source: trunk/www/views/experiments/bioassaysets/list_bioassaysets.jsp @ 4889

<%-- $Id: list_bioassaysets.jsp 4889 2009-04-06 12:52:39Z nicklas $
  ------------------------------------------------------------------
  Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
  Copyright (C) 2007 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 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.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.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="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="t" uri="/WEB-INF/tab.tld" %>
<%@ taglib prefix="p" uri="/WEB-INF/path.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);
    }
    parent.addChild(bas);
  }
}

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, Collection<String> closed)
{
  StringBuilder sb = new StringBuilder();
  Tree.Entry<BasicItem> rootEntry = tree.getEntry(root);
  if (rootEntry == null) return "";
  
  List<Tree.Entry<BasicItem>> children = rootEntry.getChildren();
  if (children != null)
  {
    for (Tree.Entry<BasicItem> child : children)
    {
      BasicItem node = child.getNode();
      int id = node.getId();
      String var = node.getType().name() + "_" + id;
      String name = ((Nameable)node).getName();
      
      String folderIcon = node.getType() == Item.BIOASSAYSET ?
        "BioAssaySet" : "Transformation";
      sb.append("var ").append(var);
      if (root == null)
      {
        sb.append(" = JoustMenu.addMenuItem(-1");
      }
      else
      {
        String rootVar = root.getType().name() + "_" + root.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 ((closed == null || !closed.contains(var)) && child.getNumChildren() > 0)
      {
        sb.append("JoustMenu.menuItems[").append(var).append("].isOpen = true;\n");
      }
      sb.append(generateTree(tree, node, closed));
    }
  }
  return sb.toString();
}
%>
<%
final int experimentId = Values.getInt(request.getParameter("experiment_id"));
final SessionControl sc = Base.getExistingSessionControl(pageContext, Permission.DENIED, itemType);
final String ID = sc.getId();
final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null);
final ItemContext tc = sc.getCurrentContext(Item.TRANSFORMATION);

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;
try
{
  final Experiment experiment = Experiment.getById(dc, experimentId);
  final boolean createPermission = experiment.hasPermission(Permission.WRITE);
  final boolean deletePermission = createPermission;
  final boolean writePermission = createPermission;

  final ItemQuery<BioAssaySet> query = Base.getConfiguredQuery(cc, true, experiment.getBioAssaySets(), mode);
  final ItemQuery<Transformation> transformationQuery = experiment.getTransformations();
  Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
  try
  {
    analysisTree = getAnalysisTree(dc, query, transformationQuery);
  }
  catch (Throwable t)
  {
    cc.setMessage(t.getMessage());
  }
  // Contains the ID:s of the bioassaysets that are closed in the tree
  Collection<String> closed = (Collection<String>)cc.getObject("closed");
  int numListed = 0;
  %>
  <base:page title="<%=title%>" type="<%=mode.getPageType()%>">
  <base:head scripts="table.js,tabcontrol.js,newjoust.js" styles="table.css,headertabcontrol.css,path.css,newjoust.css">
    <script language="JavaScript">
    function switchTab(tabControlId, tabId)
    {
      if (tabId == 'properties' || tabId == 'overview')
      {
        location.href = '../index.jsp?ID=<%=ID%>&cmd=ViewItem&item_id=<%=experimentId%>&tab='+tabId;
      }
      else
      {
        TabControl.setActiveTab(tabControlId, tabId);
      }
    }
    </script>
  </base:head>
  
  <base:body >
    <p>
    <p:path>
      <p:pathelement title="Experiments" href="<%="../index.jsp?ID="+ID%>" />
      <p:pathelement title="<%=HTML.encodeTags(experiment.getName())%>" />
    </p:path>

    <t:tabcontrol id="main" active="bioassaysets" switch="switchTab">
    <t:tab id="properties" title="Properties" />
    
    <t:tab id="bioassaysets" title="Bioassay sets">
    
      <jsp:include page="analysis_tree.jsp">
        <jsp:param name="ID" value="<%=ID%>" />
        <jsp:param name="experiment_id" value="<%=experimentId%>" />
      </jsp:include>
    
    <base:buttongroup align="center">
      <base:button onclick="returnSelected();" title="Ok" visible="<%=mode.hasOkButton()%>" />
      <base:button onclick="window.close();" title="Cancel" visible="<%=mode.hasCancelButton()%>" />
      <base:button onclick="window.close();" title="Close" visible="<%=mode.hasCloseButton()%>" />
    </base:buttongroup>
    </t:tab>
    <t:tab id="overview" title="Overview" 
      tooltip="Display a tree overview of related items" />
    </t:tabcontrol>

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