObject("export.formatter.&parents(name)", new NameableFormatter());
    cc.setObject("export.formatter.&children(name)", new NameableFormatter());
    cc.setObject("export.formatter.&rawBioAssays(name)", new NameableFormatter());
    
    // Register dataloaders
    String bioassayParameter = "bioassay";
    // Physical bioassays
    ItemQuery<PhysicalBioAssay> physicalQuery = PhysicalBioAssay.getQuery();
    physicalQuery.include(cc.getInclude());
    physicalQuery.join(Hql.innerJoin("derivedBioAssays", "dba"));
    physicalQuery.restrict(Restrictions.eq(Hql.alias("dba"), Expressions.parameter(bioassayParameter)));
    physicalQuery.order(Orders.asc(Hql.property("name")));
    cc.setObject("export.dataloader.&physicalBioAssays(name)", new ItemQueryLoader(physicalQuery, bioassayParameter));

    // Parent bioassays
    ItemQuery<DerivedBioAssay> parentQuery = DerivedBioAssay.getQuery();
    parentQuery.include(cc.getInclude());
    parentQuery.join(Hql.innerJoin("children", "c"));
    parentQuery.restrict(Restrictions.eq(Hql.alias("c"), Expressions.parameter(bioassayParameter)));
    parentQuery.order(Orders.asc(Hql.property("name")));
    cc.setObject("export.dataloader.&parents(name)", new ItemQueryLoader(parentQuery, bioassayParameter));

    // Child bioassays
    ItemQuery<DerivedBioAssay> childQuery = DerivedBioAssay.getQuery();
    childQuery.include(cc.getInclude());
    childQuery.join(Hql.innerJoin("parents", "p"));
    childQuery.restrict(Restrictions.eq(Hql.alias("p"), Expressions.parameter(bioassayParameter)));
    childQuery.order(Orders.asc(Hql.property("name")));
    cc.setObject("export.dataloader.&children(name)", new ItemQueryLoader(childQuery, bioassayParameter));
    
    // Child raw bioassays
    ItemQuery<RawBioAssay> rawQuery = RawBioAssay.getQuery();
    rawQuery.include(cc.getInclude());
    rawQuery.restrict(Restrictions.eq(Hql.property("parentBioAssay"), Expressions.parameter(bioassayParameter)));
    rawQuery.order(Orders.asc(Hql.property("name")));
    cc.setObject("export.dataloader.&rawBioAssays(name)", new ItemQueryLoader(rawQuery, 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+"&item_id="+itemId
  +(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
    ItemContext cc = 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
    ItemContext cc = 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);
    forward = 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();
    
    DerivedBioAssay bas = (DerivedBioAssay)cc.getObject("item");
    if (bas == null)
    {
      bas = DerivedBioAssay.getNew(dc, Values.getBoolean(request.getParameter("isRoot")), null);
      dc.saveItem(bas);
      message = "Derived bioassay created";
    }
    else
    {
      dc.reattachItem(bas, false);
      message = "Derived bioassay updated";
    }

    JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.item(itemType), bas);
    ExtensionsInvoker invoker = EditUtil.useOnSaveExtensions(jspContext);
    try
    {
      bas.setName(Values.getStringOrNull(request.getParameter("name")));
      bas.setDescription(Values.getStringOrNull(request.getParameter("description")));
  
      int subtypeId = Values.getInt(request.getParameter("subtype_id"), -1);
      ItemSubtype subtype = null;
      if (subtypeId >= 0) // < 0 = denied or unchanged
      {
        subtype = subtypeId == 0 ? null : ItemSubtype.getById(dc, subtypeId);
        bas.setItemSubtype(subtype);
        if (subtype != null) cc.setRecent(subtype, maxRecent);
      }
      
      int extractId = Values.getInt(request.getParameter("extract_id"), -1);
      if (extractId >= 0) // < 0 = denied or unchanged
      {
        Extract extract = extractId == 0 ? null : Extract.getById(dc, extractId);
        bas.setExtract(extract);
      }

      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);
        bas.setProtocol(pt);
        if (pt != null) cc.setRecent(pt, subtype, maxRecent);
      }
      
      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);
        bas.setHardware(hw);
        if (hw != null) cc.setRecent(hw, subtype, maxRecent);
      }

      int softwareId = Values.getInt(request.getParameter("software_id"), -1);
      if (softwareId >= 0) // < 0 denied or unchanged
      {
        Software sw = softwareId == 0 ? null : Software.getById(dc, softwareId);
        bas.setSoftware(sw);
        if (sw != null) cc.setRecent(sw, subtype, maxRecent);
      }
      
      if (bas.isRoot())
      {
        // A root derived bioassay set may have physical bioassays as parents
        String[] removePhysicalBioAssays = Values.getString(request.getParameter("-PHYSICALBIOASSAY")).split(",");
        for (int i = 0; i < removePhysicalBioAssays.length; ++i)
        {
          int pbaId = Values.getInt(removePhysicalBioAssays[i], -1);
          if (pbaId != -1) bas.removePhysicalBioAssay(PhysicalBioAssay.getById(dc, pbaId));
        }
        
        String[] addPhysicalBioAssays = Values.getString(request.getParameter("+PHYSICALBIOASSAY")).split(",");
        for (int i = 0; i < addPhysicalBioAssays.length; ++i)
        {
          int pbaId = Values.getInt(addPhysicalBioAssays[i], -1);
          if (pbaId != -1) bas.addPhysicalBioAssay(PhysicalBioAssay.getById(dc, pbaId));
        }
      }
      else
      {
        // A non-root derived bioassay set may have other derived bioassays as parents
        String[] removeParents = Values.getString(request.getParameter("-DERIVEDBIOASSAY")).split(",");
        for (int i = 0; i < removeParents.length; ++i)
        {
          int parentId = Values.getInt(removeParents[i], -1);
          if (parentId != -1) bas.removeParent(DerivedBioAssay.getById(dc, parentId));
        }
        
        String[] addParents = Values.getString(request.getParameter("+DERIVEDBIOASSAY")).split(",");
        for (int i = 0; i < addParents.length; ++i)
        {
          int parentId = Values.getInt(addParents[i], -1);
          if (parentId != -1) bas.addParent(DerivedBioAssay.getById(dc, parentId));
        }
      }
      
      // Data files tab
      boolean validate = Values.getBoolean(request.getParameter("datafiles.validate"));
      Base.updateFiles(dc, bas, request, validate, cc, maxRecent);
      
      // Annotations tab
      Base.updateAnnotations(dc, bas, bas, 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.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.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.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.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 ("InheritAnnotations".equals(cmd))
  {
    // Change owner of items selected on a list page
    dc = sc.newDbControl();
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    Set<AnnotatedItem> items = new HashSet<AnnotatedItem>();
    for (Integer id : cc.getSelected())
    {
      if (id != null) items.add((AnnotatedItem)itemType.getById(dc, id));
    }
    dc.close();
    cc.setObject("AnnotatedItems", items);
    redirect = "../../common/annotations/batch_inherit.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<DerivedBioAssay> query = DerivedBioAssay.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+bioassay+sets";
  }
  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+bioassay+set";
  }
  else if ("ImportItems".equals(cmd))
  {
    // Run an import plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<DerivedBioAssay> query = DerivedBioAssay.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+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);
    final ItemQuery<DerivedBioAssay> query = DerivedBioAssay.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 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 ("NewMergedDerivedBioAssay".equals(cmd))
  {
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    cc.setId(0);
    forward = editPage + "&useParents=DERIVEDBIOASSAY";
  }
  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));
}
%>