Save very large EM networks to a file in the session.

Refs #482

Author: mikekucera

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

@@ -52,6 +52,7 @@
 public class CyActivator extends AbstractCyActivator {
 
 	public static final String APP_NAME = "EnrichmentMap";
+	public static final String SESSION_DATA_FOLDER = "EnrichmentMap.Data.1";
 
 	private Injector injector;
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/io/ModelSerializer.java

@@ -1,6 +1,13 @@
 package org.baderlab.csplugins.enrichmentmap.model.io;
 
 import java.awt.Color;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.Reader;
+import java.io.StringReader;
+import java.io.StringWriter;
 import java.lang.reflect.Type;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -46,6 +53,18 @@ public static String serialize(EnrichmentMap map) {
 	}
 
 	public static String serialize(EnrichmentMap map, boolean pretty) {
+		var writer = new StringWriter();
+		serialize(map, pretty, writer);
+		return writer.toString();
+	}
+	
+	public static void serialize(EnrichmentMap map, File file) throws IOException {
+		try(var writer = new FileWriter(file)) {
+			serialize(map, true, writer);
+		}
+	}
+	
+	private static void serialize(EnrichmentMap map, boolean pretty, Appendable writer) {
 		// When saving to the session file DO NOT enable pretty printing, the Cytoscape
 		// CSV parser is very slow for multi-line text
 		GsonBuilder builder = new GsonBuilder()
@@ -54,16 +73,28 @@ public static String serialize(EnrichmentMap map, boolean pretty) {
 				.registerTypeHierarchyAdapter(Color.class, new ColorAdapter())
 				.serializeSpecialFloatingPointValues(); // really important, we allow NaN in expression files
 
-		if (pretty) {
+		if(pretty)
 			builder.setPrettyPrinting();
-		}
 
 		Gson gson = builder.create();
-		String json = gson.toJson(map);
-		return json;
+		gson.toJson(map, writer);
+		
+	}
+	
+	public static EnrichmentMap deserialize(File file) throws IOException {
+		try(var reader = new FileReader(file)) {
+			return deserialize(reader);
+		}
 	}
 
 	public static EnrichmentMap deserialize(String json) {
+		try(var reader = new StringReader(json)) {
+			return deserialize(reader);
+		}
+	}
+	
+	
+	private static EnrichmentMap deserialize(Reader reader) {
 		Type immutableIntSetType = new TypeToken<ImmutableSet<Integer>>() {}.getType();
 
 		Gson gson = new GsonBuilder()
@@ -74,7 +105,7 @@ public static EnrichmentMap deserialize(String json) {
 				.registerTypeAdapter(immutableIntSetType, new ImmutableIntSetAdapter()).create();
 
 		try {
-			EnrichmentMap map = gson.fromJson(json, EnrichmentMap.class);
+			EnrichmentMap map = gson.fromJson(reader, EnrichmentMap.class);
 			for (EMDataSet dataset : map.getDataSetList()) {
 				dataset.setParent(map);
 			}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/io/SessionListener.java

@@ -1,5 +1,8 @@
 package org.baderlab.csplugins.enrichmentmap.model.io;
 
+import java.io.File;
+import java.util.List;
+
 import javax.swing.JFrame;
 import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
@@ -44,7 +47,14 @@ public void handleEvent(SessionLoadedEvent event) {
 	@Override
 	public void handleEvent(SessionAboutToBeSavedEvent event) {
 		if(sessionIsActuallySaving()) {
-			save();
+			List<File> files = save();
+			if(files != null && !files.isEmpty()) {
+				try {
+					event.addAppFiles(CyActivator.SESSION_DATA_FOLDER, files);
+				} catch (Exception e) {
+					e.printStackTrace();
+				}
+			}
 		}
 	}
 
@@ -60,11 +70,12 @@ private boolean sessionIsActuallySaving() {
 		return false;
 	}
 
-	public void save() {
-		modelIO.saveModel();
+	public List<File> save() {
 		if(!headless) {
 			viewIO.saveView();
 		}
+		List<File> files = modelIO.saveModel();
+		return files;
 	}
 
 	public void restore(CySession session) {