source: trunk/www/admin/annotationtypes/index.jsp @ 5156

<%-- $Id: index.jsp 5156 2009-10-22 07:09:52Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2005 Nicklas Nordborg
  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 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.AnnotationType"
  import="net.sf.basedb.core.AnnotationTypeCategory"
  import="net.sf.basedb.core.Quantity"
  import="net.sf.basedb.core.Unit"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.ItemContext"
  import="net.sf.basedb.core.Metadata"
  import="net.sf.basedb.core.Type"
  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.Expressions"
  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.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.plugins.ItemQueryLoader"
  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="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.Collection"
  import="java.util.Arrays"
  import="java.util.Date"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%!
  private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,valueType,requiredForMiame,itemTypes,description");
  private static final Item itemType = Item.ANNOTATIONTYPE;
  
  private static void registerExportUtils(ItemContext cc)
  {
    // Register formatter
    cc.setObject("export.formatter.&categories(name)", new NameableFormatter());
    
    // Register dataloader
    String typeParameter = "annotationType";
    ItemQuery<AnnotationTypeCategory> categoryQuery = AnnotationTypeCategory.getQuery();
    categoryQuery.include(cc.getInclude());
    categoryQuery.join(Hql.innerJoin("annotationTypes", "atp"));
    categoryQuery.restrict(Restrictions.eq(Hql.alias("atp"), Expressions.parameter(typeParameter)));
    categoryQuery.order(Orders.asc(Hql.property("name")));
    cc.setObject("export.dataloader.&categories(name)", new ItemQueryLoader(categoryQuery, typeParameter));
  }
%>
<%
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_annotationtypes.jsp?ID="+ID
  +(mode == null ? "" : "&mode="+mode)
  +(callback == null ? "" : "&callback="+callback)
  +(itemId == null ? "" : "&item_id="+itemId);
final String viewPage = "view_annotationtype.jsp?ID="+ID;
final String editPage = "edit_annotationtype.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);
    redirect = editPage+"&value_type="+request.getParameter("value_type");
  }
  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();
    AnnotationType annotationType = (AnnotationType)cc.getObject("item");
    if (annotationType == null)
    {
      Type valueType = Type.valueOf(request.getParameter("value_type"));
      annotationType = AnnotationType.getNew(dc, valueType);
      message = "Annotation type created";
      dc.saveItem(annotationType);
    }
    else
    {
      dc.reattachItem(annotationType, false);
      message = "Annotation type updated";
    }
    
    annotationType.setName(Values.getStringOrNull(request.getParameter("name")));
    annotationType.setDescription(Values.getStringOrNull(request.getParameter("description")));
    annotationType.setExternalId(Values.getStringOrNull(request.getParameter("external_id")));
    annotationType.setMultiplicity(Values.getInt(request.getParameter("multiplicity"), 0));
    annotationType.setDefaultValue(request.getParameter("defaultValue"));
    annotationType.setRequiredForMiame(Values.getBoolean(request.getParameter("required_for_miame")));
    annotationType.setProtocolParameter(Values.getBoolean(request.getParameter("is_protocol_parameter")));
    if (annotationType.getValueType().canEnumerate())
    {
      annotationType.setEnumeration(!"box".equals(request.getParameter("interface")));
    }
    
    // Options tab
    Type valueType = annotationType.getValueType();
    if (valueType == Type.INT || valueType == Type.LONG)
    {
      annotationType.setMinValueLong(Values.getLong(request.getParameter("minValue"), null));
      annotationType.setMaxValueLong(Values.getLong(request.getParameter("maxValue"), null));
      annotationType.setWidth(Values.getInt(request.getParameter("width"), 40));
      if (annotationType.isEnumeration())
      {
        Object[] values = null;
        if (valueType == Type.INT)
        {
          values = Values.getInt(request.getParameter("values").split("[\n\r]+"));
        }
        else
        {
          values = Values.getLong(request.getParameter("values").split("[\n\r]+"));
        }
        annotationType.setValues(Arrays.asList(values));
        annotationType.setDisplayAsList("list".equals(request.getParameter("interface")));
      }
    }
    else if (valueType == Type.FLOAT || valueType == Type.DOUBLE)
    {
      annotationType.setMinValueDouble(Values.getDouble(request.getParameter("minValue"), null));
      annotationType.setMaxValueDouble(Values.getDouble(request.getParameter("maxValue"), null));
      annotationType.setWidth(Values.getInt(request.getParameter("width"), 40));
      if (annotationType.isEnumeration())
      {
        Object[] values = null;
        if (valueType == Type.FLOAT)
        {
          values = Values.getFloat(request.getParameter("values").split("[\n\r]+"));
        }
        else
        {
          values = Values.getDouble(request.getParameter("values").split("[\n\r]+"));
        }
        annotationType.setValues(Arrays.asList(values));
        annotationType.setDisplayAsList("list".equals(request.getParameter("interface")));
      }
    }
    else if (valueType == Type.STRING)
    {
      annotationType.setMaxLength(Values.getInteger(request.getParameter("maxLength"), null));
      annotationType.setWidth(Values.getInt(request.getParameter("width"), 40));
      if (annotationType.isEnumeration())
      {
        String[] values = request.getParameter("values").split("[\n\r]+");
        annotationType.setValues(Arrays.asList(values));
        annotationType.setDisplayAsList("list".equals(request.getParameter("interface")));
      }
    }
    else if (valueType == Type.TEXT)
    {
      annotationType.setWidth(Values.getInt(request.getParameter("width"), 40));
      annotationType.setHeight(Values.getInt(request.getParameter("height"), 10));
    }
    else if (valueType == Type.DATE)
    {
      annotationType.setWidth(Values.getInt(request.getParameter("width"), 40));
      if (annotationType.isEnumeration())
      {
        Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
        Date[] values = Values.getDate(request.getParameter("values").split("[\n\r]+"), dateFormatter);
        annotationType.setValues(Arrays.asList(values));
        annotationType.setDisplayAsList("list".equals(request.getParameter("interface")));
      }
    }
    
    // Item types tab
    Set<Item> allItems = Metadata.getAnnotatableItems();
    String[] enabled = request.getParameterValues("enabled");
    Collection<String> enabledItems = enabled != null ? Arrays.asList(enabled) : new ArrayList<String>();
    for (Item item : allItems)
    {
      if (enabledItems.contains(item.name()))
      {
        annotationType.enableForItem(item);
      }
      else
      {
        annotationType.disableForItem(item);
      }
    }
    
    // Units tab
    if (valueType.isNumerical())
    {
      int unitId = Values.getInt(request.getParameter("unit_id"), -1);
      if (unitId >= 0) // < 0 = denied or unchanged
      {
        Unit unit = unitId == 0 ? null : Unit.getById(dc, unitId);
        annotationType.setDefaultUnit(unit);
      }
      
      String[] removeUnits = Values.getString(request.getParameter("removeUsableUnits")).split(",");
      for (int i = 0; i < removeUnits.length; ++i)
      {
        int uId = Values.getInt(removeUnits[i], -1);
        if (uId != -1) annotationType.removeUsableUnit(Unit.getById(dc, uId));
      }
      
      String[] addUnits = Values.getString(request.getParameter("addUsableUnits")).split(",");
      for (int i = 0; i < addUnits.length; ++i)
      {
        int uId = Values.getInt(addUnits[i], -1);
        if (uId != -1) annotationType.addUsableUnit(Unit.getById(dc, uId));
      }
    }
    
    // Categories tab
    String[] removeCategories = Values.getString(request.getParameter("removeCategories")).split(",");
    for (int i = 0; i < removeCategories.length; ++i)
    {
      int categoryId = Values.getInt(removeCategories[i], -1);
      if (categoryId != -1) annotationType.removeCategory(AnnotationTypeCategory.getById(dc, categoryId));
    }
    
    String[] addCategories = Values.getString(request.getParameter("addCategories")).split(",");
    for (int i = 0; i < addCategories.length; ++i)
    {
      int categoryId = Values.getInt(addCategories[i], -1);
      if (categoryId != -1) annotationType.addCategory(AnnotationTypeCategory.getById(dc, categoryId));
    }

    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 ("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<AnnotationType> query = AnnotationType.getQuery(null);
    cc.configureQuery(query, true);
    cc.setQuery(query);
    registerExportUtils(cc);
    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+annotation+types";
  }
  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+annotation+type";
  }
  else if ("ImportItems".equals(cmd))
  {
    // Run an import plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<AnnotationType> query = AnnotationType.getQuery(null);
    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+annotation+types";
  }
  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+annotation+typey";
  }
  else if ("RunListPlugin".equals(cmd))
  {
    // Run another plugin in a list context
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    final ItemQuery<AnnotationType> query = AnnotationType.getQuery(null);
    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));
}
%>