update rest of repo, partly using original github repo

- update xtext versions
- use constants for version of most packages
- try to silence "illegal-access"-warning (without success yet)

trainbenchmark/build.gradle

@@ -15,7 +15,7 @@ subprojects {
 
 	artifacts.archives packageSources
 	repositories {
-		jcenter()
+		mavenCentral()
 		maven { url "https://repo.eclipse.org/content/groups/acceleo" }
 		maven { url "https://repo.eclipse.org/content/groups/viatra2" }
 		maven { url "https://oss.sonatype.org/content/repositories/snapshots" }
@@ -27,11 +27,14 @@ subprojects {
 ext {
 	commonsExecVersion = '1.3'
 	commonsIoVersion = '2.5'
+	commonsLangVersion = '2.4'
 	emfVersion = '2.10.0-v20140514-1158'
-	tinkerGraphVersion = '3.2.5'
-	ingraphVersion = '0.1.0'
-	viatraVersion = '1.6.1'
+	guavaVersion = '23.0'
+	jacksonVersion = '2.12.4'
 	junitVersion = '4.12'
-	kryoVersion = '4.0.0'
+	kryoVersion = '4.0.2'
 	slf4jVersion = '1.7.10'
+	tinkerGraphVersion = '3.2.5'
+	viatraVersion = '1.6.1'
+	xtextVersion = '2.23.0'
 }

trainbenchmark/trainbenchmark-config/build.gradle

 dependencies {
-  compile group: 'commons-lang', name: 'commons-lang', version:'2.4'
-  compile group: 'com.google.guava', name: 'guava', version: '19.0'
+  compile group: 'commons-lang', name: 'commons-lang', version: commonsLangVersion
+  compile group: 'com.google.guava', name: 'guava', version: guavaVersion
   compile group: 'com.esotericsoftware', name: 'kryo-shaded', version: kryoVersion
 }

trainbenchmark/trainbenchmark-format-emf-model/.classpath

 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src">
-		<attributes>
-			<attribute name="FROM_GRADLE_MODEL" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" path="build/xcore/main">
-		<attributes>
-			<attribute name="FROM_GRADLE_MODEL" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" path="xtend-gen">
-		<attributes>
-			<attribute name="FROM_GRADLE_MODEL" value="true"/>
-		</attributes>
-	</classpathentry>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="src" path="build/xcore/main"/>
+	<classpathentry kind="src" path="xtend-gen"/>
 	<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.buildship.core.gradleclasspathcontainer"/>
-	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

trainbenchmark/trainbenchmark-format-emf-model/.project

@@ -6,12 +6,12 @@
 	</projects>
 	<buildSpec>
 		<buildCommand>
-			<name>org.eclipse.xtext.ui.shared.xtextBuilder</name>
+			<name>org.eclipse.jdt.core.javabuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>
 		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
+			<name>org.eclipse.xtext.ui.shared.xtextBuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>

trainbenchmark/trainbenchmark-format-emf-model/build.gradle

 plugins {
-    id "org.xtext.builder" version "1.0.0"
+    id "org.xtext.builder" version "2.0.8"
+	id 'java'
 }
 
 apply plugin: 'org.xtext.xtend'
 apply from: "${rootDir}/gradle/source-layout-xcore.gradle"
 
-ext {
-	xtextVersion = '2.13.0'
-}
-
- configurations.all {
-   resolutionStrategy.force 'org.antlr:antlr-runtime:3.2'
- }
-
 dependencies {
 	compile "org.eclipse.xtext:org.eclipse.xtext.xbase:${xtextVersion}"
 	compile 'org.eclipse.emf:org.eclipse.emf.ecore.xcore.lib:+'
@@ -33,6 +26,10 @@ sourceSets {
 	}
 }
 
+configurations.all {
+	resolutionStrategy.force 'org.antlr:antlr-runtime:3.2'
+}
+
 xtext {
 	version = "${xtextVersion}"
 	languages {

trainbenchmark/trainbenchmark-generator-emf/src/main/java/hu/bme/mit/trainbenchmark/generator/emf/EmfSerializer.java

@@ -85,7 +85,7 @@ public class EmfSerializer extends ModelSerializer<EmfGeneratorConfig> {
 		final RailwayElement railwayElement = (RailwayElement) RailwayFactory.eINSTANCE.create(clazz);
 		railwayElement.setId(id);
 		for (final Entry<String, ? extends Object> attribute : attributes.entrySet()) {
-			setAttribute(clazz, railwayElement, attribute.getKey(), attribute.getValue());
+			setEmfAttribute(clazz, railwayElement, attribute.getKey(), attribute.getValue());
 		}
 
 		switch (type) {
@@ -128,10 +128,10 @@ public class EmfSerializer extends ModelSerializer<EmfGeneratorConfig> {
 	public void setAttribute(final String type, final Object node, final String key, final Object value)
 			throws IOException {
 		final EClass clazz = (EClass) RailwayPackage.eINSTANCE.getEClassifier(type);
-		setAttribute(clazz, (RailwayElement) node, key, value);
+		setEmfAttribute(clazz, (RailwayElement) node, key, value);
 	}
 
-	protected void setAttribute(final EClass clazz, final RailwayElement node, final String key, Object value) {
+	protected void setEmfAttribute(final EClass clazz, final RailwayElement node, final String key, Object value) {
 		// change the enum value from the
 		// hu.bme.mit.trainbenchmark.constants.Signal enum to the
 		// hu.bme.mit.trainbenchmark.railway.Signal enum

trainbenchmark/trainbenchmark-generator-graph-tinkerpop/src/main/java/hu/bme/mit/trainbenchmark/generator/graph/tinkerpop/TinkerGraphSerializer.java

@@ -12,20 +12,19 @@
 
 package hu.bme.mit.trainbenchmark.generator.graph.tinkerpop;
 
-import java.io.IOException;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import javax.xml.stream.XMLStreamException;
-
+import hu.bme.mit.trainbenchmark.constants.ModelConstants;
+import hu.bme.mit.trainbenchmark.generator.ModelSerializer;
+import hu.bme.mit.trainbenchmark.generator.graph.tinkerpop.config.TinkerGraphFormat;
+import hu.bme.mit.trainbenchmark.generator.graph.tinkerpop.config.TinkerGraphGeneratorConfig;
 import org.apache.tinkerpop.gremlin.structure.Vertex;
 import org.apache.tinkerpop.gremlin.structure.io.Io.Builder;
 import org.apache.tinkerpop.gremlin.structure.io.IoCore;
 import org.apache.tinkerpop.gremlin.tinkergraph.structure.TinkerGraph;
 
-import hu.bme.mit.trainbenchmark.generator.ModelSerializer;
-import hu.bme.mit.trainbenchmark.generator.graph.tinkerpop.config.TinkerGraphFormat;
-import hu.bme.mit.trainbenchmark.generator.graph.tinkerpop.config.TinkerGraphGeneratorConfig;
+import javax.xml.stream.XMLStreamException;
+import java.io.IOException;
+import java.util.Map;
+import java.util.Map.Entry;
 
 public class TinkerGraphSerializer extends ModelSerializer<TinkerGraphGeneratorConfig> {
 
@@ -51,6 +50,7 @@ public class TinkerGraphSerializer extends ModelSerializer<TinkerGraphGeneratorC
 		// NOTE: multiple inheritance is not supported
 		final Vertex vertex = graph.addVertex(type);
 
+		vertex.property(ModelConstants.ID, id);
 		for (final Entry<String, ? extends Object> attribute : attributes.entrySet()) {
 			final String key = attribute.getKey();
 			Object value = attribute.getValue();

trainbenchmark/trainbenchmark-generator-jastadd-manual-intrinsic/build.gradle

@@ -12,5 +12,5 @@ shadowJar {
 dependencies {
     compile project(':trainbenchmark-tool')
     compile project(':trainbenchmark-generator')
-    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.8.8.1'
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: jacksonVersion
 }

trainbenchmark/trainbenchmark-generator-jastadd-manual/build.gradle

@@ -12,5 +12,5 @@ shadowJar {
 dependencies {
     compile project(':trainbenchmark-tool')
     compile project(':trainbenchmark-generator')
-    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.8.8.1'
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: jacksonVersion
 }

trainbenchmark/trainbenchmark-generator-jastadd-relast/build.gradle

@@ -13,5 +13,5 @@ dependencies {
     compile project(':trainbenchmark-tool')
     compile project(':trainbenchmark-generator')
     compile project(':trainbenchmark-tool-jastadd-relast')
-    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.8.8.1'
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: jacksonVersion
 }

trainbenchmark/trainbenchmark-generator/src/main/java/hu/bme/mit/trainbenchmark/generator/runner/GeneratorRunner.java

@@ -19,7 +19,7 @@ public class GeneratorRunner {
 
 		final String projectName = String.format("trainbenchmark-generator-%s", gc.getProjectName());
 		final String jarPath = String.format("../%s/build/libs/%s-1.0.0-SNAPSHOT-fat.jar", projectName, projectName);
-		final String javaCommand = String.format("java -Xms%s -Xmx%s -server -jar %s %s", ec.getXms(), ec.getXmx(),
+		final String javaCommand = String.format("java --illegal-access=permit -Xms%s -Xmx%s -server -jar %s %s", ec.getXms(), ec.getXmx(),
 				jarPath, configPath);
 
 		final CommandLine cmdLine = CommandLine.parse(javaCommand);

trainbenchmark/trainbenchmark-scripts/build.gradle

 dependencies {
-    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.2.3'
-    compile group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.3.0'
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: jacksonVersion
+    compile group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: jacksonVersion
 
     compile project(':trainbenchmark-generator')
     compile project(':trainbenchmark-generator-emf')

trainbenchmark/trainbenchmark-scripts/src/main/java/de/tudresden/inf/st/train/scripts/BenchmarkMain.java

@@ -8,6 +8,8 @@ import hu.bme.mit.trainbenchmark.config.ExecutionConfig;
 import hu.bme.mit.trainbenchmark.constants.RailwayOperation;
 
 import java.io.IOException;
+import java.lang.reflect.Field;
+import java.lang.reflect.Method;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
@@ -18,6 +20,24 @@ import java.util.Optional;
  */
 public class BenchmarkMain {
 
+  public static void disableAccessWarnings() {
+    try {
+      Class<?> unsafeClass = Class.forName("sun.misc.Unsafe");
+      Field field = unsafeClass.getDeclaredField("theUnsafe");
+      field.setAccessible(true);
+      Object unsafe = field.get(null);
+
+      Method putObjectVolatile = unsafeClass.getDeclaredMethod("putObjectVolatile", Object.class, long.class, Object.class);
+      Method staticFieldOffset = unsafeClass.getDeclaredMethod("staticFieldOffset", Field.class);
+
+      Class<?> loggerClass = Class.forName("jdk.internal.module.IllegalAccessLogger");
+      Field loggerField = loggerClass.getDeclaredField("logger");
+      Long offset = (Long) staticFieldOffset.invoke(unsafe, loggerField);
+      putObjectVolatile.invoke(unsafe, loggerClass, offset, null);
+    } catch (Exception ignored) {
+    }
+  }
+
   @SuppressWarnings("unchecked")
   private static void runBenchmarkSeries(BenchmarkConfigBaseBuilder configBaseBuilder, BenchmarkConfigBuilder configBuilder,
                                          ExecutionConfig ec, ModelSetConfig modelSetConfig, BenchmarkSettingsBasics bbs) {
@@ -61,6 +81,8 @@ public class BenchmarkMain {
     }
     String benchmarkVariant = args[0];
 
+    disableAccessWarnings();
+
     // read basic settings (min, maxsize, etc.)
     ObjectMapper mapper = Utils.getMapper();
     BenchmarkSettingsBasics bbs = Utils.readFromResource(mapper, "basic-settings.json",

trainbenchmark/trainbenchmark-tool-jastadd-base/src/main/java/de/tudresden/inf/st/train/jastadd/JastaddAbstractBenchmarkScenario.java

@@ -17,14 +17,36 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.PrintStream;
+import java.lang.reflect.Field;
+import java.lang.reflect.Method;
 
 public abstract class JastaddAbstractBenchmarkScenario<TBenchmarkConfigWrapper extends JastaddAbstractBenchmarkConfig> extends
   BenchmarkScenario<JastaddMatch, JastaddDriver, TBenchmarkConfigWrapper> {
 
   protected final CacheCounterReceiver receiver = new CacheCounterReceiver();
 
+  @SuppressWarnings("unchecked")
+  public static void disableAccessWarnings() {
+    try {
+      Class unsafeClass = Class.forName("sun.misc.Unsafe");
+      Field field = unsafeClass.getDeclaredField("theUnsafe");
+      field.setAccessible(true);
+      Object unsafe = field.get(null);
+
+      Method putObjectVolatile = unsafeClass.getDeclaredMethod("putObjectVolatile", Object.class, long.class, Object.class);
+      Method staticFieldOffset = unsafeClass.getDeclaredMethod("staticFieldOffset", Field.class);
+
+      Class loggerClass = Class.forName("jdk.internal.module.IllegalAccessLogger");
+      Field loggerField = loggerClass.getDeclaredField("logger");
+      Long offset = (Long) staticFieldOffset.invoke(unsafe, loggerField);
+      putObjectVolatile.invoke(unsafe, loggerClass, offset, null);
+    } catch (Exception ignored) {
+    }
+  }
+
   public JastaddAbstractBenchmarkScenario(final TBenchmarkConfigWrapper bc, boolean flushCaches) throws Exception {
     super(new JastaddDriverFactory(flushCaches), new JastaddModelOperationFactory(), new JastaddMatchComparator(), bc);
+    disableAccessWarnings();
 
     ((JastaddDriverFactory)driverFactory).setReceiver(receiver);
   }

trainbenchmark/trainbenchmark-tool-jastadd-base/tasks.gradle

@@ -78,7 +78,7 @@ clean {
 
 dependencies {
     compile project(':trainbenchmark-tool')
-    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.8.8.1'
+    compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: jacksonVersion
 }
 
 test {

trainbenchmark/trainbenchmark-tool-viatra-patterns/.classpath

 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src">
-		<attributes>
-			<attribute name="FROM_GRADLE_MODEL" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" path="src-gen">
-		<attributes>
-			<attribute name="FROM_GRADLE_MODEL" value="true"/>
-		</attributes>
-	</classpathentry>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="src" path="src-gen"/>
 	<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.buildship.core.gradleclasspathcontainer"/>
-	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

trainbenchmark/trainbenchmark-tool-viatra-patterns/.project

@@ -6,22 +6,22 @@
 	</projects>
 	<buildSpec>
 		<buildCommand>
-			<name>org.eclipse.viatra.query.tooling.ui.projectbuilder</name>
+			<name>org.eclipse.jdt.core.javabuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>
 		<buildCommand>
-			<name>org.eclipse.xtext.ui.shared.xtextBuilder</name>
+			<name>org.eclipse.buildship.core.gradleprojectbuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>
 		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
+			<name>org.eclipse.viatra.query.tooling.ui.projectbuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>
 		<buildCommand>
-			<name>org.eclipse.buildship.core.gradleprojectbuilder</name>
+			<name>org.eclipse.xtext.ui.shared.xtextBuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>

trainbenchmark/trainbenchmark-tool/src/main/java/hu/bme/mit/trainbenchmark/benchmark/driver/Driver.java

@@ -16,8 +16,6 @@ package hu.bme.mit.trainbenchmark.benchmark.driver;
  * 
  * @author szarnyasg
  *
- * @param <TElement>
- *            the type of the individual model elements
  */
 public abstract class Driver {