source: trunk/www/views/experiments/index.jsp @ 5878

<%-- $Id: index.jsp 5878 2011-11-17 11:41:31Z 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 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.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.ReporterCloneTemplate"
  import="net.sf.basedb.core.ReporterCloneBatcher"
  import="net.sf.basedb.core.PluginDefinition"
  import="net.sf.basedb.core.Job"
  import="net.sf.basedb.core.ItemParameterType"
  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.SimpleProgressReporter"
  import="net.sf.basedb.core.snapshot.SnapshotManager"
  import="net.sf.basedb.plugins.CloneReportersPlugin"
  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="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="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, false);
      message = "Experiment updated";
    }

    JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.item(Item.EXPERIMENT), experiment);
    ExtensionsInvoker invoker = EditUtil.useOnSaveExtensions(jspContext);
    try
    {
      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));
      }
      
      // 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.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 ("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<Experiment> query = Experiment.getQuery();
    dc = sc.newDbControl();
    cc.configureQuery(dc, query, true);
    dc.close();
    cc.setQuery(query);
    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+experiments";
  }
  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+experiment";
  }
  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();
    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+experiments";
  }
  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+experiment";
  }
  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();
    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 ("AutoInherit".equals(cmd))
  {
    Integer[] annotationTypeIds = Values.getInt(request.getParameterValues("autoinherit"));
    int numInherited = 0;
    int numRawBioAssays = 0;
    if (annotationTypeIds.length > 0)
    {
      dc = sc.newDbControl();
      SimpleProgressReporter progress = new SimpleProgressReporter(null);
      sc.setSessionSetting("progress.autoinherit", progress);
      Experiment exp = Experiment.getById(dc, Values.getInt(itemId));
      List<AnnotationType> annotationTypes = new ArrayList<AnnotationType>(annotationTypeIds.length);
      for (int atId : annotationTypeIds)
      {
        annotationTypes.add(AnnotationType.getById(dc, atId));
      }
      ItemQuery<RawBioAssay> query = exp.getRawBioAssays();
      query.include(Include.ALL);
      query.setItemPermission(Permission.WRITE);
      SnapshotManager manager = new SnapshotManager();
      List<RawBioAssay> all = query.list(dc);
      int total = all.size();
      int done = 0;
      for (RawBioAssay rba : all)
      {
        progress.display(10+(90 * done) / total, "Processing <i>" + rba.getName() + "</i>...");
        ++done;
        int inherited = rba.getAnnotationSet().autoInherit(dc, annotationTypes, manager, false);
        numInherited += inherited;
        if (inherited > 0) numRawBioAssays++;
      }
      message = numInherited + " annotation(s) inherited by " + numRawBioAssays + " raw bioassay(s)";
      progress.display(100, message);
      dc.commit();
    }
    redirect = viewPage;
  }
  else if ("CloneReporters".equals(cmd))
  {
    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, defaultContext);
    final int maxRecent = Base.getMaxRecent(sc);
    
    dc = sc.newDbControl();
    ReporterCloneTemplate template = ReporterCloneTemplate.getById(dc, Values.getInt(request.getParameter("reporterclonetemplate_id")));
    cc.setRecent(template, maxRecent);
    
    Experiment exp = Experiment.getById(dc, Values.getInt(itemId));
    
    PluginDefinition clonePlugin = PluginDefinition.getByClassName(dc, CloneReportersPlugin.class.getName());
    Job cloneJob = Job.getNew(dc, clonePlugin, null, exp);
    cloneJob.setName("Cloning reporters using template '" + template.getName() + "'");
    cloneJob.setDescription(Values.getStringOrNull(request.getParameter("description")));
    cloneJob.setParameterValue("template", "Reporter clone template", null, 
      new ItemParameterType<ReporterCloneTemplate>(ReporterCloneTemplate.class, null), template);
    dc.saveItem(cloneJob);
    dc.commit();
    
    redirect = "../jobs/index.jsp?ID=" + ID + "&cmd=ViewItem&item_id="+cloneJob.getId();
  }
  else if ("RemoveClonedReporters".equals(cmd))
  {
    
    dc = sc.newDbControl();
    Experiment exp = Experiment.getById(dc, Values.getInt(itemId));
    ReporterCloneBatcher batcher = exp.getReporterCloneBatcher(dc);
    batcher.dropClonedReporters();
    dc.commit();
    
    message = "The cloned reporter annotations has been removed";
    
  }
  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));
}
%>