Join: use soft reference delegates for instances

common/plugins/eu.esdihumboldt.hale.common.align/plugin.xml

@@ -610,6 +610,10 @@
             allowAll="false"
             class="eu.esdihumboldt.hale.common.align.transformation.function.impl.NoResultException">
       </allow>
+      <allow
+            allowAll="false"
+            class="eu.esdihumboldt.hale.common.align.transformation.function.impl.FamilyInstanceDelegate">
+      </allow>
    </extension>
 
 </plugin>

common/plugins/eu.esdihumboldt.hale.common.align/src/eu/esdihumboldt/hale/common/align/transformation/function/impl/FamilyInstanceDelegate.java

@@ -0,0 +1,64 @@
+/*
+ * Copyright (c) 2016 Data Harmonisation Panel
+ * 
+ * All rights reserved. This program and the accompanying materials are made
+ * available under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation, either version 3 of the License,
+ * or (at your option) any later version.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this distribution. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ * Contributors:
+ *     wetransform GmbH
+ */
+
+package eu.esdihumboldt.hale.common.align.transformation.function.impl;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+
+import eu.esdihumboldt.hale.common.instance.model.FamilyInstance;
+import eu.esdihumboldt.hale.common.instance.model.InstanceCollection;
+import eu.esdihumboldt.hale.common.instance.model.InstanceReference;
+import eu.esdihumboldt.hale.common.instance.model.impl.SoftInstanceDelegate;
+
+/**
+ * Family instance delegating to a soft reference that is refreshed via an
+ * InstanceReference.
+ * 
+ * @author Simon Templer
+ */
+public class FamilyInstanceDelegate extends SoftInstanceDelegate implements FamilyInstance {
+
+	private final Collection<FamilyInstance> children;
+
+	/**
+	 * Constructs the delegating instance.
+	 * 
+	 * @param ref the instance reference
+	 * @param collection the instance collection to resolved the reference from
+	 */
+	public FamilyInstanceDelegate(InstanceReference ref, InstanceCollection collection) {
+		super(ref, collection);
+		children = new ArrayList<FamilyInstance>();
+	}
+
+	/**
+	 * @see FamilyInstance#getChildren()
+	 */
+	@Override
+	public Collection<FamilyInstance> getChildren() {
+		return Collections.unmodifiableCollection(children);
+	}
+
+	/**
+	 * 
+	 * @see FamilyInstance#addChild(FamilyInstance)
+	 */
+	@Override
+	public void addChild(FamilyInstance child) {
+		children.add(child);
+	}
+}

common/plugins/eu.esdihumboldt.hale.common.instance.orient/.classpath

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 	<classpathentry kind="src" path="src"/>
 	<classpathentry kind="output" path="bin"/>

common/plugins/eu.esdihumboldt.hale.common.instance.orient/.settings/org.eclipse.jdt.core.prefs

@@ -1,5 +1,5 @@
-#Updated from default preferences Jul 24, 2013 2:15:11 PM
-#Wed Jul 24 14:15:11 CEST 2013
+#Updated from default preferences Jul 11, 2016 3:40:58 PM
+#Mon Jul 11 15:40:58 CEST 2016
 eclipse.preferences.version=1
 org.eclipse.jdt.core.builder.cleanOutputFolder=clean
 org.eclipse.jdt.core.builder.duplicateResourceTask=warning
@@ -20,9 +20,10 @@ org.eclipse.jdt.core.codeComplete.staticFieldSuffixes=
 org.eclipse.jdt.core.codeComplete.staticFinalFieldPrefixes=
 org.eclipse.jdt.core.codeComplete.staticFinalFieldSuffixes=
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
+org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.7
+org.eclipse.jdt.core.compiler.compliance=1.8
 org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
@@ -107,7 +108,7 @@ org.eclipse.jdt.core.compiler.problem.unusedParameterWhenOverridingConcrete=disa
 org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
 org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning
 org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
-org.eclipse.jdt.core.compiler.source=1.7
+org.eclipse.jdt.core.compiler.source=1.8
 org.eclipse.jdt.core.formatter.align_type_members_on_columns=false
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=16
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=0

common/plugins/eu.esdihumboldt.hale.common.instance.orient/META-INF/MANIFEST.MF

@@ -4,7 +4,7 @@ Bundle-Name: Instance model based on Orient DB
 Bundle-SymbolicName: eu.esdihumboldt.hale.common.instance.orient;singleton:=true
 Bundle-Version: 2.9.5.qualifier
 Bundle-Vendor: data harmonisation panel
-Bundle-RequiredExecutionEnvironment: JavaSE-1.7
+Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: eu.esdihumboldt.hale.common.instance;bundle-version="2.5.0",
  com.vividsolutions.jts;bundle-version="1.12.0",
  eu.esdihumboldt.hale.common.schema;bundle-version="2.5.0",

common/plugins/eu.esdihumboldt.hale.common.instance.orient/src/eu/esdihumboldt/hale/common/instance/orient/storage/BrowseOrientInstanceCollection.java

@@ -150,8 +150,7 @@ public Instance next() {
 				allowUpdate = true; // allow updating in hasNext
 				Instance instance = new OInstance(doc, getCurrentType(), ref.getDatabase(),
 						dataSet);
-				handle.addReference(instance);
-				return instance;
+				return handle.addInstance(instance);
 			}
 			else {
 				throw new IllegalStateException(

common/plugins/eu.esdihumboldt.hale.common.instance.orient/src/eu/esdihumboldt/hale/common/instance/orient/storage/DatabaseHandle.java

@@ -17,15 +17,22 @@
 package eu.esdihumboldt.hale.common.instance.orient.storage;
 
 import java.lang.ref.Reference;
+import java.util.Arrays;
 import java.util.Set;
 
+import javax.xml.namespace.QName;
+
 import com.google.common.base.FinalizablePhantomReference;
 import com.google.common.base.FinalizableReferenceQueue;
 import com.google.common.collect.Sets;
 import com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx;
 
 import de.fhg.igd.slf4jplus.ALogger;
 import de.fhg.igd.slf4jplus.ALoggerFactory;
+import eu.esdihumboldt.hale.common.instance.model.Group;
+import eu.esdihumboldt.hale.common.instance.model.Instance;
+import eu.esdihumboldt.hale.common.instance.model.impl.GroupDecorator;
+import eu.esdihumboldt.hale.common.instance.model.impl.InstanceDecorator;
 
 /**
  * Database handle that manages objects referencing the database object. It will
@@ -80,7 +87,10 @@ public void finalizeReferent() {
 	}
 
 	/**
-	 * Add an object that references the database connection
+	 * Add an object that references the database connection.
+	 * 
+	 * It is preferred to use {@link #addInstance(Instance)} or
+	 * {@link #addGroup(Group)} instead.
 	 * 
 	 * @param object the object referencing the database
 	 */
@@ -98,6 +108,77 @@ public void finalizeReferent() {
 		count++;
 	}
 
+	/**
+	 * Augment an instance and add a reference for the database connection.
+	 * Makes sure child instances or groups also reference the database
+	 * connection.
+	 * 
+	 * @param instance the instance to augment
+	 * @return the augmented instance
+	 */
+	public Instance addInstance(Instance instance) {
+		if (instance == null) {
+			return null;
+		}
+
+		Instance result = new InstanceDecorator(instance) {
+
+			@Override
+			public Object[] getProperty(QName propertyName) {
+				return augmentValues(getOriginalInstance().getProperty(propertyName));
+			}
+
+		};
+		addReference(result);
+		return result;
+	}
+
+	/**
+	 * Augment a group and add a reference for the database connection. Makes
+	 * sure child instances or groups also reference the database connection.
+	 * 
+	 * @param group the group to augment
+	 * @return the augmented group
+	 */
+	public Group addGroup(Group group) {
+		if (group == null) {
+			return null;
+		}
+
+		Group result = new GroupDecorator(group) {
+
+			@Override
+			public Object[] getProperty(QName propertyName) {
+				return augmentValues(getOriginalGroup().getProperty(propertyName));
+			}
+
+		};
+		addReference(result);
+		return result;
+	}
+
+	/**
+	 * Augment an array of values.
+	 * 
+	 * @param values the values to augment
+	 * @return the augmented objects
+	 */
+	protected Object[] augmentValues(Object[] values) {
+		if (values == null) {
+			return null;
+		}
+
+		return Arrays.stream(values).map(value -> {
+			if (value instanceof Instance) {
+				return addInstance((Instance) value);
+			}
+			if (value instanceof Group) {
+				return addGroup((Group) value);
+			}
+			return value;
+		}).toArray();
+	}
+
 	private synchronized void removeReference() {
 		count--;
 		tryClose();

common/plugins/eu.esdihumboldt.hale.common.instance.orient/src/eu/esdihumboldt/hale/common/instance/orient/storage/OrientInstanceReference.java

@@ -26,6 +26,7 @@
 import eu.esdihumboldt.hale.common.instance.model.DataSet;
 import eu.esdihumboldt.hale.common.instance.model.Instance;
 import eu.esdihumboldt.hale.common.instance.model.InstanceReference;
+import eu.esdihumboldt.hale.common.instance.model.impl.InstanceDecorator;
 import eu.esdihumboldt.hale.common.instance.orient.OInstance;
 import eu.esdihumboldt.hale.common.schema.model.TypeDefinition;
 import net.jcip.annotations.Immutable;
@@ -124,6 +125,10 @@ public static InstanceReference createReference(Instance instance) {
 					"Instance data set may not be null for retrieving reference");
 		}
 
+		while (instance instanceof InstanceDecorator) {
+			instance = ((InstanceDecorator) instance).getOriginalInstance();
+		}
+
 		OInstance inst = (OInstance) instance;
 		ORID id = inst.getDocument().getIdentity();
 
@@ -147,18 +152,7 @@ public Instance load(LocalOrientDB lodb, Object owner) {
 			if (document != null) {
 				OInstance instance = new OInstance(document, getTypeDefinition(), db.getDatabase(),
 						getDataSet());
-				handle.addReference(instance);
-				return instance;
-				/*
-				 * Alternative: Returning a copy of the instance.
-				 * 
-				 * But this can be very expensive if dealing with an instance
-				 * with deep sub-structures. Example: A Merge on ~150 GML
-				 * features took ~200 times longer (over 6 minutes instead of 2
-				 * seconds) when copying instances that were retrieved through
-				 * instance references.
-				 */
-//				return new DefaultInstance(instance);
+				return handle.addInstance(instance);
 			}
 			else
 				return null;

common/plugins/eu.esdihumboldt.hale.common.instance.orient/src/eu/esdihumboldt/hale/common/instance/orient/storage/SQLQueryInstanceCollection.java

@@ -97,8 +97,7 @@ public Instance next() {
 					TypeDefinition type = types.getType(typeName);
 					// TODO react in case it is not found?
 					Instance instance = new OInstance(doc, type, ref.getDatabase(), dataSet);
-					handle.addReference(instance);
-					return instance;
+					return handle.addInstance(instance);
 				} catch (DecoderException e) {
 					throw new IllegalStateException("Failed to decode instance type", e);
 				}

common/plugins/eu.esdihumboldt.hale.common.instance/src/eu/esdihumboldt/hale/common/instance/model/impl/GroupDecorator.java

@@ -0,0 +1,65 @@
+/*
+ * Copyright (c) 2016 wetransform GmbH
+ * 
+ * All rights reserved. This program and the accompanying materials are made
+ * available under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation, either version 3 of the License,
+ * or (at your option) any later version.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this distribution. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ * Contributors:
+ *     wetransform GmbH <http://www.wetransform.to>
+ */
+
+package eu.esdihumboldt.hale.common.instance.model.impl;
+
+import javax.xml.namespace.QName;
+
+import eu.esdihumboldt.hale.common.instance.model.Group;
+import eu.esdihumboldt.hale.common.schema.model.DefinitionGroup;
+
+/**
+ * Group decorator class.
+ * 
+ * @author Simon Templer
+ */
+public class GroupDecorator implements Group {
+
+	private final Group group;
+
+	/**
+	 * Constructs the decorator with the given group.
+	 * 
+	 * @param group the group to decorate
+	 */
+	public GroupDecorator(Group group) {
+		this.group = group;
+	}
+
+	/**
+	 * Returns the original group.
+	 * 
+	 * @return the original group
+	 */
+	public Group getOriginalGroup() {
+		return group;
+	}
+
+	@Override
+	public Object[] getProperty(QName propertyName) {
+		return group.getProperty(propertyName);
+	}
+
+	@Override
+	public Iterable<QName> getPropertyNames() {
+		return group.getPropertyNames();
+	}
+
+	@Override
+	public DefinitionGroup getDefinition() {
+		return group.getDefinition();
+	}
+
+}