Changeset 6728

Timestamp:

Feb 13, 2015, 9:00:01 AM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #1910: Disable annotation inheritance for annotation types

Added AnnotationType.getDisableInheritance() which is a flag that if set will disable the inheritance. Schema version is updated and all existing annotation types are set to FALSE.

A permission check when calling AnnotationSet.inheritAnnotation has been implemented and setting the flag with AnnotationType.setDisableInheritance() will trigger a removal of existing inherited annotations.

This should complete the core part of the functionality but we also need some supporting functionality (mainly in the gui).

Location:

trunk

Files:

• src/core/common-queries.xml (modified) (1 diff)
• src/core/net/sf/basedb/core/AnnotationSet.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/AnnotationType.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/Install.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Update.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/data/AnnotationTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/snapshot/SnapshotManager.java (modified) (1 diff)
• www/admin/annotationtypes/edit_annotationtype.jsp (modified) (1 diff)
• www/admin/annotationtypes/index.jsp (modified) (1 diff)
• www/admin/annotationtypes/list_annotationtypes.jsp (modified) (2 diffs)
• www/admin/annotationtypes/view_annotationtype.jsp (modified) (1 diff)

trunk/src/core/common-queries.xml

@@ -1949 +1949 @@
   </query>
   
+  <query id="LOAD_ANNOTATIONSET_INHERITING_ANNOTATIONTYPE" type="SQL">
+    <sql>
+      SELECT [ia].[annotationset_id] FROM [InheritedAnnotations] [ia]
+      INNER JOIN [Annotations] [a] ON [a].[id] = [ia].[annotation_id]
+      WHERE [a].[annotationtype_id] = :annotationType
+    </sql>
+    <description>
+      An SQL query that load the ID of all annotation sets that
+      are inheriting a given annotation type.
+    </description>
+  </query>
+  
+  <query id="DELETE_INHERITED_ANNOTATIONS" type="SQL">
+    <sql>
+      DELETE FROM [InheritedAnnotations]
+      WHERE [annotation_id] IN (
+        SELECT [id] FROM [Annotations] WHERE [annotationtype_id] = :annotationType
+      )
+    </sql>
+    <description>
+      An SQL query that delete all directly inherited annotations of the specified 
+      annotation type.
+    </description>
+  </query>
+  
   <query id="UPDATE_BYTES_FOR_EXPERIMENT" type="HQL">
     <sql>

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

@@ -755 +755 @@
     @throws PermissionDeniedException If the logged in user
       doesn't have write permission for this annotation set or
-      use permission for the annotation
+      use permission for the annotation or if the annotation type is not
+      enabled for inheritance
     @throws InvalidDataException If the annotation is null
   */
@@ -764 +765 @@
     if (annotation == null) throw new InvalidUseOfNullException("annotation");
     annotation.checkPermission(Permission.USE);
+    if (annotation.getAnnotationType().getDisableInheritance())
+    {
+      throw new PermissionDeniedException("Inheritance has been disabled on " + annotation.getAnnotationType());
+    }
     if (getData().getInherited().add(annotation.getData()))
     {

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

@@ -913 +913 @@
   }
 
-  
+  /**
+    If this flag is set, annotations of this type can't be inherited
+    to child items. Use this to prevent sensitive data from being used
+    in other contexts.
+    @since 3.5
+  */
+  public boolean getDisableInheritance()
+  {
+    return getData().getDisableInheritance();
+  }
+  
+  /**
+    If this flag is set, annotations of this type can't be inherited
+    to child items. Use this to prevent sensitive data from being used
+    in other contexts. Changing this from FALSE to TRUE will automatically
+    trigger a database action that remove all existing inherited annotations
+    of this type.
+    @throws PermissionDeniedException If the logged in user doesn't
+      have write permission
+    @since 3.5
+  */
+  public void setDisableInheritance(boolean disableInheritance)
+    throws PermissionDeniedException
+  {
+    checkPermission(Permission.WRITE);
+    if (disableInheritance && !getData().getDisableInheritance() && isInDatabase())
+    {
+      getDbControl().addTransactionalAction(new RemoveInheritedAnnotationsAction(this));
+    }
+    getData().setDisableInheritance(disableInheritance);
+  }
+
   /**
     Get the minumum allowed value for an {@link Type#INT} or {@link Type#LONG}
@@ -1408 +1439 @@
   }
   
+  static class RemoveInheritedAnnotationsAction
+    implements TransactionalAction
+  {
+    private final AnnotationType at;
+    
+    public RemoveInheritedAnnotationsAction(AnnotationType at)
+    {
+      this.at = at;
+    }
+
+    @Override
+    public void onBeforeCommit() 
+    {
+      // Verify that the disable flag is still set
+      if (at.getDisableInheritance())
+      {
+        DbControl dc = at.getDbControl();
+        org.hibernate.Session session = dc.getHibernateSession();
+        
+        org.hibernate.Query query = HibernateUtil.getPredefinedSQLQuery(session, "LOAD_ANNOTATIONSET_INHERITING_ANNOTATIONTYPE");
+        query.setInteger("annotationType", at.getId());
+        List<Integer> ids = HibernateUtil.loadList(Integer.class, query, dc.getSessionControl());
+        SnapshotManager.removeSnapshots(ids);
+        
+        query = HibernateUtil.getPredefinedSQLQuery(session, "DELETE_INHERITED_ANNOTATIONS");
+        query.setInteger("annotationType", at.getId());
+        query.executeUpdate();
+      }
+    }
+
+    // Nothing to do
+    @Override
+    public void onAfterCommit() 
+    {}
+
+    // Nothing to do
+    @Override
+    public void onRollback() 
+    {}
+    
+  }
 }

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

@@ -118 +118 @@
     method.
   */
-  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(118).intValue();
+  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(119).intValue();
   
   public static synchronized int createTables(SchemaGenerator.Mode mode, ProgressReporter progress,

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

@@ -210 +210 @@
     </td>
   </tr>
+  <tr>
+    <td>119</td>
+    <td>
+      Added {@link AnnotationTypeData#getDisableInheritance()}.
+      The update will set the value to FALSE for all existing annotation types.
+    </td>
+  </tr>
   </table>
 
@@ -331 +338 @@
       }
       
-      if (schemaVersion < 118)
-      {
-        if (progress != null) progress.display((int)(progress_current), "--Updating schema version: " + schemaVersion + " -> 118...");
-        // Schemaversion 118 only updates the version number
-        schemaVersion = setSchemaVersionInTransaction(session, 118);
+      if (schemaVersion < 119)
+      {
+        if (progress != null) progress.display((int)(progress_current), "--Updating schema version: " + schemaVersion + " -> 119...");
+        // Schemaversion 118-119 only updates the version number
+        schemaVersion = setSchemaVersionInTransaction(session, 119);
         progress_current += progress_step;
       }
@@ -568 +575 @@
           "SET sv.appId = :appId WHERE sv.appId IS NULL");
         query.setString("appId", SchemaVersionData.BASE_APP_ID);
+        query.executeUpdate();
+      }
+      
+      if (schemaVersion < 119)
+      {
+        // Set disableInheritance=false on all annotation types
+        org.hibernate.Query query = HibernateUtil.createQuery(session, 
+          "UPDATE AnnotationTypeData at " +
+          "SET at.disableInheritance = false " +
+          "WHERE at.disableInheritance IS NULL");
         query.executeUpdate();
       }

trunk/src/core/net/sf/basedb/core/data/AnnotationTypeData.java

@@ -264 +264 @@
   }
 
+  private boolean disableInheritance;
+  /**
+    If this flag is set, annotation of this type can't be inherited.
+    @since 3.5
+    @hibernate.property column="`disable_inherit`" type="boolean" not-null="true"
+  */
+  public boolean getDisableInheritance()
+  {
+    return disableInheritance;
+  }
+  public void setDisableInheritance(boolean disableInheritance)
+  {
+    this.disableInheritance = disableInheritance;
+  }
+  
   private Set<Integer> itemTypes;
   /**

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

@@ -76 +76 @@
     String cacheKey = getCacheKey(annotationSetId);
     return cache.delete(cacheKey, 1000);
+  }
+  
+  /**
+    Removes a list of snapshots from the static cache.
+    @param annotationSetIds A list with IDs of annotation set  s
+    @return The number of successfully removed snapshots
+    @since 3.5
+  */
+  public static int removeSnapshots(List<Integer> annotationSetIds)
+  {
+    StaticCache cache = Application.getStaticCache();
+    int removed = 0;
+    for (Integer i : annotationSetIds)
+    {
+      String cacheKey = getCacheKey(i);
+      if (cache.delete(cacheKey, 1000)) removed++;
+    }
+    return removed;
   }
   

trunk/www/admin/annotationtypes/edit_annotationtype.jsp

@@ -398 +398 @@
         <td></td>
       </tr>
+      <tr>
+        <th><label for="disable_inheritance">Disable inheritance</label></th>
+        <td><input type="checkbox" name="disable_inheritance" id="disable_inheritance" value="1" 
+          <%=(annotationType != null && annotationType.getDisableInheritance()) || 
+            (annotationType == null && Values.getBoolean(cc.getPropertyValue("disableInheritance"))) ? "checked" : ""%>
+          >
+        </td>
+        <td></td>
+      </tr>
       <tr class="dynamic">
         <th>Description</th>

trunk/www/admin/annotationtypes/index.jsp

@@ -191 +191 @@
       annotationType.setProtocolParameter(Values.getBoolean(request.getParameter("is_protocol_parameter")));
       annotationType.setDisableLogOfValues(Values.getBoolean(request.getParameter("disable_log")));
+      annotationType.setDisableInheritance(Values.getBoolean(request.getParameter("disable_inheritance")));
       if (annotationType.getValueType().canEnumerate())
       {

trunk/www/admin/annotationtypes/list_annotationtypes.jsp

@@ -281 +281 @@
       />
       <tbl:columndef 
+        id="disableInheritance"
+        property="disableInheritance"
+        datatype="boolean"
+        title="Disable inheritance"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
+      />
+      <tbl:columndef 
         id="isEnumeration"
         property="enumeration"
@@ -603 +612 @@
                 <tbl:cell column="isProtocolParameter"><%=item.isProtocolParameter() ? "yes" : "no"%></tbl:cell>
                 <tbl:cell column="disableLogOfValues"><%=item.getDisableLogOfValues() ? "yes" : "no"%></tbl:cell>
+                <tbl:cell column="disableInheritance"><%=item.getDisableInheritance() ? "yes" : "no"%></tbl:cell>
                 <tbl:cell column="multiplicity"><%=item.getMultiplicity() == 0 ? "<i>- unlimited -</i>" : item.getMultiplicity()%></tbl:cell>
                 <tbl:cell column="defaultValue"><%=HTML.encodeTags(item.getDefaultValue())%></tbl:cell>

trunk/www/admin/annotationtypes/view_annotationtype.jsp

@@ -278 +278 @@
         <th>Disable change log</th>
         <td><%=annotationType.getDisableLogOfValues() ? "yes" : "no"%></td>
+      </tr>
+      <tr>
+        <th>Disable inheritance</th>
+        <td><%=annotationType.getDisableInheritance() ? "yes" : "no"%></td>
       </tr>
       <tr>