Fixing json serialization/deserialization issues

.classpath

@@ -22,7 +22,7 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>

.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,6 @@
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
+encoding//src/test/resources=UTF-8
+encoding/<project>=UTF-8

.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.8

src/main/java/org/gcube/informationsystem/base/reference/AccessType.java

@@ -5,6 +5,8 @@ package org.gcube.informationsystem.base.reference;
 
 import java.util.Arrays;
 
+import org.gcube.informationsystem.base.impl.properties.BasePropertyImpl;
+import org.gcube.informationsystem.base.reference.properties.BaseProperty;
 import org.gcube.informationsystem.context.impl.entities.ContextImpl;
 import org.gcube.informationsystem.context.impl.relations.IsParentOfImpl;
 import org.gcube.informationsystem.context.reference.entities.Context;
@@ -27,13 +29,15 @@ import org.gcube.informationsystem.model.reference.properties.Property;
 import org.gcube.informationsystem.model.reference.relations.ConsistsOf;
 import org.gcube.informationsystem.model.reference.relations.IsRelatedTo;
 import org.gcube.informationsystem.model.reference.relations.Relation;
+import org.gcube.informationsystem.types.impl.TypeDefinitionImpl;
 import org.gcube.informationsystem.types.impl.entities.EntityTypeDefinitionImpl;
 import org.gcube.informationsystem.types.impl.properties.PropertyDefinitionImpl;
 import org.gcube.informationsystem.types.impl.properties.PropertyTypeDefinitionImpl;
 import org.gcube.informationsystem.types.impl.relations.RelationTypeDefinitionImpl;
+import org.gcube.informationsystem.types.reference.TypeDefinition;
 import org.gcube.informationsystem.types.reference.entities.EntityTypeDefinition;
 import org.gcube.informationsystem.types.reference.properties.PropertyDefinition;
-import org.gcube.informationsystem.types.reference.properties.PropertyTypeDefiniton;
+import org.gcube.informationsystem.types.reference.properties.PropertyTypeDefinition;
 import org.gcube.informationsystem.types.reference.relations.RelationTypeDefinition;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -44,17 +48,20 @@ import org.slf4j.LoggerFactory;
  * Enumerates the basic type names.
  */
 public enum AccessType {
-
+	
-	PROPERTY_DEFINITION(PropertyDefinition.class, PropertyDefinition.NAME, PropertyDefinitionImpl.class, null),
+	BASE_PROPERTY(BaseProperty.class, BaseProperty.NAME, BasePropertyImpl.class, null),
-	PROPERTY_TYPE_DEFINITION(PropertyTypeDefiniton.class, PropertyTypeDefiniton.NAME, PropertyTypeDefinitionImpl.class, null),
 	PROPERTY(Property.class, Property.NAME, PropertyImpl.class, DummyProperty.class),
 	
 	CONTEXT(Context.class, Context.NAME, ContextImpl.class, null),
 	IS_PARENT_OF(IsParentOf.class, IsParentOf.NAME, IsParentOfImpl.class, null),
 	
+	PROPERTY_DEFINITION(PropertyDefinition.class, PropertyDefinition.NAME, PropertyDefinitionImpl.class, null),
+	
+	TYPE_DEFINITION(TypeDefinition.class, TypeDefinition.NAME, TypeDefinitionImpl.class, null),
+	PROPERTY_TYPE_DEFINITION(PropertyTypeDefinition.class, PropertyTypeDefinition.NAME, PropertyTypeDefinitionImpl.class, null),
 	ENTITY_TYPE_DEFINITION(EntityTypeDefinition.class, EntityTypeDefinition.NAME, EntityTypeDefinitionImpl.class, null),
 	RELATION_TYPE_DEFINITION(RelationTypeDefinition.class, RelationTypeDefinition.NAME, RelationTypeDefinitionImpl.class, null),
-		
+	
 	ENTITY(Entity.class, Entity.NAME, EntityImpl.class, null),
 	RESOURCE(Resource.class, Resource.NAME, ResourceImpl.class, DummyResource.class),
 	FACET(Facet.class, Facet.NAME, FacetImpl.class, DummyFacet.class),

src/main/java/org/gcube/informationsystem/types/TypeBinder.java

@@ -1,7 +1,6 @@
 package org.gcube.informationsystem.types;
 
 import java.lang.reflect.Field;
-import java.util.ArrayList;
 import java.util.List;
 
 import org.gcube.informationsystem.base.reference.ISManageable;
@@ -9,9 +8,6 @@ import org.gcube.informationsystem.types.impl.TypeDefinitionImpl;
 import org.gcube.informationsystem.types.reference.TypeDefinition;
 import org.gcube.informationsystem.utils.ISMapper;
 
-import com.fasterxml.jackson.databind.JavaType;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
 /**
  * @author Luca Frosini (ISTI - CNR)
  */
@@ -19,7 +15,8 @@ public class TypeBinder {
 
 	private final static String NAME = "NAME";
 	
-	public static <ISM extends ISManageable> String serializeTypeDefinition(TypeDefinition<ISM> typeDefinition) throws Exception{
+	@SuppressWarnings("rawtypes")
+	public static String serializeTypeDefinition(TypeDefinition typeDefinition) throws Exception{
 		/*
 		ObjectMapper mapper = new ObjectMapper();
 		String json = mapper.writeValueAsString(typeDefinition);
@@ -33,23 +30,37 @@ public class TypeBinder {
 		return ISMapper.marshal(typeDefinition);
 	}
 
-	public static <ISM extends ISManageable> TypeDefinition<ISM> deserializeTypeDefinition(String json) throws Exception{
+	@SuppressWarnings("rawtypes")
+	public static TypeDefinition deserializeTypeDefinition(String json) throws Exception{
+		/*
 		ObjectMapper mapper = new ObjectMapper();
 		@SuppressWarnings("unchecked")
 		TypeDefinition<ISM> readValue = mapper.readValue(json, TypeDefinition.class);
+		*/
+		TypeDefinition readValue = ISMapper.unmarshal(TypeDefinition.class, json);
 		return readValue;
 	}
 	
 	public static <ISM extends ISManageable> String serializeTypeDefinitions(List<TypeDefinition<ISM>> typeDefinitions) throws Exception{
+		/*
 		ObjectMapper mapper = new ObjectMapper();
 		String json = mapper.writeValueAsString(typeDefinitions);
 		return json;
+		*/
+		String json = ISMapper.marshal(typeDefinitions);
+		return json;
+		
 	}
 	
-	public static <ISM extends ISManageable> List<TypeDefinition<ISM>> deserializeTypeDefinitions(String json) throws Exception{
+	@SuppressWarnings("rawtypes")
+	public static List<TypeDefinition> deserializeTypeDefinitions(String json) throws Exception{
+		/*
 		ObjectMapper mapper = new ObjectMapper();
 		JavaType type = mapper.getTypeFactory().constructCollectionType(ArrayList.class, TypeDefinition.class) ;
 		return mapper.readValue(json, type);
+		*/
+		List<TypeDefinition> list = ISMapper.unmarshalList(TypeDefinition.class, json);
+		return list;
 	}
 	
 	public static <ISM extends ISManageable> TypeDefinition<ISM> createTypeDefinition(Class<ISM> clz) {

src/main/java/org/gcube/informationsystem/types/impl/TypeDefinitionImpl.java

@@ -28,7 +28,7 @@ import com.fasterxml.jackson.annotation.JsonTypeName;
 
 // @JsonAutoDetect(fieldVisibility=JsonAutoDetect.Visibility.ANY)
 @JsonTypeName(value=TypeDefinition.NAME)
-public class TypeDefinitionImpl<ISM extends ISManageable> extends ISManageableImpl implements TypeDefinition<ISM> {
+public abstract class TypeDefinitionImpl<ISM extends ISManageable> extends ISManageableImpl implements TypeDefinition<ISM> {
 
 	/**
 	 * Generated Serial Version UID
@@ -50,7 +50,9 @@ public class TypeDefinitionImpl<ISM extends ISManageable> extends ISManageableIm
 		Set<String> interfaceList = new HashSet<>();
 		
 		if(type==baseClass){
-			interfaceList.add(topSuperClass);
+			if(topSuperClass!=null) {
+				interfaceList.add(topSuperClass);
+			}
 			return interfaceList;
 		}
 		
@@ -104,12 +106,14 @@ public class TypeDefinitionImpl<ISM extends ISManageable> extends ISManageableIm
 		} else if(BaseProperty.class.isAssignableFrom(clz)){
 			return new PropertyTypeDefinitionImpl(clz);
 		} else if(TypeDefinition.class.isAssignableFrom(clz)) {
-			return new TypeDefinitionImpl(clz);
+			return new DummyTypeDefinitionImpl(clz);
 		} else {
 			throw new RuntimeException("Serialization required");
 		}
 	}
 	
+	protected TypeDefinitionImpl() {}
+	
 	protected TypeDefinitionImpl(Class<ISM> clz) {
 		this.name = TypeBinder.getType(clz);
 		this.description = TypeBinder.getStaticStringFieldByName(clz, DESCRIPTION, "");

src/main/java/org/gcube/informationsystem/types/impl/entities/EntityTypeDefinitionImpl.java

@@ -16,7 +16,7 @@ import org.gcube.informationsystem.utils.ISMapper;
 import com.fasterxml.jackson.annotation.JsonTypeName;
 
 @JsonTypeName(value=EntityTypeDefinition.NAME)
-public class EntityTypeDefinitionImpl<E extends BaseEntity> extends TypeDefinitionImpl<E> implements EntityTypeDefinition<E> {
+public final class EntityTypeDefinitionImpl<E extends BaseEntity> extends TypeDefinitionImpl<E> implements EntityTypeDefinition<E> {
 
 	/**
 	 * Generated Serial Version UID
@@ -25,6 +25,10 @@ public class EntityTypeDefinitionImpl<E extends BaseEntity> extends TypeDefiniti
 
 	private static final String VERTEX_CLASS_NAME = "V";
 	
+	protected EntityTypeDefinitionImpl() {
+		super();
+	}
+	
 	public EntityTypeDefinitionImpl(Class<E> clz) {
 		super(clz);
 		

src/main/java/org/gcube/informationsystem/types/impl/properties/PropertyDefinitionImpl.java

@@ -65,7 +65,9 @@ public final class PropertyDefinitionImpl implements PropertyDefinition {
 		return name;
 	}
 	
-	
+	protected PropertyDefinitionImpl() {
+		
+	}
 	
 	public PropertyDefinitionImpl(ISProperty propertyAnnotation, Method method) {
 		String name = propertyAnnotation.name().isEmpty()?getPropertyNameFromMethodName(method):propertyAnnotation.name();

src/main/java/org/gcube/informationsystem/types/impl/properties/PropertyTypeDefinitionImpl.java

@@ -3,22 +3,26 @@ package org.gcube.informationsystem.types.impl.properties;
 import org.gcube.informationsystem.base.reference.properties.BaseProperty;
 import org.gcube.informationsystem.types.impl.TypeDefinitionImpl;
 import org.gcube.informationsystem.types.reference.TypeDefinition;
-import org.gcube.informationsystem.types.reference.properties.PropertyTypeDefiniton;
+import org.gcube.informationsystem.types.reference.properties.PropertyTypeDefinition;
 
 import com.fasterxml.jackson.annotation.JsonTypeName;
 
-@JsonTypeName(value=PropertyTypeDefiniton.NAME)
+@JsonTypeName(value=PropertyTypeDefinition.NAME)
-public class PropertyTypeDefinitionImpl<P extends BaseProperty> extends TypeDefinitionImpl<P> implements PropertyTypeDefiniton<P> {
+public final class PropertyTypeDefinitionImpl<P extends BaseProperty> extends TypeDefinitionImpl<P> implements PropertyTypeDefinition<P> {
 	
 	/**
 	 * Generated Serial Version UID
 	 */
 	private static final long serialVersionUID = 7532701373450638829L;
 
+	protected PropertyTypeDefinitionImpl() {
+		super();
+	}
+	
 	public PropertyTypeDefinitionImpl(Class<P> clz) {
 		super(clz);
 		this.superClasses = retrieveSuperClasses(clz, BaseProperty.class, clz == BaseProperty.class ? null : BaseProperty.NAME);
-		if(PropertyTypeDefiniton.class.isAssignableFrom(clz)) {
+		if(PropertyTypeDefinition.class.isAssignableFrom(clz)) {
 			this.superClasses.add(TypeDefinition.class.getSimpleName());
 		}
 	}

src/main/java/org/gcube/informationsystem/types/impl/relations/RelationTypeDefinitionImpl.java

@@ -20,7 +20,7 @@ import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonTypeName;
 
 @JsonTypeName(value=RelationTypeDefinition.NAME)
-public class RelationTypeDefinitionImpl<Out extends BaseEntity, In extends BaseEntity, Rel extends BaseRelation<Out,In>>
+public final class RelationTypeDefinitionImpl<Out extends BaseEntity, In extends BaseEntity, Rel extends BaseRelation<Out,In>>
 		extends TypeDefinitionImpl<Rel> implements RelationTypeDefinition<Out,In,Rel> {
 
 	/**
@@ -35,6 +35,10 @@ public class RelationTypeDefinitionImpl<Out extends BaseEntity, In extends BaseE
 	@JsonInclude(JsonInclude.Include.NON_NULL) 
 	protected String targetType;
 	
+	protected RelationTypeDefinitionImpl() {
+		super();
+	}
+	
 	public RelationTypeDefinitionImpl(Class<Rel> clz) {
 		super(clz);
 		

src/main/java/org/gcube/informationsystem/types/reference/properties/PropertyTypeDefinition.java

@@ -9,8 +9,8 @@ import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 
 @JsonIgnoreProperties(ignoreUnknown = true)
 @JsonDeserialize(as = PropertyTypeDefinitionImpl.class)
-public interface PropertyTypeDefiniton<P extends BaseProperty> extends TypeDefinition<P>, BaseProperty {
+public interface PropertyTypeDefinition<P extends BaseProperty> extends TypeDefinition<P>, BaseProperty {
 	
-	public static final String NAME = "PropertyTypeDefiniton"; // PropertyTypeDefiniton.class.getSimpleName();
+	public static final String NAME = "PropertyTypeDefinition"; // PropertyTypeDefinition.class.getSimpleName();
 	
 }

src/main/java/org/gcube/informationsystem/utils/ISMapper.java

@@ -63,7 +63,13 @@ public abstract class ISMapper {
 		
 		SchemaAction schemaAction = new ObjectMappingERAction(mapper);
 		try {
-			ISMDiscovery.manageISM(schemaAction);
+			List<Package> packages = new ArrayList<Package>();
+			for(AccessType accessType : accessTypes) {
+				Class<ISManageable> clz = accessType.getTypeClass();
+				packages.add(clz.getPackage());
+			}
+			ISMDiscovery.manageISM(schemaAction, packages.toArray(new Package[]{}));
+			
 		} catch(Exception e) {
 			logger.error("Error registering types", e);
 		}

src/main/java/org/gcube/informationsystem/utils/discovery/ISMDiscovery.java

@@ -13,7 +13,6 @@ import org.gcube.informationsystem.base.reference.ISManageable;
 import org.gcube.informationsystem.base.reference.entities.BaseEntity;
 import org.gcube.informationsystem.base.reference.properties.BaseProperty;
 import org.gcube.informationsystem.base.reference.relations.BaseRelation;
-import org.gcube.informationsystem.model.reference.properties.Property;
 import org.gcube.informationsystem.types.annotations.ISProperty;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -76,7 +75,7 @@ public class ISMDiscovery<ISM extends ISManageable> {
 			analizeISM(parent);
 		}
 		
-		if(root == Property.class) {
+		if(root == BaseProperty.class) {
 			
 			for(Method m : clz.getDeclaredMethods()) {
 				m.setAccessible(true);
@@ -116,8 +115,9 @@ public class ISMDiscovery<ISM extends ISManageable> {
 	@SuppressWarnings("unchecked")
 	public static void manageISM(SchemaAction schemaAction, Package... packages) throws Exception {
 		ISMDiscovery<BaseProperty> propertyDiscovery = new ISMDiscovery<>(BaseProperty.class);
-		if(Objects.nonNull(packages))
+		if(Objects.nonNull(packages)) {
 			Arrays.stream(packages).forEach(p -> propertyDiscovery.addPackage(p));
+		}
 		propertyDiscovery.discover();
 		for(Class<BaseProperty> property : propertyDiscovery.getDiscovered()) {
 			logger.trace("Going to manage : {}", property);
@@ -125,8 +125,9 @@ public class ISMDiscovery<ISM extends ISManageable> {
 		}
 		
 		ISMDiscovery<BaseEntity> entityDiscovery = new ISMDiscovery<>(BaseEntity.class);
-		if(Objects.nonNull(packages))
+		if(Objects.nonNull(packages)) {
 			Arrays.stream(packages).forEach(p -> entityDiscovery.addPackage(p));
+		}
 		entityDiscovery.discover();
 		
 		for(Class<BaseEntity> entity : entityDiscovery.getDiscovered()) {