Refactored preferences support with JpaPreferencesManager

10 files changed, 531 insertions, 400 deletions

diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/JptJpaCorePlugin.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/JptJpaCorePlugin.java
index 2c784e51c7..2d0c954774 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/JptJpaCorePlugin.java
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/JptJpaCorePlugin.java
@@ -10,13 +10,13 @@
 package org.eclipse.jpt.jpa.core;
 
 import java.util.Hashtable;
+
 import javax.xml.parsers.SAXParserFactory;
+
 import org.eclipse.core.resources.IProject;
 import org.eclipse.core.resources.IWorkspace;
-import org.eclipse.core.resources.ProjectScope;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IPath;
-import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.IStatus;
 import org.eclipse.core.runtime.Path;
 import org.eclipse.core.runtime.Platform;
@@ -24,30 +24,22 @@ import org.eclipse.core.runtime.Plugin;
 import org.eclipse.core.runtime.QualifiedName;
 import org.eclipse.core.runtime.Status;
 import org.eclipse.core.runtime.content.IContentType;
-import org.eclipse.core.runtime.jobs.Job;
-import org.eclipse.core.runtime.preferences.DefaultScope;
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
-import org.eclipse.core.runtime.preferences.IScopeContext;
-import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.jpt.common.core.JptResourceType;
 import org.eclipse.jpt.common.utility.internal.StringTools;
 import org.eclipse.jpt.jpa.core.context.XmlContextNode;
 import org.eclipse.jpt.jpa.core.internal.InternalJpaProjectManager;
-import org.eclipse.jpt.jpa.core.internal.JptCoreMessages;
 import org.eclipse.jpt.jpa.core.internal.platform.JpaPlatformManagerImpl;
-import org.eclipse.jpt.jpa.core.internal.prefs.JpaPreferenceInitializer;
+import org.eclipse.jpt.jpa.core.internal.prefs.JpaPreferencesManager;
 import org.eclipse.jpt.jpa.core.platform.GenericPlatform;
 import org.eclipse.jpt.jpa.core.platform.JpaPlatformDescription;
 import org.eclipse.jpt.jpa.core.platform.JpaPlatformManager;
 import org.eclipse.jst.j2ee.internal.J2EEConstants;
-import org.eclipse.osgi.util.NLS;
 import org.eclipse.wst.common.componentcore.internal.util.IModuleConstants;
 import org.eclipse.wst.common.project.facet.core.FacetedProjectFramework;
 import org.eclipse.wst.common.project.facet.core.IProjectFacet;
 import org.eclipse.wst.common.project.facet.core.IProjectFacetVersion;
 import org.eclipse.wst.common.project.facet.core.ProjectFacetsManager;
 import org.osgi.framework.BundleContext;
-import org.osgi.service.prefs.BackingStoreException;
 import org.osgi.service.prefs.Preferences;
 import org.osgi.util.tracker.ServiceTracker;
 
@@ -74,8 +66,6 @@ public class JptJpaCorePlugin
 	private volatile boolean active = false;
 	private final Hashtable<IWorkspace, InternalJpaProjectManager> jpaProjectManagers = new Hashtable<IWorkspace, InternalJpaProjectManager>();
 	private volatile ServiceTracker<?, SAXParserFactory> parserTracker;
-	private static volatile boolean flushPreferences = true;
-
 
 	// ********** public constants **********
 
@@ -94,50 +84,6 @@ public class JptJpaCorePlugin
 	public static final String LEGACY_PLUGIN_ID_ = LEGACY_PLUGIN_ID + '.';
 
 	/**
-	 * The key for storing a JPA project's platform ID in the Eclipse
-	 * project's preferences.
-	 */
-	private static final String JPA_PLATFORM_PREF_KEY = LEGACY_PLUGIN_ID_ + "platform";  //$NON-NLS-1$
-
-	/**
-	 * The old key for storing the default JPA platform ID in the workspace preferences.
-	 * @deprecated  As of version 2.3.  Instead use {@link #DEFAULT_JPA_PLATFORM_1_0_PREF_KEY} or 
-	 * 		{@link #DEFAULT_JPA_PLATFORM_2_0_PREF_KEY}
-	 */
-	@Deprecated
-	public static final String DEFAULT_JPA_PLATFORM_PREF_KEY = "defaultJpaPlatform"; //$NON-NLS-1$
-	
-	/**
-	 * The key for storing the default JPA platform ID for JPA 1.0 in the workspace preferences.
-	 */
-	public static final String DEFAULT_JPA_PLATFORM_1_0_PREF_KEY = 
-			DEFAULT_JPA_PLATFORM_PREF_KEY + "_" + JpaFacet.VERSION_1_0.getVersionString(); //$NON-NLS-1$
-	
-	/**
-	 * The key for storing the default JPA platform ID for JPA 2.0 in the workspace preferences.
-	 */
-	public static final String DEFAULT_JPA_PLATFORM_2_0_PREF_KEY = 
-			DEFAULT_JPA_PLATFORM_PREF_KEY + "_" + JpaFacet.VERSION_2_0.getVersionString(); //$NON-NLS-1$
-	
-	/**
-	 * The key for storing a JPA project's "discover" flag in the Eclipse
-	 * project's preferences.
-	 */
-	public static final String DISCOVER_ANNOTATED_CLASSES = PLUGIN_ID_ + "discoverAnnotatedClasses";  //$NON-NLS-1$
-
-	//bug 354780 - made the mistake of changing the project metadata in the 3.0 release
-	private static final String LEGACY_DISCOVER_ANNOTATED_CLASSES = LEGACY_PLUGIN_ID_ + "discoverAnnotatedClasses";  //$NON-NLS-1$
-
-	/**
-	 * The key for storing the name of a JPA project's metamodel source folder
-	 * in the Eclipse project's preferences.
-	 */
-	public static final String METAMODEL_SOURCE_FOLDER_NAME = PLUGIN_ID_ + "metamodelSourceFolderName";  //$NON-NLS-1$
-
-	//bug 354780 - made the mistake of changing the project metadata in the 3.0 release
-	private static final String LEGACY_METAMODEL_SOURCE_FOLDER_NAME = LEGACY_PLUGIN_ID_ + "metamodelSourceFolderName";  //$NON-NLS-1$
-
-	/**
 	 * The key for storing a JPA project's data source connection profile name
 	 * in the Eclipse project's persistent properties.
 	 */
@@ -232,12 +178,10 @@ public class JptJpaCorePlugin
 		return Platform.getContentTypeManager().getContentType(contentType);
 	}
 	
-	
 	// ********** singleton **********
 
 	static JptJpaCorePlugin INSTANCE;
 
-
 	// ********** public static methods **********
 
 	/**
@@ -289,138 +233,41 @@ public class JptJpaCorePlugin
 				: new Path("/");  //$NON-NLS-1$
 	}
 	
-	public static void initializeDefaultPreferences() {
-		IEclipsePreferences node = getDefaultPreferences();
-
-		// default JPA platforms
-		JpaPlatformDescription defaultPlatform_1_0 = 
-				JpaPlatformManagerImpl.instance().getDefaultJpaPlatform(JpaFacet.VERSION_1_0);
-		if (defaultPlatform_1_0 == null) {
-			defaultPlatform_1_0 = GenericPlatform.VERSION_1_0;
-		}
-		node.put(DEFAULT_JPA_PLATFORM_1_0_PREF_KEY, defaultPlatform_1_0.getId());
-		
-		JpaPlatformDescription defaultPlatform_2_0 = 
-				JpaPlatformManagerImpl.instance().getDefaultJpaPlatform(JpaFacet.VERSION_2_0);
-		if (defaultPlatform_2_0 == null) {
-			defaultPlatform_2_0 = GenericPlatform.VERSION_2_0;
-		}
-		node.put(DEFAULT_JPA_PLATFORM_2_0_PREF_KEY, defaultPlatform_2_0.getId());
-	}
-	
-	/**
-	 * Return the default Dali preferences
-	 * @see JpaPreferenceInitializer
-	 */
-	public static IEclipsePreferences getDefaultPreferences() {
-		return getPreferences(DefaultScope.INSTANCE);
-	}
-
-	/**
-	 * Return the Dali preferences for the current workspace instance.
-	 */
-	public static IEclipsePreferences getWorkspacePreferences() {
-		return getPreferences(InstanceScope.INSTANCE);
-	}
-	
-	/**
-	 * Set the workspace preference.
-	 */
-	public static void setWorkspacePreference(String preferenceKey, String preferenceValue) {
-		IEclipsePreferences prefs = getWorkspacePreferences();
-		prefs.put(preferenceKey, preferenceValue);
-		flush(prefs);
-	}
-
-	/**
-	 * Return the Dali preferences for the specified Eclipse project.
-	 */
-	public static IEclipsePreferences getProjectPreferences(IProject project) {
-		return getPreferences(new ProjectScope(project));
-	}
-	
-	/**
-	 * Set the project preference
-	 */
-	public static void setProjectPreference(IProject project, String preferenceKey, String preferenceValue) {
-		IEclipsePreferences prefs = getProjectPreferences(project);
-		if (preferenceValue == null) {
-			prefs.remove(preferenceKey);
-		}
-		else {
-			prefs.put(preferenceKey, preferenceValue);
-		}
-		flush(prefs);
-	}
-	
-	/**
-	 * Set the project preference
-	 */
-	public static void setProjectPreference(IProject project, String preferenceKey, boolean preferenceValue) {
-		IEclipsePreferences prefs = getProjectPreferences(project);
-		prefs.putBoolean(preferenceKey, preferenceValue);
-		flush(prefs);
-	}
-	
-	/**
-	 * Clears the project of JPA-specific preferences
-	 */
-	public static void clearProjectPreferences(IProject project) {
-		clearProjectPreferences(
-				project, 
-				JPA_PLATFORM_PREF_KEY,
-				DISCOVER_ANNOTATED_CLASSES,
-				METAMODEL_SOURCE_FOLDER_NAME,
-				LEGACY_DISCOVER_ANNOTATED_CLASSES,
-				LEGACY_METAMODEL_SOURCE_FOLDER_NAME);
-	}
-	
-	/**
-	 * Clears the specified preferences
-	 */
-	public static void clearProjectPreferences(IProject project, String ... preferenceKeys) {
-		IEclipsePreferences prefs = getProjectPreferences(project);
-		for (String preferenceKey : preferenceKeys) {
-			prefs.remove(preferenceKey);
-		}
-		flush(prefs);
-	}
-	
-	/**
-	 * Return the Dali preferences for the specified context.
-	 */
-	private static IEclipsePreferences getPreferences(IScopeContext context) {
-		return context.getNode(LEGACY_PLUGIN_ID);
-	}
-	
 	/**
 	 * Return the default {@link JpaPlatformDescription} for new JPA projects with the given JPA facet version.
 	 */
 	public static JpaPlatformDescription getDefaultJpaPlatform(IProjectFacetVersion jpaFacetVersion) {
-		JpaPlatformDescription defaultPlatform = 
-				getDefaultJpaPlatform(jpaFacetVersion, getWorkspacePreferences(), getDefaultPreferences());
+		JpaPlatformDescription defaultPlatform = 	getDefaultJpaPlatform(
+							jpaFacetVersion, 
+							JpaPreferencesManager.getWorkspacePreferences(), 
+							JpaPreferencesManager.getDefaultPreferences());
 		if (defaultPlatform == null) {
 			// if the platform ID stored in the workspace prefs is invalid (i.e. null), look in the default prefs
-			defaultPlatform = getDefaultJpaPlatform(jpaFacetVersion, getDefaultPreferences());
+			defaultPlatform = getDefaultJpaPlatform(
+						jpaFacetVersion, 
+						JpaPreferencesManager.getDefaultPreferences());
 		}
 		return defaultPlatform;
 	}
 	
 	private static JpaPlatformDescription getDefaultJpaPlatform(IProjectFacetVersion jpaFacetVersion, Preferences ... nodes) {
-		JpaPlatformDescription defaultDefaultPlatform = 
-				getDefaultJpaPlatform(jpaFacetVersion, DEFAULT_JPA_PLATFORM_PREF_KEY, null, nodes);
+		JpaPlatformDescription defaultDefaultPlatform = getDefaultJpaPlatform(
+							jpaFacetVersion, 
+							JpaPreferencesManager.DEFAULT_JPA_PLATFORM_PREF_KEY, 
+							null, 
+							nodes);
 		String preferenceKey = null;
 		if (jpaFacetVersion.equals(JpaFacet.VERSION_1_0)) {
 			if (defaultDefaultPlatform == null) {
 				defaultDefaultPlatform = GenericPlatform.VERSION_1_0;
 			}
-			preferenceKey = DEFAULT_JPA_PLATFORM_1_0_PREF_KEY; 
+			preferenceKey = JpaPreferencesManager.DEFAULT_JPA_PLATFORM_1_0_PREF_KEY; 
 		}
 		else if (jpaFacetVersion.equals(JpaFacet.VERSION_2_0)) {
 			if (defaultDefaultPlatform == null) {
 				defaultDefaultPlatform = GenericPlatform.VERSION_2_0;
 			}
-			preferenceKey = DEFAULT_JPA_PLATFORM_2_0_PREF_KEY;
+			preferenceKey = JpaPreferencesManager.DEFAULT_JPA_PLATFORM_2_0_PREF_KEY;
 		}
 		else {
 			throw new IllegalArgumentException("Illegal JPA facet version: " + jpaFacetVersion); //$NON-NLS-1$
@@ -453,22 +300,22 @@ public class JptJpaCorePlugin
 	public static void setDefaultJpaPlatformId(String jpaFacetVersion, String platformId) {
 		String preferenceKey = null;
 		if (JpaFacet.VERSION_1_0.getVersionString().equals(jpaFacetVersion)) {
-			preferenceKey = DEFAULT_JPA_PLATFORM_1_0_PREF_KEY;
+			preferenceKey = JpaPreferencesManager.DEFAULT_JPA_PLATFORM_1_0_PREF_KEY;
 		}
 		else if (JpaFacet.VERSION_2_0.getVersionString().equals(jpaFacetVersion)) {
-			preferenceKey = DEFAULT_JPA_PLATFORM_2_0_PREF_KEY;
+			preferenceKey = JpaPreferencesManager.DEFAULT_JPA_PLATFORM_2_0_PREF_KEY;
 		}
 		else {
 			throw new IllegalArgumentException("Illegal JPA facet version: " + jpaFacetVersion); //$NON-NLS-1$
 		}
-		setWorkspacePreference(preferenceKey, platformId);
+		JpaPreferencesManager.setWorkspacePreference(preferenceKey, platformId);
 	}
 	
 	/**
 	 * Return the JPA platform ID associated with the specified Eclipse project.
 	 */
 	public static String getJpaPlatformId(IProject project) {
-		return getProjectPreferences(project).get(JPA_PLATFORM_PREF_KEY, GenericPlatform.VERSION_1_0.getId());
+		return (new JpaPreferencesManager(project)).getJpaPlatformId();
 	}
 	
 	/**
@@ -483,27 +330,15 @@ public class JptJpaCorePlugin
 	 * Set the JPA platform ID associated with the specified Eclipse project.
 	 */
 	public static void setJpaPlatformId(IProject project, String jpaPlatformId) {
-		setProjectPreference(project, JPA_PLATFORM_PREF_KEY, jpaPlatformId);
-	}
-
-	/**
-	 * Return the preferences key used to look up an Eclipse project's
-	 * JPA platform ID.
-	 */
-	public static String getJpaPlatformIdPrefKey() {
-		return JPA_PLATFORM_PREF_KEY;
+		(new JpaPreferencesManager(project)).setJpaPlatformId(jpaPlatformId);
 	}
 
 	/**
 	 * Return the JPA "discover" flag associated with the specified
 	 * Eclipse project.
 	 */
-	public static boolean discoverAnnotatedClasses(IProject project) {
-		if (getProjectPreferences(project).get(DISCOVER_ANNOTATED_CLASSES, null) != null) {
-			return getProjectPreferences(project).getBoolean(DISCOVER_ANNOTATED_CLASSES, false);
-		}
-		//bug 354780 - made the mistake of changing the project metadata in the 3.0 release
-		return getProjectPreferences(project).getBoolean(LEGACY_DISCOVER_ANNOTATED_CLASSES, false);
+	public static boolean getDiscoverAnnotatedClasses(IProject project) {
+		return (new JpaPreferencesManager(project)).getDiscoverAnnotatedClasses();
 	}
 
 	/**
@@ -511,7 +346,7 @@ public class JptJpaCorePlugin
 	 * Eclipse project.
 	 */
 	public static void setDiscoverAnnotatedClasses(IProject project, boolean discoverAnnotatedClasses) {
-		setProjectPreference(project, DISCOVER_ANNOTATED_CLASSES, discoverAnnotatedClasses);
+		(new JpaPreferencesManager(project)).setDiscoverAnnotatedClasses(discoverAnnotatedClasses);
 	}
 
 	/**
@@ -519,12 +354,7 @@ public class JptJpaCorePlugin
 	 * specified Eclipse project.
 	 */
 	public static String getMetamodelSourceFolderName(IProject project) {
-		String metamodelSourceFolderName = getProjectPreferences(project).get(METAMODEL_SOURCE_FOLDER_NAME, null);
-		if (metamodelSourceFolderName != null) {
-			return metamodelSourceFolderName;
-		}
-		//bug 354780 - made the mistake of changing the project metadata in the 3.0 release
-		return getProjectPreferences(project).get(LEGACY_METAMODEL_SOURCE_FOLDER_NAME, null);
+		return (new JpaPreferencesManager(project)).getMetamodelSourceFolderName();
 	}
 
 	/**
@@ -532,59 +362,9 @@ public class JptJpaCorePlugin
 	 * specified Eclipse project.
 	 */
 	public static void setMetamodelSourceFolderName(IProject project, String metamodelSourceFolderName) {
-		setProjectPreference(project, METAMODEL_SOURCE_FOLDER_NAME, metamodelSourceFolderName);
-		//bug 354780 - made the mistake of changing the project metadata in the 3.0 release.
-		//make sure legacy setting is removed when turning off metamodel gen, if we don't then
-		//there will be no way to turn off meatamodel gen without sacrificing backwards compatibility
-		if(metamodelSourceFolderName == null) {
-			setProjectPreference(project, LEGACY_METAMODEL_SOURCE_FOLDER_NAME, null);
-		}
-		
-	}
-
-	/**
-	 * This method is called (via reflection) when the test plug-in is loaded.
-	 * The preferences end up getting flushed after the test case has deleted
-	 * its project, resulting in resource exceptions in the log, e.g.
-	 * <pre>
-	 *     Resource '/JpaProjectManagerTests' is not open.
-	 * </pre>
-	 * See <code>JptJpaCoreTestsPlugin.start(BundleContext)</code>
-	 */
-	@SuppressWarnings("unused")
-	private static void doNotFlushPreferences() {
-		flushPreferences = false;
-	}
-
-	/**
-	 * Flush preferences in an asynchronous Job because the flush request will
-	 * trigger a lock on the project, which can cause us some deadlocks (e.g.
-	 * when deleting the metamodel source folder).
-	 * Note: the flush will also remove the prefs node if it is empty
-	 */
-	private static void flush(IEclipsePreferences prefs) {
-		if (flushPreferences) {
-			new PreferencesFlushJob(prefs).schedule();
-		}
-	}
-
-	private static class PreferencesFlushJob extends Job {
-		private final IEclipsePreferences prefs;
-		PreferencesFlushJob(IEclipsePreferences prefs) {
-			super(NLS.bind(JptCoreMessages.PREFERENCES_FLUSH_JOB_NAME, prefs.absolutePath()));
-			this.prefs = prefs;
-		}
-		@Override
-		protected IStatus run(IProgressMonitor monitor) {
-			try {
-				this.prefs.flush();
-			} catch(BackingStoreException ex) {
-				log(ex);
-			}
-			return Status.OK_STATUS;
-		}
+		(new JpaPreferencesManager(project)).setMetamodelSourceFolderName(metamodelSourceFolderName);
 	}
-
+	
 	/**
 	 * Return the name of the connection profile associated with the specified
 	 * Eclipse project.
@@ -717,8 +497,7 @@ public class JptJpaCorePlugin
         INSTANCE.getLog().log(status);
     }
 
-
-	// ********** plug-in implementation **********
+	// ********** plug-in implementation **************************************************
 
 	public JptJpaCorePlugin() {
 		super();
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/InternalJpaProjectManager.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/InternalJpaProjectManager.java
index 9369ca97a9..5d4ab4175f 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/InternalJpaProjectManager.java
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/InternalJpaProjectManager.java
@@ -630,7 +630,7 @@ public class InternalJpaProjectManager
 		config.setConnectionProfileName(JptJpaCorePlugin.getConnectionProfileName(project));
 		config.setUserOverrideDefaultCatalog(JptJpaCorePlugin.getUserOverrideDefaultCatalog(project));
 		config.setUserOverrideDefaultSchema(JptJpaCorePlugin.getUserOverrideDefaultSchema(project));
-		config.setDiscoverAnnotatedClasses(JptJpaCorePlugin.discoverAnnotatedClasses(project));
+		config.setDiscoverAnnotatedClasses(JptJpaCorePlugin.getDiscoverAnnotatedClasses(project));
 		config.setMetamodelSourceFolderName(JptJpaCorePlugin.getMetamodelSourceFolderName(project));
 		return config;
 	}
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/facet/JpaFacetUninstallDelegate.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/facet/JpaFacetUninstallDelegate.java
index b71b2ce923..1559337946 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/facet/JpaFacetUninstallDelegate.java
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/facet/JpaFacetUninstallDelegate.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2006, 2010 Oracle. All rights reserved.
+ * Copyright (c) 2006, 2012 Oracle. All rights reserved.
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v1.0, which accompanies this distribution
  * and is available at http://www.eclipse.org/legal/epl-v10.html.
@@ -13,6 +13,7 @@ import org.eclipse.core.resources.IProject;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.jpt.jpa.core.JptJpaCorePlugin;
+import org.eclipse.jpt.jpa.core.internal.prefs.JpaValidationPreferencesManager;
 import org.eclipse.wst.common.project.facet.core.IDelegate;
 import org.eclipse.wst.common.project.facet.core.IProjectFacetVersion;
 
@@ -22,7 +23,7 @@ public class JpaFacetUninstallDelegate
 	public void execute(IProject project, IProjectFacetVersion fv,
 			Object config, IProgressMonitor monitor) throws CoreException {
 		
-		JptJpaCorePlugin.clearProjectPreferences(project);
+		(new JpaValidationPreferencesManager(project)).clearProjectPreferences();
 		JptJpaCorePlugin.clearProjectPersistentProperties(project);
 	}
 }
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/prefs/JpaPreferenceInitializer.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/prefs/JpaPreferenceInitializer.java
index d6fd0418ca..c8136cf4b4 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/prefs/JpaPreferenceInitializer.java
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/prefs/JpaPreferenceInitializer.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2006, 2009 Oracle. All rights reserved.
+ * Copyright (c) 2006, 2012 Oracle. All rights reserved.
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v1.0, which accompanies this distribution
  * and is available at http://www.eclipse.org/legal/epl-v10.html.
@@ -10,7 +10,6 @@
 package org.eclipse.jpt.jpa.core.internal.prefs;
 
 import org.eclipse.core.runtime.preferences.AbstractPreferenceInitializer;
-import org.eclipse.jpt.jpa.core.JptJpaCorePlugin;
 
 /**
  * Class used to initialize default preference values.
@@ -21,6 +20,6 @@ public class JpaPreferenceInitializer
 {
 	@Override
 	public void initializeDefaultPreferences() {
-		JptJpaCorePlugin.initializeDefaultPreferences();
+		JpaPreferencesManager.initializeDefaultPreferences();
 	}
 }
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/prefs/JpaPreferencesManager.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/prefs/JpaPreferencesManager.java
new file mode 100644
index 0000000000..ad2e9e34ce
--- /dev/null
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/prefs/JpaPreferencesManager.java
@@ -0,0 +1,360 @@
+/*******************************************************************************
+* Copyright (c) 2012 Oracle. All rights reserved.
+* This program and the accompanying materials are made available under the
+* terms of the Eclipse Public License v1.0, which accompanies this distribution
+* and is available at http://www.eclipse.org/legal/epl-v10.html.
+* 
+* Contributors:
+*     Oracle - initial API and implementation
+*******************************************************************************/
+package org.eclipse.jpt.jpa.core.internal.prefs;
+
+import org.eclipse.core.resources.IProject;
+import org.eclipse.core.resources.ProjectScope;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.core.runtime.IStatus;
+import org.eclipse.core.runtime.Status;
+import org.eclipse.core.runtime.jobs.Job;
+import org.eclipse.core.runtime.preferences.DefaultScope;
+import org.eclipse.core.runtime.preferences.IEclipsePreferences;
+import org.eclipse.core.runtime.preferences.IScopeContext;
+import org.eclipse.core.runtime.preferences.InstanceScope;
+import org.eclipse.jpt.jpa.core.JpaFacet;
+import org.eclipse.jpt.jpa.core.JptJpaCorePlugin;
+import org.eclipse.jpt.jpa.core.internal.JptCoreMessages;
+import org.eclipse.jpt.jpa.core.internal.platform.JpaPlatformManagerImpl;
+import org.eclipse.jpt.jpa.core.platform.GenericPlatform;
+import org.eclipse.jpt.jpa.core.platform.JpaPlatformDescription;
+import org.eclipse.osgi.util.NLS;
+import org.osgi.service.prefs.BackingStoreException;
+
+/**
+ *  JptPreferencesManager
+ */
+public class JpaPreferencesManager
+{
+	private final IProject project;
+
+	private static volatile boolean flushPreferences = true;
+
+	// ********** public constants **********
+	
+	/**
+	 * The key for storing a JPA project's platform ID in the Eclipse
+	 * project's preferences.
+	 */
+	protected static final String JPA_PLATFORM_PREF_KEY = JptJpaCorePlugin.LEGACY_PLUGIN_ID_ + "platform";  //$NON-NLS-1$
+
+	/**
+	 * The old key for storing the default JPA platform ID in the workspace preferences.
+	 * @deprecated  As of version 2.3.  Instead use {@link #DEFAULT_JPA_PLATFORM_1_0_PREF_KEY} or 
+	 * 		{@link #DEFAULT_JPA_PLATFORM_2_0_PREF_KEY}
+	 */
+	@Deprecated
+	public static final String DEFAULT_JPA_PLATFORM_PREF_KEY = "defaultJpaPlatform"; //$NON-NLS-1$
+	
+	/**
+	 * The key for storing the default JPA platform ID for JPA 1.0 in the workspace preferences.
+	 */
+	public static final String DEFAULT_JPA_PLATFORM_1_0_PREF_KEY = 
+			DEFAULT_JPA_PLATFORM_PREF_KEY + "_" + JpaFacet.VERSION_1_0.getVersionString(); //$NON-NLS-1$
+	
+	/**
+	 * The key for storing the default JPA platform ID for JPA 2.0 in the workspace preferences.
+	 */
+	public static final String DEFAULT_JPA_PLATFORM_2_0_PREF_KEY = 
+			DEFAULT_JPA_PLATFORM_PREF_KEY + "_" + JpaFacet.VERSION_2_0.getVersionString(); //$NON-NLS-1$
+
+	/**
+	 * The key for storing a JPA project's "discover" flag in the Eclipse
+	 * project's preferences.
+	 */
+	public static final String DISCOVER_ANNOTATED_CLASSES = JptJpaCorePlugin.PLUGIN_ID_ + "discoverAnnotatedClasses";  //$NON-NLS-1$
+
+	//bug 354780 - made the mistake of changing the project metadata in the 3.0 release
+	protected static final String LEGACY_DISCOVER_ANNOTATED_CLASSES = JptJpaCorePlugin.LEGACY_PLUGIN_ID_ + "discoverAnnotatedClasses";  //$NON-NLS-1$
+
+	/**
+	 * The key for storing the name of a JPA project's metamodel source folder
+	 * in the Eclipse project's preferences.
+	 */
+	public static final String METAMODEL_SOURCE_FOLDER_NAME = JptJpaCorePlugin.PLUGIN_ID_ + "metamodelSourceFolderName";  //$NON-NLS-1$
+
+	//bug 354780 - made the mistake of changing the project metadata in the 3.0 release
+	protected static final String LEGACY_METAMODEL_SOURCE_FOLDER_NAME = JptJpaCorePlugin.LEGACY_PLUGIN_ID_ + "metamodelSourceFolderName";  //$NON-NLS-1$
+
+	
+	// ********** static methods **************************************************
+	
+	public static void clearWorkspacePreferences() throws BackingStoreException {
+		getWorkspacePreferences().clear();
+	}
+
+	// ********** preferences **********
+
+	/**
+	 * Return the Dali preferences for the specified context.
+	 */
+	private static IEclipsePreferences getPreferences(IScopeContext context) {
+		return context.getNode(JptJpaCorePlugin.LEGACY_PLUGIN_ID);
+	}
+
+	/**
+	 * Return the Dali preferences for the current workspace instance.
+	 */
+	public static IEclipsePreferences getWorkspacePreferences() {
+		return getPreferences(InstanceScope.INSTANCE);
+	}
+	
+	/**
+	 * Return the default Dali preferences
+	 * @see JpaPreferenceInitializer
+	 */
+	 public static IEclipsePreferences getDefaultPreferences() {
+		return getPreferences(DefaultScope.INSTANCE);
+	}
+	
+	public static void initializeDefaultPreferences() {
+		IEclipsePreferences node = getDefaultPreferences();
+
+		// default JPA platforms
+		JpaPlatformDescription defaultPlatform_1_0 = 
+				JpaPlatformManagerImpl.instance().getDefaultJpaPlatform(JpaFacet.VERSION_1_0);
+		if (defaultPlatform_1_0 == null) {
+			defaultPlatform_1_0 = GenericPlatform.VERSION_1_0;
+		}
+		node.put(DEFAULT_JPA_PLATFORM_1_0_PREF_KEY, defaultPlatform_1_0.getId());
+		
+		JpaPlatformDescription defaultPlatform_2_0 = 
+				JpaPlatformManagerImpl.instance().getDefaultJpaPlatform(JpaFacet.VERSION_2_0);
+		if (defaultPlatform_2_0 == null) {
+			defaultPlatform_2_0 = GenericPlatform.VERSION_2_0;
+		}
+		node.put(DEFAULT_JPA_PLATFORM_2_0_PREF_KEY, defaultPlatform_2_0.getId());
+	}
+
+	// ********** workspace preference **********
+
+	public static String getWorkspacePreference(String key, String defaultValue) {
+		return getWorkspacePreferences().get(key, defaultValue);
+	}
+
+	public static String getWorkspacePreference(String key) {
+		return getWorkspacePreferences().get(key, null);
+	}
+
+	public static void setWorkspacePreference(String key, String value) {
+		IEclipsePreferences wkspPrefs = getWorkspacePreferences();
+		if(value == null) {
+			wkspPrefs.remove(key);
+		}
+		else {
+			wkspPrefs.put(key, value);
+		}
+		flush(wkspPrefs);
+	}
+
+	// ********** private static methods **********
+
+	/**
+	 * This method is called (via reflection) when the test plug-in is loaded.
+	 * The preferences end up getting flushed after the test case has deleted
+	 * its project, resulting in resource exceptions in the log, e.g.
+	 * <pre>
+	 *     Resource '/JpaProjectManagerTests' is not open.
+	 * </pre>
+	 * See <code>JptJpaCoreTestsPlugin.start(BundleContext)</code>
+	 */
+	@SuppressWarnings("unused")
+	private static void doNotFlushPreferences() {
+		flushPreferences = false;
+	}
+
+	/**
+	 * Flush preferences in an asynchronous Job because the flush request will
+	 * trigger a lock on the project, which can cause us some deadlocks (e.g.
+	 * when deleting the metamodel source folder).
+	 * Note: the flush will also remove the prefs node if it is empty
+	 */
+	private static void flush(IEclipsePreferences prefs) {
+		if (flushPreferences) {
+			new PreferencesFlushJob(prefs).schedule();
+		}
+	}
+
+	private static class PreferencesFlushJob extends Job {
+		private final IEclipsePreferences prefs;
+		PreferencesFlushJob(IEclipsePreferences prefs) {
+			super(NLS.bind(JptCoreMessages.PREFERENCES_FLUSH_JOB_NAME, prefs.absolutePath()));
+			this.prefs = prefs;
+		}
+		@Override
+		protected IStatus run(IProgressMonitor monitor) {
+			try {
+				this.prefs.flush();
+			} 
+			catch(BackingStoreException ex) {
+				JptJpaCorePlugin.log(ex);
+			}
+			return Status.OK_STATUS;
+		}
+	}
+
+	// ********** implementation **************************************************
+
+	public JpaPreferencesManager(IProject project) {
+		if(project == null) {
+			throw new RuntimeException("Project is null"); 	//$NON-NLS-1$
+		}
+		this.project = project;
+	}
+
+	// ********** query **********
+
+	public String getPreference(String key) {
+		String preference = this.getProjectPreference(key);
+		
+		// check workspace preferences if not a project preference
+		if(preference == null) {
+			preference = getWorkspacePreference(key);
+		}
+		return preference;
+	}
+
+	// ********** preferences **********
+
+	/**
+	 * Return the Dali preferences for the specified Eclipse project.
+	 */
+	protected IEclipsePreferences getProjectPreferences() {
+		return getPreferences(new ProjectScope(this.project));
+	}
+	
+	/**
+	 * Clears the project of JPA-specific preferences
+	 */
+	public void clearProjectPreferences() {
+		this.clearProjectPreferences(
+				JPA_PLATFORM_PREF_KEY,
+				DISCOVER_ANNOTATED_CLASSES,
+				METAMODEL_SOURCE_FOLDER_NAME,
+				LEGACY_DISCOVER_ANNOTATED_CLASSES,
+				LEGACY_METAMODEL_SOURCE_FOLDER_NAME);
+	}
+	
+	/**
+	 * Clears the specified preferences
+	 */
+	public void clearProjectPreferences(String ... preferenceKeys) {
+		IEclipsePreferences projectPrefs = this.getProjectPreferences();
+		for(String preferenceKey : preferenceKeys) {
+			projectPrefs.remove(preferenceKey);
+		}
+		flush(projectPrefs);
+	}
+
+	// ********** project preference **********
+
+	public String getProjectPreference(String key, String defaultValue) {
+		return this.getProjectPreferences().get(key, defaultValue);
+	}
+	
+	public String getProjectPreference(String key) {
+		return this.getProjectPreferences().get(key, null);
+	}
+	
+	public void setProjectPreference(String key, String value) {
+		IEclipsePreferences projectPrefs = this.getProjectPreferences();
+		if(value == null) {
+			projectPrefs.remove(key);
+		}
+		else {
+			projectPrefs.put(key, value);
+		}
+		flush(projectPrefs);
+	}
+
+	public boolean getProjectPreference(String key, boolean defaultBooleanValue) {
+		return this.getProjectPreferences().getBoolean(key, defaultBooleanValue);
+	}
+
+	public void setProjectPreference(String key, boolean booleanValue) {
+		IEclipsePreferences projectPrefs = this.getProjectPreferences();
+		if( ! booleanValue) {
+			projectPrefs.remove(key);
+		}
+		else {
+			projectPrefs.putBoolean(key, booleanValue);
+		}
+		flush(projectPrefs);
+	}
+
+	// ********** getters/setters *********
+
+	/**
+	 * Return the JPA platform ID associated with the specified Eclipse project.
+	 */
+	public String getJpaPlatformId() {
+		return this.getProjectPreference(JPA_PLATFORM_PREF_KEY, GenericPlatform.VERSION_1_0.getId());
+	}
+
+	/**
+	 * Set the JPA platform ID associated with the specified Eclipse project.
+	 */
+	public void setJpaPlatformId(String jpaPlatformId) {
+		this.setProjectPreference(JPA_PLATFORM_PREF_KEY, jpaPlatformId);
+	}
+
+	/**
+	 * Return the JPA "discover" flag associated with the specified
+	 * Eclipse project.
+	 */
+	public boolean getDiscoverAnnotatedClasses() {
+		if (this.getProjectPreference(DISCOVER_ANNOTATED_CLASSES, null) != null) {
+			return this.getProjectPreference(DISCOVER_ANNOTATED_CLASSES, false);
+		}
+		//bug 354780 - made the mistake of changing the project metadata in the 3.0 release
+		return this.getProjectPreference(LEGACY_DISCOVER_ANNOTATED_CLASSES, false);
+	}
+	
+	 /** 
+	  * Set the JPA "discover" flag associated with the specified
+	 * Eclipse project.
+	 */
+	public void setDiscoverAnnotatedClasses(boolean discoverAnnotatedClasses) {
+		this.setProjectPreference(DISCOVER_ANNOTATED_CLASSES, discoverAnnotatedClasses);
+	}
+
+	/**
+	 * Return the name of the metamodel source folder associated with the
+	 * specified Eclipse project.
+	 */
+	public String getMetamodelSourceFolderName() {
+		String metamodelSourceFolderName = this.getProjectPreference(METAMODEL_SOURCE_FOLDER_NAME, null);
+		if (metamodelSourceFolderName != null) {
+			return metamodelSourceFolderName;
+		}
+		//bug 354780 - made the mistake of changing the project metadata in the 3.0 release
+		return this.getProjectPreference(LEGACY_METAMODEL_SOURCE_FOLDER_NAME, null);
+	}
+
+	/**
+	 * Set the name of the metamodel source folder associated with the
+	 * specified Eclipse project.
+	 */
+	public void setMetamodelSourceFolderName(String metamodelSourceFolderName) {
+		this.setProjectPreference(METAMODEL_SOURCE_FOLDER_NAME, metamodelSourceFolderName);
+		//bug 354780 - made the mistake of changing the project metadata in the 3.0 release.
+		//make sure legacy setting is removed when turning off metamodel gen, if we don't then
+		//there will be no way to turn off meatamodel gen without sacrificing backwards compatibility
+		if(metamodelSourceFolderName == null) {
+			this.setProjectPreference(LEGACY_METAMODEL_SOURCE_FOLDER_NAME, null);
+		}
+	}
+
+	// ********** protected methods **********
+	
+	protected IProject getProject() {
+		return this.project;
+	}
+}
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/prefs/JpaValidationPreferencesManager.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/prefs/JpaValidationPreferencesManager.java
new file mode 100644
index 0000000000..a721373cb5
--- /dev/null
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/prefs/JpaValidationPreferencesManager.java
@@ -0,0 +1,127 @@
+/*******************************************************************************
+* Copyright (c) 2012 Oracle. All rights reserved.
+* This program and the accompanying materials are made available under the
+* terms of the Eclipse Public License v1.0, which accompanies this distribution
+* and is available at http://www.eclipse.org/legal/epl-v10.html.
+* 
+* Contributors:
+*     Oracle - initial API and implementation
+*******************************************************************************/
+package org.eclipse.jpt.jpa.core.internal.prefs;
+
+import org.eclipse.core.resources.IProject;
+import org.eclipse.core.resources.IResource;
+import org.eclipse.jpt.common.utility.internal.Tools;
+import org.eclipse.wst.validation.internal.provisional.core.IMessage;
+
+/**
+ *  JpaValidationPreferencesManager
+ */
+public class JpaValidationPreferencesManager extends JpaPreferencesManager
+{
+	/*
+	 * prefix for all preference strings.  This is only used internally.
+	 * Clients of get*LevelProblemPrefernce() and set*LevelProblemPreference 
+	 * should not include the prefix.
+	 */
+	private static final String PROBLEM_PREFIX = "problem."; //$NON-NLS-1$
+
+	public static final String ERROR = "error"; //$NON-NLS-1$
+	public static final String WARNING = "warning"; //$NON-NLS-1$
+	public static final String INFO = "info"; //$NON-NLS-1$
+	public static final String IGNORE = "ignore"; //$NON-NLS-1$
+
+	public static final int NO_SEVERITY_PREFERENCE = -1;
+
+	public static final String WORKSPACE_PREFERENCES_OVERRIDEN = "workspace_preferences_overriden"; //$NON-NLS-1$
+
+	// ********** public static methods **********
+
+	/**
+	 * Returns only the severity level of a given problem preference.  This does not
+	 * include information on whether the problem is ignored.  See isProblemIgnored.
+	 * @return an IMessage severity level
+	 */
+	public static int getProblemSeverityPreference(IResource targetObject, String messageId) {
+		String problemPreference = (new JpaValidationPreferencesManager(targetObject.getProject())).
+															getPreference(appendProblemPrefix(messageId));
+
+		if(problemPreference == null) {
+			return NO_SEVERITY_PREFERENCE;
+		} 
+		else if (problemPreference.equals(ERROR)) {
+			return IMessage.HIGH_SEVERITY;
+		} 
+		else if (problemPreference.equals(WARNING)) {
+			return IMessage.NORMAL_SEVERITY;
+		} 
+		else if (problemPreference.equals(INFO)) {
+			return IMessage.LOW_SEVERITY;
+		}
+		return NO_SEVERITY_PREFERENCE;
+	}
+
+	// ********** workspace preference **********
+
+	/**
+	 * Returns the String value of the problem preference from the workspace preferences
+	 */
+	public static String getWorkspaceLevelProblemPreference(String messageId) {
+		return getWorkspacePreference(appendProblemPrefix(messageId));
+	}
+	
+	public static void setWorkspaceLevelProblemPreference(String messageId, String problemPreference) {
+		setWorkspacePreference(appendProblemPrefix(messageId), problemPreference);
+	}
+	
+	protected static String appendProblemPrefix(String messageId) {
+		return PROBLEM_PREFIX + messageId;
+	}
+
+	// ********** implementation **************************************************
+
+	public JpaValidationPreferencesManager(IProject project) {
+		
+		super(project);
+	}
+
+	// ********** behavior **********
+
+	/**
+	 * Return whether the specified problem should <em>not</em> be ignored based
+	 * on project or workspace preferences.
+	 */
+	public boolean problemIsNotIgnored(String messageId) {
+		return ! problemIsIgnored(messageId);
+	}
+
+	/**
+	 * Return whether the specified problem should be ignored based on project or
+	 * workspace preferences.
+	 */
+	public boolean problemIsIgnored(String messageId) {
+		return Tools.valuesAreEqual(this.getPreference(appendProblemPrefix(messageId)), IGNORE);
+	}
+
+	public boolean projectHasSpecificOptions() {
+		return this.getProjectPreference(WORKSPACE_PREFERENCES_OVERRIDEN, false);
+	}
+
+	public void setProjectHasSpecificOptions(boolean booleanValue) {
+		this.setProjectPreference(WORKSPACE_PREFERENCES_OVERRIDEN, booleanValue);
+	}
+	
+	// ********** project preference **********
+
+	/**
+	 * Returns the String value of the problem preference from the project preferences
+	 */
+	public String getProjectLevelProblemPreference(String messageId) {
+		return this.getProjectPreference(appendProblemPrefix(messageId));
+	}
+	
+	public void setProjectLevelProblemPreference(String messageId, String problemPreference) {
+		this.setProjectPreference(appendProblemPrefix(messageId), problemPreference);
+	}
+	
+}
\ No newline at end of file
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/validation/DefaultJpaValidationMessages.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/validation/DefaultJpaValidationMessages.java
index 366250c267..7a0dd08990 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/validation/DefaultJpaValidationMessages.java
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/validation/DefaultJpaValidationMessages.java
@@ -15,6 +15,7 @@ import org.eclipse.jpt.common.core.utility.TextRange;
 import org.eclipse.jpt.common.utility.internal.StringTools;
 import org.eclipse.jpt.jpa.core.JpaNode;
 import org.eclipse.jpt.jpa.core.JptJpaCorePlugin;
+import org.eclipse.jpt.jpa.core.internal.prefs.JpaValidationPreferencesManager;
 import org.eclipse.wst.validation.internal.core.Message;
 import org.eclipse.wst.validation.internal.provisional.core.IMessage;
 
@@ -96,8 +97,8 @@ public class DefaultJpaValidationMessages {
 	{
 		public IMessage buildMessage(int severity, String messageId, String[] parms, IResource targetObject) {
 			// check for preference override
-			int prefSeverity = JpaValidationPreferences.getProblemSeverityPreference(targetObject, messageId);
-			if (prefSeverity != JpaValidationPreferences.NO_SEVERITY_PREFERENCE){
+			int prefSeverity = JpaValidationPreferencesManager.getProblemSeverityPreference(targetObject, messageId);
+			if (prefSeverity != JpaValidationPreferencesManager.NO_SEVERITY_PREFERENCE){
 				severity = prefSeverity;
 			}
 			IMessage message = new Message(JpaValidationMessages.BUNDLE_NAME, severity, messageId, parms, targetObject);
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/validation/JpaValidationPreferences.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/validation/JpaValidationPreferences.java
deleted file mode 100644
index da9b129a1b..0000000000
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/validation/JpaValidationPreferences.java
+++ /dev/null
@@ -1,138 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2005, 2012 Oracle. All rights reserved.
- * This program and the accompanying materials are made available under the
- * terms of the Eclipse Public License v1.0, which accompanies this distribution
- * and is available at http://www.eclipse.org/legal/epl-v10.html.
- * 
- * Contributors:
- *     Oracle - initial API and implementation
- ******************************************************************************/
-package org.eclipse.jpt.jpa.core.internal.validation;
-
-import org.eclipse.core.resources.IProject;
-import org.eclipse.core.resources.IResource;
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
-import org.eclipse.jpt.common.utility.internal.Tools;
-import org.eclipse.jpt.jpa.core.JptJpaCorePlugin;
-import org.eclipse.wst.validation.internal.provisional.core.IMessage;
-import org.osgi.service.prefs.BackingStoreException;
-
-//TODO:  Probably want to merge the behavior in this class into JptJpaCorePlugin
-public class JpaValidationPreferences {
-
-	/*
-	 * prefix for all preference strings.  This is only used internally.
-	 * Clients of get*LevelProblemPrefernce() and set*LevelProblemPreference 
-	 * should not include the prefix.
-	 */
-	private static final String PROBLEM_PREFIX = "problem."; //$NON-NLS-1$
-
-	public static final String ERROR = "error"; //$NON-NLS-1$
-	public static final String WARNING = "warning"; //$NON-NLS-1$
-	public static final String INFO = "info"; //$NON-NLS-1$
-	public static final String IGNORE = "ignore"; //$NON-NLS-1$
-
-	static final int NO_SEVERITY_PREFERENCE = -1;
-
-	public static final String WORKSPACE_PREFERENCES_OVERRIDEN = "workspace_preferences_overriden"; //$NON-NLS-1$
-
-	/**
-	 * Returns only the severity level of a given problem preference.  This does not
-	 * include information on whether the problem is ignored.  See isProblemIgnored.
-	 * @return an IMessage severity level
-	 */
-	public static int getProblemSeverityPreference(IResource targetObject, String messageId) {
-		String problemPreference = getPreference(targetObject.getProject(), messageId);
-		
-		if (problemPreference == null){
-			return NO_SEVERITY_PREFERENCE;
-		}
-		if (problemPreference.equals(ERROR)){
-			return IMessage.HIGH_SEVERITY;
-		}
-		if (problemPreference.equals(WARNING)){
-			return IMessage.NORMAL_SEVERITY;
-		}
-		if (problemPreference.equals(INFO)){
-			return IMessage.LOW_SEVERITY;
-		}
-		return NO_SEVERITY_PREFERENCE;
-	}
-
-	/**
-	 * Return whether the specified problem should <em>not</em> be ignored based
-	 * on project or workspace preferences.
-	 */
-	public static boolean problemIsNotIgnored(IProject project, String messageId) {
-		return ! problemIsIgnored(project, messageId);
-	}
-
-	/**
-	 * Return whether the specified problem should be ignored based on project or
-	 * workspace preferences.
-	 */
-	public static boolean problemIsIgnored(IProject project, String messageId) {
-		return Tools.valuesAreEqual(getPreference(project, messageId), IGNORE);
-	}
-
-	private static String getPreference(IProject project, String messageId) {
-		String problemPreference = null;
-		problemPreference = getProjectLevelProblemPreference(project, messageId);
-		//if severity is still null, check the workspace preferences
-		if (problemPreference == null) {
-			problemPreference = getWorkspaceLevelProblemPreference(messageId);
-		}
-		return problemPreference;
-	}
-
-	/**
-	 * Returns the String value of the problem preference from the project preferences
-	 */
-	public static String getProjectLevelProblemPreference(IProject project, String messageId){
-		return getPreference(JptJpaCorePlugin.getProjectPreferences(project), messageId);
-	}
-
-	public static void setProjectLevelProblemPreference(IProject project, String messageId, String problemPreference) {
-		IEclipsePreferences projectPreferences = JptJpaCorePlugin.getProjectPreferences(project);
-		setPreference(projectPreferences, messageId, problemPreference);
-		flush(projectPreferences);
-	}
-
-	/**
-	 * Returns the String value of the problem preference from the workspace preferences
-	 */
-	public static String getWorkspaceLevelProblemPreference(String messageId){
-		return getPreference(JptJpaCorePlugin.getWorkspacePreferences(), messageId);
-	}
-
-	public static void setWorkspaceLevelProblemPreference(String messageId, String problemPreference) {
-		IEclipsePreferences workspacePreferences = JptJpaCorePlugin.getWorkspacePreferences();
-		setPreference(workspacePreferences, messageId, problemPreference);
-		flush(workspacePreferences);
-	}
-
-	private static String getPreference(IEclipsePreferences preferences, String messageId) {
-		return preferences.get(appendProblemPrefix(messageId), null);
-	}
-
-	private static void setPreference(IEclipsePreferences preferences, String messageId, String problemPreference) {
-		if (problemPreference == null){
-			preferences.remove(appendProblemPrefix(messageId));
-		}
-		else {
-			preferences.put(appendProblemPrefix(messageId), problemPreference);
-		}
-	}
-
-	private static String appendProblemPrefix(String messageId) {
-		return PROBLEM_PREFIX + messageId;
-	}
-
-	public static void flush(IEclipsePreferences prefs) {
-		try {
-			prefs.flush();
-		} catch(BackingStoreException ex) {
-			JptJpaCorePlugin.log(ex);
-		}
-	}
-}
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/validation/JpaValidator.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/validation/JpaValidator.java
index 05d2881d19..00da287307 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/validation/JpaValidator.java
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/internal/validation/JpaValidator.java
@@ -16,6 +16,7 @@ import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.jpt.jpa.core.JpaProject;
 import org.eclipse.jpt.jpa.core.JptJpaCorePlugin;
+import org.eclipse.jpt.jpa.core.internal.prefs.JpaValidationPreferencesManager;
 import org.eclipse.wst.validation.AbstractValidator;
 import org.eclipse.wst.validation.ValidationResult;
 import org.eclipse.wst.validation.ValidationState;
@@ -90,7 +91,7 @@ public class JpaValidator
 		this.clearMarkers(project);
 		for (IMessage message : messages) {
 			// check preferences for IGNORE
-			if (JpaValidationPreferences.problemIsNotIgnored(project, message.getId())) {
+			if ((new JpaValidationPreferencesManager(project)).problemIsNotIgnored(message.getId())) {
 				reporter.addMessage(this, message);
 			}
 		}
diff --git a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/jpql/JpaJpqlQueryHelper.java b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/jpql/JpaJpqlQueryHelper.java
index e5af6f7bc3..0b1c7ee76f 100644
--- a/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/jpql/JpaJpqlQueryHelper.java
+++ b/jpa/plugins/org.eclipse.jpt.jpa.core/src/org/eclipse/jpt/jpa/core/jpql/JpaJpqlQueryHelper.java
@@ -14,6 +14,7 @@
 package org.eclipse.jpt.jpa.core.jpql;
 
 import java.util.List;
+
 import org.eclipse.core.resources.IResource;
 import org.eclipse.jpt.common.core.internal.utility.SimpleTextRange;
 import org.eclipse.jpt.common.core.utility.TextRange;
@@ -21,9 +22,9 @@ import org.eclipse.jpt.jpa.core.JpaProject;
 import org.eclipse.jpt.jpa.core.context.AttributeMapping;
 import org.eclipse.jpt.jpa.core.context.NamedQuery;
 import org.eclipse.jpt.jpa.core.context.persistence.PersistenceUnit;
+import org.eclipse.jpt.jpa.core.internal.prefs.JpaValidationPreferencesManager;
 import org.eclipse.jpt.jpa.core.internal.validation.DefaultJpaValidationMessages;
 import org.eclipse.jpt.jpa.core.internal.validation.JpaValidationMessages;
-import org.eclipse.jpt.jpa.core.internal.validation.JpaValidationPreferences;
 import org.eclipse.jpt.jpa.core.jpql.spi.JpaManagedTypeProvider;
 import org.eclipse.jpt.jpa.core.jpql.spi.JpaQuery;
 import org.eclipse.persistence.jpa.jpql.AbstractJPQLQueryHelper;
@@ -180,7 +181,7 @@ public abstract class JpaJpqlQueryHelper extends AbstractJPQLQueryHelper {
 	}
 
 	protected int getValidationPreference(NamedQuery namedQuery) {
-		return JpaValidationPreferences.getProblemSeverityPreference(
+		return JpaValidationPreferencesManager.getProblemSeverityPreference(
 			namedQuery.getResource(),
 			JpaValidationMessages.JPQL_QUERY_VALIDATION
 		);
@@ -212,7 +213,7 @@ public abstract class JpaJpqlQueryHelper extends AbstractJPQLQueryHelper {
 	 * @return The global severity for validating JPQL queries
 	 */
 	protected int severity(IResource targetObject) {
-		return JpaValidationPreferences.getProblemSeverityPreference(
+		return JpaValidationPreferencesManager.getProblemSeverityPreference(
 			targetObject,
 			JpaValidationMessages.JPQL_QUERY_VALIDATION
 		);