Fixed serialization of unknown properties

src/main/java/org/gcube/informationsystem/base/impl/properties/PropertyElementImpl.java

@@ -41,7 +41,6 @@ public class PropertyElementImpl extends ElementImpl implements Property {
 		super();
 		this.additionalProperties = new HashMap<>();
 		this.allowedAdditionalKeys = new HashSet<>();
-		this.allowedAdditionalKeys.add(SUPERTYPES_PROPERTY);
 	}
 
 	@Override

src/main/java/org/gcube/informationsystem/contexts/impl/entities/ContextImpl.java

@@ -4,17 +4,25 @@
 package org.gcube.informationsystem.contexts.impl.entities;
 
 import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
+import java.util.Set;
 import java.util.UUID;
 
+import org.gcube.com.fasterxml.jackson.annotation.JsonIgnore;
 import org.gcube.com.fasterxml.jackson.annotation.JsonSetter;
 import org.gcube.com.fasterxml.jackson.annotation.JsonTypeName;
 import org.gcube.com.fasterxml.jackson.core.JsonProcessingException;
 import org.gcube.informationsystem.base.impl.entities.EntityElementImpl;
+import org.gcube.informationsystem.base.reference.Element;
 import org.gcube.informationsystem.contexts.impl.relations.IsParentOfImpl;
 import org.gcube.informationsystem.contexts.reference.entities.Context;
 import org.gcube.informationsystem.contexts.reference.relations.IsParentOf;
 import org.gcube.informationsystem.model.impl.properties.MetadataImpl;
+import org.gcube.informationsystem.model.reference.properties.Property;
+import org.gcube.informationsystem.serialization.ElementMapper;
 import org.gcube.informationsystem.utils.UUIDManager;
 
 /**
@@ -34,10 +42,21 @@ public final class ContextImpl extends EntityElementImpl implements Context {
 	protected IsParentOf parent;
 	protected List<IsParentOf> children;
 	
+	@JsonIgnore
+	protected Map<String, Object> additionalProperties;
+	
+	@JsonIgnore
+	/**
+	 * Used to allow to have an additional property starting with '_' or '@'
+	 */
+	protected final Set<String> allowedAdditionalKeys;
+	
 	protected ContextImpl() {
 		super();
 		this.parent = null;
 		this.children = new ArrayList<>();
+		this.additionalProperties = new HashMap<>();
+		this.allowedAdditionalKeys = new HashSet<>();
 	}
 	
 	public ContextImpl(UUID uuid) {
@@ -158,4 +177,55 @@ public final class ContextImpl extends EntityElementImpl implements Context {
 		children.add(isParentOf);
 	}
 
+	@Override
+	public Map<String, Object> getAdditionalProperties() {
+		return additionalProperties;
+	}
+
+	@Override
+	public void setAdditionalProperties(Map<String, Object> additionalProperties) {
+		this.additionalProperties = additionalProperties;
+	}
+
+	@Override
+	public Object getAdditionalProperty(String key) {
+		return additionalProperties.get(key);
+	}
+
+	@Override
+	public void setAdditionalProperty(String key, Object value) {
+		
+		if(!allowedAdditionalKeys.contains(key)){
+			if(key.startsWith("_")) {
+				return;
+			}
+			if(key.startsWith("@")) {
+				return;
+			}
+		}
+		
+		/*
+		Additional properties are not deserialized to the proper property type.
+		The first attempt was to try to write a specific deserializer but it fails.	
+		This fix the issue.
+		*/
+		try {
+			if(value instanceof Map<?,?>) {
+				@SuppressWarnings("unchecked")
+				Map<String, Object> map = (Map<String,Object>) value;
+				if(map.containsKey(Element.TYPE_PROPERTY)) {
+					String reserialized = ElementMapper.getObjectMapper().writeValueAsString(map);
+					Property property = ElementMapper.unmarshal(Property.class, reserialized);
+					value = property;
+				}
+			}
+		}catch (Throwable e) {
+			e.getMessage();
+			// Any type of error/exception must be catched
+		}
+		/* END of fix to properly deserialize Property types*/
+		
+		this.additionalProperties.put(key, value);
+	}
+
 }

src/main/java/org/gcube/informationsystem/contexts/reference/entities/Context.java

@@ -4,19 +4,25 @@
 package org.gcube.informationsystem.contexts.reference.entities;
 
 import java.util.List;
+import java.util.Map;
 import java.util.UUID;
 
+import org.gcube.com.fasterxml.jackson.annotation.JsonAnyGetter;
+import org.gcube.com.fasterxml.jackson.annotation.JsonAnySetter;
 import org.gcube.com.fasterxml.jackson.annotation.JsonGetter;
 import org.gcube.com.fasterxml.jackson.annotation.JsonIgnore;
 import org.gcube.com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import org.gcube.com.fasterxml.jackson.annotation.JsonPropertyOrder;
 import org.gcube.com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import org.gcube.com.fasterxml.jackson.databind.annotation.JsonSerialize;
 import org.gcube.informationsystem.base.reference.Element;
 import org.gcube.informationsystem.base.reference.IdentifiableElement;
+import org.gcube.informationsystem.base.reference.SchemaMixedElement;
 import org.gcube.informationsystem.base.reference.entities.EntityElement;
 import org.gcube.informationsystem.contexts.impl.entities.ContextImpl;
 import org.gcube.informationsystem.contexts.reference.relations.IsParentOf;
 import org.gcube.informationsystem.model.reference.relations.Relation;
+import org.gcube.informationsystem.serialization.AdditionalPropertiesSerializer;
 import org.gcube.informationsystem.types.annotations.ISProperty;
 import org.gcube.informationsystem.types.reference.Change;
 import org.gcube.informationsystem.types.reference.TypeMetadata;
@@ -31,14 +37,59 @@ import org.gcube.informationsystem.utils.Version;
 @JsonPropertyOrder({ Element.TYPE_PROPERTY, IdentifiableElement.ID_PROPERTY, IdentifiableElement.METADATA_PROPERTY})
 @TypeMetadata(name = Context.NAME, description = "This type is the used to define a Context", version = Version.MINIMAL_VERSION_STRING)
 @Change(version = Version.MINIMAL_VERSION_STRING, description = Version.MINIMAL_VERSION_DESCRIPTION)
-public interface Context extends EntityElement {
+public interface Context extends EntityElement, SchemaMixedElement {
 
 	public static final String NAME = "Context"; // Context.class.getSimpleName();
 
 	public static final String NAME_PROPERTY = "name";
 	public static final String PARENT_PROPERTY = "parent";
 	public static final String CHILDREN_PROPERTY = "children";
-
+	
+	/**
+	 * {
+	 * 	...
+	 * 	"availableAt" : [
+	 * 		"https://i-marine.d4science.org/group/alienandinvasivespecies", 
+	 * 		"https://services.d4science.org/group/alienandinvasivespecies"
+	 * 	]
+	 * 	...
+	 * }
+	 * For non VRE context this field could be null or could have multiple value
+	 * For VRE it is normally one value only (but some exception could exists
+	 */
+	public static final String AVAILABLE_AT_PROPERTY = "availableAt";
+	
+	// 
+	/**
+	 * This information is provided to allowed user only (by role)
+	 * {
+	 * 	...
+	 * 	"fullpaths" : [
+	 * 		{
+	 * 			"fullpath": "/gcube/devsec/myTest",
+	 * 			"time": "2023-12-11 15:35:41.289 +0000", // Same of creationTime in metadata
+	 * 		},
+	 * 		{
+	 * 			"fullpath": "/gcube/devsec/myTestVRE",
+	 * 			"time": "2023-12-13 16:13:12.336 +0000", 
+	 * 		}
+	 * 		{
+	 * 			"fullpath": "/gcube/devsec/myVRE",
+	 * 			"time": "2023-12-18 12:37:48.172 +0000", // Same of lastUpdateTime in metadata
+	 * 		}
+	 * 	]
+	 * 	...
+	 * }
+	 */
+	public static final String CONTEXT_FULLPATH_CHANGES_LOG_PROPERTY = "fullpathChangelog";
+	
+	/**
+	 * This information is provided to allowed user only (by role)
+	 * The symmetric key for the context
+	 */
+	public static final String CONTEXT_KEY_PROPERTY = "key";
+	
+	
 	@ISProperty(name = NAME_PROPERTY, mandatory = true, nullable = false)
 	public String getName();
 
@@ -66,5 +117,20 @@ public interface Context extends EntityElement {
 	public void addChild(Context child);
 
 	public void addChild(IsParentOf isParentOf);
+	
+	@JsonAnyGetter
+	@JsonSerialize(using = AdditionalPropertiesSerializer.class)
+	@Override
+	public Map<String,Object> getAdditionalProperties();
+	
+	@Override
+	public void setAdditionalProperties(Map<String,Object> additionalProperties);
+	
+	@Override
+	public Object getAdditionalProperty(String key);
+	
+	@JsonAnySetter
+	@Override
+	public void setAdditionalProperty(String key, Object value);
 
 }

src/main/java/org/gcube/informationsystem/model/impl/entities/FacetImpl.java

@@ -11,7 +11,6 @@ import java.util.Set;
 import org.gcube.com.fasterxml.jackson.annotation.JsonIgnore;
 import org.gcube.com.fasterxml.jackson.annotation.JsonTypeName;
 import org.gcube.informationsystem.base.reference.Element;
-import org.gcube.informationsystem.model.reference.ModelElement;
 import org.gcube.informationsystem.model.reference.entities.Facet;
 import org.gcube.informationsystem.model.reference.properties.Property;
 import org.gcube.informationsystem.serialization.ElementMapper;
@@ -40,8 +39,6 @@ public abstract class FacetImpl extends EntityImpl implements Facet {
 		super();
 		this.additionalProperties = new HashMap<>();
 		this.allowedAdditionalKeys = new HashSet<>();
-		this.allowedAdditionalKeys.add(ModelElement.SUPERTYPES_PROPERTY);
-		this.allowedAdditionalKeys.add(ModelElement.EXPECTED_TYPE_PROPERTY);
 	}
 	
 	@Override

src/main/java/org/gcube/informationsystem/model/impl/relations/RelationImpl.java

@@ -53,7 +53,6 @@ public abstract class RelationImpl<S extends Resource, T extends Entity>
 		super();
 		this.additionalProperties = new HashMap<>();
 		this.allowedAdditionalKeys = new HashSet<>();
-		this.allowedAdditionalKeys.add(SUPERTYPES_PROPERTY);
 	}
 
 	protected RelationImpl(S source, T target,

src/main/java/org/gcube/informationsystem/serialization/ElementMapper.java

@@ -25,6 +25,7 @@ import org.gcube.com.fasterxml.jackson.databind.ObjectMapper;
 import org.gcube.com.fasterxml.jackson.databind.SerializationFeature;
 import org.gcube.com.fasterxml.jackson.databind.exc.InvalidTypeIdException;
 import org.gcube.com.fasterxml.jackson.databind.node.ArrayNode;
+import org.gcube.com.fasterxml.jackson.databind.node.JsonNodeType;
 import org.gcube.com.fasterxml.jackson.databind.node.ObjectNode;
 import org.gcube.com.fasterxml.jackson.databind.node.TextNode;
 import org.gcube.informationsystem.base.reference.AccessType;
@@ -32,6 +33,7 @@ import org.gcube.informationsystem.base.reference.Element;
 import org.gcube.informationsystem.discovery.Discovery;
 import org.gcube.informationsystem.discovery.knowledge.Knowledge;
 import org.gcube.informationsystem.model.reference.ModelElement;
+import org.gcube.informationsystem.model.reference.properties.Property;
 import org.gcube.informationsystem.types.TypeMapper;
 import org.gcube.informationsystem.types.reference.Type;
 import org.slf4j.Logger;
@@ -207,24 +209,26 @@ public abstract class ElementMapper {
 		ArrayNode arrayNode = (ArrayNode) objectNode.get(ModelElement.SUPERTYPES_PROPERTY);
 		
 		String candidatedSupertype = null;
-		for(int i = 0; i < arrayNode.size(); i++) {
-			String superType = arrayNode.get(i).asText();
-			if(knownTypes.containsKey(superType)) {
-				candidatedSupertype = superType;
-				try {
-					// Checking if it is one of the base type. In some cases we need to use dummy 
-					// implementation
-					AccessType accessType = AccessType.getAccessType(superType);
-					// It is one of the BaseType. 
-					// Looking if we need to set the dummy implementation class
-					if(accessType.getDummyImplementationClass()!=null) {
-						// This should not happen because the type has been assigned already to the dummy class.
-						candidatedSupertype = accessType.getDummyImplementationClass().getSimpleName();
+		if(arrayNode!=null) {
+			for(int i = 0; i < arrayNode.size(); i++) {
+				String superType = arrayNode.get(i).asText();
+				if(knownTypes.containsKey(superType)) {
+					candidatedSupertype = superType;
+					try {
+						// Checking if it is one of the base type. In some cases we need to use dummy 
+						// implementation
+						AccessType accessType = AccessType.getAccessType(superType);
+						// It is one of the BaseType. 
+						// Looking if we need to set the dummy implementation class
+						if(accessType.getDummyImplementationClass()!=null) {
+							// This should not happen because the type has been assigned already to the dummy class.
+							candidatedSupertype = accessType.getDummyImplementationClass().getSimpleName();
+						}
+					} catch(Exception ex) {
+						// can continue discovery
 					}
-				} catch(Exception ex) {
-					// can continue discovery
+					break;
 				}
-				break;
 			}
 		}
 			
@@ -243,7 +247,17 @@ public abstract class ElementMapper {
 	}
 	
 	protected static JsonNode analizeTypes(ObjectNode objectNode) {
-		String cls = objectNode.get(Element.TYPE_PROPERTY).asText();
+		String cls = null;
+		
+		JsonNode typeJN = objectNode.get(Element.TYPE_PROPERTY);
+		if(typeJN !=null) {
+			cls = objectNode.get(Element.TYPE_PROPERTY).asText();
+		}
+		
+		if(cls==null && objectNode.getNodeType()==JsonNodeType.OBJECT) {
+			cls = Property.NAME;
+		}
+		
 		if(!knownTypes.containsKey(cls)) {
 			objectNode = setTypeToBestAvailable(objectNode);
 		}
@@ -267,7 +281,7 @@ public abstract class ElementMapper {
 		}
 		return objectNode;
 	}
-	
+
 	protected static ArrayNode analizeTypes(ArrayNode arrayNode) {
 		ArrayNode ret = mapper.createArrayNode();
 		

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

@@ -33,7 +33,11 @@ public class UUIDUtility {
 	}
 	
 	public static String getUUIDAsString(JsonNode jsonNode){
-		return getUUID(jsonNode).toString();
+		UUID uuid = getUUID(jsonNode);
+		if(uuid!=null) {
+			return uuid.toString();
+		}
+		return null;
 	}
 	
 	public static String getUUIDAsString(String json) throws JsonProcessingException, IOException{