Merge branch 'release/1.1.0'

.travis.yml

@@ -7,5 +7,6 @@ branches:
   only:
     - develop
     - master
+
 after_success:
-  - mvn clean cobertura:cobertura coveralls:cobertura
+  - mvn clean cobertura:cobertura coveralls:report

pom.xml

@@ -5,7 +5,7 @@
 	<properties>
 		<bundle.symbolicName>org.cytoscape.rest.cy-rest</bundle.symbolicName>
 		<bundle.namespace>org.cytoscape.rest</bundle.namespace>
-		<maven-compiler-plugin.version>3.2</maven-compiler-plugin.version>
+		<maven-compiler-plugin.version>3.3</maven-compiler-plugin.version>
 		<osgi.api.version>4.2.0</osgi.api.version>
 		<junit.version>4.12</junit.version>
 		<jersey.version>2.18</jersey.version>
@@ -17,7 +17,7 @@
 
 	<groupId>org.cytoscape</groupId>
 	<artifactId>cy-rest</artifactId>
-	<version>0.9.17</version>
+	<version>1.1.0</version>
 	<packaging>bundle</packaging>
 	<name>cyREST</name>
 
@@ -79,7 +79,7 @@
 			<plugin>
 				<groupId>org.apache.felix</groupId>
 				<artifactId>maven-bundle-plugin</artifactId>
-				<version>2.5.3</version>
+				<version>2.5.4</version>
 				<extensions>true</extensions>
 				<configuration>
 					<instructions>
@@ -150,12 +150,19 @@
 			<plugin>
 				<groupId>org.eluder.coveralls</groupId>
 				<artifactId>coveralls-maven-plugin</artifactId>
-				<version>2.2.0</version>
+				<version>3.1.0</version>
 			</plugin>
 			<plugin>
 				<groupId>org.codehaus.mojo</groupId>
 				<artifactId>cobertura-maven-plugin</artifactId>
 				<version>2.6</version>
+				<dependencies>
+					<dependency>
+						<groupId>org.ow2.asm</groupId>
+						<artifactId>asm</artifactId>
+						<version>5.0.3</version>
+					</dependency>
+				</dependencies>
 				<configuration>
 					<format>xml</format>
 					<maxmem>256m</maxmem>
@@ -177,7 +184,7 @@
 			</dependency>
 		</dependencies>
 	</dependencyManagement>
-	
+
 	<dependencies>
 		<!-- Cytoscape 3 Dependencies -->
 		<dependency>
@@ -259,7 +266,7 @@
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-databind</artifactId>
-			<version>2.5.3</version>
+			<version>2.5.4</version>
 		</dependency>
 
 		<!-- Jersey -->

src/main/java/org/cytoscape/rest/internal/CyActivator.java

@@ -12,6 +12,7 @@
 import org.cytoscape.io.read.InputStreamTaskFactory;
 import org.cytoscape.io.util.StreamUtil;
 import org.cytoscape.io.write.CyNetworkViewWriterFactory;
+import org.cytoscape.io.write.PresentationWriterFactory;
 import org.cytoscape.io.write.VizmapWriterFactory;
 import org.cytoscape.model.CyNetworkFactory;
 import org.cytoscape.model.CyNetworkManager;
@@ -83,6 +84,10 @@ public void start(BundleContext bc) {
 		final MappingFactoryManager mappingFactoryManager = new MappingFactoryManager();
 		registerServiceListener(bc, mappingFactoryManager, "addFactory", "removeFactory",
 				VisualMappingFunctionFactory.class);
+
+		final GraphicsWriterManager graphicsWriterManager = new GraphicsWriterManager();
+		registerServiceListener(bc, graphicsWriterManager, "addFactory", "removeFactory",
+				PresentationWriterFactory.class);
 
 		@SuppressWarnings("unchecked")
 		final CyProperty<Properties> cyPropertyServiceRef = getService(bc, CyProperty.class,
@@ -156,7 +161,7 @@ public void start(BundleContext bc) {
 				networkSelectedNodesAndEdgesTaskFactory, edgeListReaderFactory, netViewFact, tableFactory, fitContent,
 				new EdgeBundlerImpl(edgeBundler), renderingEngineManager, sessionManager, 
 				saveSessionAsTaskFactory, openSessionTaskFactory, newSessionTaskFactory, desktop, 
-				new LevelOfDetails(showDetailsTaskFactory), selectFirstNeighborsTaskFactory);
+				new LevelOfDetails(showDetailsTaskFactory), selectFirstNeighborsTaskFactory, graphicsWriterManager);
 				this.grizzlyServerManager = new GrizzlyServerManager(binder, cyPropertyServiceRef);
 		try {
 			this.grizzlyServerManager.startServer();

src/main/java/org/cytoscape/rest/internal/GraphicsWriterManager.java

@@ -0,0 +1,39 @@
+package org.cytoscape.rest.internal;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+import org.cytoscape.io.CyFileFilter;
+import org.cytoscape.io.write.PresentationWriterFactory;
+
+public class GraphicsWriterManager {
+
+	private final Map<String, PresentationWriterFactory> factories;
+
+	public GraphicsWriterManager() {
+		factories = new HashMap<>();
+	}
+
+	public PresentationWriterFactory getFactory(final String fileType) {
+		return factories.get(fileType);
+	}
+
+	@SuppressWarnings("rawtypes")
+	public void addFactory(PresentationWriterFactory factory, Map properties) {
+		final CyFileFilter ff = factory.getFileFilter();
+		final Set<String> ext = ff.getExtensions();
+
+		final String firstExt = ext.iterator().next();
+		System.out.println("Got writer: " + firstExt);
+
+		factories.put(firstExt, factory);
+	}
+
+	@SuppressWarnings("rawtypes")
+	public void removeFactory(PresentationWriterFactory factory, Map properties) {
+		final CyFileFilter ff = factory.getFileFilter();
+		final Set<String> ext = ff.getExtensions();
+		factories.remove(ext.iterator().next());
+	}
+}

src/main/java/org/cytoscape/rest/internal/resource/NetworkResource.java

@@ -66,7 +66,7 @@ public class NetworkResource extends AbstractResource {
 	protected SelectFirstNeighborsTaskFactory selectFirstNeighborsTaskFactory;
 
 	// Preset types
-	private static final String DEF_COLLECTION_PREFIX = "Posted: ";
+	private static final String DEF_COLLECTION_PREFIX = "Created by cyREST: ";
 
 	public NetworkResource() {
 		super();
@@ -82,8 +82,9 @@ public NetworkResource() {
 	@GET
 	@Path("/count")
 	@Produces(MediaType.APPLICATION_JSON)
-	public String getNetworkCount() {
-		return getNumberObjectString(JsonTags.COUNT, networkManager.getNetworkSet().size());
+	public Response getNetworkCount() {
+		final String result = getNumberObjectString(JsonTags.COUNT, networkManager.getNetworkSet().size());
+		return Response.ok(result).build();
 	}
 
 	/**
@@ -97,8 +98,9 @@ public String getNetworkCount() {
 	@GET
 	@Path("/{networkId}/nodes/count")
 	@Produces(MediaType.APPLICATION_JSON)
-	public String getNodeCount(@PathParam("networkId") Long networkId) {
-		return getNumberObjectString(JsonTags.COUNT, getCyNetwork(networkId).getNodeCount());
+	public Response getNodeCount(@PathParam("networkId") Long networkId) {
+		final String result = getNumberObjectString(JsonTags.COUNT, getCyNetwork(networkId).getNodeCount());
+		return Response.ok(result).build();
 	}
 
 	/**
@@ -113,8 +115,9 @@ public String getNodeCount(@PathParam("networkId") Long networkId) {
 	@GET
 	@Path("/{networkId}/edges/count")
 	@Produces(MediaType.APPLICATION_JSON)
-	public String getEdgeCount(@PathParam("networkId") Long networkId) {
-		return getNumberObjectString(JsonTags.COUNT, getCyNetwork(networkId).getEdgeCount());
+	public Response getEdgeCount(@PathParam("networkId") Long networkId) {
+		final String result = getNumberObjectString(JsonTags.COUNT, getCyNetwork(networkId).getEdgeCount());
+		return Response.ok(result).build();
 	}
 
 
@@ -265,7 +268,7 @@ public Response getSelectedNodes(@PathParam("networkId") Long networkId) {
 	@GET
 	@Path("/{networkId}/nodes/selected/neighbors")
 	@Produces(MediaType.APPLICATION_JSON)
-	public Response getNeighbors(@PathParam("networkId") Long networkId) {
+	public Response getNeighborsSelected(@PathParam("networkId") Long networkId) {
 		final CyNetwork network = getCyNetwork(networkId);
 		final List<CyNode> selectedNodes = CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true);
 
@@ -461,14 +464,15 @@ public Collection<Long> getAdjEdges(@PathParam("networkId") Long networkId, @Pat
 	@GET
 	@Path("/{networkId}/nodes/{nodeId}/pointer")
 	@Produces(MediaType.APPLICATION_JSON)
-	public String getNetworkPointer(@PathParam("networkId") Long networkId, @PathParam("nodeId") Long nodeId) {
+	public Response getNetworkPointer(@PathParam("networkId") Long networkId, @PathParam("nodeId") Long nodeId) {
 		final CyNetwork network = getCyNetwork(networkId);
 		final CyNode node = getNode(network, nodeId);
 		final CyNetwork pointer = node.getNetworkPointer();
 		if (pointer == null) {
 			throw getError("Could not find network pointer.", new RuntimeException(), Response.Status.NOT_FOUND);
 		}
-		return getNumberObjectString(JsonTags.NETWORK_SUID, pointer.getSUID());
+
+		return Response.ok(getNumberObjectString(JsonTags.NETWORK_SUID, pointer.getSUID())).build();
 	}
 
 	/**
@@ -486,11 +490,12 @@ public String getNetworkPointer(@PathParam("networkId") Long networkId, @PathPar
 	@GET
 	@Path("/{networkId}/nodes/{nodeId}/neighbors")
 	@Produces(MediaType.APPLICATION_JSON)
-	public Collection<Long> getNeighbours(@PathParam("networkId") Long networkId, @PathParam("nodeId") Long nodeId) {
+	public Response getNeighbours(@PathParam("networkId") Long networkId, @PathParam("nodeId") Long nodeId) {
 		final CyNetwork network = getCyNetwork(networkId);
 		final CyNode node = getNode(network, nodeId);
 		final List<CyNode> nodes = network.getNeighborList(node, Type.ANY);
-		return getGraphObjectArray(nodes);
+
+		return Response.status(Response.Status.OK).entity(getGraphObjectArray(nodes)).build();
 	}
 
 	/**
@@ -501,11 +506,9 @@ public Collection<Long> getNeighbours(@PathParam("networkId") Long networkId, @P
 	 * @return
 	 */
 	private final Collection<Long> getGraphObjectArray(final Collection<? extends CyIdentifiable> objects) {
-		final Collection<Long> suids = new ArrayList<Long>();
-		for (final CyIdentifiable obj : objects) {
-			suids.add(obj.getSUID());
-		}
-		return suids;
+		return objects.stream()
+			.map(CyIdentifiable::getSUID)
+			.collect(Collectors.toList());
 	}
 
 	/**
@@ -529,7 +532,7 @@ private final Collection<Long> getGraphObjectArray(final Collection<? extends Cy
 	@Path("/{networkId}/nodes")
 	@Consumes(MediaType.APPLICATION_JSON)
 	@Produces(MediaType.APPLICATION_JSON)
-	public String createNode(@PathParam("networkId") Long networkId, final InputStream is) {
+	public Response createNode(@PathParam("networkId") Long networkId, final InputStream is) {
 		final CyNetwork network = getCyNetwork(networkId);
 		final ObjectMapper objMapper = new ObjectMapper();
 		JsonNode rootNode = null;
@@ -566,7 +569,8 @@ public String createNode(@PathParam("networkId") Long networkId, final InputStre
 			} catch (Exception e) {
 				throw getError("Could not create node list.", e, Response.Status.INTERNAL_SERVER_ERROR);
 			}
-			return result;
+
+			return Response.status(Response.Status.CREATED).entity(result).build();
 		} else {
 			throw getError("Need to post as array.", new IllegalArgumentException(),
 					Response.Status.PRECONDITION_FAILED);
@@ -598,7 +602,7 @@ public String createNode(@PathParam("networkId") Long networkId, final InputStre
 	@Path("/{networkId}/edges")
 	@Consumes(MediaType.APPLICATION_JSON)
 	@Produces(MediaType.APPLICATION_JSON)
-	public String createEdge(@PathParam("networkId") Long networkId, final InputStream is) {
+	public Response createEdge(@PathParam("networkId") Long networkId, final InputStream is) {
 		final CyNetwork network = getCyNetwork(networkId);
 		final ObjectMapper objMapper = new ObjectMapper();
 
@@ -665,9 +669,10 @@ public String createEdge(@PathParam("networkId") Long networkId, final InputStre
 				stream.close();
 				updateViews(network);
 			} catch (Exception e) {
+				e.printStackTrace();
 				throw getError("Could not create edge.", e, Response.Status.INTERNAL_SERVER_ERROR);
 			}
-			return result;
+			return Response.status(Response.Status.CREATED).entity(result).build();
 		} else {
 			throw getError("Need to POST as array.", new IllegalArgumentException(),
 					Response.Status.INTERNAL_SERVER_ERROR);
@@ -683,11 +688,11 @@ public String createEdge(@PathParam("networkId") Long networkId, final InputStre
 	 */
 	@DELETE
 	@Path("/")
-	public void deleteAllNetworks() {
-		final Set<CyNetwork> allNetworks = this.networkManager.getNetworkSet();
-		for (final CyNetwork network : allNetworks) {
-			this.networkManager.destroyNetwork(network);
-		}
+	public Response deleteAllNetworks() {
+		this.networkManager.getNetworkSet().stream()
+			.forEach(network->this.networkManager.destroyNetwork(network));
+
+		return Response.ok().build();
 	}
 
 	/**
@@ -715,6 +720,7 @@ public Response deleteAllNodes(@PathParam("networkId") Long networkId) {
 		final CyNetwork network = getCyNetwork(networkId);
 		network.removeNodes(network.getNodeList());
 		updateViews(network);
+
 		return Response.ok().build();
 	}
 
@@ -726,10 +732,12 @@ public Response deleteAllNodes(@PathParam("networkId") Long networkId) {
 	 */
 	@DELETE
 	@Path("/{networkId}/edges")
-	public void deleteAllEdges(@PathParam("networkId") Long networkId) {
+	public Response deleteAllEdges(@PathParam("networkId") Long networkId) {
 		final CyNetwork network = getCyNetwork(networkId);
 		network.removeEdges(network.getEdgeList());
 		updateViews(network);
+
+		return Response.ok().build();
 	}
 
 
@@ -743,7 +751,7 @@ public void deleteAllEdges(@PathParam("networkId") Long networkId) {
 	 */
 	@DELETE
 	@Path("/{networkId}/nodes/{nodeId}")
-	public void deleteNode(@PathParam("networkId") Long networkId, @PathParam("nodeId") Long nodeId) {
+	public Response deleteNode(@PathParam("networkId") Long networkId, @PathParam("nodeId") Long nodeId) {
 		final CyNetwork network = getCyNetwork(networkId);
 		final CyNode node = network.getNode(nodeId);
 		if (node == null) {
@@ -753,6 +761,8 @@ public void deleteNode(@PathParam("networkId") Long networkId, @PathParam("nodeI
 		nodes.add(node);
 		network.removeNodes(nodes);
 		updateViews(network);
+
+		return Response.ok().build();
 	}
 
 
@@ -767,7 +777,7 @@ public void deleteNode(@PathParam("networkId") Long networkId, @PathParam("nodeI
 	 */
 	@DELETE
 	@Path("/{networkId}/edges/{edgeId}")
-	public void deleteEdge(@PathParam("networkId") Long networkId, @PathParam("edgeId") Long edgeId) {
+	public Response deleteEdge(@PathParam("networkId") Long networkId, @PathParam("edgeId") Long edgeId) {
 		final CyNetwork network = getCyNetwork(networkId);
 		final CyEdge edge = network.getEdge(edgeId);
 		if (edge == null) {
@@ -777,6 +787,8 @@ public void deleteEdge(@PathParam("networkId") Long networkId, @PathParam("edgeI
 		edges.add(edge);
 		network.removeEdges(edges);
 		updateViews(network);
+
+		return Response.ok().build();
 	}
 
 	/**
@@ -849,6 +861,7 @@ public String createNetwork(@DefaultValue(DEF_COLLECTION_PREFIX) @QueryParam("co
 		try {
 			reader.run(new HeadlessTaskMonitor());
 		} catch (Exception e) {
+			e.printStackTrace();
 			throw getError("Could not parse the given network JSON.", e, Response.Status.PRECONDITION_FAILED);
 		}