Changeset 3875

Timestamp:

Oct 24, 2007, 12:53:33 PM (15 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #806: Experimental factor values display on Experiment page can only display one annotation of each type

The same bug was also present in the Experiment overview

Location:

trunk

Files:

• src/core/net/sf/basedb/core/AnnotationSet.java (modified) (6 diffs)
• src/core/net/sf/basedb/core/AnnotationType.java (modified) (5 diffs)
• src/core/net/sf/basedb/util/BioAssaySetUtil.java (modified) (3 diffs)
• src/core/net/sf/basedb/util/overview/ExperimentOverview.java (modified) (5 diffs)
• www/views/experiments/overview/info.jsp (modified) (3 diffs)
• www/views/experiments/view_experiment.jsp (modified) (2 diffs)

trunk/src/core/net/sf/basedb/core/AnnotationSet.java

@@ -25 +25 @@
 package net.sf.basedb.core;
 
+import java.util.LinkedList;
+import java.util.List;
 import java.util.Set;
 
@@ -263 +265 @@
       and the annotation type isn't valid for this type of item
     @throws BaseException If there is another error
-    @see #findAnnotation(AnnotationType)
+    @see #findAnnotations(DbControl, AnnotationType, boolean)
   */
   public Annotation getAnnotation(AnnotationType annotationType)
@@ -313 +315 @@
     @param annotationType The annotation type to look for
     @return An <code>Annotation</code> object or null
-   */
-  public Annotation findAnnotation(AnnotationType annotationType)
+    @deprecated Use {@link #findAnnotations(DbControl, AnnotationType, boolean)} instead
+  */
+  public Annotation xfindAnnotation(AnnotationType annotationType)
     throws PermissionDeniedException
   {
+    List<Annotation> annotations = findAnnotations(getDbControl(), annotationType, null);
+    return annotations.size() > 0 ? annotations.get(0) : null;
+  }
+  
+  /**
+    Find annotations of the specified annotation type among all annotations
+    including the inherted annotations. This method will search for 
+    annotations in the following order:
+    <ol>
+    <li>The primary annotations
+    <li>The inherited annotations
+    <li>The inherited annotation sets
+    </ol>
+    If no annotation of the specified type is found, an empty list is returned.
+    
+    @param dc The DbControl to use for database access
+    @param annotationType The annotation type to look for
+    @param findInherited TRUE if the method always should try to find inherited annotations,
+      FALSE if it never should try, or null if it only should try if it hasn't found any
+      annotation so far
+    @return A list <code>Annotation</code> objects (may be empty)
+  */
+  public List<Annotation> findAnnotations(DbControl dc, AnnotationType annotationType, Boolean findInherited)
+    throws PermissionDeniedException
+  {
     if (annotationType == null) throw new InvalidUseOfNullException("annotationType");
+    // List for storing the result
+    List<Annotation> annotations = new LinkedList<Annotation>();
     
-    Annotation a = null;
-    AnnotationData ad = null;
-    
-    org.hibernate.Session session = getDbControl().getHibernateSession();
-    
+    org.hibernate.Session session = dc.getHibernateSession();
     // Find primary annotation
     org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, "GET_PRIMARY_ANNOTATION");
@@ -334 +360 @@
     query.setEntity("annotationType", annotationType.getData());
     query.setEntity("annotationSet", this.getData());
-    ad = HibernateUtil.loadData(AnnotationData.class, query);
+    AnnotationData ad = HibernateUtil.loadData(AnnotationData.class, query);
+    if (ad != null) annotations.add(dc.getItem(Annotation.class, ad));
     
-    if (ad == null)
-    {
-      // Find inherited
+    if (Boolean.TRUE.equals(findInherited) || (annotations.isEmpty() && findInherited == null))
+    {
+      // Find among inherited annotations
       query = HibernateUtil.getPredefinedQuery(session, "GET_DIRECTLY_INHERITED_ANNOTATION");
       /*
@@ -349 +376 @@
       query.setEntity("annotationType", annotationType.getData());
       query.setEntity("annotationSet", this.getData());
-      ad = HibernateUtil.loadData(AnnotationData.class, query);
-    }
-
-    if (ad == null)
+      List<AnnotationData> inherited = HibernateUtil.loadList(AnnotationData.class, query, dc.getSessionControl());
+      for (AnnotationData a : inherited)
+      {
+        annotations.add(dc.getItem(Annotation.class, a));
+      }
+    }
+  
+    if (Boolean.TRUE.equals(findInherited) || (annotations.isEmpty() && findInherited == null))
     {
       // Find among inherited annotation sets
@@ -365 +396 @@
       query.setEntity("annotationType", annotationType.getData());
       query.setEntity("annotationSet", this.getData());
-      ad = HibernateUtil.loadData(AnnotationData.class, query);
-    }
-    
-    if (ad != null)
-    {
-      a = getDbControl().getItem(Annotation.class, ad);
-    }
-    return a;
-  }
+      List<AnnotationData> inherited = HibernateUtil.loadList(AnnotationData.class, query, dc.getSessionControl());
+      for (AnnotationData a : inherited)
+      {
+        annotations.add(dc.getItem(Annotation.class, a));
+      }
+    }
+    return annotations;
+  } 
   
   /**

trunk/src/core/net/sf/basedb/core/AnnotationType.java

@@ -1001 +1001 @@
         if (minValue != null && maxValue != null)
         {
-          throw new NumberOutOfRangeException(this.toString(), intValue.intValue(), minValue.intValue(), maxValue.intValue());
+          throw new NumberOutOfRangeException(this.getName(), intValue.intValue(), minValue.intValue(), maxValue.intValue());
         }
         else if (minValue != null)
         {
-          throw new NumberOutOfRangeException(this.toString(), intValue.intValue(), minValue.intValue(), false);
+          throw new NumberOutOfRangeException(this.getName(), intValue.intValue(), minValue.intValue(), false);
         }
         else if (maxValue != null)
         {
-          throw new NumberOutOfRangeException(this.toString(), intValue.intValue(), maxValue.intValue(), true);
+          throw new NumberOutOfRangeException(this.getName(), intValue.intValue(), maxValue.intValue(), true);
         }
       }
@@ -1024 +1024 @@
         if (minValue != null && maxValue != null)
         {
-          throw new NumberOutOfRangeException(this.toString(), longValue.longValue(), minValue.longValue(), maxValue.longValue());
+          throw new NumberOutOfRangeException(this.getName(), longValue.longValue(), minValue.longValue(), maxValue.longValue());
         }
         else if (minValue != null)
         {
-          throw new NumberOutOfRangeException(this.toString(), longValue.longValue(), minValue.longValue(), false);
+          throw new NumberOutOfRangeException(this.getName(), longValue.longValue(), minValue.longValue(), false);
         }
         else if (maxValue != null)
         {
-          throw new NumberOutOfRangeException(this.toString(), longValue.longValue(), maxValue.longValue(), true);
+          throw new NumberOutOfRangeException(this.getName(), longValue.longValue(), maxValue.longValue(), true);
         }
       }
@@ -1047 +1047 @@
         if (minValue != null && maxValue != null)
         {
-          throw new NumberOutOfRangeException(this.toString(), floatValue.floatValue(), minValue.floatValue(), maxValue.floatValue());
+          throw new NumberOutOfRangeException(this.getName(), floatValue.floatValue(), minValue.floatValue(), maxValue.floatValue());
         }
         else if (minValue != null)
         {
-          throw new NumberOutOfRangeException(this.toString(), floatValue.floatValue(), minValue.floatValue(), false);
+          throw new NumberOutOfRangeException(this.getName(), floatValue.floatValue(), minValue.floatValue(), false);
         }
         else if (maxValue != null)
         {
-          throw new NumberOutOfRangeException(this.toString(), floatValue.floatValue(), maxValue.floatValue(), true);
+          throw new NumberOutOfRangeException(this.getName(), floatValue.floatValue(), maxValue.floatValue(), true);
         }
       }
@@ -1070 +1070 @@
         if (minValue != null && maxValue != null)
         {
-          throw new NumberOutOfRangeException(this.toString(), doubleValue.doubleValue(), minValue.doubleValue(), maxValue.doubleValue());
+          throw new NumberOutOfRangeException(this.getName(), doubleValue.doubleValue(), minValue.doubleValue(), maxValue.doubleValue());
         }
         else if (minValue != null)
         {
-          throw new NumberOutOfRangeException(this.toString(), doubleValue.doubleValue(), minValue.doubleValue(), false);
+          throw new NumberOutOfRangeException(this.getName(), doubleValue.doubleValue(), minValue.doubleValue(), false);
         }
         else if (maxValue != null)
         {
-          throw new NumberOutOfRangeException(this.toString(), doubleValue.doubleValue(), maxValue.doubleValue(), true);
+          throw new NumberOutOfRangeException(this.getName(), doubleValue.doubleValue(), maxValue.doubleValue(), true);
         }
       }
@@ -1088 +1088 @@
       if (stringValue.length() > maxLength)
       {
-        throw new StringTooLongException(this.toString(), stringValue, maxLength);
+        throw new StringTooLongException(this.getName(), stringValue, maxLength);
       }
     }

trunk/src/core/net/sf/basedb/util/BioAssaySetUtil.java

@@ -48 +48 @@
 import net.sf.basedb.util.jep.ScoreFunction;
 
+import java.util.List;
 import java.util.Set;
 import java.util.TreeSet;
@@ -83 +84 @@
     if (bioAssay.isAnnotated())
     {
-      Annotation a = bioAssay.getAnnotationSet().findAnnotation(annotationType);
-      if (a != null) allValues.addAll(a.getValues());
+      List<Annotation> all = bioAssay.getAnnotationSet().findAnnotations(dc, annotationType, true);
+      for (Annotation a : all)
+      {
+        if (a != null) allValues.addAll(a.getValues());
+      }
     }
     for (RawBioAssay rb : rbaQuery.list(dc))
@@ -90 +94 @@
       if (rb.isAnnotated())
       {
-        Annotation a =  rb.getAnnotationSet().findAnnotation(annotationType);
-        if (a != null) allValues.addAll(a.getValues());
+        List<Annotation> all =  rb.getAnnotationSet().findAnnotations(dc, annotationType, true);
+        for (Annotation a : all)
+        {
+          if (a != null) allValues.addAll(a.getValues());
+        }
       }
     }

trunk/src/core/net/sf/basedb/util/overview/ExperimentOverview.java

@@ -1635 +1635 @@
     ItemQuery<AnnotationType> parameterQuery = initQuery(protocol.getParameters(), null, "name");
     List<AnnotationType> parameters = parameterQuery.list(dc);
-    Node parameterNode = null;
+    Node parametersNode = null;
     if (parameters.size() > 0)
     {
-      parameterNode = new Node("parameters", "Parameters", protocolNode);
+      parametersNode = new Node("parameters", "Parameters", protocolNode);
       for (AnnotationType pp : parameters)
       {
-        new Node("parameter."+pp.getId(), pp.getName(), parameterNode, pp);
+        Node parameterNode = new Node("parameter."+pp.getId(), pp.getName(), parametersNode, pp);
         
         // Check if a value for this parameter has been specified
@@ -1647 +1647 @@
         {
           failures.add(new Failure(Validator.MISSING_PARAMETER, parentNode, 
-            "Missing parameter value: " + pp.getName(), 
-            new Fix("Add parameter value for: " + pp.getName(), parentItem, pp, false)));
-        }
-      }
-    }
-    return parameterNode;
+            "Missing value for parameter: " + pp.getName(), 
+            new Fix("Add value for: " + pp.getName(), parentItem, pp, false)));
+        }
+        else
+        {
+          Annotation a = as.getAnnotation(pp);
+          try
+          {
+            List<?> values = a.getValues();
+            if (values != null)
+            {
+              for (Object value : values)
+              {
+                pp.validateAnnotationValue(value);
+              }
+            }
+          }
+          catch (InvalidDataException ex)
+          {
+            failures.add(new Failure(Validator.ANNOTATION_INVALID_VALUE, parentNode, ex.getMessage(),
+              new Fix("Change parameter value", parentItem, pp, false),
+              new Fix("Change parameter restrictions", pp)
+            ));
+          }
+          
+        }
+      }
+    }
+    return parametersNode;
   }
   
@@ -1658 +1681 @@
     Add annotations child node to an annotatable item. Creates a 
     folder-type child node with the name <code>annotations</code> and inside
-    it item-type nodes with the name <code>annotation.ID</code> for each
+    it item-type nodes with the name <code>annotationtype.ID</code> for each
     annotation (primary and inherited). ID is the ID of the annotation type.
+    If the logged in user doesn't have read permission for a particular annotation
+    type a node with the name <code>annotation.ID</code> is created instead. In this
+    case the ID is the ID of the annotation.
     @see Protocol#getParameters()
   */
@@ -1759 +1785 @@
     if (parent.isAnnotated())
     {
-      annotationTypes.clear();
+      //annotationTypes.clear();
       AnnotationSet as = parent.getAnnotationSet();
       ItemQuery<Annotation> annotationQuery = initQuery(as.getAllInheritedAnnotations(), "at", "name");
@@ -1775 +1801 @@
           {
             at = a.getAnnotationType();
-            atNode = new Node("annotationtype."+at.getId(), at.getName(), annotationsNode, at);
             if (annotationTypes.containsKey(at))
             {
               duplicates.add(at);
+              atNode = annotationTypes.get(at);
             }
             else
             {
               annotationTypes.put(at, atNode);
+              atNode = new Node("annotationtype."+at.getId(), at.getName(), annotationsNode, at);
             }
           }

trunk/www/views/experiments/overview/info.jsp

@@ -59 +59 @@
   import="java.util.LinkedList"
   import="java.util.Iterator"
+  import="java.util.Collection"
+  import="java.util.Collections"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
@@ -287 +289 @@
       
       <%
-      if (item instanceof Annotatable)
-      {
-        Annotatable annotatable = (Annotatable)item;
+      List<Annotation> annotations = null;
+      String annotationsTitle = "";
+      Annotatable annotatable = null;
+      if (item instanceof Annotation)
+      {
+        Annotation a = (Annotation)item;
+        dc.reattachItem(a);
+        annotatable = a.getAnnotationSet().getItem();
+        annotations = Collections.singletonList(a);
+        annotationsTitle = "Annotation values";
+      }
+      else if (item instanceof AnnotationType)
+      {
+        if (node.getName().startsWith("parameter"))
+        {
+          annotatable = (Annotatable)node.getParent().getParent().getParent().getItem();
+        }
+        else
+        {
+          annotatable = (Annotatable)node.getParent().getParent().getItem();
+        }
+        dc.reattachItem((BasicItem)annotatable);
         if (annotatable.isAnnotated())
         {
-          dc.reattachItem(item);
-          AnnotationSet as = AnnotationSet.getById(dc, annotatable.getAnnotationSet().getId());
-          List<Node> annotationNodes = new ArrayList<Node>();
-          
-          // Load annotations
-          Node annotationsFolder = node.getChild("annotations");
-          if (annotationsFolder != null && annotationsFolder.getChildren() != null)
-          {
-            annotationNodes.addAll(annotationsFolder.getChildren());
-          }
-          
-          // Load protocol parameters
+          annotations = annotatable.getAnnotationSet().findAnnotations(dc, (AnnotationType)item, true);
+        }
+        annotationsTitle = "Annotation values";
+      }
+      else if (item instanceof Annotatable)
+      {
+        annotationsTitle = "Annotations &amp; protocol parameters";
+        annotatable = (Annotatable)item;
+        if (annotatable.isAnnotated())
+        {
+          dc.reattachItem((BasicItem)annotatable);
+  
+          // Load annotations & protocol parameters
+          List<Node> nodes = new LinkedList<Node>();
+          Node folder = node.getChild("annotations");
+          if (folder != null && folder.getChildren() != null) nodes.addAll(folder.getChildren());
           Node protocolNode = node.getChild("protocol");
-          if (protocolNode != null)
-          {
-            Node parametersFolder = protocolNode.getChild("parameters");
-            if (parametersFolder != null && parametersFolder.getChildren() != null)
+          folder = protocolNode == null ? null : protocolNode.getChild("parameters");
+          if (folder != null && folder.getChildren() != null) nodes.addAll(folder.getChildren());
+          if (nodes.size() > 0)
+          {
+            annotations = new LinkedList<Annotation>();
+            for (Node n : nodes)
             {
-              annotationNodes.addAll(parametersFolder.getChildren());
+              BasicItem aItem = n.getItem();
+              if (aItem instanceof Annotation)
+              {
+                annotations.add((Annotation)aItem);
+              }
+              else if (aItem instanceof AnnotationType)
+              {
+                annotations.addAll(annotatable.getAnnotationSet().findAnnotations(dc, (AnnotationType)aItem, true));
+              }
             }
           }
+        }
+      }
+      if (annotations != null && annotations.size() > 0)
+      {
+        %>
+        <h4><%=annotationsTitle%></h4>
+        <table border=0 cellspacing=0 cellpadding=0>
+        <%
+        for (Annotation a : annotations)
+        {
+          a = Annotation.getById(dc, a.getId());
+          AnnotationType at = null;
+          Annotatable annotationOwner = null;
+          try
+          {
+            at = a.getAnnotationType();
+          }
+          catch (Throwable t)
+          {}
+          try
+          {
+            annotationOwner = a.getAnnotationSet().getItem();
+          }
+          catch (Throwable t)
+          {}
+          String icon = at != null && at.isProtocolParameter() ? 
+              "parameter.gif" : "joust/annotation.gif";
+          String editLink = null;
+          String editTooltip = null;
+          if (annotatable.hasPermission(Permission.WRITE) && at != null)
+          {
+            if (annotatable.equals(annotationOwner))
+            {
+              editLink = "editAnnotation('" + annotatable.getType().name() + "', " + annotatable.getId() + ", " + at.getId() + ")";
+              editTooltip = "Edit the values of this annotation";
+            }
+            else
+            {
+              editLink = "editInheritedAnnotation('" + annotatable.getType().name() + "', " + annotatable.getId() + ", " + at.getId() + ")";
+              editTooltip = "Inherit this annotation from another item";
+            }
+          }
           %>
-          <h4>Annotations &amp; protocol parameters</h4>
-          <table border=0 cellspacing=0 cellpadding=0>
-          <%
-          for (Node annotationNode : annotationNodes)
-          {
-            BasicItem aItem = annotationNode.getItem();
-            AnnotationType at = null;
-            Annotation a = null;
-            String editLink = null;
-            if (aItem instanceof AnnotationType)
-            {
-              at = (AnnotationType)aItem;
-              a = as.findAnnotation(at);
-              if (item.hasPermission(Permission.WRITE))
-              {
-                if (as.hasAnnotation(at))
-                {
-                  editLink = "editAnnotation('" + item.getType().name() + "', " + item.getId() + ", " + at.getId() + ")";
-                }
-                else
-                {
-                  editLink = "editInheritedAnnotation('" + item.getType().name() + "', " + item.getId() + ", " + at.getId() + ")";
-                }
-              }
-            }
-            else if (aItem instanceof Annotation)
-            {
-              a = Annotation.getById(dc, aItem.getId());
-            }
-            if (a != null)
-            {
-              boolean hasWarnings = annotationNode.getNumWarnings() > 0;
-              boolean hasErrors = annotationNode.getNumErrors() > 0;
-              String icon = hasErrors ? "error.gif" : hasWarnings ? "warning.gif" : null;
-              if (icon == null)
-              {
-                if (annotationNode.getName().startsWith("parameter"))
-                {
-                  icon = "parameter.gif";
-                }
-                else
-                {
-                  icon = "joust/annotation.gif";
-                }
-              }
-              %>
-              <tr><td><base:icon visible="<%=icon != null%>" image="<%=icon%>" />&nbsp;</td>
-              <td><b>
-                <%
-                if (at != null && at.hasPermission(Permission.WRITE))
+          <tr>
+            <td><base:icon visible="<%=icon != null%>" image="<%=icon%>" />&nbsp;</td>
+            <td>
+              <%
+              if (at != null)
+              {
+                if (at.hasPermission(Permission.WRITE))
                 {
                   %>
                   <a href="javascript:editItem('<%=at.getType().name()%>', <%=at.getId()%>)" 
-                    title="Edit this annotation type"><%=HTML.encodeTags(annotationNode.getTitle())%></a>
+                    title="Edit this annotation type"><%=HTML.encodeTags(at.getName())%></a>
                   <%
                 }
@@ -373 +407 @@
                 {
                   %>
-                  <%=HTML.encodeTags(annotationNode.getTitle())%>
+                  <%=HTML.encodeTags(at.getName())%>
                   <%
                 }
-                %></b>
-              </td>
-              <td>&nbsp;</td>
-              <td><%=Values.getString(a.getValues(), ", ", true)%></td>
-              <td>&nbsp;:
+              }
+              else
+              {
+                %>
+                <%=a.getValueType() %>
                 <%
-                if (editLink != null)
-                {
-                  %><base:icon image="edit.gif" onclick="<%=editLink%>" 
-                    tooltip="Edit the values of this annotation" />
+              }
+              %>
+            </td>
+            <td>
+              <%
+              if (annotationOwner != null && !annotationOwner.equals(annotatable))
+              {
+                %>
+                <base:icon image="bullet.gif" tooltip="Annotation is inherited from" />
+                <%
+                String ownerName = annotationOwner instanceof Nameable ?
+                    ((Nameable)annotationOwner).getName() : annotationOwner.toString();
+                if (annotationOwner.hasPermission(Permission.WRITE))
+                {
+                  %>
+                  <a href="javascript:editItem('<%=annotationOwner.getType().name()%>', <%=annotationOwner.getId()%>)" 
+                    title="Edit this item"><%=HTML.encodeTags(ownerName)%></a>
                   <%
                 }
-                %>
-              </td>
-              <%
-            }
-          }
-          %>
-          </table>
+                else
+                {
+                  %>
+                  <%=HTML.encodeTags(ownerName)%>
+                  <%
+                }
+              }
+              %>
+            </td>
+            <td><base:icon image="bullet.gif" /></td>
+            <td><%=Values.getString(a.getValues(), ", ", true)%></td>
+            <td>&nbsp;
+              <%
+              if (editLink != null)
+              {
+                %><base:icon image="edit.gif" onclick="<%=editLink%>" 
+                  tooltip="<%=editTooltip%>" />
+                <%
+              }
+              %>
+            </td>
+          </tr>
           <%
         }
+        %>
+        </table>
+        <%
       }
       %>

trunk/www/views/experiments/view_experiment.jsp

@@ -66 +66 @@
   import="java.util.HashSet"
   import="java.util.List"
+  import="java.util.LinkedList"
   import="java.util.Date"
 %>
@@ -515 +516 @@
               {
                 String value = "<i>- none -</i>";
-                Annotation a = as == null ? null : as.findAnnotation(at);
-                List<?> factorValues = a == null ? null : a.getValues();
-                if (factorValues != null) usedFactorValues.get(at).addAll(factorValues);
-                Annotatable aItem = null;
-                try
+                List<Annotation> all = as == null ? null : as.findAnnotations(dc, at, true);
+                Map<Annotatable, List> factorValues = new HashMap<Annotatable, List>();
+                if (all != null && all.size() > 0)
                 {
-                  aItem = a.getAnnotationSet().getItem();
+                  for (Annotation a : all)
+                  {
+                    List values = a.getValues();
+                    usedFactorValues.get(at).addAll(values);
+                    Annotatable aItem = null;
+                    try
+                    {
+                      aItem = a.getAnnotationSet().getItem();
+                    }
+                    catch (Throwable t)
+                    {}
+                    List toAdd = factorValues.get(aItem);
+                    if (toAdd == null)
+                    {
+                      toAdd = new LinkedList();
+                      factorValues.put(aItem, toAdd);
+                    }
+                    toAdd.addAll(values);
+                  }
                 }
-                catch (Throwable t)
-                {}
+                
                 %>
                 <tbl:cell column="<%="at"+at.getId()%>"
-                  ><tbl:cellvalue list="<%=factorValues%>" />
-                <%
-                if (aItem != null && aItem.hasPermission(Permission.WRITE))
-                {
-                  %>: <base:icon image="edit.gif" 
-                    onclick="<%="editAnnotation('"+aItem.getType().name()+"',"+aItem.getId()+","+at.getId()+")"%>" 
-                    tooltip="Modify the values of this experimental factor" />
+                  >
                   <%
-                }
-                %>
+                  for (Map.Entry<Annotatable, List> entry : factorValues.entrySet())
+                  {
+                    Annotatable aItem = entry.getKey();
+                    List values = entry.getValue();
+                    %>
+                    <tbl:cellvalue list="<%=values%>" />
+                    <%
+                    if (aItem != null && aItem.hasPermission(Permission.WRITE))
+                    {
+                      %>: <base:icon image="edit.gif" 
+                        onclick="<%="editAnnotation('"+aItem.getType().name()+"',"+aItem.getId()+","+at.getId()+")"%>" 
+                        tooltip="Modify the values of this experimental factor" />
+                      <%
+                    }
+                  }
+                  %>
                 </tbl:cell>
                 <%