Fix some issues on unuserialize

msi.gama.core/src/msi/gama/kernel/simulation/SimulationAgent.java

@@ -972,6 +972,10 @@ public void executeAction(final IExecutable executable) {
 	@Override
 	public void updateWith(final IScope scope, final SavedAgent sa) {
 
+		Double seedValue = null;
+		String rngValue = null;
+		Integer usageValue = null;		
+
 		// This list is updated during all the updateWith of the simulation.
 		// When all the agents will be created (end of this updateWith),
 		// all the references will be replaced by the corresponding agent.
@@ -989,9 +993,23 @@ public void updateWith(final IScope scope, final SavedAgent sa) {
 				((IReference) attrValue).setAgentAndAttrName(this, varName);
 				if (!list_ref.contains(attrValue)) { list_ref.add((IReference) attrValue); }
 			}
+
+			// If attributes are related to the RNG, we keep them to initialise the RNG later, in the proper order.
+			if(varName.equals(IKeyword.SEED)) {
+				seedValue = (Double) attrValue;
+			} else if(varName.equals(IKeyword.RNG)) {
+				rngValue = (String) attrValue;
+			} else if(varName.equals(SimulationAgent.USAGE)) {
+				usageValue = (Integer) attrValue;
+			} else {
+				this.setDirectVarValue(scope, varName, attrValue);				
+			}
 
-			this.setDirectVarValue(scope, varName, attrValue);
 		}
+
+		// Update RNG
+		setRandomGenerator(new RandomUtils(seedValue, rngValue));
+		setUsage(usageValue);
 
 		// Update Clock
 		final Object cycle = sa.getAttributeValue("cycle");
@@ -1012,7 +1030,6 @@ public void updateWith(final IScope scope, final SavedAgent sa) {
 		if (savedAgentInnerPop != null) {
 			for (final String savedAgentMicroPopName : savedAgentInnerPop.keySet()) {
 				final IPopulation<? extends IAgent> simuMicroPop = getPopulationFor(savedAgentMicroPopName);
-				// final IPopulation<? extends IAgent> simuMicroPop = getMicroPopulation(savedAgentMicroPopName);
 
 				if (simuMicroPop != null) {
 					// Build a map name::innerPopAgentSavedAgt :
@@ -1061,9 +1078,6 @@ public void updateWith(final IScope scope, final SavedAgent sa) {
 					for (final IAgent remainingAgent : mapSimuAgtName.values()) {
 						// Kill them all
 						remainingAgent.dispose();
-						// simuMicroPop.killMembers();
-						// microPop.clear();
-						// microPop.firePopulationCleared();
 					}
 				}
 			}

msi.gama.core/src/msi/gama/metamodel/topology/CompoundSpatialIndex.java

@@ -283,7 +283,11 @@ public void remove(final ISpecies species) {
 	public void update(final IScope scope, final Envelope envelope, final boolean parallel) {
 		this.bounds = envelope;
 		this.parallel = parallel;
-		for (ISpecies species : spatialIndexes.keySet()) {
+
+		final WeakHashMap<ISpecies, ISpatialIndex> spatialIndexesTmp = new WeakHashMap<>();
+		spatialIndexesTmp.putAll(spatialIndexes);
+
+		for (ISpecies species : spatialIndexesTmp.keySet()) {
 			remove(species);
 			add(scope, species, true);
 		}

ummisco.gama.serialize/src/ummisco/gama/serializer/gamaType/converters/GamaAgentConverter.java

@@ -33,12 +33,17 @@
 @SuppressWarnings ({ "rawtypes" })
 public class GamaAgentConverter implements Converter {
 
+	/** The convert scope. */
+	ConverterScope convertScope;
+
 	/**
-	 * Instantiates a new gama agent converter.
+	 * Instantiates a new gama list converter.
 	 *
 	 * @param s the s
 	 */
-	public GamaAgentConverter(final ConverterScope s) {}
+	public GamaAgentConverter(final ConverterScope s) {
+		convertScope = s;
+	}
 
 	@Override
 	public boolean canConvert(final Class arg0) {
@@ -61,7 +66,6 @@ public boolean canConvert(final Class arg0) {
 		}
 
 		return false;
-		// return (arg0.equals(GamlAgent.class) || arg0.equals(MinimalAgent.class));
 	}
 
 	@Override
@@ -73,11 +77,9 @@ public void marshal(final Object arg0, final HierarchicalStreamWriter writer, fi
 		DEBUG.OUT("ConvertAnother : AgentConverter " + agt.getClass());
 		// System.out.println("ConvertAnother : AgentConverter " + agt.getClass());
 
-		// ReferenceSavedAgent refAft = new ReferenceSavedAgent(agt, null, (ReferenceToAgent) null);
 		final ReferenceAgent refAft = new ReferenceAgent(null, null, agt);
 		context.convertAnother(refAft);
 
-		// writer.setValue(agt.getName());
 		DEBUG.OUT("===========END ConvertAnother : GamaAgent");
 		// System.out.println("===========END ConvertAnother : GamaAgent");
 
@@ -88,27 +90,10 @@ public void marshal(final Object arg0, final HierarchicalStreamWriter writer, fi
 	public Object unmarshal(final HierarchicalStreamReader reader, final UnmarshallingContext arg1) {
 		// TODO manage MinimalAgent and MinimalGridAgent
 		reader.moveDown();
-		// SimulationAgent simAgt = convertScope.getSimulationAgent();
-		// List<IAgent> lagt;
-		// if(simAgt == null) {
-		// lagt = (convertScope.getScope()).getSimulation().getAgents(convertScope.getScope());
-		// } else {
-		// lagt = simAgt.getAgents(convertScope.getScope());
-		// }
 		final ReferenceAgent agt = (ReferenceAgent) arg1.convertAnother(null, ReferenceAgent.class);
-
-		// boolean found = false;
-		// int i = 0;
-		// IAgent agt = null;
-		// while(!found && (i < lagt.size())) {
-		// if(lagt.get(i).getName().equals(reader.getValue())) {
-		// found = true;
-		// agt = lagt.get(i);
-		// }
-		// i++;
-		// }
 		reader.moveUp();
-		return agt;
+
+		return agt.getReferencedAgent(convertScope.getScope().getSimulation());
 	}
 
 }

ummisco.gama.serialize/src/ummisco/gama/serializer/gamaType/reduced/GamaListReducer.java

@@ -60,8 +60,12 @@ public IList constructObject(final IScope scope) {
 			i++;
 		}
 
-		return isReference ? new ReferenceList(this)
-				: GamaListFactory.create(scope, contentTypeListReducer, valuesListReducer);
+		if(isReference) {
+			unreferenceReducer(scope.getSimulation());
+			return new ReferenceList(this);
+		} else {
+			return GamaListFactory.create(scope, contentTypeListReducer, valuesListReducer);
+		}
 	}
 
 	/**

ummisco.gama.serialize/src/ummisco/gama/serializer/gamaType/reference/ReferenceAgent.java

@@ -102,6 +102,10 @@ public boolean equals(final Object o) {
 		if (o == this) return true;
 		return false;
 	}
+
+	public IAgent getReferencedAgent(final SimulationAgent sim) {
+		return attributeValue.getReferencedAgent(sim);
+	}
 
 	@Override
 	public int hashCode() {

ummisco.gama.serialize/src/ummisco/gama/serializer/gamaType/reference/ReferenceList.java

@@ -13,7 +13,6 @@
 import java.util.ArrayList;
 
 import msi.gama.kernel.simulation.SimulationAgent;
-import msi.gama.metamodel.agent.IAgent;
 import msi.gama.util.GamaList;
 import msi.gama.util.IReference;
 import ummisco.gama.serializer.gamaType.reduced.GamaListReducer;
@@ -36,6 +35,7 @@ public class ReferenceList extends GamaList implements IReference {
 	 */
 	public ReferenceList(GamaListReducer l) {
 		super(l.getValuesListReducer().size(), l.getContentTypeListReducer());
+		this.addAll(l.getValuesListReducer());
 		agtAttr = new ArrayList<AgentAttribute>();		
 		listReducer = l;
 	}