Add Command for exporting PNG. Code cleanup.

Refs #385

Author: mikekucera

EnrichmentMapPlugin/pom.xml

@@ -189,6 +189,12 @@
 			<version>2.0</version>
 			<scope>provided</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.glassfish.jersey.media</groupId>
+			<artifactId>jersey-media-multipart</artifactId>
+			<version>2.0</version>
+			<scope>provided</scope>
+		</dependency>
 		<dependency>
 			<groupId>io.swagger</groupId>
 			<artifactId>swagger-annotations</artifactId>

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CommandModule.java

@@ -6,6 +6,7 @@
 import org.baderlab.csplugins.enrichmentmap.commands.EMBuildCommandTask;
 import org.baderlab.csplugins.enrichmentmap.commands.EMGseaCommandTask;
 import org.baderlab.csplugins.enrichmentmap.commands.ExportModelJsonCommandTask;
+import org.baderlab.csplugins.enrichmentmap.commands.ExportNetworkImageCommandTask;
 import org.baderlab.csplugins.enrichmentmap.commands.ExportPDFCommandTask;
 import org.baderlab.csplugins.enrichmentmap.commands.MastermapCommandTask;
 import org.baderlab.csplugins.enrichmentmap.commands.MastermapListCommandTask;
@@ -101,5 +102,11 @@ public CommandTaskFactory provideExportPDF(Provider<ExportPDFCommandTask> taskPr
 		String desc = "Exports the contents of the Heat Map panel to a PDF file.";
 		return CommandTaskFactory.create("export pdf", desc, null, taskProvider);
 	}
+	
+	@ProvidesIntoSet
+	public CommandTaskFactory provideExportImage(Provider<ExportNetworkImageCommandTask> taskProvider) {
+		String desc = "Exports the network view to an image file in the users home directory.";
+		return CommandTaskFactory.create("export png", desc, null, taskProvider);
+	}
 
 }

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/CyActivator.java

@@ -14,9 +14,9 @@
 import org.baderlab.csplugins.enrichmentmap.commands.tunables.MannWhitRanksTunableHandlerFactory;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
 import org.baderlab.csplugins.enrichmentmap.model.io.SessionListener;
-import org.baderlab.csplugins.enrichmentmap.rest.BuildResource;
 import org.baderlab.csplugins.enrichmentmap.rest.ExpressionsResource;
 import org.baderlab.csplugins.enrichmentmap.rest.ModelResource;
+import org.baderlab.csplugins.enrichmentmap.rest.UploadFileResource;
 import org.baderlab.csplugins.enrichmentmap.style.ChartFactoryManager;
 import org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder;
 import org.baderlab.csplugins.enrichmentmap.style.charts.radialheatmap.RadialHeatMapChartFactory;
@@ -76,7 +76,7 @@ public void start(BundleContext bc) {
 		// jax-rs (CyREST) resources
 		registerService(bc, injector.getInstance(ExpressionsResource.class), ExpressionsResource.class);
 		registerService(bc, injector.getInstance(ModelResource.class), ModelResource.class);
-		registerService(bc, injector.getInstance(BuildResource.class), BuildResource.class);
+		registerService(bc, injector.getInstance(UploadFileResource.class), UploadFileResource.class);
 
 		// CyProperty
 		CyProperty<Properties> cyProperty = injector.getInstance(Key.get(new TypeLiteral<CyProperty<Properties>>(){}));

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/ExportNetworkImageCommandTask.java

@@ -0,0 +1,39 @@
+package org.baderlab.csplugins.enrichmentmap.commands;
+
+import java.nio.file.Paths;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.UUID;
+
+import org.cytoscape.command.CommandExecutorTaskFactory;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskMonitor;
+
+import com.google.inject.Inject;
+
+/**
+ * There is already a command in Cytoscape to export a network image. This command
+ * is different in that it always exports to the user's home directory, and it
+ * never prompts for overwrite permission.
+ */
+public class ExportNetworkImageCommandTask extends AbstractTask {
+
+	@Inject private CommandExecutorTaskFactory commandTaskFactory;
+	
+	@Override
+	public void run(TaskMonitor taskMonitor) {
+		String fileName = "em_network_" + UUID.randomUUID() + ".png";
+		String homeDir = System.getProperty("user.home");
+		String filePath = Paths.get(homeDir, fileName).toString();
+		
+		Map<String,Object> args = new HashMap<>();
+		args.put("options", "PNG (*.png)");
+		args.put("outputFile", filePath);
+		args.put("view", "CURRENT"); // required
+		
+		TaskIterator commandTasks = commandTaskFactory.createTaskIterator("view", "export", args, null);
+		insertTasksAfterCurrentTask(commandTasks);
+	}
+	
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/rest/BuildResource.java

@@ -0,0 +1,66 @@
+package org.baderlab.csplugins.enrichmentmap.rest;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.attribute.FileAttribute;
+
+import javax.ws.rs.Consumes;
+import javax.ws.rs.POST;
+import javax.ws.rs.Produces;
+import javax.ws.rs.core.MediaType;
+import javax.ws.rs.core.Response;
+
+import org.glassfish.jersey.media.multipart.FormDataParam;
+
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+
+
+@Api(tags="Apps: EnrichmentMap")
+@javax.ws.rs.Path("/enrichmentmap/fileupload")
+public class UploadFileResource {
+	
+	private Path tempDir = null;
+	
+	
+	@POST
+	@javax.ws.rs.Path("/")
+	@Consumes(MediaType.MULTIPART_FORM_DATA)
+	@Produces(MediaType.APPLICATION_JSON)
+	@ApiOperation(value="Upload a file.",
+		notes=""
+	)
+	public Response uploadFile(@FormDataParam("file") InputStream in) {
+		try {
+			synchronized(this) {
+				if(tempDir == null) {
+					tempDir = Files.createTempDirectory("em_fileupload_", new FileAttribute<?>[0]);
+				}
+			}
+			
+			File tempFile = Files.createTempFile(tempDir, "em_", "", new FileAttribute<?>[0]).toFile();
+			tempFile.deleteOnExit();
+			
+			try(FileOutputStream out = new FileOutputStream(tempFile)) {
+				int read = 0;
+				byte[] bytes = new byte[1024];
+				while((read = in.read(bytes)) != -1) {
+					out.write(bytes, 0, read);
+				}
+				out.flush();
+			}
+			
+			String absPath = tempFile.getAbsolutePath();
+			String response = String.format("{\"path\" : \"%s\"}", absPath);
+			return Response.status(200).entity(response).build();
+			
+		} catch(Exception e) {
+			e.printStackTrace();
+			return Response.serverError().build();
+		} 
+	}
+
+}