Node view will be used for exporting network view.

Author: keiono

README.md

@@ -1,16 +1,19 @@
 Cytoscape to D3.js Exporter
 ============
+## Release history
+* 9/15/2014 - Version 1.0.1 released.  Node locations (x, y) will be added as node property when user select Network and View.
+ 
 
 ## What is this for?
-This is a [Cytoscape 3]() App for exporting network and its data table to [D3.js](http://d3js.org/) compatible JSON.  D3.js is a general data visualization JavaScript library, and some of its presets support network/tree style data.  This App directly creates JSON file for those presets from Cytoscape network and data tables.
+This is a [Cytoscape](http://www.cytoscape.org/) App for exporting network and its data table to [D3.js](http://d3js.org/) compatible JSON.  D3.js is a general data visualization JavaScript library, and some of its presets support network/tree style data.  This App directly creates JSON file for those presets from Cytoscape network and data tables.
 
 Currently, this App supports:
 
 * Network JSON for force layout ([example](http://bl.ocks.org/mbostock/4062045))
 * Tree JSON ([example](http://mbostock.github.io/d3/talk/20111018/tree.html))
 
 ## How to Use
-Build, and install the JAR file from Cytoscape's App manager.  You can export your network and its data table as JSON from *File-->Export-->Network*.
+Build, and install the JAR file from Cytoscape's App manager or simply install from Cytoscape App Store.  You can export your network and its data table as JSON from *File → Export → Network*.
 
 **For Tree data, you need to select root node manually (simply click the root node before exporting)**.
 

pom.xml

@@ -7,12 +7,13 @@
 		<bundle.symbolicName>org.cytoscape.d3js-exporter</bundle.symbolicName>
 		<bundle.namespace>org.cytoscape.d3</bundle.namespace>
 		<cytoscape.api.version>3.1.0</cytoscape.api.version>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 	</properties>
 
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.cytoscape</groupId>
 	<artifactId>d3js-exporter</artifactId>
-	<version>1.0.0</version>
+	<version>1.0.1</version>
 
 	<name>D3.js Exporter</name>
 
@@ -69,7 +70,7 @@
 			<plugin>
 				<groupId>org.apache.felix</groupId>
 				<artifactId>maven-bundle-plugin</artifactId>
-				<version>2.4.0</version>
+				<version>2.5.3</version>
 				<extensions>true</extensions>
 				<configuration>
 					<instructions>
@@ -78,7 +79,7 @@
 						<Export-Package>${bundle.namespace}</Export-Package>
 						<Private-Package>${bundle.namespace}.internal.*</Private-Package>
 						<Bundle-Activator>${bundle.namespace}.internal.CyActivator</Bundle-Activator>
-						<Embed-Dependency>*;scope=!provided;groupId=!org.cytoscape</Embed-Dependency>
+						<Embed-Dependency>*;scope=!provided;scope=!test;groupId=!org.cytoscape</Embed-Dependency>
 						<Embed-Transitive>true</Embed-Transitive>
 						<Import-Package>*;resolution:=optional</Import-Package>
 					</instructions>
@@ -120,6 +121,7 @@
 			<groupId>org.osgi</groupId>
 			<artifactId>org.osgi.core</artifactId>
 			<version>4.2.0</version>
+			<scope>provided</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.ops4j.pax.logging</groupId>
@@ -161,15 +163,10 @@
 		</dependency>
 
 		<!-- 3rd party libraries -->
-		<dependency>
-			<groupId>com.fasterxml.jackson.core</groupId>
-			<artifactId>jackson-core</artifactId>
-			<version>2.2.2</version>
-		</dependency>
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-databind</artifactId>
-			<version>2.2.2</version>
+			<version>2.4.2</version>
 		</dependency>
 
 		<!-- Testing -->

src/main/java/org/cytoscape/d3/internal/serializer/D3CyNetworkSerializer.java

@@ -15,7 +15,7 @@ public class D3CyNetworkSerializer extends JsonSerializer<CyNetwork> {
 	public void serialize(final CyNetwork network, JsonGenerator jgen, SerializerProvider provider)
 			throws IOException, JsonProcessingException {
 		final D3JsonBuilder builder = new D3JsonBuilder();
-		builder.serializeNetwork(network, jgen, provider);
+		builder.serializeNetwork(network, null, jgen, provider);
 	}
 
 	@Override

src/main/java/org/cytoscape/d3/internal/serializer/D3CyNetworkViewSerializer.java

@@ -19,7 +19,7 @@ public void serialize(final CyNetworkView networkView, JsonGenerator jgen, Seria
 
 		final D3JsonBuilder builder = new D3JsonBuilder();
 		final CyNetwork network = networkView.getModel();
-		builder.serializeNetwork(network, jgen, provider);
+		builder.serializeNetwork(network, networkView, jgen, provider);
 	}
 
 

src/main/java/org/cytoscape/d3/internal/serializer/D3JsonBuilder.java

@@ -8,6 +8,9 @@
 import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyNode;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.presentation.property.BasicVisualLexicon;
 
 import com.fasterxml.jackson.core.JsonGenerator;
 import com.fasterxml.jackson.core.JsonProcessingException;
@@ -20,8 +23,10 @@ public class D3JsonBuilder {
 	private static final String SOURCE = "source";
 	private static final String TARGET= "target";
 	private static final String ID = "id";
+	private static final String X = "x";
+	private static final String Y = "y";
 
-	protected final void serializeNetwork(final CyNetwork network, JsonGenerator jgen, SerializerProvider provider)
+	protected final void serializeNetwork(final CyNetwork network, final CyNetworkView view, JsonGenerator jgen, SerializerProvider provider)
 			throws IOException, JsonProcessingException {
 
 		// Write array
@@ -40,6 +45,12 @@ protected final void serializeNetwork(final CyNetwork network, JsonGenerator jge
 			jgen.writeStartObject();
 
 			jgen.writeStringField(ID, node.getSUID().toString());
+			if(view != null) {
+				// View is available.  Pick (x,y)
+				final View<CyNode> nodeView = view.getNodeView(node);
+				jgen.writeNumberField(X, nodeView.getVisualProperty(BasicVisualLexicon.NODE_X_LOCATION));
+				jgen.writeNumberField(Y, nodeView.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION));
+			}
 
 			// Write CyRow in "data" field
 			jgen.writeObject(network.getRow(node));

src/main/java/org/cytoscape/d3/internal/writer/D3NetworkViewWriter.java

@@ -2,15 +2,11 @@
 
 import java.io.OutputStream;
 import java.io.OutputStreamWriter;
-import java.nio.charset.Charset;
-import java.nio.charset.CharsetEncoder;
 
 import org.cytoscape.io.write.CyWriter;
 import org.cytoscape.task.AbstractNetworkViewTask;
 import org.cytoscape.view.model.CyNetworkView;
 import org.cytoscape.work.TaskMonitor;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
@@ -27,25 +23,26 @@ public D3NetworkViewWriter(final OutputStream outputStream, final CyNetworkView
 			final ObjectMapper networkView2jsonMapper) {
 		super(networkView);
 
-		if(outputStream == null)
+		if (outputStream == null)
 			throw new NullPointerException("Output Stream is null.");
-		
-		if(networkView2jsonMapper == null)
+
+		if (networkView2jsonMapper == null)
 			throw new NullPointerException("Object Mapper is null.");
-		
+
 		this.outputStream = outputStream;
 		this.networkView2jsonMapper = networkView2jsonMapper;
 	}
 
 	@Override
 	public void run(TaskMonitor taskMonitor) throws Exception {
 		if (taskMonitor != null) {
-			taskMonitor.setTitle("Writing Network View to D3.js Style JSON...");
-			taskMonitor.setProgress(0);
+			taskMonitor.setTitle("Writing Network View to D3-Style JSON");
+			taskMonitor.setStatusMessage("Writing D3 style JSON...");
+			taskMonitor.setProgress(-1.0);
 		}
 		networkView2jsonMapper.writeValue(new OutputStreamWriter(outputStream, EncodingUtil.getEncoder()), view);
 		outputStream.close();
-		
+
 		if (taskMonitor != null) {
 			taskMonitor.setStatusMessage("Success.");
 			taskMonitor.setProgress(1.0);

src/main/java/org/cytoscape/d3/internal/writer/D3NetworkWriter.java

@@ -1,15 +1,12 @@
 package org.cytoscape.d3.internal.writer;
 
 import java.io.OutputStream;
-import java.nio.charset.Charset;
-import java.nio.charset.CharsetEncoder;
+import java.io.OutputStreamWriter;
 
 import org.cytoscape.io.write.CyWriter;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.task.AbstractNetworkTask;
 import org.cytoscape.work.TaskMonitor;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
@@ -33,14 +30,16 @@ public D3NetworkWriter(final OutputStream outputStream, final CyNetwork network,
 	@Override
 	public void run(TaskMonitor taskMonitor) throws Exception {
 		if (taskMonitor != null) {
-			taskMonitor.setTitle("Writing to D3.js style JSON...");
-			taskMonitor.setProgress(0);
+			taskMonitor.setTitle("Writing to D3-Style JSON");
+			taskMonitor.setStatusMessage("Writing network in D3.js format...");
+			taskMonitor.setProgress(-1.0);
 		}
-		network2jsonMapper.writeValue(outputStream, network);
+
+		network2jsonMapper.writeValue(new OutputStreamWriter(outputStream, EncodingUtil.getEncoder()), network);
 		outputStream.close();
-		
+
 		if (taskMonitor != null) {
-			taskMonitor.setTitle("Success.");
+			taskMonitor.setStatusMessage("Success.");
 			taskMonitor.setProgress(1.0);
 		}
 	}

src/test/java/org/cytoscape/d3/D3WriterTest.java

@@ -136,5 +136,8 @@ private void readAndTest(final File outFile, CyNetwork network) throws IOExcepti
 		assertTrue(nodes.isArray());
 		assertNotNull(edges);
 		assertTrue(edges.isArray());
+		
+		assertEquals(5, nodes.size());
+		assertEquals(4, edges.size());
 	}
 }