Changeset 2166

Timestamp:

Apr 19, 2006, 3:30:05 PM (17 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #96 and #158:

• Inherit annotations
• Resizable annotation tab for most items but mostly needed for BioSource/BioSample?

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/Annotation.java (modified) (5 diffs)
• src/core/net/sf/basedb/core/AnnotationSet.java (modified) (9 diffs)
• src/core/net/sf/basedb/core/Hybridization.java (modified) (2 diffs)
• src/core/net/sf/basedb/util/Tree.java (modified) (2 diffs)
• www/common/annotations/annotate.jsp (modified) (3 diffs)
• www/common/annotations/inherit.jsp (modified) (1 diff)
• www/common/annotations/list_annotations.jsp (modified) (6 diffs)
• www/common/plugin/configure.jsp (modified) (1 diff)
• www/include/scripts/annotations.js (modified) (2 diffs)
• www/include/scripts/linkitems.js (modified) (1 diff)
• www/include/scripts/newjoust.js (modified) (7 diffs)
• www/include/styles/parameters.css (modified) (1 diff)
• www/views/rawbioassays/view_rawbioassay.jsp (modified) (1 diff)
• www/views/scans/view_scan.jsp (modified) (1 diff)

trunk/src/clients/web/net/sf/basedb/clients/web/Base.java

@@ -719 +719 @@
     throws ItemModifiedException, BaseException
   {
+    // Modified annotations
     String modified = Values.getStringOrNull(request.getParameter("modifiedAnnotations"));
     if (modified != null)
@@ -751 +752 @@
       }
     }
+    
+    // Inherited annotations and annotation sets
+    
+    // Annotations that are no longer inherited
+    String removed = Values.getStringOrNull(request.getParameter("removedAnnotations"));
+    if (removed != null)
+    {
+      String[] removedAnnotations = removed.split(",");
+      AnnotationSet newAs = newItem.getAnnotationSet();
+      for (int i = 0; i < removedAnnotations.length; ++i)
+      {
+        int annotationId = Values.getInt(removedAnnotations[i], -1);
+        if (annotationId != -1)
+        {
+          newAs.removeInheritedAnnotation(Annotation.getById(dc, annotationId));
+        }
+      }
+    }
+    
+    // Annotations that we now are inheriting
+    String added = Values.getStringOrNull(request.getParameter("addedAnnotations"));
+    if (added != null)
+    {
+      String[] addedAnnotations = added.split(",");
+      AnnotationSet newAs = newItem.getAnnotationSet();
+      for (int i = 0; i < addedAnnotations.length; ++i)
+      {
+        int annotationId = Values.getInt(addedAnnotations[i], -1);
+        if (annotationId != -1)
+        {
+          newAs.inheritAnnotation(Annotation.getById(dc, annotationId));
+        }
+      }
+    }
+
+    // Annotation sets that are no longer inherited
+    String removedSets = Values.getStringOrNull(request.getParameter("removedAnnotationSets"));
+    if (removedSets != null)
+    {
+      String[] removedAnnotationSets = removedSets.split(",");
+      AnnotationSet newAs = newItem.getAnnotationSet();
+      for (int i = 0; i < removedAnnotationSets.length; ++i)
+      {
+        int annotationSetId = Values.getInt(removedAnnotationSets[i], -1);
+        if (annotationSetId != -1)
+        {
+          newAs.removeInheritedAnnotationSet(AnnotationSet.getById(dc, annotationSetId));
+        }
+      }
+    }
+    
+    // Annotation sets that we now are inheriting
+    String addedSets = Values.getStringOrNull(request.getParameter("addedAnnotationSets"));
+    if (addedSets != null)
+    {
+      String[] addedAnnotationSets = addedSets.split(",");
+      AnnotationSet newAs = newItem.getAnnotationSet();
+      for (int i = 0; i < addedAnnotationSets.length; ++i)
+      {
+        int annotationSetId = Values.getInt(addedAnnotationSets[i], -1);
+        if (annotationSetId != -1)
+        {
+          newAs.inheritAnnotationSet(AnnotationSet.getById(dc, annotationSetId));
+        }
+      }
+    }
   }
   

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

@@ -26 +26 @@
 
 import net.sf.basedb.core.data.AnnotationData;
+import net.sf.basedb.core.query.EntityQuery;
 
 import java.util.List;
@@ -55 +56 @@
   
   /**
+    This filter gives everybody read permission to annotations.
+  */
+  private static final QueryRuntimeFilter RUNTIME_FILTER = new QueryRuntimeFilterImpl();
+
+  /**
     Create a new annotation.
     @param dc The DbControl object
@@ -103 +109 @@
   static ItemQuery<Annotation> getQuery()
   {
-    return new ItemQuery<Annotation>(Annotation.class);
+    return new ItemQuery<Annotation>(Annotation.class, RUNTIME_FILTER);
   }
   
@@ -153 +159 @@
     {
       granted |= Permission.grant(Permission.CREATE, Permission.READ, Permission.WRITE, Permission.DELETE);
+    }
+    else if (as.hasPermission(Permission.USE))
+    {
+      granted |= Permission.grant(Permission.USE);
     }
     else if (as.hasPermission(Permission.READ))
@@ -267 +277 @@
   }
 
+  private static class QueryRuntimeFilterImpl
+    implements QueryRuntimeFilter
+  {
+    public void enableFilters(QueryRuntimeFilterManager manager, EntityQuery query, DbControl dc)
+    {
+      // Do not add any filters.
+    }
+  }
 }
 

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

@@ -25 +25 @@
 package net.sf.basedb.core;
 
+import net.sf.basedb.core.query.EntityQuery;
+import net.sf.basedb.core.query.Expression;
+import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.core.query.Hql;
@@ -60 +63 @@
   
   /**
+    This filter gives everybody read permission to annotations.
+  */
+  private static final QueryRuntimeFilter RUNTIME_FILTER = new QueryRuntimeFilterImpl();
+
+  /**
     Create a new annotation set for the specified item.
     @see AnnotatedItem#getAnnotationSet()
@@ -70 +78 @@
     return as;
   }
-  
+  /**
+    Get an <code>AnnotationSet</code> item when you know the id.
+  
+    @param dc The <code>DbControl</code> which will be used for
+      permission checking and database access.
+    @param id The id of the item to load
+    @return The <code>AnnotationSet</code> item
+    @throws ItemNotFoundException If an item with the specified 
+      id is not found
+    @throws PermissionDeniedException If the logged in user doesn't 
+      have read permission to the item
+    @throws BaseException If there is another error
+  */
+  public static AnnotationSet getById(DbControl dc, int id)
+    throws ItemNotFoundException, PermissionDeniedException, BaseException
+  {
+    AnnotationSet as = dc.loadItem(AnnotationSet.class, id);
+    if (as == null) throw new ItemNotFoundException("AnnotationSet[id="+id+"]");
+    return as;
+  } 
   /**
     Get a {@link ItemQuery} object configured to retrieve <code>AnnotationSet</code> 
@@ -79 +106 @@
   static ItemQuery<AnnotationSet> getQuery()
   {
-    return new ItemQuery<AnnotationSet>(AnnotationSet.class);
+    return new ItemQuery<AnnotationSet>(AnnotationSet.class, RUNTIME_FILTER);
   }
 
@@ -131 +158 @@
   }
   /**
-    READ permission is granted if the logged in user has READ permission on 
-    the associated item. CREATE, WRITE and DELETE permissions are granted
+    READ permission is granted to all users. CREATE, WRITE and DELETE permissions are granted
     if the logged in user has WRITE permission on the associated item.
   */
@@ -138 +164 @@
     throws BaseException
   { 
-    Annotatable item = getItem();     
-    if (item.hasPermission(Permission.WRITE))
+    Annotatable item = null;
+    try
+    {
+      item = getItem();     
+    }
+    catch (PermissionDeniedException ex)
+    {}
+    if (item != null && item.hasPermission(Permission.WRITE))
     {
       granted |= Permission.grant(Permission.CREATE, Permission.READ, Permission.WRITE, Permission.DELETE);       
     }
-    else if (item.hasPermission(Permission.READ))
+    else if (item != null && item.hasPermission(Permission.USE))
+    {
+      granted |= Permission.grant(Permission.USE);
+    }
+    else
     {
       granted |= Permission.grant(Permission.READ);       
@@ -400 +436 @@
   
   /**
-    Get a query that returns all inherited annotations in this annotation set.
+    Get a query that returns directly inherited annotations in this annotation set.
+    Directly inherited annotations are annotations that are linked to this annotation
+    set.
+    @see #inheritAnnotation(Annotation)
     @return An <code>ItemQuery</code> object
   */
@@ -418 +457 @@
   
   /**
+      Get a query that returns all inherited (directly and indirectly) annotations in
+      this annotation set. The directy inherited annotations include annotations added
+      by {@link #inheritAnnotation(Annotation)}, the indirectly inherited annotations
+      include annotations in annotation sets added by 
+      {@link #inheritAnnotationSet(AnnotationSet)}
+      
+      @see #getInheritedAnnotations()
+    @return An <code>ItemQuery</code> object
+  */
+  public ItemQuery<Annotation> getAllInheritedAnnotations()
+  {
+    ItemQuery<Annotation> query = Annotation.getQuery();
+    query.joinPermanent(Hql.leftJoin("inheritingSets", "direct"));
+    query.joinPermanent(Hql.leftJoin("annotationSet.inheritingSets", "indirect"));
+    Expression thisEntity = Expressions.parameter("annotationSet", this.getId(), Type.INT);
+    query.restrictPermanent(
+      Restrictions.or(
+        Restrictions.eq(Hql.alias("direct"), thisEntity),
+        Restrictions.eq(Hql.alias("indirect"), thisEntity)
+      )
+    );
+    return query;
+  }
+  
+  /**
     Inherit an annotation set.
     @param annotationSet The annotation set to inherit
@@ -495 +559 @@
     return query;
   }
+  
+  private static class QueryRuntimeFilterImpl
+    implements QueryRuntimeFilter
+  {
+    public void enableFilters(QueryRuntimeFilterManager manager, EntityQuery query, DbControl dc)
+    {
+      // Do not add any filters.
+    }
+  }
 }

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

@@ -117 +117 @@
   */
   /**
-    Get the labeled extracts and array slide
+    Get the labeled extracts and array slide.
   */
   public Set<Annotatable> getAnnotatableParents()
@@ -125 +125 @@
     try
     {
-      annotatable.addAll(getCreationEvent().getSources().list(getDbControl()));
+      ItemQuery<? extends MeasuredBioMaterial> sources = getCreationEvent().getSources();
+      sources.include(Include.MINE, Include.SHARED, Include.OTHERS, Include.IN_PROJECT);
+      annotatable.addAll(sources.list(getDbControl()));
       if (getData().getArraySlide() != null) annotatable.add(getArraySlide());
     }

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

@@ -256 +256 @@
       Add a child to the node.
       @param child The child to add
+      @return The <code>Entry</code> object of the new child node
       @throws IllegalArgumentException If the child already exists in the tree
     */
-    public void addChild(E child)
+    public Entry<E> addChild(E child)
     {
       if (tree.contains(child))
@@ -264 +265 @@
         throw new IllegalArgumentException("Element '" + child + "' is already in the tree.");
       }
-      tree.addEntry(new Entry<E>(tree, child, this));
+      Entry<E> childEntry = new Entry<E>(tree, child, this);
+      tree.addEntry(childEntry);
+      return childEntry;
     }
 

trunk/www/common/annotations/annotate.jsp

@@ -59 +59 @@
 try
 {
-//  final Annotatable item = (Annotatable)sc.getSessionSetting(itemType.name()+".item");
   final Annotatable item = itemId == 0 ? null : (Annotatable)itemType.getById(dc, itemId);
-  if (item != null) dc.reattachItem((BasicItem)item);
   final String clazz = "class=\"text\"" ;
 
@@ -110 +108 @@
       }
       icon = "<img id=\"icon_"+at.getId()+"\" src=\"../../images/"+icon+"\" class=\"icon\">";
-      sb.append("<div class=\"pluginparameter\" id=\"prompt_"+at.getId()+"\" onclick=\"parametersOnClick('"+at.getId()+"')\" onmouseover=\"Main.addClass(this, 'hover')\" onmouseout=\"Main.removeClass(this, 'hover')\" title=\""+fullLabel+"\">"+icon+label+"</div>");
+      sb.append("<div class=\"param\" id=\"prompt_"+at.getId()+"\" onclick=\"parametersOnClick('"+at.getId()+"')\" onmouseover=\"Main.addClass(this, 'hover')\" onmouseout=\"Main.removeClass(this, 'hover')\" title=\""+fullLabel+"\">"+icon+label+"</div>");
       %>
-      //new AnnotationType(<%=at.getId()%>, '<%=HTML.javaScriptEncode(at.getName())%>', '<%=at.getValueType().name()%>', <%=at.getMultiplicity()%>, <%=at.isEnumeration()%>, values);
       new Parameter('<%=at.getId()%>', '<%=HTML.javaScriptEncode(at.getName())%>', <%=at.getMultiplicity()%>, <%=at.isEnumeration()%>, false, values);
       <%
@@ -351 +348 @@
   <base:body onload="init()" style="background: #E0E0E0;">
     <form name="annotations">
-    <table class="form" cellspacing="2" border="0" cellpadding="0">
+    <table class="form" cellspacing="2" border="0" cellpadding="0" width="100%">
     <tr valign="top">
-      <td>
-        <div class="parameterlist" style="height: <%=(int)(scale*320)%>px; width:<%=(int)(scale*240)%>px;">
+      <td width="50%">
+        <div class="parameterlist" style="height: <%=(int)(scale*320)%>px;">
         <%=sb.toString()%>
         </div>
         <base:icon image="hasvalues.gif" /> = has value(s)
       </td>
-      <td>&nbsp;</td>
-      <td>
+      <td width="50%">
 
         <div id="valuecontainer" style="display: none;">

trunk/www/common/annotations/inherit.jsp

@@ -30 +30 @@
 --%>
 <%@ page
-
+  import="net.sf.basedb.core.SessionControl"
+  import="net.sf.basedb.core.DbControl"
+  import="net.sf.basedb.core.Item"
+  import="net.sf.basedb.core.Type"
+  import="net.sf.basedb.core.BasicItem"
+  import="net.sf.basedb.core.Permission"
+  import="net.sf.basedb.core.Annotatable"
+  import="net.sf.basedb.core.AnnotationSet"
+  import="net.sf.basedb.core.Annotation"
+  import="net.sf.basedb.core.ItemQuery"
+  import="net.sf.basedb.core.Include"
+  import="net.sf.basedb.core.Nameable"
+  import="net.sf.basedb.core.ItemResultList"
+  import="net.sf.basedb.core.AnnotationType"
+  import="net.sf.basedb.core.PermissionDeniedException"
+  import="net.sf.basedb.core.query.Orders"
+  import="net.sf.basedb.core.query.Hql"
+  import="net.sf.basedb.util.Tree"
+  import="net.sf.basedb.clients.web.Base"
+  import="net.sf.basedb.clients.web.util.HTML"
+  import="net.sf.basedb.clients.web.util.Values"
+  import="java.util.List"
+  import="java.util.Set"
+  import="java.util.HashSet"
+  import="java.util.Map"
+  import="java.util.HashMap"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
-
+<%!
+private void loadParents(Set<AnnotationSet> parentAnnotations, Annotatable item)
+{
+  Set<Annotatable> parents = item.getAnnotatableParents();
+  if (parents == null) return;
+  for (Annotatable parent : parents)
+  {
+    if (parent != null && !parentAnnotations.contains(parent))
+    {
+      if (parent.hasPermission(Permission.USE) && parent.isAnnotated())
+      {
+        AnnotationSet as = parent.getAnnotationSet();
+        parentAnnotations.add(as);
+      }
+      loadParents(parentAnnotations, parent);
+    }
+  }
+}
+
+private String generateJoustTree(Set<AnnotationSet> parentAnnotations, Set<Annotation> inheritedAnnotations, Set<AnnotationSet> inheritedSets)
+{
+  StringBuilder sb = new StringBuilder();
+  String itemIcon = "Folder";
+  String annotationIcon = "Document";
+  
+  for (AnnotationSet as : parentAnnotations)
+  {
+    //Annotatable item = entry.getKey();
+    // AnnotationSet as = item.getAnnotationSet();
+    Annotatable item = null;
+    try
+    {
+      item = as.getItem();
+    }
+    catch (PermissionDeniedException ex)
+    {}
+    
+    boolean setInherited = inheritedSets.contains(as);
+
+    String input = "<input type=\"checkbox\""+
+      " name=\"AS"+as.getId()+"\""+
+      (setInherited ? " checked" : "")+
+      " onclick=\"itemOnToggle(event, "+as.getId()+")\""+
+      ">";
+    String name = item == null ? "<i>- denied -</i>" : 
+      HTML.javaScriptEncode(((Nameable)item).getName()) + " (" + item.getType() + ")";
+    sb.append("var item").append(as.getId());
+    sb.append(" = JoustMenu.addMenuItem(-1"); 
+    sb.append(",'").append(itemIcon).append("'");
+    sb.append(",'").append(input).append(name).append("'");
+    sb.append(", 'itemOnClick(event, ").append(as.getId()).append(")'");
+    sb.append(", '', 'AS").append(as.getId()).append("', true);\n");
+
+    List<Annotation> annotations = as.getAnnotations().list(as.getDbControl());
+    for (Annotation a : annotations)
+    {
+      boolean inherited = inheritedAnnotations.contains(a);
+      AnnotationType at = null;
+      String annotationName = "<i>- denied -</i>";
+      try
+      {
+        at = a.getAnnotationType();
+        annotationName = at.getName();
+      }
+      catch (PermissionDeniedException ex)
+      {}
+      String values = Values.getString(a.getValues(), ", ", true);
+      name = HTML.javaScriptEncode(annotationName +
+        " [" + Values.trimString(values, 20)+"]");
+      input = "<input type=\"checkbox\""+
+        " name=\"A"+a.getId()+"\""+
+        (inherited || setInherited ? " checked" : "")+
+        (setInherited ? " disabled" : "")+
+        " onclick=\"annotationOnToggle(event, "+a.getId()+")\""+
+        ">";
+      sb.append("JoustMenu.addChildItem(item" + as.getId());
+      sb.append(",'").append(annotationIcon).append("'");
+      sb.append(",'").append(input).append(name).append("'");
+      sb.append(", 'annotationOnClick(event, ").append(a.getId()).append(")'");
+      sb.append(", '', 'A").append(a.getId()).append("');\n");
+      sb.append("annotationValues['A").append(a.getId()).append("'] = ");
+      sb.append("'").append(HTML.javaScriptEncode(values)).append("';\n");
+    }
+  }
+  return sb.toString();
+}
+%>
+<%
+final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
+final String ID = sc.getId();
+final float scale = Base.getScale(sc);
+final Item itemType = Item.valueOf(request.getParameter("item_type"));
+final int itemId = Values.getInt(request.getParameter("item_id"));
+
+final DbControl dc = sc.newDbControl();
+ItemResultList<AnnotationType> annotationTypes = null;
+try
+{
+  final Annotatable item = itemId == 0 ? null : (Annotatable)itemType.getById(dc, itemId);
+  
+  // Get all annotated parents and their annotation sets
+  Set<AnnotationSet> parentAnnotations = new HashSet<AnnotationSet>();
+  loadParents(parentAnnotations, item);
+
+//  Map<Annotatable, Set<Annotation>> annotatedParents = new HashMap<Annotatable, Set<Annotation>>();
+//  loadParents(annotatedParents, item);
+  
+  // Get the currently inherited annotations
+  final AnnotationSet as = item.isAnnotated() ? item.getAnnotationSet() : null;
+  Set<Annotation> inheritedAnnotations = null;
+  Set<AnnotationSet> inheritedSets = null;
+  if (as != null)
+  {
+    ItemQuery<Annotation> inheritedQuery = as.getInheritedAnnotations();
+    inheritedQuery.order(Orders.asc(Hql.property("annotationSet")));
+    inheritedQuery.order(Orders.asc(Hql.property("annotationType.name")));
+    inheritedAnnotations = new HashSet<Annotation>(inheritedQuery.list(dc));
+    for (Annotation a : inheritedAnnotations)
+    {
+      AnnotationSet from = a.getAnnotationSet();
+      if (!parentAnnotations.contains(from) && from.hasPermission(Permission.USE))
+      {
+        parentAnnotations.add(from);
+      }
+    }
+    
+    ItemQuery<AnnotationSet> setQuery = as.getInheritedAnnotationSets();
+    inheritedSets = new HashSet<AnnotationSet>(setQuery.list(dc));
+    for (AnnotationSet ias : inheritedSets)
+    {
+      //Annotatable from = ias.getItem();
+      if (!parentAnnotations.contains(ias) && ias.hasPermission(Permission.USE))
+      {
+        parentAnnotations.add(ias);
+      }
+    }
+  }
+  %>
   <base:page type="popup" title="Inherit annotations">
-  <base:head />
-  <base:body >
+  <base:head  scripts="annotations.js,parameters.js,newjoust.js,linkitems.js" styles="parameters.css,newjoust.css">
+  <script language="JavaScript">
+  var annotationValues = new Array();
+  function init()
+  {
+    IconStore.init();
+    <%=generateJoustTree(parentAnnotations, inheritedAnnotations, inheritedSets)%>
+    JoustMenu.alwaysSendOnClickToSelected = true;
+    JoustMenu.draw('joust');
+  }
+  function itemOnClick(event, annotationSetId)
+  {
+    var frm = document.forms['annotations'];
+    frm['AS'+annotationSetId].checked = !frm['AS'+annotationSetId].checked;
+    itemOnToggle(event, annotationSetId);
+  }
+  
+  function itemOnToggle(event, annotationSetId)
+  {
+    //alert('itemOnClick: '+annotationSetId);
+    var frm = document.forms['annotations'];
+
+    var linkedItem = Link.getItem('AS', annotationSetId);
+    if (!linkedItem)
+    {
+      linkedItem = new Item('AS', annotationSetId);
+    }
+    var checked = frm['AS'+annotationSetId].checked;
+    linkedItem.action += checked ? 1 : -1;
+
+    frm['AS'+annotationSetId].checked = checked;
+    var menuItem = JoustMenu.menuItems['AS'+annotationSetId];
+    var childIndex = menuItem.firstChildIndex;
+    while (childIndex != -1)
+    {
+      var childMenuItem = JoustMenu.menuItems[childIndex];
+      frm[childMenuItem.externalId].checked = checked;
+      frm[childMenuItem.externalId].disabled = checked;
+      childIndex = childMenuItem.nextItemIndex;
+      
+      var annotationId = childMenuItem.externalId.substr(1);
+      annotationItem = Link.getItem('A', annotationId);
+      if (!annotationItem) annotationItem = new Item('A', annotationId);
+      annotationItem.action = -1;
+    }
+    event.cancelBubble = true;
+  }
+  
+  function annotationOnClick(event, annotationId)
+  {
+    var frm = document.forms['annotations'];
+    var annotation = frm['A'+annotationId];
+    if (!annotation.disabled)
+    {
+      annotation.checked = !annotation.checked;
+      annotationOnToggle(event, annotationId);
+    }
+    document.getElementById('annotationValues').innerHTML = annotationValues['A'+annotationId];
+  }
+  
+  function annotationOnToggle(event, annotationId)
+  {
+    //alert('itemOnClick: '+annotationSetId);
+    var frm = document.forms['annotations'];
+
+    var linkedItem = Link.getItem('A', annotationId);
+    if (!linkedItem)
+    {
+      linkedItem = new Item('A', annotationId);
+    }
+    var checked = frm['A'+annotationId].checked;
+    linkedItem.action += checked ? 1 : -1;
     
-  TODO
-  
+    frm['A'+annotationId].checked = checked;
+    event.cancelBubble = true;
+  }
+
+  </script>
+  </base:head>
+  <base:body onload="init()" style="background: #E0E0E0;">
+
+  <form name="annotations">
+  <table class="form" cellspacing="2" border="0" cellpadding="0" width="100%">
+  <tr valign="top">
+  <td width="50%">
+    <div id="joust" class="joust parameterlist" 
+      style="height: <%=(int)(scale*320)%>px;">
+    </div>
+  </td>
+  <td width="50%">
+    <b>Annotation values</b>
+    <div id="annotationValues">
+    </div>
+  </td>
+  </tr>
+  </table>
+      
+  </form>
   </base:body>
   </base:page>
-
+  <%
+}
+finally
+{
+  if (dc != null) dc.close();
+}
+%>
+

trunk/www/common/annotations/list_annotations.jsp

@@ -33 +33 @@
   import="net.sf.basedb.core.AnnotationType"
   import="net.sf.basedb.core.AnnotationSet"
+  import="net.sf.basedb.core.Annotation"
   import="net.sf.basedb.core.Annotatable"
+  import="net.sf.basedb.core.Nameable"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.PermissionDeniedException"
+  import="net.sf.basedb.core.query.Orders"
+  import="net.sf.basedb.core.query.Hql"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.util.HTML"
@@ -58 +62 @@
   final ItemResultList<AnnotationType> annotationTypes = annotationTypeQuery.list(dc);
   final Annotatable item = (Annotatable)itemType.getById(dc, itemId);
+
+  final AnnotationSet as = item.isAnnotated() ? item.getAnnotationSet() : null;
+  ItemResultList<Annotation> inheritedAnnotations = null;
+  if (as != null)
+  {
+    ItemQuery<Annotation> inheritedQuery = as.getAllInheritedAnnotations();
+    inheritedQuery.order(Orders.asc(Hql.property("annotationSet")));
+    inheritedQuery.order(Orders.asc(Hql.property("annotationType.name")));
+    inheritedAnnotations = inheritedQuery.list(dc);
+  }
   %>
 
@@ -63 +77 @@
   <base:head />
   <base:body>
-
       <%
       if (annotationTypes.size() == 0)
@@ -69 +82 @@
         %>
         <h4>Primary annotations</h4>
-        No annotation types has been defined for this type of item.
+        No annotation types has been defined for this type of item 
+        (or you don't have permission to view them).
         <%
       }
@@ -98 +112 @@
             <tbl:rows>
             <%
-            AnnotationSet as = item.isAnnotated() ? item.getAnnotationSet() : null;
             for (AnnotationType at : annotationTypes)
             {
@@ -120 +133 @@
       %>
 
-      <h4>Inherited annotations</h4>
-      TODO
+      <%
+      if (inheritedAnnotations == null || inheritedAnnotations.size() == 0)
+      {
+        %>
+        <h4>Inherited annotations</h4>
+        No annotations are inherited by this item.
+        <%
+      }
+      else
+      {
+        %>
+        <h4 class="docked">Inherited annotations</h4>
+        <tbl:table
+          id="inheritedAnnotations"
+          clazz="itemlist"
+          columns="all"
+          >
+          <tbl:columndef 
+            id="annotation"
+            title="Annotation"
+          />
+          <tbl:columndef 
+            id="item"
+            title="From item"
+          />
+          <tbl:columndef 
+            id="values"
+            title="Values"
+          />
+          <tbl:columndef 
+            id="description"
+            title="Description"
+          />
+          <tbl:data>
+            <tbl:columns>
+            </tbl:columns>
+            <tbl:rows>
+            <%
+            String denied = "<i>- denied -</i>";
+            for (Annotation a : inheritedAnnotations)
+            {
+              AnnotationType at = null;
+              String name = denied;
+              String description = "";
+              try
+              {
+                at = a.getAnnotationType();
+                name = HTML.encodeTags(at.getName());
+                description = HTML.encodeTags(at.getDescription());
+              }
+              catch (PermissionDeniedException ex)
+              {}
+              Nameable aItem = null;
+              String itemName = denied;
+              try
+              {
+                aItem = (Nameable)a.getAnnotationSet().getItem();
+                itemName = HTML.encodeTags(aItem.getName() + " (" + aItem.getType() + ")");
+              }
+              catch (PermissionDeniedException ex)
+              {}
+              List<?> values = a.getValues();
+              %>
+              <tbl:row>
+                <tbl:cell column="annotation"><%=name%></tbl:cell>
+                <tbl:cell column="item"><%=itemName%></tbl:cell>
+                <tbl:cell column="values"><%=values == null || values.size() == 0 ? "<i>- no values -</i>" : Values.getString(values, ", ", true)%></tbl:cell>
+                <tbl:cell column="description"><%=description%></tbl:cell>
+              </tbl:row>
+              <%
+            }
+            %>
+            </tbl:rows>
+          </tbl:data>
+        </tbl:table>
+        <%
+      }
+      %>
       </div>
 

trunk/www/common/plugin/configure.jsp

@@ -145 +145 @@
             }
             icon = "<img id=\"icon_"+name+"\" src=\"../../images/"+icon+"\" class=\"icon\">";
-            sb.append("<div class=\"pluginparameter\" id=\"prompt_"+name+"\" onclick=\"parametersOnClick('"+name+"')\" onmouseover=\"Main.addClass(this, 'hover')\" onmouseout=\"Main.removeClass(this, 'hover')\" title=\""+fullLabel+"\">"+icon+label+"</div>");
+            sb.append("<div class=\"param\" id=\"prompt_"+name+"\" onclick=\"parametersOnClick('"+name+"')\" onmouseover=\"Main.addClass(this, 'hover')\" onmouseout=\"Main.removeClass(this, 'hover')\" title=\""+fullLabel+"\">"+icon+label+"</div>");
             %>
             var values = new Array();

trunk/www/include/scripts/annotations.js

@@ -3 +3 @@
   BioArray Software Environment (BASE) - http://base.thep.lu.se/
   Copyright (C) 2002-2004 Lao Saal, Carl Troein,
-  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
+  Johan Vallon-Christersson, Jari H??kkinen, Nicklas Nordborg
 
   This file is part of BASE.
@@ -71 +71 @@
   this.addInheritedAnnotationsToForm = function(theFrame, frm)
   {
-    // TODO
+    var addedAnnotations = theFrame.Link.getActionIds(1, 'A');
+    var removedAnnotations = theFrame.Link.getActionIds(-1, 'A');
+    var addedAnnotationSets = theFrame.Link.getActionIds(1, 'AS');
+    var removedAnnotationSets = theFrame.Link.getActionIds(-1, 'AS');
+
+    if (frm.addedAnnotations)
+    {
+      frm.addedAnnotations.value = addedAnnotations.join(',');
+    }
+    else
+    {
+      Forms.createHidden(frm, 'addedAnnotations', addedAnnotations.join(','));
+    }
+    if (frm.removedAnnotations)
+    {
+      frm.removedAnnotations.value = removedAnnotations.join(',');
+    }
+    else
+    {
+      Forms.createHidden(frm, 'removedAnnotations', removedAnnotations.join(','));
+    }
+    if (frm.addedAnnotationSets)
+    {
+      frm.addedAnnotationSets.value = addedAnnotationSets.join(',');
+    }
+    else
+    {
+      Forms.createHidden(frm, 'addedAnnotationSets', addedAnnotationSets.join(','));
+    }
+    if (frm.removedAnnotationSets)
+    {
+      frm.removedAnnotationSets.value = removedAnnotationSets.join(',');
+    }
+    else
+    {
+      Forms.createHidden(frm, 'removedAnnotationSets', removedAnnotationSets.join(','));
+    }
   }
-  
 }
 

trunk/www/include/scripts/linkitems.js

@@ -3 +3 @@
   BioArray Software Environment (BASE) - http://base.thep.lu.se/
   Copyright (C) 2002-2004 Lao Saal, Carl Troein,
-  Johan Vallon-Christersson, Jari Häkkinen, Nicklas Nordborg
+  Johan Vallon-Christersson, Jari H?kkinen, Nicklas Nordborg
 
   This file is part of BASE.

trunk/www/include/scripts/newjoust.js

@@ -40 +40 @@
 function JoustMenuClass()
 {
+  this.alwaysSendOnClickToSelected = false;
   this.firstItemIndex = -1;
   this.lastItemIndex = -1;
@@ -101 +102 @@
     @return The index of the new item
   */
-  this.addMenuItem = function(afterItemIndex, iconName, text, onclick, tooltip, externalId) 
+  this.addMenuItem = function(afterItemIndex, iconName, text, onclick, tooltip, externalId, isOpen) 
   {
     var afterItem = this.menuItems[afterItemIndex];
@@ -112 +113 @@
     var insertIndex = this.menuItems.length;
 
-    var menuItem = new MenuItem(this, insertIndex, iconName, text, onclick, tooltip, nextItemIndex, previousItemIndex, parentItemIndex, externalId);
+    var menuItem = new MenuItem(this, insertIndex, iconName, text, onclick, tooltip, nextItemIndex, previousItemIndex, parentItemIndex, externalId, isOpen);
     this.menuItems[insertIndex] = menuItem;
     if (!this.menuItems[externalId]) this.menuItems[externalId] = menuItem;
@@ -147 +148 @@
     @return The index of the new item
   */
-  this.addChildItem = function(parentItemIndex, iconName, text, onclick, tooltip, externalId)
+  this.addChildItem = function(parentItemIndex, iconName, text, onclick, tooltip, externalId, isOpen)
   {
     var parentItem = this.menuItems[parentItemIndex];
     if (!parentItem)
     {
-      return this.addMenuItem(-1, iconName, text, onclick, tooltip);
+      return this.addMenuItem(-1, iconName, text, onclick, tooltip, externalId, isOpen);
     }
     var afterItem = this.menuItems[parentItem.lastChildIndex];
     if (afterItem)
     {
-      parentItem.lastChildIndex = this.addMenuItem(parentItem.lastChildIndex, iconName, text, onclick, tooltip, externalId);
+      parentItem.lastChildIndex = this.addMenuItem(parentItem.lastChildIndex, iconName, text, onclick, tooltip, externalId, isOpen);
       return parentItem.lastChildIndex;
     }
     var insertIndex = this.menuItems.length;
-    var menuItem = new MenuItem(this, insertIndex, iconName, text, onclick, tooltip, -1, -1, parentItemIndex, externalId);
+    var menuItem = new MenuItem(this, insertIndex, iconName, text, onclick, tooltip, -1, -1, parentItemIndex, externalId, isOpen);
     this.menuItems[insertIndex] = menuItem;
     if (!this.menuItems[externalId]) this.menuItems[externalId] = menuItem;
@@ -213 +214 @@
   {
     var menuItem = this.menuItems[menuItemIndex];
-    if (!menuItem || menuItemIndex == this.selectedItemIndex) return;
+    if (!menuItem) return;
     
-    if (this.selectedItemIndex != -1)
-    {
-      var current = this.menuItems[this.selectedItemIndex];
-      current.isSelected = false;
-      this.updateIconsAndText(this.selectedItemIndex);
-    }
-    menuItem.isSelected = true;
-    if (menuItem.parentItemIndex != -1) this.open(menuItem.parentItemIndex);
-    this.selectedItemIndex = menuItemIndex;
-    this.updateIconsAndText(menuItemIndex);
-    eval(menuItem.onclick);
+    if (menuItemIndex != this.selectedItemIndex)
+    {
+      if (this.selectedItemIndex != -1)
+      {
+        var current = this.menuItems[this.selectedItemIndex];
+        current.isSelected = false;
+        this.updateIconsAndText(this.selectedItemIndex);
+      }
+      menuItem.isSelected = true;
+      if (menuItem.parentItemIndex != -1) this.open(menuItem.parentItemIndex);
+      this.selectedItemIndex = menuItemIndex;
+      this.updateIconsAndText(menuItemIndex);
+      eval(menuItem.onclick);
+    }
+    else if (this.alwaysSendOnClickToSelected)
+    {
+      eval(menuItem.onclick);
+    }
   }
 
@@ -279 +287 @@
   @param parentItemIndex The index of the parent menu item, or -1 if this is on the root level
 */
-function MenuItem(menu, index, iconName, text, onclick, tooltip, nextItemIndex, previousItemIndex, parentItemIndex, externalId)
+function MenuItem(menu, index, iconName, text, onclick, tooltip, nextItemIndex, previousItemIndex, parentItemIndex, externalId, isOpen)
 {
   this.menu = menu;
@@ -291 +299 @@
   this.parentItemIndex = parentItemIndex;
   this.externalId = externalId;
-  this.isOpen = false;
+  this.isOpen = isOpen;
   this.isSelected = false;
   this.firstChildIndex = -1;

trunk/www/include/styles/parameters.css

@@ -41 +41 @@
 }
 
-.parameterlist .pluginparameter {
+.parameterlist .param {
 
 }
 
-.parameterlist .icon {
+.parameterlist .param .icon {
   padding-right: 4px;
 }
-.parameterlist .hover {
+.parameterlist .param.hover {
   background: #E0E0E0;
   cursor: pointer;
 }
 
-.parameterlist .selected {
+.parameterlist .param.selected {
   color: #FFFFFF;
   background: #445577;

trunk/www/views/rawbioassays/view_rawbioassay.jsp

@@ -294 +294 @@
       <tr>
         <td class="prompt">Protocol</td>
-        <td><%=Base.getEncodedName(currentProtocol, !readCurrentProtocol)%></td>
+        <td><%=Base.getEncodedName(currentProtocol, !readCurrentProtocol, "../../admin/protocols/index.jsp?ID="+ID)%></td>
       </tr>
       <tr>
         <td class="prompt">Scan</td>
-        <td><%=Base.getEncodedName(currentScan, !readCurrentScan)%></td>
+        <td><%=Base.getEncodedName(currentScan, !readCurrentScan, "../scans/index.jsp?ID="+ID)%></td>
       </tr>
       <tr>
         <td class="prompt">Software</td>
-        <td><%=Base.getEncodedName(currentSoftware, !readCurrentSoftware)%></td>
+        <td><%=Base.getEncodedName(currentSoftware, !readCurrentSoftware, "../../admin/sfotware/index.jsp?ID="+ID)%></td>
       </tr>
       <tr>
         <td class="prompt">Array design</td>
-        <td><%=Base.getEncodedName(currentArrayDesign, !readCurrentArrayDesign)%></td>
+        <td><%=Base.getEncodedName(currentArrayDesign, !readCurrentArrayDesign, "../../lims/arraydesigns/index.jsp?ID="+ID)%></td>
       </tr>
       <tr>

trunk/www/views/scans/view_scan.jsp

@@ -249 +249 @@
       <tr>
         <td class="prompt">Hybridization</td>
-        <td><%=Base.getEncodedName(currentHybridization, !readCurrentHybridization)%></td>
+        <td><%=Base.getEncodedName(currentHybridization, !readCurrentHybridization, "../hybridizations/index.jsp?ID="+ID)%></td>
       </tr>
       <tr>
         <td class="prompt">Scanner</td>
-        <td><%=Base.getEncodedName(currentScanner, !readCurrentScanner)%></td>
+        <td><%=Base.getEncodedName(currentScanner, !readCurrentScanner, "../../admin/hardware/index.jsp?ID="+ID)%></td>
       </tr>
       <tr>
         <td class="prompt">Protocol</td>
-        <td><%=Base.getEncodedName(currentProtocol, !readCurrentProtocol)%></td>
+        <td><%=Base.getEncodedName(currentProtocol, !readCurrentProtocol, "../../admin/protocol/index.jsp?ID="+ID)%></td>
       </tr>
       <tr>