Changeset 5132

Timestamp:

Oct 14, 2009, 1:55:03 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1404: Use cached annotations in "item overview"

This should fix the ticket. But there are so many different error-handling cases to test that I want to keep it open a bit more...

Location:

trunk

Files:

• src/core/net/sf/basedb/core/snapshot/AnnotationFilter.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/GenericOverview.java (modified) (4 diffs)
• src/core/net/sf/basedb/util/overview/Node.java (modified) (4 diffs)
• src/core/net/sf/basedb/util/overview/OverviewContext.java (modified) (2 diffs)
• src/core/net/sf/basedb/util/overview/loader/AnnotationLoader.java (modified) (3 diffs)
• src/core/net/sf/basedb/util/overview/validator/AnnotationValidator.java (modified) (4 diffs)
• www/common/overview/info.jsp (modified) (11 diffs)

trunk/src/core/net/sf/basedb/core/snapshot/AnnotationFilter.java

@@ -67 +67 @@
     @param a A specific annotation, or null to match any annotation
   */
-  public void setAnnotationType(Annotation a)
+  public void setAnnotation(Annotation a)
   {
     this.annotationId = a == null ? 0 : a.getId();

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

@@ -35 +35 @@
 import net.sf.basedb.core.query.Order;
 import net.sf.basedb.core.query.Orders;
+import net.sf.basedb.core.snapshot.SnapshotManager;
 import net.sf.basedb.util.overview.cache.NodeCache;
 import net.sf.basedb.util.overview.loader.NodeLoader;
@@ -92 +93 @@
   private final Project project;
   private final BasicItem rootItem;
+  private final SnapshotManager snapshotManager;
   private Node rootNode;
   private Map<String, Node> allNodes;
@@ -114 +116 @@
     this.rootItem = rootItem;
     this.project = project;
+    this.snapshotManager = new SnapshotManager();
     reset(dc);
   }
@@ -137 +140 @@
   {
     return nodeValidatorFactory;
+  }
+
+  /**
+    Get the current snapshot manager.
+    @since 2.14
+  */
+  @Override
+  public SnapshotManager getSnapshotManager()
+  {
+    return snapshotManager;
   }
 

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

@@ -22 +22 @@
 package net.sf.basedb.util.overview;
 
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.LinkedList;
 import java.util.List;
@@ -51 +53 @@
 */
 public class Node
+  implements Comparable<Node>
 {
   private final String name;
@@ -310 +313 @@
   
   /**
+    Sorts the list of child nodes.
+    @param comparator A comparator that determines the sort order, 
+      if not specifed, they children are sorted according to their
+      title
+    @since 2.14
+   */
+  public void sortChildren(Comparator<? super Node> comparator)
+  {
+    if (children == null) return;
+    Collections.sort(children, comparator);
+  }
+  
+  /**
     Sets a flag to indicate that all children has been loaded.
     @since 2.10
@@ -495 +511 @@
   }
   
+  @Override
+  public int compareTo(Node o)
+  {
+    return title.compareTo(o.title);
+  }
+
+  
   public String toString()
   {

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

@@ -27 +27 @@
 import net.sf.basedb.core.Project;
 import net.sf.basedb.core.query.Order;
+import net.sf.basedb.core.snapshot.SnapshotManager;
 import net.sf.basedb.util.overview.cache.NodeCache;
 import net.sf.basedb.util.overview.loader.NodeLoader;
@@ -60 +61 @@
   public NodeValidatorFactory getNodeValidatorFactory();
 
+  /**
+    Get the snapshot manager that is used to load annotation
+    values.
+    @since 2.14
+  */
+  public SnapshotManager getSnapshotManager();
+  
   /**
     Get the project the overview is using as the "current" project.

trunk/src/core/net/sf/basedb/util/overview/loader/AnnotationLoader.java

@@ -22 +22 @@
 package net.sf.basedb.util.overview.loader;
 
+import java.util.List;
+
 import net.sf.basedb.core.Annotatable;
 import net.sf.basedb.core.Annotation;
@@ -27 +29 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Item;
-import net.sf.basedb.core.ItemQuery;
-import net.sf.basedb.core.ItemResultIterator;
 import net.sf.basedb.core.PermissionDeniedException;
 import net.sf.basedb.core.Protocol;
-import net.sf.basedb.core.query.Hql;
-import net.sf.basedb.core.query.Orders;
+import net.sf.basedb.core.snapshot.AnnotationSnapshot;
+import net.sf.basedb.core.snapshot.SnapshotManager;
 import net.sf.basedb.util.overview.OverviewContext;
 import net.sf.basedb.util.overview.node.AnnotationNameGenerator;
@@ -82 +82 @@
       folderNode = new Node("annotations", "Annotations", parentNode, ChildNodeDirection.NONE);
       AnnotationSet as = parent.getAnnotationSet();
-      
-      // Primary annotations
-      ItemQuery<Annotation> query = context.initQuery(as.getAnnotations(), "annotationType.name");
-      ItemResultIterator<Annotation> it = query.iterate(dc);
-      while (it.hasNext())
+      SnapshotManager snapshotManager = context.getSnapshotManager();
+            
+      List<AnnotationSnapshot> all = snapshotManager.findAnnotations(dc, parent, null, true);
+      for (AnnotationSnapshot a : all)
       {
-        Annotation a = it.next();
-              
+        Annotation ann = a.getAnnotation(dc);
         // Annotations that are protocol parameters are handled by ProtocolParameterLoader        
-        if (protocol != null && protocol.isParameter(a))
+        if (!a.isInherited() && protocol != null && protocol.isParameter(ann))
         {
           /* #### CONTINUE-STATEMENT #### */
           continue;       
         }
-        createItemNode(nf, a, null, false, folderNode, ChildNodeDirection.NONE);
+        createItemNode(nf, ann, null, false, folderNode, ChildNodeDirection.NONE);
       }
-      
-      // Inherited annotations
-      query = context.initQuery(as.getAllInheritedAnnotations(), 
-          Orders.asc(Hql.property("at", "name")));
-      query.join(Hql.innerJoin(null, "annotationType", "at", true));
-      it = query.iterate(dc);
-      while (it.hasNext())
-      {
-        Annotation a = it.next();
-        createItemNode(nf, a, null, false, folderNode, ChildNodeDirection.NONE);
-      }
+      folderNode.sortChildren(null);
     }
     postValidateFolder(nf, folderNode, parentNode, false);

trunk/src/core/net/sf/basedb/util/overview/validator/AnnotationValidator.java

@@ -28 +28 @@
 import net.sf.basedb.core.Annotatable;
 import net.sf.basedb.core.Annotation;
-import net.sf.basedb.core.AnnotationSet;
 import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.BasicItem;
@@ -38 +37 @@
 import net.sf.basedb.core.ItemResultIterator;
 import net.sf.basedb.core.PermissionDeniedException;
+import net.sf.basedb.core.snapshot.AnnotationFilter;
+import net.sf.basedb.core.snapshot.AnnotationSnapshot;
+import net.sf.basedb.core.snapshot.SnapshotManager;
 import net.sf.basedb.util.overview.Fix;
 import net.sf.basedb.util.overview.OverviewContext;
@@ -85 +87 @@
     Annotatable parent = (Annotatable)parentNode.getItem(dc);
     Item parentItemType = parentNode.getItemType();
-    AnnotationSet annotationSet = parent.getAnnotationSet();
     
     Annotation a = (Annotation)node.getItem();
-    boolean isPrimary = a.belongsTo(annotationSet);
+    SnapshotManager manager = context.getSnapshotManager();
+    // The primary use of the snapshot is to load the values if the annotation is a primary annotation
+    // Thus, we do not search inherited annotations
+    List<AnnotationSnapshot> snapshots = manager.findAnnotations(dc, parent, new AnnotationFilter(a), false);
+    AnnotationSnapshot snapshot = snapshots.size() > 0 ? snapshots.get(0) : null;
+    boolean isPrimary = snapshot != null && !snapshot.isInherited();
 
     AnnotationType at = null;
@@ -120 +126 @@
         try
         {
-          List<?> values = a.getValues();
+          List<?> values = snapshot.getValues();
           if (values != null)
           {

trunk/www/common/overview/info.jsp

@@ -31 +31 @@
   import="net.sf.basedb.core.AnnotationType"
   import="net.sf.basedb.core.Annotation"
+  import="net.sf.basedb.core.Protocol"
   import="net.sf.basedb.core.FileStoreEnabled"
   import="net.sf.basedb.core.FileSetMember"
@@ -39 +40 @@
   import="net.sf.basedb.core.PermissionDeniedException"
   import="net.sf.basedb.core.ItemNotFoundException"
+  import="net.sf.basedb.core.snapshot.SnapshotManager"
+  import="net.sf.basedb.core.snapshot.AnnotationSetSnapshot"
+  import="net.sf.basedb.core.snapshot.AnnotationSnapshot"
+  import="net.sf.basedb.core.snapshot.AnnotationTypeFilter"
+  import="net.sf.basedb.core.snapshot.AnnotationFilter"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.util.HTML"
@@ -92 +98 @@
 try
 {
-  GenericOverview overview = OverviewUtil.getCurrentOverview(sc);
+  final GenericOverview overview = OverviewUtil.getCurrentOverview(sc);
+  final SnapshotManager snapshotManager = overview.getSnapshotManager();
+  final AnnotationTypeFilter annotationTypeFilter = new AnnotationTypeFilter();
+  final AnnotationFilter annotationFilter = new AnnotationFilter();
   ValidationOptions options = overview.getValidationOptions();
   String nodeId = request.getParameter("nodeId");
@@ -278 +287 @@
       
       <%
-      List<Annotation> annotations = null;
+      List<AnnotationSnapshot> annotations = new LinkedList<AnnotationSnapshot>();
       String annotationsTitle = "";
       Annotatable annotatable = null;
@@ -285 +294 @@
         Annotation a = (Annotation)item;
         dc.reattachItem(a, false);
-        annotations = Collections.singletonList(a);
-        try
-        {
-          annotatable = a.getAnnotationSet().getItem();
-        }
-        catch (Throwable t)
-        {}
+        AnnotationSetSnapshot snapshot = snapshotManager.getSnapshot(dc, a.getAnnotationSet().getId());
+        annotationFilter.setAnnotationType(a);
+        annotations.addAll(snapshotManager.findAnnotations(dc, snapshot, annotationFilter, true));
+        
+        // Find the annotatable parent node
+        Node parentNode = node;
+        while (parentNode != null)
+        {
+          BasicItem parentItem = parentNode.getItem();
+          if (parentItem instanceof Annotatable)
+          {
+            annotatable = (Annotatable)parentItem;
+            break;
+          }
+          parentNode = parentNode.getParent();
+        }
         annotationsTitle = "Annotation values";
       }
@@ -301 +319 @@
         {
           BasicItem parentItem = parentNode.getItem();
-          if (parentItem instanceof Annotatable)
+          if (parentItem instanceof Annotatable && !(parentItem instanceof Protocol))
           {
             annotatable = (Annotatable)parentItem;
@@ -307 +325 @@
             if (annotatable.isAnnotated())
             {
-              annotations = annotatable.getAnnotationSet().findAnnotations(dc, (AnnotationType)item, true);
+              annotationTypeFilter.setAnnotationType((AnnotationType)item);
+              annotations.addAll(snapshotManager.findAnnotations(dc, annotatable, annotationTypeFilter, true));
             }
             annotationsTitle = "Annotation values";
@@ -322 +341 @@
         {
           dc.reattachItem((BasicItem)annotatable, false);
-  
-          // 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 && protocolNode.getChildren() != null) nodes.addAll(protocolNode.getChildren());
-          if (nodes.size() > 0)
-          {
-            annotations = new LinkedList<Annotation>();
-            for (Node n : nodes)
-            {
-              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));
-              }
-            }
-          }
+          annotations.addAll(snapshotManager.findAnnotations(dc, annotatable, null, true));
         }
       }
@@ -353 +350 @@
         <table border=0 cellspacing=0 cellpadding=0>
         <%
-        for (Annotation a : annotations)
-        {
-          a = Annotation.getById(dc, a.getId());
+        for (AnnotationSnapshot snapshot : annotations)
+        {
+          Annotation a = snapshot.getAnnotation(dc);
           String unitSymbol = a.hasUnit() ? "&nbsp;" + a.getUnitSymbol(null) : "";
           AnnotationType at = null;
@@ -361 +358 @@
           try
           {
-            at = a.getAnnotationType();
+            at = snapshot.getAnnotationType(dc);
           }
           catch (Throwable t)
@@ -367 +364 @@
           try
           {
-            annotationOwner = a.getAnnotationSet().getItem();
+            annotationOwner = snapshot.getItem(dc);
           }
           catch (Throwable t)