Changeset 104 for branches/omero

Timestamp:

06/09/05 20:03:20 (4 years ago)

Author:

jmoore

Message:

Documentation / Javadoc update. Also added some logging.

Location:

branches/omero/components

Files:

• client/src/org/openmicroscopy/omero/client/ServiceFactory.java (modified) (1 diff)
• client/src/org/openmicroscopy/omero/client/SpringHarness.java (modified) (2 diffs)
• client/src/org/openmicroscopy/omero/client/spring.xml (modified) (1 diff)
• client/test/org/openmicroscopy/omero/client/itests/OmeroHierarchyBrowsingIntegrationTest.java (modified) (4 diffs)
• client/test/org/openmicroscopy/omero/client/itests/test.xml (modified) (1 diff)
• common/.classpath (modified) (1 diff)
• common/project.xml (modified) (1 diff)
• common/src/org/openmicroscopy/omero/interfaces/HierarchyBrowsing.java (modified) (9 diffs)
• common/src/org/openmicroscopy/omero/model2/Category2.java (modified) (1 diff)
• common/src/org/openmicroscopy/omero/model2/CategoryGroup2.java (modified) (1 diff)
• common/src/org/openmicroscopy/omero/tests/AbstractOmeroHierarchyBrowserIntegrationTest.java (modified) (2 diffs)
• common/src/org/openmicroscopy/omero/tests/OMEData.java (modified) (2 diffs)
• common/src/org/openmicroscopy/omero/tests/OMEPerformanceData.java (modified) (1 diff)
• common/src/org/openmicroscopy/omero/util/Utils.java (modified) (3 diffs)
• server/src/org/openmicroscopy/omero/logic/AnnotationDao.java (modified) (1 diff)
• server/src/org/openmicroscopy/omero/logic/AnnotationDaoHibernate.java (modified) (2 diffs)
• server/src/org/openmicroscopy/omero/logic/ContainerDao.java (modified) (1 diff)
• server/src/org/openmicroscopy/omero/logic/ContainerDaoHibernate.java (modified) (2 diffs)
• server/test/org/openmicroscopy/omero/server/itests/OmeroServiceTest.java (modified) (2 diffs)
• server/test/org/openmicroscopy/omero/server/itests/OmeroThumbnailsBugTest.java (modified) (2 diffs)
• server/test/org/openmicroscopy/omero/server/utests/HierarchyBrowsingUnitTest.java (modified) (3 diffs)
• server/web/WEB-INF/config-test.xml (modified) (1 diff)
• server/web/WEB-INF/config.xml (modified) (1 diff)
• shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/AdapterUtils.java (modified) (3 diffs)
• shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/HierarchyBrowsingAdapter.java (modified) (2 diffs)
• shoola-adapter/src/org/openmicroscopy/omero/shoolaadapter/ServiceFactory.java (modified) (1 diff)
• test/src/org/openmicroscopy/omero/test/OmeroGrinderTest.java (modified) (2 diffs)
• test/src/org/openmicroscopy/shoola/env/data/t/ShoolaGrinderTest.java (modified) (1 diff)
• test/src/speed.py (modified) (2 diffs)

branches/omero/components/client/src/org/openmicroscopy/omero/client/ServiceFactory.java

@@ -1 +1 @@
 /*
- * Created on May 8, 2005
-*/
+ * org.openmicroscopy.omero.ServiceFactory
+ *
+ *------------------------------------------------------------------------------
+ *
+ *  Copyright (C) 2004 Open Microscopy Environment
+ *      Massachusetts Institute of Technology,
+ *      National Institutes of Health,
+ *      University of Dundee
+ *
+ *
+ *
+ *    This library is free software; you can redistribute it and/or
+ *    modify it under the terms of the GNU Lesser General Public
+ *    License as published by the Free Software Foundation; either
+ *    version 2.1 of the License, or (at your option) any later version.
+ *
+ *    This library 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
+ *    Lesser General Public License for more details.
+ *
+ *    You should have received a copy of the GNU Lesser General Public
+ *    License along with this library; if not, write to the Free Software
+ *    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ *
+ *------------------------------------------------------------------------------
+ */
+
 package org.openmicroscopy.omero.client;
 
+//Java imports
+
+//Third-party libraries
+
+//Application-internal dependencies
 import org.openmicroscopy.omero.interfaces.HierarchyBrowsing;
 
-/**
- * @author josh
+/** 
+ * Entry point for all client calls. Provides methods to 
+ * obtain proxies for all remote facades. 
+ * 
+ * @author  Josh Moore     
+ *                              <a href="mailto:josh.moore@gmx.de">josh.moore@gmx.de</a>
+ * @version 1.0 
+ * <small>
+ * (<b>Internal version:</b> $Rev$ $Date$)
+ * </small>
+ * @since 1.0
  */
 public class ServiceFactory {

branches/omero/components/client/src/org/openmicroscopy/omero/client/SpringHarness.java

@@ -1 +1 @@
 /*
- * Created on Jul 21, 2004
+ * org.openmicroscopy.shoola.ServiceFactory
+ *
+ *------------------------------------------------------------------------------
+ *
+ *  Copyright (C) 2004 Open Microscopy Environment
+ *      Massachusetts Institute of Technology,
+ *      National Institutes of Health,
+ *      University of Dundee
+ *
+ *
+ *
+ *    This library is free software; you can redistribute it and/or
+ *    modify it under the terms of the GNU Lesser General Public
+ *    License as published by the Free Software Foundation; either
+ *    version 2.1 of the License, or (at your option) any later version.
+ *
+ *    This library 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
+ *    Lesser General Public License for more details.
+ *
+ *    You should have received a copy of the GNU Lesser General Public
+ *    License along with this library; if not, write to the Free Software
+ *    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ *
+ *------------------------------------------------------------------------------
  */
+
 package org.openmicroscopy.omero.client;
 
+//Java imports
 import java.net.URL;
 
+//Third-party libraries
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.support.FileSystemXmlApplicationContext;
 
-/** provides all objects needed for working with the meta package 
- * within the Spring Framework.
- * @author moore
+//Application-internal dependencies
+
+
+
+/** provides context for all objects configured by the Spring Framework.
+ * 
+ * @author  Josh Moore     
+ *                              <a href="mailto:josh.moore@gmx.de">josh.moore@gmx.de</a>
+ * @version 1.0 
+ * @DEV.TODO Possibly deprecate SpringHarness, make internal to ServiceFactory.
+ * <small>
+ * (<b>Internal version:</b> $Rev$ $Date$)
+ * </small>
+ * @since 1.0
  */
 public class SpringHarness {
@@ -22 +61 @@
         path = SpringHarness.class.getClassLoader().getResource(springConfFile);
         if (path==null){
-            throw new RuntimeException("Can't find spring.xml on classpath");
+            throw new RuntimeException("Client jar corrupted. Can't find internal configuration file:\n"+springConfFile);
         }
         ctx = new FileSystemXmlApplicationContext(path.toString());

branches/omero/components/client/src/org/openmicroscopy/omero/client/spring.xml

@@ -1 +1 @@
 <?xml version="1.0" encoding="UTF-8"?>
+<!--
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+# Copyright (C) 2003 Open Microscopy Environment
+#       Massachusetts Institue of Technology,
+#       National Institutes of Health,
+#       University of Dundee
+#
+#
+#
+#    This library is free software; you can redistribute it and/or
+#    modify it under the terms of the GNU Lesser General Public
+#    License as published by the Free Software Foundation; either
+#    version 2.1 of the License, or (at your option) any later version.
+#
+#    This library 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
+#    Lesser General Public License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public
+#    License along with this library; if not, write to the Free Software
+#    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+-->
+
+<!--
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# Written by:  Josh Moore <josh.moore@gmx.de>
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+-->
+
+<!--
+
+        Configuration of client proxies.
+ 
+-->
+
 <!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN" "http://www.springframework.org/dtd/spring-beans.dtd">
 
-<beans> 
+        <beans> 
         <!-- ***** CONFIG ***** -->
         <!-- property placeholder post-processor -->

branches/omero/components/client/test/org/openmicroscopy/omero/client/itests/OmeroHierarchyBrowsingIntegrationTest.java

@@ -1 +1 @@
 /*
- * Created on Jun 7, 2005
-*/
+ * org.openmicroscopy.omero.client.itests.OmeroHierarchyBrowsingIntegrationTest
+ *
+ *------------------------------------------------------------------------------
+ *
+ *  Copyright (C) 2004 Open Microscopy Environment
+ *      Massachusetts Institute of Technology,
+ *      National Institutes of Health,
+ *      University of Dundee
+ *
+ *
+ *
+ *    This library is free software; you can redistribute it and/or
+ *    modify it under the terms of the GNU Lesser General Public
+ *    License as published by the Free Software Foundation; either
+ *    version 2.1 of the License, or (at your option) any later version.
+ *
+ *    This library 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
+ *    Lesser General Public License for more details.
+ *
+ *    You should have received a copy of the GNU Lesser General Public
+ *    License along with this library; if not, write to the Free Software
+ *    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ *
+ *------------------------------------------------------------------------------
+ */
+
 package org.openmicroscopy.omero.client.itests;
 
+//Java imports
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.Set;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+//Third-party libraries
+
+//Application-internal dependencies
 import org.openmicroscopy.omero.model.Category;
 import org.openmicroscopy.omero.model.CategoryGroup;
@@ -17 +50 @@
 import org.openmicroscopy.omero.tests.OMEPerformanceData;
 
-/**
- * @author josh
+/** Tests calls through to the database, using all necessary layers. Specifics 
+ * are available in abstract super class.
+ * 
+ * @author  Josh Moore     
+ *                              <a href="mailto:josh.moore@gmx.de">josh.moore@gmx.de</a>
+ * @version 1.0 
+ * <small>
+ * (<b>Internal version:</b> $Rev$ $Date$)
+ * </small>
+ * @since 1.0
+ * @see org.openmicroscopy.omero.tests.AbstractOmeroHierarchyBrowserIntegrationTest
  */
 public class OmeroHierarchyBrowsingIntegrationTest
@@ -28 +70 @@
      */
     protected String[] getConfigLocations() {
-        return new String[]{"org/openmicroscopy/omero/client/spring.xml"}; 
+        return new String[]{"org/openmicroscopy/omero/client/spring.xml",
+                "org/openmicroscopy/omero/client/itests/test.xml"}; 
     }
     
@@ -38 +81 @@
         super("Omero Integration Test with Data",data);
     }
-    
-    public void testContainerCallWithWrongParameters(){
-        try {
-            getHb().loadPDIHierarchy(Object.class,1);
-            fail("loadPDIHierarchy(class,int) didn't choke on bad class.");
-        } catch (IllegalArgumentException iae){
-            // We should get here. TODO log
-        }
-
-        try {
-            getHb().loadCGCIHierarchy(Object.class,1);
-            fail("loadCGCIHierarchy(class,int) didn't choke on bad class.");
-        } catch (IllegalArgumentException iae){
-            // We should get here. TODO log
-        }
-             
-       }
-    
-    String nullObj = "This should get us nothing.";
-    String emptyColl = "This collection should be empty.";
-    String nonNull = "We should get something back";
-
-    public void testNulls(){
-        // Each method should return a null or an empty set as appropriate
-        //TODO getHb().findCGCIHierarchies(     );
-        //TODO generate OMENullData(); and use it here.
-        //TODO OMEData toString();
-        
-        Set test = new HashSet();
-        test.add(new Integer(0)); // Non-existence set of ids
-        int nonExp = 0; // Non-existence experimenter ID
-        //
-        assertTrue(emptyColl,getHb().findDatasetAnnotations(test).size()==0);
-        assertTrue(emptyColl,getHb().findDatasetAnnotations(new HashSet()).size()==0);
-        //
-        assertTrue(emptyColl,getHb().findDatasetAnnotationsForExperimenter(test,nonExp).size()==0);
-        assertTrue(emptyColl,getHb().findDatasetAnnotationsForExperimenter(new HashSet(),nonExp).size()==0);
-        //
-        assertTrue(emptyColl,getHb().findImageAnnotations(test).size()==0);
-        assertTrue(emptyColl,getHb().findImageAnnotations(new HashSet()).size()==0);
-        //
-        assertTrue(emptyColl,getHb().findImageAnnotationsForExperimenter(test,nonExp).size()==0);
-        assertTrue(emptyColl,getHb().findImageAnnotationsForExperimenter(new HashSet(),nonExp).size()==0);
-        //
-        assertTrue(emptyColl,getHb().findPDIHierarchies(test).size()==0);
-        assertTrue(emptyColl,getHb().findPDIHierarchies(new HashSet()).size()==0);
-        //
-        assertNull(nullObj,getHb().loadCGCIHierarchy(CategoryGroup.class, 0));
-        assertNull(nullObj,getHb().loadCGCIHierarchy(Category.class, 0));
-        //
-        assertNull(nullObj,getHb().loadPDIHierarchy(Project.class, 0));
-        assertNull(nullObj,getHb().loadPDIHierarchy(Dataset.class, 0));
-    }
-    
-    public void testContainedImages(){
-        // Something
-        Set result = (Set) testFindPDIHierarchies();
-        assertTrue(nonNull, result != null && result.size() != 0);
-        // Not to much
-        Set test = new HashSet();
-        Iterator i = result.iterator();
-        while (i.hasNext()){
-            Object o = i.next();
-            if (o instanceof Image) {
-                test.add(o);
-            } else if (o instanceof Dataset) {
-                Dataset dd = (Dataset) o;
-                test.addAll(dd.getImages());
-            } else if (o instanceof Project) {
-                Project pd = (Project) o;
-                Iterator p = pd.getDatasets().iterator();
-                while (p.hasNext()){
-                    Dataset dd = (Dataset) p.next();
-                    test.addAll(dd.getImages());
-                }
-            }
-        }
-        assertTrue("There should only be as many images as in the data.imagesPDI", test.size() == this.getData().imgsPDI.size());
-//      TODO Make sure joins aren't leaving anything out because of empties!
-    }
-
    
 }

branches/omero/components/client/test/org/openmicroscopy/omero/client/itests/test.xml

@@ -1 +1 @@
 <?xml version="1.0" encoding="UTF-8"?>
+<!--
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+# Copyright (C) 2003 Open Microscopy Environment
+#       Massachusetts Institue of Technology,
+#       National Institutes of Health,
+#       University of Dundee
+#
+#
+#
+#    This library is free software; you can redistribute it and/or
+#    modify it under the terms of the GNU Lesser General Public
+#    License as published by the Free Software Foundation; either
+#    version 2.1 of the License, or (at your option) any later version.
+#
+#    This library 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
+#    Lesser General Public License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public
+#    License along with this library; if not, write to the Free Software
+#    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+-->
+
+<!--
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# Written by:  Josh Moore <josh.moore@gmx.de>
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+-->
+
+<!--
+
+        Test configuration for the client side. The dataSource is necessary
+        so that data can query for existing values.
+ 
+-->
 <!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN" "http://www.springframework.org/dtd/spring-beans.dtd">
 

branches/omero/components/common/.classpath

@@ -16 +16 @@
   <classpathentry kind="var" path="MAVEN_REPO/commons-lang/jars/commons-lang-2.0.jar">
   </classpathentry>
+  <classpathentry kind="var" path="MAVEN_REPO/commons-logging/jars/commons-logging-1.0.4.jar">
+  </classpathentry>
   <classpathentry kind="var" path="MAVEN_REPO/postgresql/jars/postgresql-7.4.1-jdbc3.jar">
   </classpathentry>

branches/omero/components/common/project.xml

@@ -36 +36 @@
     </dependency>
     <dependency>
+      <groupId>commons-logging</groupId>
+      <artifactId>commons-logging</artifactId>
+      <version>1.0.4</version>
+    </dependency>
+    <dependency>
       <groupId>postgresql</groupId>
       <artifactId>postgresql</artifactId>

branches/omero/components/common/src/org/openmicroscopy/omero/interfaces/HierarchyBrowsing.java

@@ -57 +57 @@
  * </small>
  * @since OME2.2
+ * @DEV.TODO Possibly change these methods to return an abstract super type 
+ * @DEV.TODO or even a concretefor these or concrete type like "Project loadPDIHierary()"
+ * @DEV.TODO Update code generation for Hibernate to include copyright. 
  */
 public interface HierarchyBrowsing
@@ -64 +67 @@
      * Loads a Project/Dataset/Image (P/D/I) hierarchy rooted by a given node.
      * <p>The root node can be either Project or Dataset.  A Project tree will
-     * be represented by {@link ProjectData}, {@link DatasetData}, and
-     * {@link ImageData} objects.  A Dataset tree will only have objects of
+     * be represented by {@link Project}, {@link Dataset}, and
+     * {@link Image} objects.  A Dataset tree will only have objects of
      * the latter two types.</p>
      * <p>This method also retrieves the Experimenters linked to the objects
      * in the tree &#151; an Experimenter is represented by an 
-     * {@link ExperimenterData} object.  Similarly, all Images will be linked
-     * to their Pixels &#151; represented by {@link PixelsData} objects.</p>
+     * {@link Experimenter} object.  Similarly, all Images will be linked
+     * to their Pixels &#151; represented by {@link Pixels} objects.</p>
      * <p>Note that objects are never duplicated.  For example, if an 
      * Experimenter owns all the objects in the retrieved tree, then those
      * objects will be linked to the <i>same</i> instance of
-     * {@link ExperimenterData}.  Or if an Image is contained in more than
-     * one Dataset in the retrieved tree, then all enclosing {@link DatasetData}
-     * objects will point to the <i>same</i> {@link ImageData} object.  And so
+     * {@link Experimenter}.  Or if an Image is contained in more than
+     * one Dataset in the retrieved tree, then all enclosing {@link Dataset}
+     * objects will point to the <i>same</i> {@link Image} object.  And so
      * on.</p>
      * 
      * @param rootNodeType  The type of the root node.  Can either be
-     *                      {@link ProjectData} or {@link DatasetData}.
+     *                      {@link Project} or {@link Dataset}.
      * @param rootNodeID    The id of the root node.
      * @return The requested node as root and all of its descendants.  The type
@@ -86 +89 @@
      */
     public Object loadPDIHierarchy(Class rootNodeType, int rootNodeID); 
-    // TODO Super Object for these or concrete "Project loadPDIHierary() / Dataset loadDIHierarchy()"??? 
     
     /**
@@ -92 +94 @@
      * given node.
      * <p>The root node can be either Category Group or Category.  A Category
-     * Group tree will be represented by {@link CategoryGroupData}, 
-     * {@link CategoryData}, and {@link ImageData} objects.  A Category tree
+     * Group tree will be represented by {@link CategoryGroup}, 
+     * {@link Category}, and {@link Image} objects.  A Category tree
      * will only have objects of the latter two types.</p>
      * <p>This method also retrieves the Experimenters linked to the objects
      * in the tree &#151; an Experimenter is represented by an 
-     * {@link ExperimenterData} object.  Similarly, all Images will be linked
-     * to their Pixels &#151; represented by {@link PixelsData} objects.</p>
+     * {@link Experimenter} object.  Similarly, all Images will be linked
+     * to their Pixels &#151; represented by {@link Pixels} objects.</p>
      * <p>Note that objects are never duplicated.  For example, if an 
      * Experimenter owns all the objects in the retrieved tree, then those
      * objects will be linked to the <i>same</i> instance of
-     * {@link ExperimenterData}.</p>
+     * {@link Experimenter}.</p>
      * 
      * @param rootNodeType  The type of the root node.  Can either be
-     *                      {@link CategoryGroupData} or {@link CategoryData}.
+     *                      {@link CategoryGroup} or {@link Category}.
      * @param rootNodeID    The id of the root node.
      * @return The requested node as root and all of its descendants.  The type
@@ -117 +119 @@
      * <p>This method will look for all the Datasets containing the specified 
      * Images and then for all Projects containing those Datasets.  In the 
-     * returned trees, Projects will be represented by {@link ProjectData}
-     * objects, Datasets by {@link DatasetData} objects, and Images by
-     * {@link ImageData} objects.</p>
+     * returned trees, Projects will be represented by {@link Project}
+     * objects, Datasets by {@link Dataset} objects, and Images by
+     * {@link Image} objects.</p>
      * <p>This method returns a <code>Set</code> with all root nodes that were
      * found.  Every root node is linked to the found objects and so on until
-     * the leaf nodes, which are {@link ImageData} objects.  Note that the type
-     * of any root node in the returned set can be {@link ProjectData}, 
-     * {@link DatasetData}, or {@link ImageData}.</p>
+     * the leaf nodes, which are {@link Image} objects.  Note that the type
+     * of any root node in the returned set can be {@link Project}, 
+     * {@link Dataset}, or {@link Image}.</p>
      * <p>For example, say that you pass in the ids of six Images: <code>i1, i2,
      * i3, i4, i5, i6</code>.  If the P/D/I hierarchy in the DB looks like this:
@@ -175 +177 @@
      * Image.  If no annotations were found for that Image, then the entry
      * will be <code>null</code>.  Otherwise it will be a <code>Set</code>
-     * containing {@link AnnotationData} objects.
+     * containing {@link Annotation} objects.
      * 
      * @param imgIDs Contains the ids of the Images.
@@ -192 +194 @@
      * Image.  If no annotations were found for that Image, then the entry
      * will be <code>null</code>.  Otherwise it will be a <code>Set</code>
-     * containing {@link AnnotationData} objects.
+     * containing {@link Annotation} objects.
      * 
      * @param imgIDs Contains the ids of the Images.
@@ -210 +212 @@
      * Dataset.  If no annotations were found for that Dataset, then the
      * entry will be <code>null</code>.  Otherwise it will be a <code>Set
-     * </code> containing {@link AnnotationData} objects.
+     * </code> containing {@link Annotation} objects.
      * 
      * @param datasetIDs Contains the ids of the Datasets.
@@ -227 +229 @@
      * Dataset.  If no annotations were found for that Image, then the entry
      * will be <code>null</code>.  Otherwise it will be a <code>Set</code>
-     * containing {@link AnnotationData} objects.
+     * containing {@link Annotation} objects.
      * 
      * @param datasetIDs Contains the ids of the Datasets.

branches/omero/components/common/src/org/openmicroscopy/omero/model2/Category2.java

@@ -1 +1 @@
 /*
- * Created on May 31, 2005
-*/
+ * org.openmicroscopy.omero.model2
+ *
+ *------------------------------------------------------------------------------
+ *
+ *  Copyright (C) 2004 Open Microscopy Environment
+ *      Massachusetts Institute of Technology,
+ *      National Institutes of Health,
+ *      University of Dundee
+ *
+ *
+ *
+ *    This library is free software; you can redistribute it and/or
+ *    modify it under the terms of the GNU Lesser General Public
+ *    License as published by the Free Software Foundation; either
+ *    version 2.1 of the License, or (at your option) any later version.
+ *
+ *    This library 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
+ *    Lesser General Public License for more details.
+ *
+ *    You should have received a copy of the GNU Lesser General Public
+ *    License along with th