Ready to benchmark.

.gitignore

@@ -60,4 +60,4 @@ atlassian-ide-plugin.xml
 # Crashlytics plugin (for Android Studio and IntelliJ)
 com_crashlytics_export_strings.xml
 
-target/
+#target/

pom.xml

@@ -155,5 +155,11 @@
             <version>3.4.0-SNAPSHOT</version>
         </dependency>
 
+        <dependency>
+            <groupId>commons-lang</groupId>
+            <artifactId>commons-lang</artifactId>
+            <version>2.6</version>
+        </dependency>
+
     </dependencies>
 </project>

queries/csmr-a.sparql

@@ -0,0 +1,13 @@
+PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+
+SELECT ?sw
+WHERE
+{
+	?sw rdf:type <http://www.emftext.org/java/statements#//Switch> .
+
+	OPTIONAL {
+	  ?sw <http://www.emftext.org/java/statements#//Switch/cases> ?sc .
+	  ?sc rdf:type <http://www.emftext.org/java/statements#//DefaultSwitchCase>
+	}
+	FILTER (!BOUND(?sc))
+}

queries/csmr-b.sparql

@@ -0,0 +1,15 @@
+SELECT ?cb
+WHERE
+{
+	?cb <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
+		<http://www.emftext.org/java/statements#//CatchBlock> .
+	?cb <http://www.emftext.org/java/statements#//CatchBlock/parameter>
+		?cbParam .
+
+	?io <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
+		<http://www.emftext.org/java/expressions#//InstanceOfExpression> .
+	?io <http://www.emftext.org/java/expressions#//InstanceOfExpression/child>
+		 ?ioChild .
+	?ioChild <http://www.emftext.org/java/references#//ElementReference/target>
+		?cbParam
+}

queries/csmr-c.sparql

@@ -0,0 +1,34 @@
+PREFIX java: <https://www.java.com/>
+PREFIX xannotations: <http://www.emftext.org/java/annotations#/>
+PREFIX xarrays: <http://www.emftext.org/java/arrays#/>
+PREFIX xclassifiers: <http://www.emftext.org/java/classifiers#/>
+PREFIX xcommons: <http://www.emftext.org/java/commons#/>
+PREFIX xcontainers: <http://www.emftext.org/java/containers#/>
+PREFIX xexpressions: <http://www.emftext.org/java/expressions#/>
+PREFIX xgenerics: <http://www.emftext.org/java/generics#/>
+PREFIX ximports: <http://www.emftext.org/java/imports#/>
+PREFIX xinstantiations: <http://www.emftext.org/java/instantiations#/>
+PREFIX xliterals: <http://www.emftext.org/java/literals#/>
+PREFIX xmembers: <http://www.emftext.org/java/members#/>
+PREFIX xmodifiers: <http://www.emftext.org/java/modifiers#/>
+PREFIX xoperators: <http://www.emftext.org/java/operators#/>
+PREFIX xparameters: <http://www.emftext.org/java/parameters#/>
+PREFIX xreferences: <http://www.emftext.org/java/references#/>
+PREFIX xstatements: <http://www.emftext.org/java/statements#/>
+PREFIX xtypes: <http://www.emftext.org/java/types#/>
+PREFIX xvariables: <http://www.emftext.org/java/variables#/>
+
+PREFIX base: <http://www.semanticweb.org/ontologies/2011/1/TrainRequirementOntology.owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl:  <http://www.w3.org/2002/07/owl#>
+PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+
+SELECT ?addEx
+WHERE
+{
+	?addEx rdf:type <http://www.emftext.org/java/expressions#//AdditiveExpression> .
+	?addEx <http://www.emftext.org/java/expressions#//AdditiveExpression/children> ?strRef .
+	?strRef <http://www.emftext.org/java/references#//StringReference/value> ""^^<http://www.w3.org/2001/XMLSchema#string> .
+	?addEx <http://www.emftext.org/java/expressions#//AdditiveExpression/additiveOperators> ?addOp .
+	?addOp rdf:type <http://www.emftext.org/java/operators#//Addition> .
+}

queries/csmr-d.sparql

@@ -0,0 +1,22 @@
+PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX java: <http://www.emftext.org/java/>
+PREFIX commons: <http://www.emftext.org/commons/>
+
+SELECT ?methodCall
+WHERE
+{
+	?ref rdf:type <java:references#//Reference> .
+	?ref <java:references#//Reference/next> ?methodCall .
+	?ref <java:references#//ElementReference/target> ?var .
+	?var rdf:type <java:variables#//Variable> .
+
+	?eqLayout rdf:type <commons:layout#//ReferenceLayoutInformation> .
+	?eqLayout <commons:layout#//LayoutInformation/visibleTokenText>
+		"equals"^^<http://www.w3.org/2001/XMLSchema#string> .
+	?eqLayout <commons:layout#//ReferenceLayoutInformation/object> ?eqEnumID .
+
+	?methodCall rdf:type <java:references#//MethodCall> .
+	?methodCall <java:references#//ElementReference/target> ?eqEnumID .
+	?methodCall <java:references#//Argumentable/arguments> ?arg .
+	?arg rdf:type <java:references#//StringReference> .
+}

src/main/java/hu/bme/mit/codemodel/jamoppdiscoverer/CommandParser.java

@@ -13,7 +13,11 @@
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.net.UnknownHostException;
-import java.util.*;
+import java.util.Arrays;
+import java.util.Set;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.TimeUnit;
 
 public class CommandParser {
 
@@ -24,7 +28,8 @@ public class CommandParser {
     protected String newFilesListPath = null;
     protected String modifiedFilesListPath = null;
     protected String deletedFilesListPath = null;
-//    protected String gitOutputPath = null;
+    protected static final int NTHREDS = 2;
+    //    protected String gitOutputPath = null;
 
     // -----------------------------------------------------------------------------------------------------------------
 
@@ -57,6 +62,77 @@ public void processArguments(String[] args) {
 
     public void execute() {
 
+        long dgStart = System.currentTimeMillis();
+        processChanges();
+        System.out.println("[DepGraph] " + (System.currentTimeMillis() - dgStart));
+
+
+        long agsStart = System.currentTimeMillis();
+        processFiles();
+        System.out.println("[ASG] " + (System.currentTimeMillis() - agsStart));
+    }
+
+    protected void processFiles() {
+        // ----------------------------------------------------------------------------------------------------- PROCESS
+
+        try {
+            DependencyManager dm = DependencyManager.getInstance();
+
+            // MultiMap of packages, and the files inside them
+            HashMultimap<String, String> packageAndFiles = HashMultimap.create();
+
+            for (String path : ChangeProcessor.getFilesToProcess()) {
+                String relativePath = RelativePath.of(path);
+
+                Dependency dependency = dm.find(relativePath);
+                if (dependency != null) {
+                    String packageName = dependency.getPackageName();
+
+                    if (!"".equals(packageName)) {
+                        packageAndFiles.get(packageName).add(relativePath);
+                    }
+                } else {
+                    packageAndFiles.get("").add(relativePath);
+                }
+            }
+
+            // processing packages separately
+            Set<String> packages = packageAndFiles.keys().elementSet();
+
+//            for (String p : packages) {
+//                FileDiscoverer packageDiscoverer = new FileDiscoverer(p);
+//
+//                for (String file : packageAndFiles.get(p)) {
+//                    packageDiscoverer.execute(new File(file));
+//                }
+//            }
+
+
+
+            ExecutorService executor = Executors.newFixedThreadPool(NTHREDS);
+
+            for (String p : packages) {
+
+                ParserProcess process = new ParserProcess(p, packageAndFiles.get(p));
+                executor.execute(process);
+
+            }
+
+            // This will make the executor accept no new threads
+            // and finish all existing threads in the queue
+            executor.shutdown();
+            // Wait until all threads are finish
+            executor.awaitTermination(9999999, TimeUnit.DAYS);
+
+
+        } catch (UnknownHostException e) {
+            e.printStackTrace();
+        } catch (InterruptedException e) {
+            e.printStackTrace();
+        }
+    }
+
+    protected void processChanges() {
         // --------------------------------------------------------------------------------------------------------- NEW
 
         if (newFilesListPath != null) {
@@ -99,53 +175,34 @@ public void execute() {
             File f = new File("toprocess/");
             FileIterator.iterate(f, new InitializationIterator());
         }
+    }
 
-        // ----------------------------------------------------------------------------------------------------- PROCESS
-
-        try {
-            DependencyManager dm = DependencyManager.getInstance();
+    protected void printHelp() {
+        HelpFormatter formatter = new HelpFormatter();
+        formatter.setWidth(120);
 
-            // MultiMap of packages, and the files inside them
-            HashMultimap<String, String> packageAndFiles = HashMultimap.create();
+        formatter.printHelp("java -jar JaMoPPDiscoverer.jar [options]", "options:", options, "", false);
+        System.out.println();
+    }
 
-            for (String path : ChangeProcessor.getFilesToProcess()) {
-                String relativePath = RelativePath.of(path);
+    protected class ParserProcess implements Runnable {
 
-                Dependency dependency = dm.find(relativePath);
-                if (dependency != null) {
-                    String packageName = dependency.getPackageName();
+        protected String packageName = null;
+        protected Set<String> files = null;
 
-                    if (!"".equals(packageName)) {
-                        packageAndFiles.get(packageName).add(relativePath);
-                    }
-                } else {
-                    packageAndFiles.get("").add(relativePath);
-                }
-            }
-
-            // processing packages separately
-            Set<String> packages = packageAndFiles.keys().elementSet();
+        public ParserProcess(String packageName, Set<String> files) {
+            this.packageName = packageName;
+            this.files = files;
+        }
 
-            for (String p : packages) {
-                FileDiscoverer packageDiscoverer = new FileDiscoverer(p);
+        @Override
+        public void run() {
+            FileDiscoverer packageDiscoverer = new FileDiscoverer(packageName);
 
-                for (String file : packageAndFiles.get(p)) {
-                    packageDiscoverer.execute(new File(file));
-                }
+            for (String file : files) {
+                packageDiscoverer.execute(new File(file));
             }
 
-
-        } catch (UnknownHostException e) {
-            e.printStackTrace();
         }
-
-    }
-
-    protected void printHelp() {
-        HelpFormatter formatter = new HelpFormatter();
-        formatter.setWidth(120);
-
-        formatter.printHelp("java -jar JaMoPPDiscoverer.jar [options]", "options:", options, "", false);
-        System.out.println();
     }
 }

src/main/java/hu/bme/mit/codemodel/jamoppdiscoverer/iterators/FileDiscoverer.java

@@ -7,6 +7,7 @@
 import hu.bme.mit.codemodel.jamoppdiscoverer.utils.RelativePath;
 import hu.bme.mit.codemodel.jamoppdiscoverer.whitepages.DependencyManager;
 import hu.bme.mit.codemodel.jamoppdiscoverer.whitepages.pojo.Dependency;
+import org.apache.commons.lang.StringEscapeUtils;
 import org.eclipse.emf.common.notify.Notifier;
 import org.eclipse.emf.common.util.EList;
 import org.eclipse.emf.common.util.TreeIterator;
@@ -27,10 +28,12 @@
 import java.io.*;
 import java.net.UnknownHostException;
 import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 public class FileDiscoverer implements FileIterator.Function {
 
-    protected static final int DEBUG_LEVEL = 0;
+    protected static final int DEBUG_LEVEL = -9001;
     protected static DependencyManager dependencyManager = null;
     private final JavaClasspath cp;
     protected String rootPath = new File("").getAbsolutePath() + "/";
@@ -42,6 +45,10 @@ public class FileDiscoverer implements FileIterator.Function {
     protected Set<Resource> basePackageResources = new HashSet<>();
     protected Long packageSize = 0L;
     protected Long packageCount = 0L;
+    protected static Pattern literalPattern = Pattern.compile("^(.*?)(\\^\\^.*)$");
+
+//    protected static ResourceSet cprs = new ResourceSetImpl();
+//    protected static JavaClasspath scp = JavaClasspath.get(cprs);
 
     public FileDiscoverer(String packageName) {
 
@@ -69,12 +76,25 @@ public FileDiscoverer(String packageName) {
 
         // init ResourceSet
         resourceSet.getLoadOptions().put(JavaClasspath.OPTION_USE_LOCAL_CLASSPATH, Boolean.TRUE);
+//        resourceSet.getLoadOptions().put(JavaClasspath.OPTION_REGISTER_STD_LIB, Boolean.TRUE);
+
         // TODO make this configurable
         resourceSet.getLoadOptions().put(IJavaOptions.DISABLE_LAYOUT_INFORMATION_RECORDING, Boolean.TRUE);
 
         cp = JavaClasspath.get(resourceSet);
-        cp.registerStdLib();
-        cp.registerSourceOrClassFileFolder(URI.createFileURI(rootPath + INPUT_DIRECTORY));
+//        scp.registerStdLib();
+//
+//        Map<String, List<String>> packageClassifierMap = scp.getPackageClassifierMap();
+//        for(String p : packageClassifierMap.keySet()) {
+//            cp.getPackageClassifierMap().put(p, new ArrayList<String>(packageClassifierMap.get(p)));
+//        }
+//
+//        resourceSet.getURIConverter().getURIMap().putAll(cprs.getURIConverter().getURIMap());
+
+//        javaClasspath.registerStdLib();
+//        resourceSet.getjavaClasspath.getDefaultImports();
+//        cp.registerStdLib();
+//        cp.registerSourceOrClassFileFolder(URI.createFileURI(rootPath + INPUT_DIRECTORY));
 
 
         loadPackageResources();
@@ -422,7 +442,17 @@ protected String exportTTL(Resource target) {
 //                    if (DEBUG_LEVEL > 0) System.out.println("\t" + _attribute.getName() + ":\t" + attributeValue + "\t" + attributeType);
 
                     String attributeString = ResourceFactory.createTypedLiteral(attribute).toString();
-                    w.println("<" + objectURI + "> <" + attributeURI + "> '''" + attributeString.replace("^^", "'''^^<") + "> .");
+                    String toSaveString = "";
+
+                    Matcher matcher = literalPattern.matcher(attributeString);
+
+                    if (matcher.matches()) {
+                        toSaveString = "'''" + StringEscapeUtils.escapeJava(matcher.group(1)) + "'''" + matcher.group(2).replace("^^", "^^<") + ">";
+                    } else {
+                        toSaveString = "'''" + attributeString.replace("^^", "'''^^<") + ">";
+                    }
+
+                    w.println("<" + objectURI + "> <" + attributeURI + "> " + toSaveString + " .");
                 }
 
                 // --------------------------------------------------------------------------------------- REFERENCE

target/.gitignore

@@ -0,0 +1,7 @@
+*
+
+!.gitignore
+
+!import-check.sh
+!transform.sh
+!transform-import-check.sh