Improved knowledge and tree solution

src/main/java/org/gcube/informationsystem/discovery/knowledge/ModelKnowledgeValidator.java

@@ -64,7 +64,7 @@ public class ModelKnowledgeValidator implements DiscoveredElementAction<Element>
 		}
 		
 		String typeName = TypeMapper.getType(e);
-		if(node.getTree().getRoot().getNodeElement() == e) {
+		if(node.getTree().getRootNode().getNodeElement() == e) {
 			logger.info("{}- Type {} is the root type", stringBuffer.toString(), typeName);
 			return;
 		}

src/main/java/org/gcube/informationsystem/model/knowledge/ModelKnowledge.java

@@ -57,9 +57,13 @@ public class ModelKnowledge<T, TI extends TypeInformation<T>> {
 		
 		AccessType[] modelTypes = AccessType.getModelTypes();
 		for(AccessType accessType : modelTypes) {
-			T t = typeInformation.getRoot(accessType);
 			
-			Tree<T> tree = new Tree<>(t, typeInformation);
+			/*
+			 * T t = typeInformation.getRoot(accessType);
+			 * Tree<T> tree = new Tree<>(t, typeInformation);
+			 */
+			
+			Tree<T> tree = new Tree<>(typeInformation);
 			trees.put(accessType, tree);
 			
 			if(accessType == AccessType.PROPERTY) {
@@ -140,6 +144,10 @@ public class ModelKnowledge<T, TI extends TypeInformation<T>> {
 			}
 		}
 		
+		if(types.size()==toRetry.size()) {
+			throw new RuntimeException("Unable to find parent for " + toRetry.toString());
+		}
+		
 		if(toRetry.size()>0) {
 			addAllType(toRetry);
 		}

src/main/java/org/gcube/informationsystem/tree/Tree.java

@@ -11,18 +11,53 @@ public class Tree<T> {
 
 	private boolean allowMultipleInheritance;
 	
-	private Node<T> root;
+	private Node<T> rootNode;
 	private NodeInformation<T> ni;
 	private Map<String, Node<T>> locate;
 	
-	public Tree(T t, NodeInformation<T> ni)  {
+	public Tree() {
 		this.allowMultipleInheritance = true;
-		this.ni = ni;
 		this.locate = new HashMap<>();
-		this.root = new Node<>(t);
-		this.root.setTree(this);
-		String identifier = ni.getIdentifier(t);
-		this.locate.put(identifier, root);
+	}
+	
+	public Tree(NodeInformation<T> ni) {
+		this();
+		setNodeInformation(ni);
+	}
+	
+	public Tree(T root, NodeInformation<T> ni)  {
+		this(ni);
+		setRoot(root);
+	}
+	
+	/**
+	 * Set the NodeInformation if and only if it was not previously set.
+	 * Otherwise this function has no effect.
+	 * @param ni the NodeInformation to set
+	 */
+	public void setNodeInformation(NodeInformation<T> ni) {
+		if(this.ni==null) {
+			this.ni = ni;
+		}
+	}
+	
+	/**
+	 * Set the root if and only if it was not previously set.
+	 * Otherwise this function has no effect.
+	 * This function raises a RuntimeException is the
+	 * NodeInformation was not previously set.
+	 * @param root the root to set
+	 */
+	public void setRoot(T root) throws RuntimeException {
+		if(this.ni==null) {
+			throw new RuntimeException("You must set the NodeInformation instance first");
+		}
+		if(this.rootNode==null) {
+			this.rootNode = new Node<>(root);
+			this.rootNode.setTree(this);
+			String identifier = ni.getIdentifier(root);
+			this.locate.put(identifier, rootNode);
+		}
 	}
 	
 	public void setAllowMultipleInheritance(boolean allowMultipleInheritance) {
@@ -43,17 +78,25 @@ public class Tree<T> {
 		Node<T> node = new Node<>(t);
 		node.setTree(this);
 		
-		Set<String> parentIdentifiers = ni.getParentIdentifiers(root.getNodeElement(), t);
-		for(String parentIdentifier : parentIdentifiers) {
-			Node<T> parentNode = locate.get(parentIdentifier);
-			if(parentNode==null) {
-				throw new RuntimeException("I can find parent for " + identifier + ". Missing parent is " + parentIdentifier);
+		Set<String> parentIdentifiers = ni.getParentIdentifiers(rootNode!= null ? rootNode.getNodeElement() : null, t);
+		if(parentIdentifiers==null || parentIdentifiers.size()==0) {
+			if(this.rootNode==null) {
+				this.rootNode = node;
+			}else {
+				throw new RuntimeException("A Tree cannot have two root. " + t.toString() + " has not parent.");
 			}
-			
-			parentNode.addChild(node);
-			
-			if(!allowMultipleInheritance) {
-				break;
+		} else {
+			for(String parentIdentifier : parentIdentifiers) {
+				Node<T> parentNode = locate.get(parentIdentifier);
+				if(parentNode==null) {
+					throw new RuntimeException("I can find parent for " + identifier + ". Missing parent is " + parentIdentifier);
+				}
+				
+				parentNode.addChild(node);
+				
+				if(!allowMultipleInheritance) {
+					break;
+				}
 			}
 		}
 		
@@ -62,16 +105,16 @@ public class Tree<T> {
 		return node;
 	}
 
-	public Node<T> getRoot() {
-		return root;
+	public Node<T> getRootNode() {
+		return rootNode;
 	}
 
 	@Override
 	public String toString() {
-		return root.toString();
+		return rootNode.toString();
 	}
 
 	public void elaborate(NodeElaborator<T> nodeElaborator) throws Exception {
-		root.elaborate(nodeElaborator);
+		rootNode.elaborate(nodeElaborator);
 	}
 }

src/main/java/org/gcube/informationsystem/types/knowledge/TypeInformation.java

@@ -19,10 +19,12 @@ public class TypeInformation implements org.gcube.informationsystem.model.knowle
 
 	@Override
 	public Set<String> getParentIdentifiers(Type root, Type type) {
-		if(type.getName().compareTo(root.getName())==0) {
+		if(root!=null && type.getName().compareTo(root.getName())==0) {
+			return new LinkedHashSet<>();
+		}
+		if(root==null && AccessType.getAccessType(type.getName())!=null) {
 			return new LinkedHashSet<>();
 		}
-		
 		return type.getExtendedTypes();
 	}
 

src/test/java/org/gcube/informationsystem/types/knowledge/ModelKnowledgeTest.java

@@ -12,7 +12,6 @@ import java.util.Map.Entry;
 import org.gcube.informationsystem.base.reference.AccessType;
 import org.gcube.informationsystem.model.knowledge.ModelKnowledge;
 import org.gcube.informationsystem.model.knowledge.UsageKnowledge;
-import org.gcube.informationsystem.queries.templates.QueryTemplateTest;
 import org.gcube.informationsystem.tree.Node;
 import org.gcube.informationsystem.tree.NodeElaborator;
 import org.gcube.informationsystem.tree.Tree;
@@ -32,7 +31,7 @@ public class ModelKnowledgeTest{
 	private static final Logger logger = LoggerFactory.getLogger(ModelKnowledgeTest.class);
 	
 	protected File getTypesDirectory() throws Exception {
-		URL logbackFileURL = QueryTemplateTest.class.getClassLoader().getResource("logback-test.xml");
+		URL logbackFileURL = ModelKnowledgeTest.class.getClassLoader().getResource("logback-test.xml");
 		File logbackFile = new File(logbackFileURL.toURI());
 		File resourcesDirectory = logbackFile.getParentFile();
 		return new File(resourcesDirectory, "types");
@@ -55,6 +54,7 @@ public class ModelKnowledgeTest{
 			String json = readFile(file);
 			List<Type> types = TypeMapper.deserializeTypeDefinitions(json);
 			modelKnowledge.addAllType(types);
+			logger.trace("-------------------------------------------------------");
 		}
 		
 		for(AccessType modelType : modelTypes) {