upgrade to Neo4j 2.0.1

DesktopNeo4j/manifest.mf

@@ -1,7 +1,7 @@
-Manifest-Version: 1.0
-AutoUpdate-Show-In-Client: false
-OpenIDE-Module: org.gephi.desktop.neo4j
-OpenIDE-Module-Layer: org/gephi/desktop/neo4j/layer.xml
-OpenIDE-Module-Localizing-Bundle: org/gephi/desktop/neo4j/Bundle.properties
-OpenIDE-Module-Specification-Version: 1.0.2
-
+Manifest-Version: 1.0
+AutoUpdate-Show-In-Client: false
+OpenIDE-Module: org.gephi.desktop.neo4j
+OpenIDE-Module-Layer: org/gephi/desktop/neo4j/layer.xml
+OpenIDE-Module-Localizing-Bundle: org/gephi/desktop/neo4j/Bundle.properties
+OpenIDE-Module-Specification-Version: 1.0.2
+

DesktopNeo4j/nbproject/project.properties

@@ -1,5 +1,5 @@
-javac.source=1.6
-javac.compilerargs=-Xlint -Xlint:-serial
-license.file=../agpl-3.0.txt
-nbm.module.author=Gephi.org
-nbm.needs.restart=true
+javac.source=1.7
+javac.compilerargs=-Xlint -Xlint:-serial
+license.file=../agpl-3.0.txt
+nbm.module.author=Gephi.org
+nbm.needs.restart=true

DesktopNeo4j/src/org/gephi/desktop/neo4j/Neo4jMenuAction.java

@@ -34,6 +34,8 @@ License, or (at your option) any later version.
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.io.File;
+import java.util.Arrays;
+import java.util.Collection;
 import javax.swing.AbstractAction;
 import javax.swing.JFileChooser;
 import javax.swing.JMenu;
@@ -56,6 +58,7 @@ License, or (at your option) any later version.
 import org.gephi.utils.longtask.spi.LongTask;
 import org.gephi.visualization.VizController;
 import org.neo4j.graphdb.GraphDatabaseService;
+import org.neo4j.kernel.StoreLockException;
 import org.netbeans.validation.api.ui.ValidationPanel;
 import org.openide.DialogDescriptor;
 import org.openide.DialogDisplayer;
@@ -180,14 +183,21 @@ private static void initProject() {
         }
     }
 
-    private static void handleLocalDatabaseError(Exception e) {
+    private static void handleLocalDatabaseError(Exception e, GraphDatabaseService db) {
         String errorMessage = null;
 
-        if (e.getClass() == Neo4jStoreAlreadyInUseException.class)
+        Collection<Class> inUseExceptions = Arrays.<Class>asList(Neo4jStoreAlreadyInUseException.class,StoreLockException.class);
+        if (inUseExceptions.contains(e.getClass()) || inUseExceptions.contains(e.getCause().getClass()))
             errorMessage = NbBundle.getMessage(Neo4jMenuAction.class, "CTL_Neo4j_DatabaseStorageAlreadyInUse");
 
         NotifyDescriptor notifyDescriptor = new NotifyDescriptor.Message(errorMessage, JOptionPane.WARNING_MESSAGE);
         DialogDisplayer.getDefault().notify(notifyDescriptor);
+
+        try {
+            if (db!=null) db.shutdown();
+        } catch(Exception ex) {
+            // ignore
+        }
     }
 
     private static class FullImportMenuAction extends AbstractAction {
@@ -213,12 +223,16 @@ public void actionPerformed(ActionEvent e) {
                 NbPreferences.forModule(Neo4jMenuAction.class).put(IMPORT_LAST_PATH, neo4jDirectory.getParentFile().getAbsolutePath());
             }
 
-            GraphDatabaseService tempGraphDB;
+            GraphDatabaseService tempGraphDB = null;
             try {
                 tempGraphDB = Neo4jUtils.localDatabase(neo4jDirectory);
             }
             catch (Neo4jStoreAlreadyInUseException storeInUseException) {
-                handleLocalDatabaseError(storeInUseException);
+                handleLocalDatabaseError(storeInUseException,tempGraphDB);
+                return;
+            }
+            catch (RuntimeException exception) {
+                handleLocalDatabaseError(exception,tempGraphDB);
                 return;
             }
 
@@ -306,12 +320,12 @@ public void actionPerformed(ActionEvent e) {
                 NbPreferences.forModule(Neo4jMenuAction.class).put(IMPORT_LAST_PATH, neo4jDirectory.getParentFile().getAbsolutePath());
             }
 
-            GraphDatabaseService tempGraphDB;
+            GraphDatabaseService tempGraphDB = null;
             try {
                 tempGraphDB = Neo4jUtils.localDatabase(neo4jDirectory);
             }
             catch (Neo4jStoreAlreadyInUseException storeInUseException) {
-                handleLocalDatabaseError(storeInUseException);
+                handleLocalDatabaseError(storeInUseException,tempGraphDB);
                 return;
             }
 
@@ -407,12 +421,12 @@ public void actionPerformed(ActionEvent e) {
 
                         @Override
                         public void run() {
-                            GraphDatabaseService tempGraphDB;
+                            GraphDatabaseService tempGraphDB = null;
                             try {
                                 tempGraphDB = Neo4jUtils.localDatabase(neo4jDirectory);
                             }
                             catch (Neo4jStoreAlreadyInUseException storeInUseException) {
-                                handleLocalDatabaseError(storeInUseException);
+                                handleLocalDatabaseError(storeInUseException,tempGraphDB);
                                 return;
                             }
 

DesktopNeo4j/src/org/gephi/desktop/neo4j/ui/util/Neo4jUtils.java

@@ -26,7 +26,7 @@ License, or (at your option) any later version.
 import org.neo4j.graphdb.GraphDatabaseService;
 import org.neo4j.graphdb.RelationshipType;
 import org.neo4j.graphdb.TransactionFailureException;
-import org.neo4j.kernel.EmbeddedGraphDatabase;
+import org.neo4j.graphdb.factory.GraphDatabaseFactory;
 
 /**
  *
@@ -40,7 +40,10 @@ private Neo4jUtils() {
     public static GraphDatabaseService localDatabase(File neo4jDirectory) throws Neo4jStoreAlreadyInUseException {
 
         try {
-            return new EmbeddedGraphDatabase(neo4jDirectory.getAbsolutePath());
+            return new GraphDatabaseFactory()
+                    .newEmbeddedDatabaseBuilder(neo4jDirectory.getAbsolutePath())
+                    .setConfig("allow_store_upgrade","true")
+                    .newGraphDatabase();
         }
         catch (TransactionFailureException e) {
             if (e.getCause() instanceof IllegalStateException)

Neo4jPlugin/manifest.mf

@@ -1,6 +1,6 @@
-Manifest-Version: 1.0
-AutoUpdate-Show-In-Client: false
-OpenIDE-Module: org.gephi.neo4j.plugin
-OpenIDE-Module-Localizing-Bundle: org/gephi/neo4j/plugin/Bundle.properties
-OpenIDE-Module-Specification-Version: 1.0.3
-
+Manifest-Version: 1.0
+AutoUpdate-Show-In-Client: false
+OpenIDE-Module: org.gephi.neo4j.plugin
+OpenIDE-Module-Localizing-Bundle: org/gephi/neo4j/plugin/Bundle.properties
+OpenIDE-Module-Specification-Version: 1.0.3
+

Neo4jPlugin/nbproject/project.properties

@@ -1,5 +1,5 @@
-javac.source=1.6
-javac.compilerargs=-Xlint -Xlint:-serial
-license.file=../agpl-3.0.txt
-nbm.module.author=Gephi.org
-nbm.needs.restart=true
+javac.source=1.7
+javac.compilerargs=-Xlint -Xlint:-serial
+license.file=../agpl-3.0.txt
+nbm.module.author=Gephi.org
+nbm.needs.restart=true

Neo4jPlugin/src/org/gephi/neo4j/plugin/impl/GraphModelImportConverter.java

@@ -41,9 +41,10 @@ License, or (at your option) any later version.
 import org.gephi.project.api.WorkspaceListener;
 import org.gephi.project.api.WorkspaceProvider;
 import org.neo4j.graphdb.GraphDatabaseService;
+import org.neo4j.graphdb.Node;
 import org.neo4j.graphdb.Relationship;
-import org.neo4j.jmx.Primitives;
-import org.neo4j.management.Neo4jManager;
+import org.neo4j.kernel.GraphDatabaseAPI;
+import org.neo4j.kernel.impl.core.NodeManager;
 import org.openide.util.Lookup;
 
 /**
@@ -264,9 +265,8 @@ public static class Neo4jGraphModel {
 
         public Neo4jGraphModel(GraphDatabaseService graphDb) {
             this.graphDb = graphDb;
-
-            int numberOfNeo4jNodeIds = (int) Neo4jManager.get().getPrimitivesBean().getNumberOfNodeIdsInUse();
-
+            NodeManager nodeManager = ((GraphDatabaseAPI)graphDb).getDependencyResolver().resolveDependency(NodeManager.class);
+            int numberOfNeo4jNodeIds = (int) nodeManager.getNumberOfIdsInUse(Node.class);
             this.neo4jToGephiNodeMap = new TLongIntHashMap(numberOfNeo4jNodeIds, 1f);
             this.gephiToNeo4jNodeMap = new TIntLongHashMap(numberOfNeo4jNodeIds, 1f);
         }

Neo4jPlugin/src/org/gephi/neo4j/plugin/impl/Neo4jDelegateProviderImpl.java

@@ -28,6 +28,7 @@ License, or (at your option) any later version.
 import org.gephi.data.properties.PropertiesColumn;
 import org.neo4j.graphdb.DynamicRelationshipType;
 import org.neo4j.graphdb.GraphDatabaseService;
+import org.neo4j.graphdb.Transaction;
 
 
 /**
@@ -57,8 +58,14 @@ public String storageEngineName() {
     @Override
     public Object getNodeAttributeValue(Long delegateId, AttributeColumn attributeColumn) {
         GraphDatabaseService graphDB = GraphModelImportConverter.getGraphDBForCurrentWorkspace();
-
-        return graphDB.getNodeById(delegateId).getProperty(attributeColumn.getId());
+        Transaction tx = graphDB.beginTx();
+        try {
+            final Object value = graphDB.getNodeById(delegateId).getProperty(attributeColumn.getId());
+            tx.success();
+            return value;
+        } finally {
+            tx.close();
+        }
     }
 
     @Override
@@ -69,25 +76,45 @@ public void setNodeAttributeValue(Long delegateId, AttributeColumn attributeColu
 
         GraphDatabaseService graphDB = GraphModelImportConverter.getGraphDBForCurrentWorkspace();
 
-        graphDB.getNodeById(delegateId).setProperty(attributeColumn.getId(), nodeValue);
+        Transaction tx = graphDB.beginTx();
+        try {
+            graphDB.getNodeById(delegateId).setProperty(attributeColumn.getId(), nodeValue);
+            tx.success();
+        } finally {
+            tx.close();
+        }
     }
 
     @Override
     public void deleteNodeAttributeValue(Long delegateId, AttributeColumn attributeColumn) {
         GraphDatabaseService graphDB = GraphModelImportConverter.getGraphDBForCurrentWorkspace();
 
-        graphDB.getNodeById(delegateId).removeProperty(attributeColumn.getId());
+        Transaction tx = graphDB.beginTx();
+        try {
+            graphDB.getNodeById(delegateId).removeProperty(attributeColumn.getId());
+            tx.success();
+        } finally {
+            tx.close();
+        }
     }
 
 
     @Override
     public Object getEdgeAttributeValue(Long delegateId, AttributeColumn attributeColumn) {
         GraphDatabaseService graphDB = GraphModelImportConverter.getGraphDBForCurrentWorkspace();
 
-        if (attributeColumn.getId().equals(PropertiesColumn.NEO4J_RELATIONSHIP_TYPE.getId()))
-            return graphDB.getRelationshipById(delegateId).getType().name();
-        else
-            return graphDB.getRelationshipById(delegateId).getProperty(attributeColumn.getId());
+        Transaction tx = graphDB.beginTx();
+        try {
+            Object value;
+            if (attributeColumn.getId().equals(PropertiesColumn.NEO4J_RELATIONSHIP_TYPE.getId()))
+                value = graphDB.getRelationshipById(delegateId).getType().name();
+            else
+                value = graphDB.getRelationshipById(delegateId).getProperty(attributeColumn.getId());
+            tx.success();
+            return value;
+        } finally {
+            tx.close();
+        }
     }
 
     @Override
@@ -98,14 +125,26 @@ public void setEdgeAttributeValue(Long delegateId, AttributeColumn attributeColu
 
         GraphDatabaseService graphDB = GraphModelImportConverter.getGraphDBForCurrentWorkspace();
 
-        graphDB.getRelationshipById(delegateId).setProperty(attributeColumn.getId(), edgeValue);
+        Transaction tx = graphDB.beginTx();
+        try {
+            graphDB.getRelationshipById(delegateId).setProperty(attributeColumn.getId(), edgeValue);
+            tx.success();
+        } finally {
+            tx.close();
+        }
     }
 
     @Override
     public void deleteEdgeAttributeValue(Long delegateId, AttributeColumn attributeColumn) {
         GraphDatabaseService graphDB = GraphModelImportConverter.getGraphDBForCurrentWorkspace();
 
-        graphDB.getRelationshipById(delegateId).removeProperty(attributeColumn.getId());
+        Transaction tx = graphDB.beginTx();
+        try {
+            graphDB.getRelationshipById(delegateId).removeProperty(attributeColumn.getId());
+            tx.success();
+        } finally {
+            tx.close();
+        }
     }
 
     public GraphItemDelegateFactoryProvider<Long> graphItemDelegateFactoryProvider() {
@@ -138,32 +177,58 @@ public static Neo4jGraphItemDelegateFactoryProviderImpl getInstance() {
         public Long createNode() {
             GraphDatabaseService graphDB = GraphModelImportConverter.getGraphDBForCurrentWorkspace();
 
-            return graphDB.createNode().getId();
+            Transaction tx = graphDB.beginTx();
+            try {
+                long id = graphDB.createNode().getId();
+                tx.success();
+                return id;
+            } finally {
+                tx.close();
+            }
         }
 
         @Override
         public void deleteNode(Long nodeId) {
             GraphDatabaseService graphDB = GraphModelImportConverter.getGraphDBForCurrentWorkspace();
 
-            graphDB.getNodeById(nodeId).delete();
+            Transaction tx = graphDB.beginTx();
+            try {
+                graphDB.getNodeById(nodeId).delete();
+                tx.success();
+            } finally {
+                tx.close();
+            }
         }
 
         @Override
         public Long createEdge(Long startNodeId, Long endNodeId) {
             GraphDatabaseService graphDB = GraphModelImportConverter.getGraphDBForCurrentWorkspace();
 
-            org.neo4j.graphdb.Node startNode = graphDB.getNodeById(startNodeId);
-            org.neo4j.graphdb.Node endNode   = graphDB.getNodeById(endNodeId);
-
-            return startNode.createRelationshipTo(endNode,
-                                                  DynamicRelationshipType.withName(DEFAULT_RELATIONSHIP_TYPE_NAME)).getId();
+            Transaction tx = graphDB.beginTx();
+            try {
+                org.neo4j.graphdb.Node startNode = graphDB.getNodeById(startNodeId);
+                org.neo4j.graphdb.Node endNode   = graphDB.getNodeById(endNodeId);
+
+                long id = startNode.createRelationshipTo(endNode,
+                                                      DynamicRelationshipType.withName(DEFAULT_RELATIONSHIP_TYPE_NAME)).getId();
+                tx.success();
+                return id;
+            } finally {
+                tx.close();
+            }
         }
 
         @Override
         public void deleteEdge(Long edgeId) {
             GraphDatabaseService graphDB = GraphModelImportConverter.getGraphDBForCurrentWorkspace();
 
-            graphDB.getRelationshipById(edgeId).delete();
+            Transaction tx = graphDB.beginTx();
+            try {
+                graphDB.getRelationshipById(edgeId).delete();
+                tx.success();
+            } finally {
+                tx.close();
+            }
         }
     }
 }

Neo4jPlugin/src/org/gephi/neo4j/plugin/impl/Neo4jImporterImpl.java

@@ -38,7 +38,6 @@ License, or (at your option) any later version.
 import org.neo4j.graphdb.traversal.Evaluators;
 import org.neo4j.graphdb.traversal.TraversalDescription;
 import org.neo4j.graphdb.traversal.Traverser;
-import org.neo4j.kernel.Traversal;
 import org.openide.util.Lookup;
 import org.openide.util.NbBundle;
 import org.openide.util.lookup.ServiceProvider;
@@ -105,7 +104,7 @@ public void importDatabase(GraphDatabaseService graphDB, long startNodeId, Trave
         NodeReturnFilter nodeReturnFilter = null;
 
         if (startNodeId != NO_START_NODE) {
-            TraversalDescription traversalDescription = Traversal.description();
+            TraversalDescription traversalDescription = graphDB.traversalDescription();
 
             traversalDescription = order.update(traversalDescription);
 
@@ -137,7 +136,7 @@ private void doImport(GraphDatabaseService graphDB, Traverser traverser, NodeRet
             importGraph(graphDB, traverser, nodeReturnFilter);
             transaction.success();
         } finally {
-            transaction.finish();
+            transaction.close();
         }
 
         Progress.finish(progressTicket);