Merge branch 'GAMA_1.8.2' of https://github.com/gama-platform/gama in…

…to GAMA_1.8.2

msi.gama.core/META-INF/MANIFEST.MF

@@ -266,6 +266,7 @@ Export-Package: msi.gama.common,
    msi.gaml.types",
  msi.gama.util.path,
  msi.gama.util.random,
+ msi.gama.util.serialize,
  msi.gama.util.tree,
  msi.gaml.architecture;
   uses:="msi.gaml.species,

msi.gama.core/src/msi/gama/util/file/json/Jsoner.java

@@ -15,13 +15,38 @@
 import java.io.StringReader;
 import java.io.StringWriter;
 import java.io.Writer;
+import java.util.Arrays;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.EnumSet;
+import java.util.HashSet;
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.Map;
 import java.util.Set;
 
+import org.geotools.data.DataUtilities;
+import org.geotools.feature.SchemaException;
+import org.geotools.feature.simple.SimpleFeatureBuilder;
+import org.geotools.geojson.feature.FeatureJSON;
+import org.geotools.geojson.geom.GeometryJSON;
+import org.opengis.feature.simple.SimpleFeature;
+import org.opengis.feature.simple.SimpleFeatureType;
+import msi.gama.common.interfaces.IKeyword;
+import msi.gama.metamodel.agent.IAgent;
+import msi.gama.metamodel.population.IPopulation;
+import msi.gama.metamodel.shape.IShape;
+import msi.gama.metamodel.topology.projection.IProjection;
+import msi.gama.runtime.IScope;
+import msi.gama.runtime.exceptions.GamaRuntimeException;
+import msi.gama.util.GamaColor;
+import msi.gama.util.GamaListFactory;
+import msi.gama.util.GamaMapFactory;
+import msi.gama.util.serialize.IStreamConverter;
+import msi.gaml.descriptions.SpeciesDescription;
+import msi.gaml.expressions.IExpression;
+import msi.gaml.statements.SaveStatement;
+
 /**
  * Jsoner provides JSON utilities for escaping strings to be JSON compatible, thread safe parsing (RFC 4627) JSON
  * strings, and serializing data to strings in JSON format.
@@ -41,6 +66,8 @@ private enum DeserializationOptions {
 		/** Whether a JsonObject can be deserialized as a root element. */
 		ALLOW_JSON_OBJECTS;
 	}
+
+	public static IStreamConverter streamConverter;
 
 	/** Flags to tweak the behavior of the primary serialization method. */
 	private enum SerializationOptions {
@@ -717,7 +744,17 @@ private static void serialize(final Object jsonSerializable, final Writer writab
 			writableDestination.write(jsonSerializable.toString());
 		} else if (jsonSerializable instanceof Boolean) {
 			writableDestination.write(jsonSerializable.toString());
-		} else if (jsonSerializable instanceof Map) {
+		} else if (jsonSerializable instanceof GamaColor) {
+			GamaColor col = (GamaColor) jsonSerializable;
+			writableDestination.write('{');
+			writableDestination.write('"'+"r"+'"'+":");
+			Jsoner.serialize(col.red(), writableDestination, flags);
+			writableDestination.write("," + '"'+"g"+'"'+":");
+			Jsoner.serialize(col.blue(), writableDestination, flags);			
+			writableDestination.write("," + '"'+"b"+'"'+":");
+			Jsoner.serialize(col.green(), writableDestination, flags);			
+			writableDestination.write('}');
+	 	} else if (jsonSerializable instanceof Map) {
 			/* Writes the map in JSON object format. */
 			boolean isFirstEntry = true;
 			@SuppressWarnings ("rawtypes") final Iterator entries = ((Map) jsonSerializable).entrySet().iterator();
@@ -874,21 +911,86 @@ private static void serialize(final Object jsonSerializable, final Writer writab
 				}
 			}
 			writableDestination.write(']');
+		} else if (jsonSerializable instanceof IAgent) {
+			IAgent agent = (IAgent) jsonSerializable;
+			final SpeciesDescription species = agent.getSpecies().getDescription();
+
+			writableDestination.write('{');
+			writableDestination.write('"'+"species"+'"'+":");
+			Jsoner.serialize(species.getSpeciesExpr().getName(), writableDestination, flags);						
+
+			for (final String var : species.getAttributeNames()) {
+				if (!NON_JSONABLE_ATTRIBUTE_NAMES.contains(var)) { 
+					writableDestination.write(',');
+					writableDestination.write('"'+var+'"');
+					writableDestination.write(":");
+
+					Object attrValue = species.getVarExpr(var, false).value(agent.getScope()) ;
+					if(attrValue instanceof IAgent) {
+						Jsoner.serialize(((IAgent) attrValue).getName(), writableDestination, flags);												
+					} else {
+						Jsoner.serialize(attrValue, writableDestination, flags);						
+					}
+				}
+			}
+			writableDestination.write('}');
+
+		} else if (jsonSerializable instanceof IShape) {
+			IShape agentOrIShape = (IShape) jsonSerializable;
+			final StringBuilder specs = new StringBuilder(1 * 20);
+			final String geomType = SaveStatement.getGeometryType(Arrays.asList( agentOrIShape ));
+			specs.append("geometry:" + geomType);
+			try {
+				final SimpleFeatureType type = DataUtilities.createType("geojson", specs.toString());
+				final SimpleFeatureBuilder builder = new SimpleFeatureBuilder(type);
+				final SimpleFeature ff = builder.buildFeature("");
+
+				SaveStatement.buildFeature(null, ff, agentOrIShape, null, Collections.EMPTY_LIST);
+
+				final FeatureJSON io = new FeatureJSON(new GeometryJSON(20));
+				writableDestination.write(io.toString(ff));
+			} catch (final ClassCastException e) {
+				e.printStackTrace();				
+			}  catch (SchemaException e) {
+				e.printStackTrace();
+			}			
 		} else {
-			/* It cannot by any measure be safely serialized according to specification. */
-			if (flags.contains(SerializationOptions.ALLOW_INVALIDS)) {
-				/* Can be helpful for debugging how it isn't valid. */
-				writableDestination.write(jsonSerializable.toString());
-			} else {
-				/* Notify the caller the cause of failure for the serialization. */
-				throw new IllegalArgumentException("Encountered a: " + jsonSerializable.getClass().getName() + " as: "
-						+ jsonSerializable.toString()
-						+ "  that isn't JSON serializable.\n  Try:\n    1) Implementing the Jsonable interface for the object to return valid JSON. If it already does it probably has a bug.\n    2) If you cannot edit the source of the object or couple it with this library consider wrapping it in a class that does implement the Jsonable interface.\n    3) Otherwise convert it to a boolean, null, number, JsonArray, JsonObject, or String value before serializing it.\n    4) If you feel it should have serialized you could use a more tolerant serialization for debugging purposes.");
+			try {
+				writableDestination.write(streamConverter.convertObjectToJSONStream(null,jsonSerializable));
+			} catch(Exception e) {
+				/* It cannot by any measure be safely serialized according to specification. */
+				if (flags.contains(SerializationOptions.ALLOW_INVALIDS)) {
+					/* Can be helpful for debugging how it isn't valid. */
+					writableDestination.write(jsonSerializable.toString());
+				} else {
+					/* Notify the caller the cause of failure for the serialization. */
+					throw new IllegalArgumentException("Encountered a: " + jsonSerializable.getClass().getName() + " as: "
+							+ jsonSerializable.toString()
+							+ "  that isn't JSON serializable.\n  Try:\n    1) Implementing the Jsonable interface for the object to return valid JSON. If it already does it probably has a bug.\n    2) If you cannot edit the source of the object or couple it with this library consider wrapping it in a class that does implement the Jsonable interface.\n    3) Otherwise convert it to a boolean, null, number, JsonArray, JsonObject, or String value before serializing it.\n    4) If you feel it should have serialized you could use a more tolerant serialization for debugging purposes.");
+				}				
 			}
 		}
-		// System.out.println(writableDestination.toString());
+
+//		else {
+//			/* It cannot by any measure be safely serialized according to specification. */
+//			if (flags.contains(SerializationOptions.ALLOW_INVALIDS)) {
+//				/* Can be helpful for debugging how it isn't valid. */
+//				writableDestination.write(jsonSerializable.toString());
+//			} else {
+//				/* Notify the caller the cause of failure for the serialization. */
+//				throw new IllegalArgumentException("Encountered a: " + jsonSerializable.getClass().getName() + " as: "
+//						+ jsonSerializable.toString()
+//						+ "  that isn't JSON serializable.\n  Try:\n    1) Implementing the Jsonable interface for the object to return valid JSON. If it already does it probably has a bug.\n    2) If you cannot edit the source of the object or couple it with this library consider wrapping it in a class that does implement the Jsonable interface.\n    3) Otherwise convert it to a boolean, null, number, JsonArray, JsonObject, or String value before serializing it.\n    4) If you feel it should have serialized you could use a more tolerant serialization for debugging purposes.");
+//			}
+//		}
+//		System.out.println(writableDestination.toString());
 	}
 
+	/** The Constant NON_SAVEABLE_ATTRIBUTE_NAMES. */
+	private static final Set<String> NON_JSONABLE_ATTRIBUTE_NAMES = new HashSet<>(Arrays.asList(IKeyword.PEERS,
+			IKeyword.HOST, IKeyword.AGENTS, IKeyword.MEMBERS));
+
+
 	/**
 	 * Serializes like the first version of this library. It has been adapted to use Jsonable for serializing custom
 	 * objects, but otherwise works like the old JSON string serializer. It will allow non-JSON values in its output

msi.gama.core/src/msi/gama/util/serialize/IStreamConverter.java

@@ -0,0 +1,7 @@
+package msi.gama.util.serialize;
+
+import msi.gama.runtime.IScope;
+
+public interface IStreamConverter {
+	 abstract String convertObjectToJSONStream(final IScope scope, final Object o);
+}

msi.gama.core/src/msi/gaml/statements/SaveStatement.java

@@ -1113,7 +1113,7 @@ public String toCleanString(final Object o) {
 	 *            the var
 	 * @return the string
 	 */
-	public String type(final ITyped var) {
+	public static String type(final ITyped var) {
 		switch (var.getGamlType().id()) {
 			case IType.BOOL:
 				return "Boolean";

ummisco.gama.java2d/src/ummisco/gama/java2d/Java2DDisplaySurface.java

@@ -761,11 +761,13 @@ public void selectAgentsAroundMouse() {
 		final int yc = mousey - origin.y;
 		final List<ILayer> layers = layerManager.getLayersIntersecting(xc, yc);
 		if (layers.isEmpty()) return;
-		try {
-			EventQueue.invokeAndWait(() -> menuManager.buildMenu(mousex, mousey, xc, yc, layers));
-		} catch (InvocationTargetException | InterruptedException e) {
-			e.printStackTrace();
-		}
+		EventQueue.invokeLater(() -> menuManager.buildMenu(mousex, mousey, xc, yc, layers));
+		// Modified for Issue #3404 -- now calls the menu asynchronously
+		// try {
+		// EventQueue.invokeAndWait(() -> menuManager.buildMenu(mousex, mousey, xc, yc, layers));
+		// } catch (InvocationTargetException | InterruptedException e) {
+		// e.printStackTrace();
+		// }
 	}
 
 	@Override

ummisco.gama.network/models/Network/2 Available protocols/HTTP Request/HTTP POST.gaml

@@ -25,9 +25,9 @@ species NetworkingAgent skills:[network] {
 	reflex send when:  cycle = 0 {
 		write "sending message ";
 
-//		do send to: "/api/user/" contents: ["POST",map(["toto"::34,"titi"::12]), map(["Content-Type"::"application/json"])];
-//		do send to: "/api/user/" contents: ["PUT",map(["toto"::34,"titi"::12]), map(["Content-Type"::"application/json"])];
-		do send to: "/api/user/" contents: ["DELETE"];
+		do send to: "/api/user/" contents: ["POST",["toto"::34,"titi"::world], ["Content-Type"::"application/json"] ];
+//		do send to: "/api/user/" contents: ["PUT",["toto"::34,"titi"::12], ["Content-Type"::"application/json"]];
+//		do send to: "/api/user/" contents: ["DELETE"];
 
 	}
 

ummisco.gama.serialize/.classpath

@@ -1,14 +1,19 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry exported="true" kind="lib" path="ext/mxparser-1.2.2.jar"/>
-	<classpathentry exported="true" kind="lib" path="ext/xstream-1.4.18.jar"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 	<classpathentry kind="src" path="src"/>
 	<classpathentry kind="src" path="gaml">
 		<attributes>
 			<attribute name="optional" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
+		<attributes>
+			<attribute name="module" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry exported="true" kind="lib" path="ext/mxparser-1.2.2.jar"/>
+	<classpathentry exported="true" kind="lib" path="ext/xstream-1.4.18.jar"/>
+	<classpathentry exported="true" kind="lib" path="ext/jettison-1.4.1.jar"/>
+	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

ummisco.gama.serialize/META-INF/MANIFEST.MF

@@ -8,7 +8,8 @@ Require-Bundle: msi.gama.core,
  msi.gaml.architecture.simplebdi;bundle-version="1.8.2"
 Bundle-ClassPath: .,
  ext/mxparser-1.2.2.jar,
- ext/xstream-1.4.18.jar
+ ext/xstream-1.4.18.jar,
+ ext/jettison-1.4.1.jar
 Export-Package: com.thoughtworks.xstream,
  com.thoughtworks.xstream.annotations,
  com.thoughtworks.xstream.converters,
@@ -34,7 +35,9 @@ Export-Package: com.thoughtworks.xstream,
  ummisco.gama.serializer.gamaType.converters,
  ummisco.gama.serializer.gamaType.reduced,
  ummisco.gama.serializer.gaml
-Import-Package: org.apache.commons.lang
+Import-Package: org.apache.commons.lang,
+ org.osgi.framework;version="1.10.0"
 Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-17
 Automatic-Module-Name: ummisco.gama.serialize
+Bundle-Activator: ummisco.gama.serializer.Activator

ummisco.gama.serialize/build.properties

@@ -6,4 +6,5 @@ bin.includes = META-INF/,\
                plugin.xml,\
                models/,\
                ext/mxparser-1.2.2.jar,\
-               ext/xstream-1.4.18.jar
+               ext/xstream-1.4.18.jar,\
+               ext/jettison-1.4.1.jar

ummisco.gama.serialize/src/ummisco/gama/serializer/Activator.java

@@ -0,0 +1,19 @@
+package ummisco.gama.serializer;
+import org.osgi.framework.BundleActivator;
+import org.osgi.framework.BundleContext;
+
+import msi.gama.util.file.json.Jsoner;
+import ummisco.gama.serializer.inject.ConverterJSON;
+
+public class Activator implements BundleActivator {
+
+	@Override
+	public void start(BundleContext context) throws Exception {
+		Jsoner.streamConverter = new ConverterJSON();		
+	}
+
+	@Override
+	public void stop(BundleContext context) throws Exception {
+		// TODO Auto-generated method stub
+	}
+}

ummisco.gama.serialize/src/ummisco/gama/serializer/factory/StreamConverter.java

@@ -16,6 +16,7 @@
 
 import com.thoughtworks.xstream.XStream;
 import com.thoughtworks.xstream.converters.Converter;
+import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver;
 import com.thoughtworks.xstream.io.xml.DomDriver;
 import com.thoughtworks.xstream.security.AnyTypePermission;
 
@@ -39,14 +40,23 @@ public abstract class StreamConverter {
 	private static Map<Class<?>, XStream> xStreamMap = Collections.synchronizedMap(new HashMap<Class<?>, XStream>());
 
 	private static XStream getXStreamInstance(Class<?> clazz) {
+		return getXStreamInstance(clazz, false);
+	}	
+
+	private static XStream getXStreamInstance(Class<?> clazz, boolean toJSON) {
 		if (xStreamMap.containsKey(clazz)) {
 			return xStreamMap.get(clazz);
 		}
 		synchronized (clazz) {
 			if (xStreamMap.containsKey(clazz)) {
 				return xStreamMap.get(clazz);
 			}
-			XStream xStream = new XStream(new DomDriver());
+			XStream xStream;
+			if(toJSON) {
+				xStream = new XStream(new JettisonMappedXmlDriver());								
+			} else {
+				xStream = new XStream(new DomDriver());				
+			}
 			xStream.ignoreUnknownElements();
 			xStream.processAnnotations(clazz);
 			xStream.addPermission(AnyTypePermission.ANY);
@@ -76,6 +86,19 @@ public static void registerConverter(final XStream st,final Converter c) {
 		st.registerConverter(c);
 	}
 
+	/**
+	 * Convert object to stream in JSON.
+	 *
+	 * @param scope
+	 *            the scope
+	 * @param o
+	 *            the o
+	 * @return the string
+	 */
+	public static synchronized String convertObjectToJSONStream(final IScope scope, final Object o) {
+		return loadAndBuild(new ConverterScope(scope),o, true).toXML(o);
+	}	
+
 	/**
 	 * Load and build.
 	 *
@@ -84,9 +107,13 @@ public static void registerConverter(final XStream st,final Converter c) {
 	 * @return the x stream
 	 */
 	public static XStream loadAndBuild(final ConverterScope cs, final Object o) {
+		return loadAndBuild(cs, o, false);
+	}	
+
+	public static XStream loadAndBuild(final ConverterScope cs, final Object o, final boolean toJSON) {
 
 		final Converter[] cnv = Converters.converterFactory(cs);
-		XStream streamer=getXStreamInstance(o.getClass());
+		XStream streamer = getXStreamInstance(o.getClass(),toJSON);		
 		for (final Converter c : cnv) { StreamConverter.registerConverter(streamer,c); }
 		// dataStreamer.setMode(XStream.ID_REFERENCES);
 		return streamer;

ummisco.gama.serialize/src/ummisco/gama/serializer/inject/ConverterJSON.java

@@ -0,0 +1,13 @@
+package ummisco.gama.serializer.inject;
+
+import msi.gama.runtime.IScope;
+import msi.gama.util.serialize.IStreamConverter;
+import ummisco.gama.serializer.factory.StreamConverter;
+
+public class ConverterJSON implements IStreamConverter {
+
+	@Override
+	public String convertObjectToJSONStream(IScope scope, Object o) {
+		return StreamConverter.convertObjectToJSONStream(scope,o);
+	}
+}