source: trunk/www/views/experiments/bioassaysets/analysis_tree.jsp @ 5674

<%-- $Id: analysis_tree.jsp 5674 2011-06-27 12:29:52Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
  Copyright (C) 2007 Johan Enell, Jari Häkkinen, Nicklas Nordborg

  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.ItemContext"
  import="net.sf.basedb.core.BasicItem"
  import="net.sf.basedb.core.Experiment"
  import="net.sf.basedb.core.BioAssaySet"
  import="net.sf.basedb.core.Transformation"
  import="net.sf.basedb.core.ExtraValue"
  import="net.sf.basedb.core.ExtraValueType"
  import="net.sf.basedb.core.AnnotationSet"
  import="net.sf.basedb.core.AnnotationType"
  import="net.sf.basedb.core.Annotation"
  import="net.sf.basedb.core.Job"
  import="net.sf.basedb.core.ItemQuery"
  import="net.sf.basedb.core.Nameable"
  import="net.sf.basedb.core.ItemResultIterator"
  import="net.sf.basedb.core.ItemResultList"
  import="net.sf.basedb.core.Permission"
  import="net.sf.basedb.core.PluginDefinition"
  import="net.sf.basedb.core.PermissionDeniedException"
  import="net.sf.basedb.core.query.Restrictions"
  import="net.sf.basedb.core.query.Expressions"
  import="net.sf.basedb.core.query.Orders"
  import="net.sf.basedb.core.query.Hql"
  import="net.sf.basedb.core.query.Restrictions"
  import="net.sf.basedb.core.plugin.GuiContext"
  import="net.sf.basedb.core.plugin.Plugin"
  import="net.sf.basedb.util.Tree"
  import="net.sf.basedb.util.Enumeration"
  import="net.sf.basedb.clients.web.Base"
  import="net.sf.basedb.clients.web.ModeInfo"
  import="net.sf.basedb.clients.web.util.HTML"
  import="net.sf.basedb.util.Values"
  import="net.sf.basedb.util.formatter.Formatter"
  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
  import="net.sf.basedb.clients.web.extensions.toolbar.ButtonAction"
  import="net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil"
  import="net.sf.basedb.clients.web.extensions.JspContext"
  import="net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer"
  import="net.sf.basedb.util.extensions.ExtensionsInvoker"
  import="net.sf.basedb.util.extensions.Renderer"
  import="java.util.Date"
  import="java.util.List"
  import="java.util.ArrayList"
  import="java.util.LinkedList"
  import="java.util.Map"
  import="java.util.HashMap"
  import="java.util.Iterator"
  import="java.util.Collection"
%>
<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
<%@ taglib prefix="ext" uri="/WEB-INF/extensions.tld" %>
<%!
  private static final Item itemType = Item.BIOASSAYSET;
  private static final GuiContext guiContext = new GuiContext(itemType, GuiContext.Type.LIST);
%>
<%!

private static void addToTree(Tree<BasicItem> tree, BioAssaySet bas)
{
  if (!tree.contains(bas))
  {
    Transformation transformation = bas.getTransformation();
    Tree.Entry<BasicItem> parent = tree.getEntry(transformation);
    if (parent == null) 
    {
      addToTree(tree, transformation);
      parent = tree.getEntry(transformation);
    }
    Tree.Entry<BasicItem> basEntry = parent.addChild(bas);
    for (ExtraValue xv : bas.getExtraValues().list(bas.getDbControl())) 
    {
      basEntry.addChild(xv);
    }
  }
}

private static void addToTree(Tree<BasicItem> tree, Transformation transformation)
{
  if (!tree.contains(transformation))
  {
    BioAssaySet source = transformation.getSource();
    Tree.Entry<BasicItem> parent = tree.getEntry(source);
    if (parent == null) 
    {
      addToTree(tree, source);
      parent = tree.getEntry(source);
    }
    parent.addChild(transformation);
  }
}

private static Tree<BasicItem> getAnalysisTree(DbControl dc, ItemQuery<BioAssaySet> bioAssaySetQuery, ItemQuery<Transformation> transformationQuery)
{
  Tree<BasicItem> tree = new Tree<BasicItem>(null);
  ItemResultList<BioAssaySet> allBioAssaySets = bioAssaySetQuery.list(dc);
  List<Integer> ids = new ArrayList<Integer>(allBioAssaySets.size());
  
  for (BioAssaySet bas : allBioAssaySets)
  {
    addToTree(tree, bas);
    ids.add(bas.getId());
  }
  
  transformationQuery.restrict(
    Restrictions.in(
      Hql.property("source.id"), 
      Expressions.parameter("bioAssaySets", ids)
    )
  );
  ItemResultList<Transformation> allTransformations = transformationQuery.list(dc);
  for (Transformation t: allTransformations)
  {
    addToTree(tree, t);
  }
  return tree;
}
String generateTree(Tree<BasicItem> tree, BasicItem root, BasicItem parentItem, Collection<String> closed)
{
  StringBuilder sb = new StringBuilder();
  Tree.Entry<BasicItem> parentEntry = tree.getEntry(parentItem);
  if (parentEntry == null) return "";
  
  if (root != null && root == parentItem)
  {
    appendNode(sb, root, null, true);
  }
  
  List<Tree.Entry<BasicItem>> children = parentEntry.getChildren();
  if (children != null)
  {
    for (Tree.Entry<BasicItem> child : children)
    {
      BasicItem node = child.getNode();
      String var = node.getType().name() + "_" + node.getId();
      appendNode(sb, node, parentItem, (closed == null || !closed.contains(var)) && child.getNumChildren() > 0);
      sb.append(generateTree(tree, root, node, closed));
    }
  }
  return sb.toString();
}

void appendNode(StringBuilder sb, BasicItem node, BasicItem parentItem, boolean open)
{
  int id = node.getId();
  String var = node.getType().name() + "_" + id;
  String name = "";
  
  Item nodeType = node.getType();
  String folderIcon = "";
  if (nodeType == Item.BIOASSAYSET)
  {
    folderIcon = "BioAssaySet";
    name = ((BioAssaySet)node).getName();
  } 
  else if (nodeType == Item.TRANSFORMATION)
  {
    Transformation t = (Transformation)node;
    folderIcon = "Transformation";
    try
    {
      if (t.getJob().getPluginDefinition().supports("net.sf.basedb.core.plugin.AnalysisFilterPlugin"))
      {
        folderIcon = "Filter";
      }
    }
    catch (Throwable tt)
    {}
    name = t.getName();
  } 
  else if (nodeType == Item.EXTRAVALUE) 
  {
    folderIcon = "ExtraValue";
    try
    {
      name = ((ExtraValue)node).getExtraValueType().getName();
    }
    catch (PermissionDeniedException ex)
    {
      name = ((ExtraValue)node).getValueType().toString();
    }
  }
  sb.append("var ").append(var);
  if (parentItem == null)
  {
    sb.append(" = JoustMenu.addMenuItem(-1");
  }
  else
  {
    String rootVar = parentItem.getType().name() + "_" + parentItem.getId();
    sb.append(" = JoustMenu.addChildItem(").append(rootVar); 
  }
  sb.append(",'").append(folderIcon).append("'");
  sb.append(",'").append(HTML.javaScriptEncode(name)).append("'");
  sb.append(", null, '', '").append(var).append("');\n");
  if (open)
  {
    sb.append("JoustMenu.menuItems[").append(var).append("].isOpen = true;\n");
  }
}
%>
<%
final int experimentId = Values.getInt(request.getParameter("experiment_id"));
final int bioAssaySetId = Values.getInt(request.getParameter("item_id"));
final int transformationId = Values.getInt(request.getParameter("transformation_id"));
final SessionControl sc = Base.getExistingSessionControl(pageContext, Permission.DENIED, itemType);
final String ID = sc.getId();
final String rootPath = request.getContextPath()+"/";
final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null);
final ItemContext tc = sc.getCurrentContext(Item.TRANSFORMATION);
final ItemContext xvc = sc.getCurrentContext(Item.EXTRAVALUE);

final ModeInfo mode = ModeInfo.get(request.getParameter("mode"));
final String callback = request.getParameter("callback");
final String title = mode.generateTitle("bioassay set", "bioassay sets");
final DbControl dc = sc.newDbControl();
Tree<BasicItem> analysisTree = null;
ItemResultList<AnnotationType> annotationTypes = null;
try
{
  Formatter<Date> dateTimeFormatter = FormatterFactory.getDateTimeFormatter(sc);
  final ItemQuery<AnnotationType> annotationTypeQuery = Base.getAnnotationTypesQuery(itemType);
  final Experiment experiment = Experiment.getById(dc, experimentId);
  final BasicItem root = transformationId == 0 ? 
      (bioAssaySetId == 0 ? null : BioAssaySet.getById(dc, bioAssaySetId))
      : Transformation.getById(dc, transformationId);
  final boolean createPermission = experiment.hasPermission(Permission.USE);
  final boolean deletePermission = createPermission;
  final boolean writePermission = createPermission;

  final ItemQuery<Transformation> transformationQuery = experiment.getTransformations();
  transformationQuery.include(cc.getInclude());
  transformationQuery.setFirstResult(0);
  transformationQuery.setMaxResults(-1);
  Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
  annotationTypes = annotationTypeQuery.list(dc);
  try
  {
    final ItemQuery<BioAssaySet> query = Base.getConfiguredQuery(dc, cc, true, experiment.getBioAssaySets(), mode);
    query.setFirstResult(0);
    query.setMaxResults(-1);
    analysisTree = getAnalysisTree(dc, query, transformationQuery);
  }
  catch (Throwable t)
  {
    cc.setMessage(t.getMessage());
    t.printStackTrace();
  }
  // Contains the ID:s of the bioassaysets that are closed in the tree
  Collection<String> closed = (Collection<String>)cc.getObject("closed");
  int numListed = 0;
  
  JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, 
    guiContext, root == null ? experiment : root);
  ExtensionsInvoker toolsInvoker = ExtensionsControl.useExtensions(jspContext, 
      "net.sf.basedb.clients.web.bioassayset.list.tools");
  ExtensionsInvoker toolbarInvoker = ToolbarUtil.useExtensions(jspContext);
  %>
  <base:page type="include">
  <base:body>
    <ext:scripts context="<%=jspContext%>" />
    <ext:stylesheets context="<%=jspContext%>" />
    <script language="JavaScript">
    var submitPage = '<%=transformationId != 0 ? "../bioassaysets/index.jsp" : "index.jsp"%>';
    var formId = 'bioAssaySets';
    function newItem()
    {
      Main.openPopup('index.jsp?ID=<%=ID%>&cmd=NewItem&experiment_id=<%=experimentId%>', 'NewBioAssaySet', 740, 540);
    }
    function editBioAssaySet(itemId)
    {
      Main.viewOrEditItem('<%=ID%>', '<%=itemType.name()%>', itemId, true);
    }
    function viewBioAssaySet(itemId)
    {
      Main.viewOrEditItem('<%=ID%>', '<%=itemType.name()%>', itemId, false);
    }
    function bioAssaySetOnClick(evt, itemId)
    {
      Table.itemOnClick(formId, evt, itemId, '<%=mode.getName()%>', viewBioAssaySet, editBioAssaySet, returnSelected);
    }
    function viewTransformation(itemId)
    {
      Main.viewOrEditItem('<%=ID%>', 'TRANSFORMATION', itemId, false);
    }
    function editTransformation(itemId)
    {
      Main.viewOrEditItem('<%=ID%>', 'TRANSFORMATION', itemId, true);
    }
    function transformationOnClick(evt, itemId)
    {
      Table.itemOnClick(formId, evt, itemId, '<%=mode.getName()%>', viewTransformation, editTransformation, returnSelected);
    }
    function viewExtraValue(itemId)
    {
      Main.viewOrEditItem('<%=ID%>', 'EXTRAVALUE', itemId, false);
    }
    function editExtraValue(itemId)
    {
      Main.viewOrEditItem('<%=ID%>', 'EXTRAVALUE', itemId, true);
    }
    function extraValueOnClick(evt, itemId)
    {
      Table.itemOnClick(formId, evt, itemId, '<%=mode.getName()%>', viewExtraValue, editExtraValue, returnSelected);
    }
    function deleteItems()
    {
      var frm = document.forms[formId];
      if (Forms.numChecked(frm) == 0)
      {
        alert('Please select at least one item in the list');
        return; 
      }
      if (Forms.numChecked(frm, /^X:/) > 0)
      {
        if (!confirm('Extra values are deleted immediately and cannot be restored. Do you want to continue?'))
        {
          return;
        }
      }
      frm.action = submitPage;
      frm.cmd.value = 'DeleteItems';
      frm.submit();
    }
    function restoreItems()
    {
      var frm = document.forms[formId];
      if (Forms.numChecked(frm) == 0)
      {
        alert('Please select at least one item in the list');
        return; 
      }
      frm.action = submitPage;
      frm.cmd.value = 'RestoreItems';
      frm.submit();
    }
    function deleteItemPermanently(itemType, itemId)
    {
      Main.deleteItemPermanently('<%=ID%>', true, itemType, itemId);
    }
    function configureColumns()
    {
      Table.configureColumns('<%=ID%>', formId, '<%=itemType.name()%>', '<%=(String)cc.getObject("defaultColumns")%>');
    }
    function runPlugin(cmd)
    {
      Table.submitToPopup(formId, cmd, 740, 540);
    }
    function filter(itemId)
    {
      Main.openPopup('../bioassaysets/index.jsp?ID=<%=ID%>&cmd=NewFilteredBioAssaySet&experiment_id=<%=experimentId%>&item_id='+itemId, 'FilterBioAssaySet', 740, 540);
    }
    function openPlotTool(itemId)
    {
      Main.openPopup('../plotter/index.jsp?ID=<%=ID%>&bioassayset_id='+itemId, 'Plotter', 1000, 700);
    }
    function openExperimentExplorer(itemId)
    {
      location.href = '../explorer/view/index.jsp?ID=<%=ID%>&bioassayset_id='+itemId;
    }
    function runAnalysisPlugin(itemId)
    {
      Main.openPopup('../bioassaysets/index.jsp?ID=<%=ID%>&cmd=RunAnalysisPlugin&experiment_id=<%=experimentId%>&item_id='+itemId, 'RunPlugin', 740, 540);
    }
    function runExportPlugin(itemId)
    {
      Main.openPopup('../bioassaysets/index.jsp?ID=<%=ID%>&cmd=ExportItem&experiment_id=<%=experimentId%>&item_id='+itemId, 'Export', 740, 540);
    }
    function copyJob(jobId)
    {
      var url = '../../../common/plugin/index.jsp?ID=<%=ID%>';
      url += '&cmd=CopyJob&job_id='+jobId;
      url += '&item_type=BIOASSAYSET&context_type=LIST'
      Main.openPopup(url, 'CopyJob', 740, 540);
    }
    function returnSelected()
    {
      Table.returnSelected(formId, <%=callback != null ? "window.opener."+callback : "null" %>);
      window.close();
    }
    function presetOnChange()
    {
      Table.presetOnChange('<%=ID%>', formId, '<%=itemType.name()%>', '<%=(String)cc.getObject("defaultColumns")%>');
    }
    
    function sendClosedWithAjax()
    {
      var request = Main.getAjaxRequest();
      if (request != null)
      {
        var frm = document.forms[formId];
        var url = '../bioassaysets/index.jsp?ID=<%=ID%>&cmd=SetClosedWithAjax';
        request.open("POST", url, true);
        var postdata = 'closed=' + frm.closed.value;
        request.setRequestHeader("Content-type", "application/x-www-form-urlencoded");
        request.setRequestHeader("Content-length", postdata.length);
        request.setRequestHeader("Connection", "close");
        request.send(postdata);
      }
    }
    
    function initTree()
    {
      var bigDir = getRoot()+'images/joust/big/';
      IconStore.init(bigDir, 18, 22);
      IconStore.addIcon('BioAssaySet', bigDir + 'bioassayset.gif', 18, 22);
      IconStore.addIcon('Transformation', bigDir + 'transformation.gif', 18, 22);
      IconStore.addIcon('Filter', bigDir + 'filter.gif', 18, 22);
      IconStore.addIcon('ExtraValue', bigDir + 'extravalue.gif', 18, 22);

      JoustMenu.toggle = function(menuItemIndex)
      {
        var menuItem = this.menuItems[menuItemIndex];
        if (!menuItem) return;
        // Switch the open/closed status and hide or show the children
        menuItem.isOpen = !menuItem.isOpen;
        if (menuItem.isOpen)
        {
          this.showChildren(menuItemIndex);
          var frm = document.forms[formId];
          frm.closed.value = frm.closed.value.replace(','+menuItem.externalId+',', ',');
        }
        else
        {
          this.hideChildren(menuItemIndex);
          var frm = document.forms[formId];
          frm.closed.value += menuItem.externalId+',';
        }
        sendClosedWithAjax();
        // alert(document.forms[formId].closed.value);
        this.updateIconsAndText(menuItemIndex);
      }
      
      JoustMenu.drawMenuItems = function(firstIndex, indentString)
      {
        var menuItem = this.menuItems[firstIndex];
        while (menuItem)
        {
          var html = menuItem.draw(indentString);
          var padIcon = IconStore.getIcon(menuItem.noOutlineIcon == true ? null : menuItem.nextItemIndex == -1 ? 'iconBlank' : 'iconLine');
          var padHtml = padIcon == null ? '' : padIcon.getImgTag();
          
          var menuDiv = document.getElementById('tree.'+menuItem.externalId);
          menuDiv.innerHTML = html;
          
          if (menuItem.firstChildIndex != -1)
          {
            this.drawMenuItems(menuItem.firstChildIndex, indentString+padHtml);
          }
          if (!menuItem.isOpen)
          {
            this.hideChildren(menuItem.index);
          }
          menuItem = this.menuItems[menuItem.nextItemIndex];
        }
        return '';
      }

      JoustMenu.hideChildren = function(menuItemIndex)
      {
        var menuItem = this.menuItems[menuItemIndex];
        if (menuItem)
        {
          var firstChildIndex = menuItem.firstChildIndex;
          var child = this.menuItems[firstChildIndex];
          while (child)
          {
            var e = document.getElementById('row.'+child.externalId);
            e.style.display = 'none';
            this.hideChildren(child.index);
            child = this.menuItems[child.nextItemIndex];
          }
        }
      }
      
      JoustMenu.showChildren = function(menuItemIndex)
      {
        var menuItem = this.menuItems[menuItemIndex];
        if (menuItem)
        {
          var firstChildIndex = menuItem.firstChildIndex;
          var child = this.menuItems[firstChildIndex];
          while (child)
          {
            var e = document.getElementById('row.'+child.externalId);
            e.style.display = Browser.isIE ? 'block' : 'table-row';
            if (child.isOpen)
            {
              this.showChildren(child.index);
            }
            child = this.menuItems[child.nextItemIndex];
          }
        }
      }

      <%=analysisTree == null ? "" : generateTree(analysisTree, root, root, closed)%>
      JoustMenu.draw('joust');
      
    }
    </script>
  

    <%
    if (cc.getMessage() != null)
    {
      %>
      <div class="error"><%=cc.getMessage()%></div>
      <%
      cc.setMessage(null);
    }
    %>
    <tbl:table 
      id="bioAssaySets" 
      clazz="itemlist" 
      columns="<%=cc.getSetting("columns")%>"
      sortby="<%=cc.getSortProperty()%>" 
      direction="<%=cc.getSortDirection()%>"
      title="<%=title%>"
      action="<%=transformationId != 0 ? "../bioassaysets/index.jsp" : "index.jsp"%>"
      sc="<%=sc%>"
      item="<%=itemType%>"
      >
      <tbl:hidden 
        name="mode" 
        value="<%=mode.getName()%>" 
      />
      <tbl:hidden 
        name="experiment_id" 
        value="<%=String.valueOf(experimentId)%>" 
      />
      <tbl:hidden 
        name="item_id" 
        value="<%=String.valueOf(bioAssaySetId)%>"
        skip="<%=bioAssaySetId == 0%>"
      />
      <tbl:hidden 
        name="transformation_id" 
        value="<%=String.valueOf(transformationId)%>"
        skip="<%=transformationId == 0%>"
      />
      <tbl:hidden 
        name="callback" 
        value="<%=callback%>" 
        skip="<%=callback == null%>" 
      />
      <tbl:hidden
        name="closed"
        value="<%=closed == null ? "," : ","+Values.getString(closed, ",", true)+","%>"
      />
      <tbl:columndef 
        id="name"
        property="name"
        datatype="string"
        title="Name"
        sortable="true" 
        filterable="true"
        exportable="true"
        show="always" 
      />
      <tbl:columndef 
        id="spots"
        property="numSpots"
        datatype="int"
        title="Spots/Values in db"
        sortable="true" 
        filterable="true"
        exportable="true"
      />
      <tbl:columndef 
        id="reporters"
        property="numReporters"
        datatype="int"
        title="Reporters in db"
        sortable="true" 
        filterable="true"
        exportable="true"
      />
      <tbl:columndef 
        id="fileSpots"
        property="numFileSpots"
        datatype="int"
        title="Spots/Values in file"
        sortable="true" 
        filterable="true"
        exportable="true"
      />
      <tbl:columndef 
        id="fileReporters"
        property="numFileReporters"
        datatype="int"
        title="Reporters in file"
        sortable="true" 
        filterable="true"
        exportable="true"
      />
      <tbl:columndef 
        id="date"
        property="transformation.job.ended"
        datatype="string"
        title="Date"
        sortable="true" 
        filterable="true"
        exportable="true"
      />
      <tbl:columndef 
        id="plugin"
        property="transformation.job.pluginDefinition.name"
        datatype="string"
        title="Plugin"
        sortable="true" 
        filterable="true"
        exportable="true"
      />
      <tbl:columndef 
        id="description"
        property="description"
        datatype="string"
        title="Description" 
        sortable="true" 
        filterable="true" 
        exportable="true"
      />
      <%
      for (AnnotationType at : annotationTypes)
      {
        Enumeration<String, String> annotationEnum = null;
        Formatter formatter = FormatterFactory.getTypeFormatter(sc, at.getValueType());
        if (at.isEnumeration())
        {
          annotationEnum = new Enumeration<String, String>();
          List<?> values = at.getValues();
          for (Object value : values)
          {
            String encoded = formatter.format(value);
            annotationEnum.add(encoded, encoded);
          }
        }
        %>
        <tbl:columndef 
          id="<%="at"+at.getId()%>"
          title="<%=HTML.encodeTags(at.getName())+" [A]"%>" 
          property="<%="#"+at.getId()%>"
          annotation="true"
          datatype="<%=at.getValueType().getStringValue()%>"
          enumeration="<%=annotationEnum%>"
          smartenum="<%=at.getDisplayAsList() %>"
          sortable="false" 
          filterable="true" 
          exportable="true"
          formatter="<%=formatter%>"
          unit="<%=at.getDefaultUnit()%>"
        />
        <%
      }
      %>
      <tbl:columndef 
        id="tools"
        title="Tools" 
      />

      <tbl:toolbar
        visible="<%=mode.hasToolbar()%>"
        >
        <tbl:button 
          disabled="<%=createPermission ? false : true%>" 
          image="<%=createPermission ? "new.gif" : "new_disabled.gif"%>" 
          onclick="newItem()" 
          title="New root bioassay set&hellip;" 
          tooltip="<%=createPermission ? "Create a new root bioassay set" : "You do not have permission to create bioassay sets"%>" 
          visible="<%=root == null && pluginCount.containsKey(Plugin.MainType.INTENSITY)%>"
        />
        <tbl:button 
          disabled="<%=deletePermission ? false : true%>" 
          image="<%=deletePermission ? "delete.gif" : "delete_disabled.gif"%>" 
          title="Delete"
          onclick="deleteItems()" 
          tooltip="<%=deletePermission ? "Delete the selected items" : "You do not have permission to delete items"%>" 
        />
        <tbl:button 
          disabled="<%=writePermission ? false : true%>" 
          image="<%=writePermission ? "restore.gif" : "restore_disabled.gif"%>" 
          onclick="restoreItems()" 
          title="Restore"
          tooltip="<%=writePermission ? "Restore the selected (deleted) items" : "You do not have permission to restore items"%>" 
        />
        <tbl:button 
          image="columns.gif" 
          onclick="configureColumns()" 
          title="Columns&hellip;" 
          tooltip="Show, hide and re-order columns" 
        />
        <tbl:button 
          image="import.gif" 
          onclick="runPlugin('ImportItems')" 
          title="Import&hellip;" 
          tooltip="Import data" 
          visible="<%=pluginCount.containsKey(Plugin.MainType.IMPORT)%>"
        />
        <tbl:button 
          image="export.gif" 
          onclick="runPlugin('ExportItems')" 
          title="Export&hellip;" 
          tooltip="Export data" 
          visible="<%=pluginCount.containsKey(Plugin.MainType.EXPORT)%>"
        />
        <tbl:button 
          image="runplugin.gif" 
          onclick="runPlugin('RunListPlugin')" 
          title="Run plugin&hellip;" 
          tooltip="Run a plugin" 
          visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>"
        />
        <ext:render extensions="<%=toolbarInvoker%>" context="<%=jspContext%>" 
          wrapper="<%=new PrefixSuffixRenderer(jspContext, "<td>", "</td>") %>"/>
      </tbl:toolbar>
      <tbl:data>
        <tbl:columns>
        <tbl:presetselector 
          clazz="columnheader"
          colspan="3"
          onchange="presetOnChange()"
        />
        </tbl:columns>
        <tr>
          <tbl:header 
            clazz="index"
            >&nbsp;</tbl:header>
          <tbl:header 
            clazz="check" 
            visible="<%=mode.hasCheck()%>"
            ><base:icon 
              image="check_uncheck.gif" 
              tooltip="Check/uncheck all" 
              onclick="Forms.checkUncheck(document.forms[formId])" style="align: left;"
            /></tbl:header>
          <tbl:header 
            clazz="check" 
            visible="<%=mode.hasRadio()%>"
            />
          <tbl:header 
            clazz="icons" 
            visible="<%=mode.hasIcons()%>"
            >&nbsp;</tbl:header>
          <tbl:propertyfilter />
        </tr>
    
          <tbl:rows>
          <%
          int index = cc.getPage()*cc.getRowsPerPage();
          int selectedItemId = cc.getId();
          if (analysisTree != null)
          {           
            Iterator<Tree.Entry<BasicItem>> baas = analysisTree.entryIterator(root);
            while (baas.hasNext())
            {
              Tree.Entry<BasicItem> entry = baas.next();
              BasicItem item = entry.getNode();
              if (item != null)
              {
                int level = entry.getDepth() - 1;
                int itemId = item.getId();
                String joustId = item.getType().name() + "_" + itemId;
                String name = "";
                String description = "";
                String tooltip = mode.isSelectionMode() ?
                    "Select this item" : "View this item" + (writePermission ? " (use CTRL, ALT or SHIFT to edit)" : "");
                String deletePermanently = "deleteItemPermanently('" + item.getType().name() + "', "+itemId+")";
                boolean removed = false;
                Transformation t = null;
                BioAssaySet bas = null;
                ExtraValue xv = null;
                PluginDefinition plugin = null;
                Job job = null;
                String prefix = "";
                ItemContext ccc = null;
                String view = "";
                String onClick = "";
                Item itemType = item.getType();
                if (itemType == Item.TRANSFORMATION)
                {
                  t = (Transformation)item;
                  removed = t.isRemoved();
                  prefix = "T:";
                  ccc = tc;
                  onClick = "transformationOnClick";
                  name = HTML.encodeTags(t.getName());
                  description = HTML.encodeTags(t.getDescription());
                  try
                  {
                    job = t.getJob();
                    plugin = job.getPluginDefinition();
                  }
                  catch (Throwable ex)
                  {}
                }
                else if (itemType == Item.BIOASSAYSET)
                {
                  bas = (BioAssaySet)item;
                  removed = bas.isRemoved();
                  ccc = cc;
                  onClick = "bioAssaySetOnClick";
                  name = HTML.encodeTags(bas.getName());
                  description = HTML.encodeTags(bas.getDescription());
                }
                else if (itemType == Item.EXTRAVALUE)
                {
                  xv = (ExtraValue)item;
                  prefix = "X:";
                  removed = false;
                  ccc = xvc;
                  onClick = "extraValueOnClick";
                  try
                  {
                    ExtraValueType xvType = xv.getExtraValueType();
                    name = HTML.encodeTags(xvType.getName());
                    description = HTML.encodeTags(xvType.getDescription());
                  }
                  catch (PermissionDeniedException ex)
                  {
                    name = xv.getValueType().toString();
                    description = "";
                  }
                  try
                  {
                    job = xv.getJob();
                    plugin = job.getPluginDefinition();
                  }
                  catch (Throwable ex)
                  {}
                }
                
                index++;
                numListed++;

                %>
                <tbl:row
                  id="<%="row."+joustId%>"
                  >
                  <tbl:header 
                    clazz="index"
                    ><%=index%></tbl:header>
                  <tbl:header 
                    clazz="check" 
                    visible="<%=mode.hasCheck()%>"
                    ><input 
                        type="checkbox" 
                        name="<%=prefix+itemId%>" 
                        value="<%=itemId%>" 
                        title="<%=name%>" 
                        <%=ccc.getSelected().contains(itemId) ? "checked" : ""%>
                      ></tbl:header>
                  <tbl:header 
                    clazz="check" 
                    visible="<%=mode.hasRadio()%>"
                    ><input 
                        type="radio" 
                        name="item_id" 
                        value="<%=itemId%>" 
                        title="<%=name%>" 
                        <%=selectedItemId == itemId ? "checked" : ""%>
                      ></tbl:header>
                  <tbl:header 
                    clazz="icons" 
                    visible="<%=mode.hasIcons()%>"
                    ><base:icon 
                      image="<%=deletePermission ? "deleted.gif" : "deleted_disabled.gif"%>"
                      onclick="<%=deletePermission ? deletePermanently : null%>"
                      tooltip="This item has been scheduled for deletion" 
                      visible="<%=removed%>"
                    />&nbsp;</tbl:header>
                  
                  <tbl:cell clazz="joustcell" column="name">
                    <div id="tree.<%=joustId%>" class="link" 
                      onclick="<%=onClick%>(<%=writePermission ? "event" : null%>, <%=itemId%>)" 
                      title="<%=tooltip%>"><%=name%>
                    </div>
                  </tbl:cell>
                  <%
                  if (t != null)
                  {
                    %>
                    <tbl:cell column="spots">&nbsp;</tbl:cell>
                    <tbl:cell column="reporters">&nbsp;</tbl:cell>
                    <tbl:cell column="fileSpots">&nbsp;</tbl:cell>
                    <tbl:cell column="fileReporters">&nbsp;</tbl:cell>
                    <tbl:cell column="tools">
                      <nobr>
                      <%
                      if (createPermission && job != null && plugin != null && plugin.isInteractive())
                      {
                        %>
                        <a href="javascript:copyJob(<%=job.getId()%>)" 
                          title="Copy this transformation"><img 
                          src="../../../images/copy.gif" border="0"></a>
                        <%
                      }
                      %>
                      <ext:render extensions="<%=toolsInvoker%>" context="<%=jspContext%>" item="<%=item%>" />
                      </nobr>
                    </tbl:cell>
                    <%
                  }
                  if (bas != null)
                  {
                    %>
                    <tbl:cell column="spots"><%=bas.getNumSpots()%></tbl:cell>
                    <tbl:cell column="reporters"><%=bas.getNumReporters()%></tbl:cell>
                    <tbl:cell column="fileSpots"><%=bas.getNumFileSpots()%></tbl:cell>
                    <tbl:cell column="fileReporters"><%=bas.getNumFileReporters()%></tbl:cell>
                    <tbl:cell column="date">&nbsp;</tbl:cell>
                    <tbl:cell column="plugin">&nbsp;</tbl:cell>
                    <%
                    AnnotationSet as = bas.isAnnotated() ? bas.getAnnotationSet() : null;
                    if (as != null)
                    {
                      for (AnnotationType at : annotationTypes)
                      {
                        if (as.hasAnnotation(at))
                        {
                          Annotation a = as.getAnnotation(at);
                          String suffix = a.getUnitSymbol(null);
                          if (suffix != null) suffix = "&nbsp;" + suffix;
                          %>
                          <tbl:cell 
                            column="<%="at"+at.getId()%>"
                            ><tbl:cellvalue 
                              list="<%=a.getValues(null)%>"
                              suffix="<%=suffix%>"
                          /></tbl:cell>
                          <%
                        }
                      }
                    }
                    %>
                    <tbl:cell column="tools">
                      <nobr>
                      <%
                      if (bas.getNumSpots() > 0)
                      {
                        %>
                        <a href="javascript:openPlotTool(<%=itemId%>)" 
                          title="A simple plot tool"><img 
                          src="../../../images/plotter.gif" border="0"></a>
                        <a href="javascript:openExperimentExplorer(<%=itemId%>)"
                          title="Experiment explorer"><img
                          src="../../../images/explorer.png" border="0"></a>
                        <%
                      }
                      %>
                      <a href="javascript:runExportPlugin(<%=itemId%>)"
                        title="Export data"><img 
                        src="../../../images/export.gif" border="0"></a>
                        
                      <%
                      if (createPermission)
                      {
                        %>
                        <a href="javascript:filter(<%=itemId%>)" 
                          title="Create a filtered bioassay set"><img 
                          src="../../../images/filter.gif" border="0"></a>
                        <a href="javascript:runAnalysisPlugin(<%=itemId%>)" title="Run an analysis plugin"><img 
                          src="../../../images/runplugin.gif" border="0"></a>
                        <%
                      }
                      %>
                      <ext:render extensions="<%=toolsInvoker%>" context="<%=jspContext%>" item="<%=item%>" />
                      </nobr>
                    </tbl:cell>
                    <%
                  }
                  if (xv != null)
                  {
                    %>
                    <tbl:cell column="spots"><%=xv.getNumValues()%></tbl:cell>
                    <tbl:cell column="reporters">&nbsp;</tbl:cell>
                    <tbl:cell column="fileSpots"><%=xv.getNumFileValues()%></tbl:cell>
                    <tbl:cell column="fileReporters">&nbsp;</tbl:cell>
                    <tbl:cell column="tools">
                      <nobr>
                      <%
                      if (createPermission && job != null && plugin != null && plugin.isInteractive())
                      {
                        %>
                        <a href="javascript:copyJob(<%=job.getId()%>)" 
                          title="Copy this extra value"><img 
                          src="../../../images/copy.gif" border="0"></a>
                        <%
                      }
                      %>
                      <ext:render extensions="<%=toolsInvoker%>" context="<%=jspContext%>" item="<%=item%>" />                            
                      </nobr>
                    </tbl:cell>
                    <%
                  }
                  %>
                  <tbl:cell column="date"><%=job == null ? "" : dateTimeFormatter.format(job.getEnded())%></tbl:cell>
                  <tbl:cell column="plugin"><%=plugin == null ? "" : Base.getLinkedName(ID, plugin, false, true)%></tbl:cell>
                  <tbl:cell column="description"><%=description%></tbl:cell>
                </tbl:row>
                <%
              }
            }
          }
          %>
          </tbl:rows>
        </tbl:data>
      <%
      if (numListed == 0)
      {
        %>
        <tbl:panel>No bioassay sets or transformations were found.</tbl:panel>
        <%
      }
      %>
    </tbl:table>

    <script language="JavaScript">
    initTree();
    </script>
  </base:body>
  </base:page>
  <%
}
finally
{
  if (dc != null) dc.close();
}
%>