Merge pull request #37 from openworm/development

Release 0.1.7

.project

@@ -15,16 +15,6 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
-			<triggers>full,incremental,</triggers>
-			<arguments>
-				<dictionary>
-					<key>LaunchConfigHandle</key>
-					<value>&lt;project&gt;/.externalToolBuilders/org.eclipse.m2e.core.maven2Builder (7).launch</value>
-				</dictionary>
-			</arguments>
-		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.m2e.core.maven2Builder</name>
 			<arguments>

.settings/org.eclipse.wst.common.project.facet.core.xml

@@ -1,9 +1,8 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<faceted-project>
-  <runtime name="Geppetto"/>
-  <installed facet="com.springsource.server.bundle" version="1.0"/>
-  <installed facet="osgi.bundle" version="4.2"/>
-  <installed facet="org.eclipse.virgo.server.bundle" version="1.0"/>
-  <installed facet="java" version="1.7"/>
-  <installed facet="jst.utility" version="1.0"/>
-</faceted-project>
+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+  <installed facet="com.springsource.server.bundle" version="1.0"/>
+  <installed facet="osgi.bundle" version="4.2"/>
+  <installed facet="org.eclipse.virgo.server.bundle" version="1.0"/>
+  <installed facet="java" version="1.7"/>
+  <installed facet="jst.utility" version="1.0"/>
+</faceted-project>

pom.xml

@@ -4,7 +4,7 @@
 	<groupId>org.geppetto</groupId>
 	<artifactId>core</artifactId>
 	<name>Geppetto Core Bundle</name>
-	<version>0.1.6</version>
+	<version>0.1.7</version>
 	<packaging>bundle</packaging>
 	<properties>
 		<github.global.server>github</github.global.server>

src/main/java/org/geppetto/core/model/IModelInterpreter.java

@@ -36,20 +36,15 @@
 import java.net.URL;
 import java.util.List;
 
-import org.geppetto.core.model.runtime.ACompositeNode;
 import org.geppetto.core.model.runtime.AspectNode;
-import org.geppetto.core.model.runtime.AspectSubTreeNode;
-import org.geppetto.core.model.runtime.EntityNode;
-import org.geppetto.core.model.runtime.RuntimeTreeRoot;
-import org.geppetto.core.model.simulation.Aspect;
 
 public interface IModelInterpreter {
 
 	IModel readModel(URL url, List<URL> recordings, String instancePath) throws ModelInterpreterException;
 
 	boolean populateModelTree(AspectNode aspectNode) throws ModelInterpreterException;
 
-	boolean populateRuntimeTree(AspectNode aspectNode);
+	boolean populateRuntimeTree(AspectNode aspectNode) throws ModelInterpreterException;;
 
 	String getName();
 }

src/main/java/org/geppetto/core/model/ModelInterpreterException.java

@@ -41,6 +41,11 @@
 public class ModelInterpreterException extends Exception
 {
 
+	public ModelInterpreterException(String message)
+	{
+		super(message);
+	}
+
 	public ModelInterpreterException(Throwable e)
 	{
 		super(e);

src/main/java/org/geppetto/core/model/runtime/AMetadataNode.java

@@ -47,6 +47,11 @@ public AMetadataNode(String name) {
 		super(name);
 	}
 
+	public AMetadataNode(String name, AValue value) {
+		super(name);
+		setValue(value);
+	}
+
 	public AValue getValue() {
 		return value;
 	}

src/main/java/org/geppetto/core/model/runtime/ANode.java

@@ -44,7 +44,7 @@ public abstract class ANode implements IVisitable
 {
 	protected ANode _parent;
 	protected String _name;
-	//protected String _metatype;
+	private String _id;
 
 	public String getMetaType(){
 		return this.getClass().getSimpleName();
@@ -70,6 +70,14 @@ public String getName()
 		return _name;
 	}
 
+	public void setId(String id){
+		this._id = id;
+	}
+
+	public String getId() {
+		return this._id;
+	}
+
 	/**
 	 * @return the next sibling of this node
 	 */

src/main/java/org/geppetto/core/model/runtime/AVisualObjectNode.java

@@ -43,7 +43,6 @@
 public abstract class AVisualObjectNode extends ANode{
 
 	private Point _position;
-	private String _id;
 
 	public AVisualObjectNode(String name) {
 		super(name);
@@ -52,14 +51,6 @@ public AVisualObjectNode(String name) {
 	public AVisualObjectNode(){
 	}
 
-	public void setId(String id) {
-		this._id = id;
-	}
-
-	public String getId(){
-		return this._id;
-	}
-
 	public void setPosition(Point position){
 		this._position = position;
 	}

src/main/java/org/geppetto/core/model/runtime/AspectNode.java

@@ -46,7 +46,6 @@
  */
 public class AspectNode extends ACompositeNode{
 
-	private String _id;
 	private VariableNode _time;
 	private IModelInterpreter _modelInterpreter;
 	private ISimulator _simulator;
@@ -81,14 +80,6 @@ public ISimulator getSimulator() {
 	public void setSimulator(ISimulator simulator) {
 		this._simulator = simulator;
 	}
-
-	public void setId(String id){
-		this._id = id;
-	}
-
-	public String getId() {
-		return this._id;
-	}
 
 	public ANode getParentEntity() {
 		return this.getParent();
@@ -114,7 +105,7 @@ public void flushSubTree(AspectTreeType tree)
 	 * @param modelTree
 	 * @return
 	 */
-	private ACompositeNode addSubTree(AspectTreeType modelTree)
+	private AspectSubTreeNode addSubTree(AspectTreeType modelTree)
 	{
 		AspectSubTreeNode subTree = new AspectSubTreeNode(modelTree);
 		addChild(subTree);
@@ -123,19 +114,19 @@ private ACompositeNode addSubTree(AspectTreeType modelTree)
 
 	/**
 	 * It creates the subtree if it doesn't exist
-	 * @param modelTree
+	 * @param treeType
 	 * @return
 	 */
-	public ACompositeNode getSubTree(AspectTreeType modelTree)
+	public AspectSubTreeNode getSubTree(AspectTreeType treeType)
 	{
 		for (ANode node:getChildren())
 		{
-			if( node.getName().equals(modelTree.toString()))
+			if( node.getName().equals(treeType.toString()))
 			{
-				return (ACompositeNode) node;
+				return (AspectSubTreeNode) node;
 			}
 		}
-		return addSubTree(modelTree);
+		return addSubTree(treeType);
 	}
 
 	@Override

src/main/java/org/geppetto/core/model/runtime/AspectSubTreeNode.java

@@ -69,16 +69,16 @@ public String toString() {
 	    }
 	}
 
-	private AspectTreeType type;
-
+	private AspectTreeType _type;
+	private boolean _modified = true;
 
 	/**
 	 * @param modelTree.toString()
 	 */
-	public AspectSubTreeNode(AspectTreeType modelTree)
+	public AspectSubTreeNode(AspectTreeType treeType)
 	{
-		super(modelTree.toString());
-		this.type = modelTree;
+		super(treeType.toString());
+		this._type = treeType;
 	}
 
 	/**
@@ -95,8 +95,16 @@ public AspectSubTreeNode(String treeType)
 		this.setName(treeType);
 	}
 
-	public String getType(){
-		return this.type.toString();
+	public AspectTreeType getType(){
+		return this._type;
+	}
+
+	public boolean isModified(){
+		return this._modified;
+	}
+
+	public void setModified(boolean mode){
+		this._modified = mode;
 	}
 
 	/**
@@ -122,6 +130,7 @@ public void flushSubTree(AspectTreeType tree)
 	private AspectSubTreeNode addSubTree(AspectTreeType treeType)
 	{
 		AspectSubTreeNode subTree = new AspectSubTreeNode(treeType.toString());
+		subTree.setId(treeType.toString());
 		addChild(subTree);
 		return subTree;
 	}

src/main/java/org/geppetto/core/model/runtime/CompositeNode.java

@@ -46,6 +46,11 @@ public CompositeNode(String name) {
 		super(name);
 	}
 
+	public CompositeNode(String name, String id) {
+		super(name);
+		setId(id);
+	}
+
 	public CompositeNode() {
 		super();
 	}

src/main/java/org/geppetto/core/model/runtime/EntityNode.java

@@ -47,7 +47,6 @@
 public class EntityNode extends ACompositeNode{
 
 	protected List<AspectNode> _aspects =new ArrayList<AspectNode>();;
-	private String _id;
 	private List<Connection> _connections;
 	private AMetadataNode _metadata;
 	private Point _position;
@@ -74,15 +73,6 @@ public void setConnections(List<Connection> connections) {
 	public List<AspectNode> getAspects() {
 		return _aspects;
 	}
-
-	public void setId(String id){
-		this._id = id;
-	}
-
-	public String getId() {
-		return this._id;
-	}
-
 
 	public AMetadataNode getMetadata() {
 		return this._metadata;
@@ -113,6 +103,14 @@ public synchronized boolean apply(IStateVisitor visitor)
 					break;
 				}
 			}
+			for(AspectNode stateNode:this.getAspects())
+			{
+				stateNode.apply(visitor);
+				if(visitor.stopVisiting())
+				{
+					break;
+				}
+			}
 		}
 		return visitor.outEntityNode( this );
 	}

src/main/java/org/geppetto/core/model/runtime/ParameterSpecificationNode.java

@@ -50,6 +50,11 @@ public ParameterSpecificationNode(String name){
 		super(name);
 	}
 
+	public ParameterSpecificationNode(String name, String id){
+		super(name);
+		setId(id);
+	}
+
 	public void setValue(PhysicalQuantity value){
 		this._value = value;
 	}

src/main/java/org/geppetto/core/model/runtime/TextMetadataNode.java

@@ -36,6 +36,7 @@
 import java.util.Map;
 
 import org.geppetto.core.model.state.visitors.IStateVisitor;
+import org.geppetto.core.model.values.AValue;
 
 /**
  * Node use for storing text metadata properties and serialization
@@ -51,6 +52,15 @@ public TextMetadataNode(String name){
 		super(name);
 	}
 
+	public TextMetadataNode(String name, AValue value){
+		super(name, value);
+	}
+
+	public TextMetadataNode(String name, String id, AValue value){
+		super(name, value);
+		setId(id);
+	}
+
 	public TextMetadataNode(){
 		super("TextMetadataNode");
 	}