Documents for algorithmic resources has been updated.

keiono · Aug 14, 2014 · 414ffac · 414ffac
1 parent 1fb7600
commit 414ffac
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Showing 9 changed files with 258 additions and 72 deletions.
diff --git a/pom.xml b/pom.xml
@@ -33,7 +33,8 @@
 			<name>Cytoscape Releases</name>
 			<url>http://code.cytoscape.org/nexus/content/repositories/releases/</url>
 		</repository>
-
+
+		<!-- For API document generation -->
 		<repository>
 			<id>miredot</id>
 			<name>MireDot Releases</name>
@@ -111,9 +112,6 @@
 					<!-- insert other configuration here (optional) -->
 					<output>
 						<title>RESTful API for Cytoscape ${rest.api.version}</title>
-						<html>
-							<jsonDoc>Disabled</jsonDoc>
-						</html>
 					</output>
 
 
@@ -127,14 +125,47 @@
 							<httpStatusCode>
 								<httpCode>412</httpCode>
 								<document>put,post</document>
-								<defaultMessage>Invalid JSON/XML input.</defaultMessage>
+								<defaultMessage>Invalid JSON input.</defaultMessage>
 							</httpStatusCode>
 						</httpStatusCodes>
 					</restModel>
 
 				</configuration>
 			</plugin>
 		</plugins>
+		<pluginManagement>
+			<plugins>
+				<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
+				<plugin>
+					<groupId>org.eclipse.m2e</groupId>
+					<artifactId>lifecycle-mapping</artifactId>
+					<version>1.0.0</version>
+					<configuration>
+						<lifecycleMappingMetadata>
+							<pluginExecutions>
+								<pluginExecution>
+									<pluginExecutionFilter>
+										<groupId>com.qmino</groupId>
+										<artifactId>
+											miredot-maven-plugin
+										</artifactId>
+										<versionRange>
+											[1.4,)
+										</versionRange>
+										<goals>
+											<goal>restdoc</goal>
+										</goals>
+									</pluginExecutionFilter>
+									<action>
+										<ignore></ignore>
+									</action>
+								</pluginExecution>
+							</pluginExecutions>
+						</lifecycleMappingMetadata>
+					</configuration>
+				</plugin>
+			</plugins>
+		</pluginManagement>
 	</build>
 
 

diff --git a/src/main/java/org/cytoscape/rest/internal/model/TableCell.java b/src/main/java/org/cytoscape/rest/internal/model/TableCell.java
@@ -0,0 +1,15 @@
+package org.cytoscape.rest.internal.model;
+
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+
+/**
+ * Wrapper class for a cell in CyTable
+ * 
+ * @author kono
+ *
+ */
+//@JsonSerialize(using=)
+public class TableCell {
+
+
+}
diff --git a/src/main/java/org/cytoscape/rest/internal/serializer/GraphObjectSerializer.java b/src/main/java/org/cytoscape/rest/internal/serializer/GraphObjectSerializer.java
@@ -193,6 +193,8 @@ private final void serializeRow(JsonGenerator generator, final CyIdentifiable ob
 			final Long targetId = ((CyEdge) obj).getSource().getSUID();
 			generator.writeNumberField("source", sourceId);
 			generator.writeNumberField("target", targetId);
+		} else {
+			generator.writeNumberField("id", obj.getSUID());
 		}
 		for (final CyColumn col : columns) {
 			final Object value = values.get(col.getName());

diff --git a/src/main/java/org/cytoscape/rest/internal/service/AbstractDataService.java b/src/main/java/org/cytoscape/rest/internal/service/AbstractDataService.java
@@ -3,10 +3,12 @@
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.util.Collection;
-import java.util.Properties;
 
+import javax.ws.rs.NotFoundException;
 import javax.ws.rs.WebApplicationException;
 import javax.ws.rs.core.Context;
+import javax.ws.rs.core.Response;
+import javax.ws.rs.core.Response.Status;
 
 import org.cytoscape.application.CyApplicationManager;
 import org.cytoscape.io.read.InputStreamTaskFactory;
@@ -41,7 +43,21 @@
 public abstract class AbstractDataService {
 
 	// TODO: do we need this level of version granularity?
-	protected static final String API_VERSION = "1.0.0";
+	protected static final String API_VERSION = "v1";
+
+	protected static final String ERROR_TAG = "\"error\":";
+
+
+	// Utilities to build error messages.
+
+	protected final WebApplicationException getError(final String errorMessage, final Status status) {
+		return new NotFoundException(Response.status(status)
+				.entity("{" + ERROR_TAG + "\"" + errorMessage + "\"}").build());
+	}
+
+	protected final WebApplicationException getError(final Exception ex, final Status status) {
+		return new NotFoundException(Response.status(status).entity(ex).build());
+	}
 
 
 	@Context
@@ -100,12 +116,12 @@ public AbstractDataService() {
 
 	protected final CyNetwork getCyNetwork(final Long id) {
 		if(id == null) {
-			throw new WebApplicationException("Network SUID is null.", 500);
+			throw getError("SUID is null.", Response.Status.NOT_FOUND);
 		}
 
 		final CyNetwork network = networkManager.getNetwork(id);
 		if (network == null) {
-			throw new WebApplicationException("Could not find network with SUID: " + id, 404);
+			throw getError("Could not find network with SUID: " + id, Response.Status.NOT_FOUND);
 		}
 		return network;
 	}
@@ -123,7 +139,7 @@ protected final Collection<CyNetworkView> getCyNetworkViews(final Long id) {
 	protected final CyNode getNode(final CyNetwork network, final Long nodeId) {
 		final CyNode node = network.getNode(nodeId);
 		if (node == null) {
-			throw new WebApplicationException("Could not find object: " + nodeId, 404);
+			throw getError("Could not find node with SUID: " + nodeId, Response.Status.NOT_FOUND);
 		}
 		return node;
 	}

diff --git a/src/main/java/org/cytoscape/rest/internal/service/AlgorithmicService.java b/src/main/java/org/cytoscape/rest/internal/service/AlgorithmicService.java
@@ -1,20 +1,15 @@
 package org.cytoscape.rest.internal.service;
 
-import java.io.File;
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import java.util.Set;
 
-import javax.activation.MimetypesFileTypeMap;
 import javax.inject.Singleton;
 import javax.ws.rs.GET;
-import javax.ws.rs.NotFoundException;
 import javax.ws.rs.Path;
 import javax.ws.rs.PathParam;
 import javax.ws.rs.Produces;
-import javax.ws.rs.WebApplicationException;
 import javax.ws.rs.core.Context;
 import javax.ws.rs.core.MediaType;
 import javax.ws.rs.core.Response;
@@ -27,105 +22,137 @@
 import org.cytoscape.work.TaskIterator;
 import org.cytoscape.work.TaskMonitor;
 
+
+
+/**
+ * Algorithmic resources.  Essentially, this is a high-level task executor.
+ * 
+ * @author kono
+ *
+ */
 @Singleton
 @Path("/v1/apply")
 public class AlgorithmicService extends AbstractDataService {
 
 	@Context
 	private TaskMonitor headlessTaskMonitor;
-	
+
 	@Context
 	private CyLayoutAlgorithmManager layoutManager;
 
+
+	/**
+	 * 
+	 * @summary Apply layout to a network
+	 * 
+	 * @param algorithmName Name of layout algorithm ("circular", "force-directed", etc.)
+	 * @param networkId Target network SUID
+	 * 
+	 * @return Success message
+	 */
 	@GET
-	@Path("/layouts/{algorithmName}/{targetId}")
+	@Path("/layouts/{algorithmName}/{networkId}")
 	@Produces(MediaType.APPLICATION_JSON)
-	public String applyLayout(@PathParam("algorithmName") String algorithmName, @PathParam("targetId") Long targetId) {
-
-		final CyNetwork network = getCyNetwork(targetId);
-		Collection<CyNetworkView> views = this.networkViewManager.getNetworkViews(network);
+	public Response applyLayout(@PathParam("algorithmName") String algorithmName, @PathParam("networkId") Long networkId) {
+		final CyNetwork network = getCyNetwork(networkId);
+		final Collection<CyNetworkView> views = this.networkViewManager.getNetworkViews(network);
 		if (views.isEmpty()) {
-			throw new NotFoundException("View is not available for the network " + targetId);
+			throw getError("Could not find view for the network with SUID: " + networkId, Response.Status.NOT_FOUND);
 		}
 
 		final CyNetworkView view = views.iterator().next();
 		final CyLayoutAlgorithm layout = this.layoutManager.getLayout(algorithmName);
-
+		if(layout == null) {
+			throw getError("No such layout algorithm: " + algorithmName, Response.Status.NOT_FOUND);
+		}
+
 		final TaskIterator itr = layout.createTaskIterator(view, layout.getDefaultLayoutContext(),
 				CyLayoutAlgorithm.ALL_NODE_VIEWS, "");
 		try {
 			itr.next().run(headlessTaskMonitor);
 		} catch (Exception e) {
-			e.printStackTrace();
+			throw getError(e, Response.Status.INTERNAL_SERVER_ERROR);
 		}
-		return "{\"status\":\"OK\"}";
+		return Response.status(Response.Status.OK).entity("{\"message\":\"Layout finished.\"}").build();
 	}
 
 
+
+
+	/**
+	 * Apply Visual Style to a network.
+	 * 
+	 * @param styleName Visual Style name (title)
+	 * @param networkId Target network SUID
+	 * 
+	 * @return Success message.
+	 */
 	@GET
-	@Path("/styles/{styleName}/{targetId}")
+	@Path("/styles/{styleName}/{networkId}")
 	@Produces(MediaType.APPLICATION_JSON)
-	public String applyStyle(@PathParam("styleName") String styleName, @PathParam("targetId") Long targetId) {
+	public Response applyStyle(@PathParam("styleName") String styleName, @PathParam("networkId") Long networkId) {
 
-		final CyNetwork network = getCyNetwork(targetId);
+		final CyNetwork network = getCyNetwork(networkId);
 		final Set<VisualStyle> styles = vmm.getAllVisualStyles();
 		VisualStyle targetStyle = null;
-		for(final VisualStyle style:styles) {
+		for (final VisualStyle style : styles) {
 			final String name = style.getTitle();
-			if(name.equals(styleName)) {
+			if (name.equals(styleName)) {
 				targetStyle = style;
 				break;
 			}
 		}
-		if(targetStyle == null) {
-			throw new NotFoundException("Could not find Visual Style: " + styleName);
+
+		if (targetStyle == null) {
+			throw getError("Visual Style does not exist: " + styleName, Response.Status.NOT_FOUND);
 		}
-		
+
 		Collection<CyNetworkView> views = this.networkViewManager.getNetworkViews(network);
 		if (views.isEmpty()) {
-			throw new NotFoundException("View is not available for the network " + targetId);
+			throw getError("Network view does not exist for the network with SUID: " + networkId, Response.Status.NOT_FOUND);
 		}
 
-
 		final CyNetworkView view = views.iterator().next();
 		vmm.setVisualStyle(targetStyle, view);
 		vmm.setCurrentVisualStyle(targetStyle);
 		targetStyle.apply(view);
-		
-		return "{\"status\":\"OK\"}";
+
+		return Response.status(Response.Status.OK).entity("{\"message\":\"Visual Style applied.\"}").build();
 	}
 
+	/**
+	 * @summary Get list of available layout algorithm names
+	 * 
+	 * @return List of layout algorithm names.
+	 */
 	@GET
 	@Path("/layouts")
 	@Produces(MediaType.APPLICATION_JSON)
-	public String getLayouts() {
+	public Collection<String> getLayoutNames() {
 		final Collection<CyLayoutAlgorithm> layouts = layoutManager.getAllLayouts();
-		final List<String> layoutNames= new ArrayList<String>();
-		for(final CyLayoutAlgorithm layout: layouts) {
+		final List<String> layoutNames = new ArrayList<String>();
+		for (final CyLayoutAlgorithm layout : layouts) {
 			layoutNames.add(layout.getName());
 		}
-		try {
-			return getNames(layoutNames);
-		} catch (IOException e) {
-			throw new WebApplicationException(e, 500);
-		}
+		return layoutNames;
 	}
+
 
-
-
+	/**
+	 * @summary Get list of all Visual Style names.
+	 * 
+	 * @return List of Style names.
+	 * 
+	 */
 	@GET
-	@Path("/images/{image}")
-	@Produces("image/*")
-	public Response getImage(@PathParam("image") String image) {
-		// TODO implement this
-		File f = new File(image);
-
-
-		if (!f.exists()) {
-			throw new WebApplicationException(404);
+	@Path("/styles")
+	@Produces(MediaType.APPLICATION_JSON)
+	public Collection<String> getStyleNames() {
+		final Set<VisualStyle> styles = vmm.getAllVisualStyles();
+		final List<String> styleNames = new ArrayList<String>();
+		for (final VisualStyle style : styles) {
+			styleNames.add(style.getTitle());
 		}
-
-		final String mt = new MimetypesFileTypeMap().getContentType(f);
-		return Response.ok(f, mt).build();
+		return styleNames;
 	}
-}
+}
diff --git a/src/main/java/org/cytoscape/rest/internal/service/NetworkDataService.java b/src/main/java/org/cytoscape/rest/internal/service/NetworkDataService.java
@@ -27,6 +27,7 @@
 import javax.ws.rs.core.Context;
 import javax.ws.rs.core.HttpHeaders;
 import javax.ws.rs.core.MediaType;
+import javax.ws.rs.core.Response;
 
 import org.cytoscape.io.read.CyNetworkReader;
 import org.cytoscape.io.write.CyWriter;
@@ -302,7 +303,7 @@ public String getEdge(@PathParam("networkId") Long networkId, @PathParam("edgeId
 		final CyNetwork network = getCyNetwork(networkId);
 		final CyEdge edge = network.getEdge(edgeId);
 		if (edge == null) {
-			throw new NotFoundException("Could not find edge with SUID: " + edgeId);
+			throw getError("Could not find edge with SUID: " + edgeId, Response.Status.NOT_FOUND);
 		}
 		return getGraphObject(network, edge);
 	}
@@ -854,11 +855,11 @@ private final String getNetworkString(final CyNetwork network) {
 		CyWriter writer = cytoscapeJsWriterFactory.createWriter(stream, network);
 		String jsonString = null;
 		try {
-			writer.run(null);
+			writer.run(new HeadlessTaskMonitor());
 			jsonString = stream.toString();
 			stream.close();
 		} catch (Exception e) {
-			e.printStackTrace();
+			throw getError(e, Response.Status.PRECONDITION_FAILED);
 		}
 		return jsonString;
 	}