Clean Sonar bugs and smells

.gitignore

@@ -2,6 +2,10 @@ build/
 .gradle/
 /bin/
 
+.idea/
+*.iml
+*.class
+
 .settings/
 .classpath
 .project

analyzer/BoSC.java

@@ -1,23 +1,20 @@
+package analyzer;
+
 import java.util.ArrayList;
-import java.util.Collections;
 
 /**
  * Bag of System Calls
  *
  * @author AmrAbed
- *
  */
-public class BoSC extends ArrayList<Byte>
-{
+public class BoSC extends ArrayList<Byte> {
 	private static final long serialVersionUID = 1L;
 
-	public BoSC(String string)
-	{
+	public BoSC(String string) {
 		string = string.replace("[", "");
 		string = string.replace("]", "");
 
-		for (String value : string.split(","))
-		{
+		for (String value : string.split(",")) {
 			add(Byte.parseByte(value.trim()));
 		}
 	}

analyzer/Database.java

@@ -1,3 +1,5 @@
+package analyzer;
+
 import java.io.BufferedReader;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
@@ -10,118 +12,96 @@
  * Normal-behavior Database
  *
  * @author AmrAbed
- *
  */
-public class Database extends HashMap<BoSC, Long>
-{
+public class Database extends HashMap<BoSC, Long> {
 	private static final long serialVersionUID = 1L;
 
 	/**
 	 * Create normal-behavior database from a dump file
 	 *
-	 * @param filePath
-	 *            path to the dump file
-	 * @throws NumberFormatException
+	 * @param filePath path to the dump file
 	 * @throws IOException
 	 */
-	public Database(String filePath) throws NumberFormatException, IOException
-	{
-		if (filePath != null)
-		{
-			final BufferedReader reader = new BufferedReader(new FileReader(filePath));
-			String line;
-			while ((line = reader.readLine()) != null)
-			{
-				final String[] words = line.split("\t");
-				put(new BoSC(words[0]), Long.parseLong(words[1]));
+	public Database(String filePath) throws IOException {
+		if (filePath != null) {
+			try (final BufferedReader reader = new BufferedReader(new FileReader(filePath))) {
+				String line;
+				while ((line = reader.readLine()) != null) {
+					final String[] words = line.split("\t");
+					put(new BoSC(words[0]), Long.parseLong(words[1]));
+				}
+			} finally {
+				reader.close();
 			}
-			reader.close();
 		}
 	}
 
-	public void add(BoSC bosc)
-	{
-		if (bosc == null)
-		{
+	public void add(BoSC bosc) {
+		if (bosc == null) {
 			return;
 		}
 
-		if (containsKey(bosc))
-		{
+		if (containsKey(bosc)) {
 			replace(bosc, get(bosc) + 1);
-		}
-		else
-		{
+		} else {
 			put(bosc, 1L);
 		}
 	}
 
-	public void commit(Database change)
-	{
-		for (BoSC bosc : change.keySet())
-		{
+	public void commit(Database change) {
+		for (BoSC bosc : change.keySet()) {
 			long value = change.get(bosc);
-			if (this.containsKey(bosc))
-			{
+			if (this.containsKey(bosc)) {
 				value += this.get(bosc);
 			}
 			this.put(bosc, value);
 		}
 	}
 
-	private double getNorm()
-	{
+	private double getNorm() {
 		double norm = 0;
-		for (BoSC bosc : keySet())
-		{
+		for (BoSC bosc : keySet()) {
 			long val = get(bosc);
 			norm += val * val;
 		}
 		return Math.sqrt(norm);
 	}
 
-	public double calculateSimilarity(Database other)
-	{
-		if (this.isEmpty() || other.isEmpty())
-		{
+	public double calculateSimilarity(Database other) {
+		if (this.isEmpty() || other.isEmpty()) {
 			return 0;
 		}
 
 		double dot = 0;
-		double norm1 = this.getNorm(), norm2 = other.getNorm();
-		for (BoSC bosc : keySet())
-		{
-//			System.out.print(bosc + " -> ");
-			if (other.containsKey(bosc))
-			{
+		double norm1 = this.getNorm();
+		double norm2 = other.getNorm();
+		for (BoSC bosc : keySet()) {
+			if (other.containsKey(bosc)) {
 				long value1 = other.get(bosc);
 				long value2 = this.get(bosc);
-//                                System.out.print("found (Frequencies: " + value2 + " & " + value1 + ")");
 				dot += value1 * value2;
 			}
 		}
 		return dot / (norm1 * norm2);
 	}
 
-	public void dump(String file) throws FileNotFoundException
-	{
-		try (PrintStream out = new PrintStream(file))
-		{
-			for (BoSC bosc : keySet())
-			{
+	public void dump(String file) throws FileNotFoundException {
+		try (PrintStream out = new PrintStream(file)) {
+			for (BoSC bosc : keySet()) {
 				out.println(bosc + "\t" + get(bosc));
 			}
 		}
 	}
 
 	@Override
-	public String toString()
-	{
-		String output = new String();
-		for (ArrayList<Byte> entry : keySet())
-		{
-			output += entry + " => " + get(entry) + "\n";
+	public String toString() {
+		final StringBuilder output = new StringBuilder();
+		for (Entry<BoSC, Long>  entry : entrySet()) {
+			output.append(entry.getKey());
+			output.append(" => ");
+			output.append(entry.getValue());
+			output.append('\n');
 		}
-		return output;
+		return output.toString();
 	}
 }

analyzer/aggregate/Aggregator.java

@@ -0,0 +1,21 @@
+package analyzer.aggregate;
+
+import java.util.logging.Logger;
+import java.util.logging.Level;
+
+import analyzer.Database;
+
+public class Aggregator {
+	public static void main(String[] args) {
+		try {
+			final Database db1 = new Database(args[0]);
+			final Database db2 = new Database(args[1]);
+
+			db1.commit(db2);
+			db1.dump(args[2]);
+
+		} catch (Exception e) {
+			Logger.getLogger(Logger.GLOBAL_LOGGER_NAME).log(Level.SEVERE, e.toString());
+		}
+	}
+}

analyzer/compare/Comparator.java

@@ -0,0 +1,20 @@
+package analyzer.compare;
+
+import java.util.logging.Logger;
+import java.util.logging.Level;
+
+import analyzer.Database;
+
+public class Comparator {
+	public static void main(String[] args) {
+		try {
+			final Database db1 = new Database(args[0]);
+			final Database db2 = new Database(args[1]);
+			final double similarity = db1.calculateSimilarity(db2);
+			Logger.getLogger(Logger.GLOBAL_LOGGER_NAME).log(Level.INFO, () -> "Similaity: " + similarity);
+
+		} catch (Exception e) {
+			Logger.getLogger(Logger.GLOBAL_LOGGER_NAME).log(Level.SEVERE, e.toString());
+		}
+	}
+}

build.gradle

@@ -1,5 +1,4 @@
 apply plugin: 'java'
-apply plugin: 'eclipse'
 apply plugin: 'application'
 
 mainClassName = 'edu.vt.rhids.main.RHIDS'
@@ -16,11 +15,10 @@ task createJar(type: Jar) {
     with jar
 }
 
-
 repositories {
     mavenCentral()
 }
 
 dependencies {
-    compile group: 'commons-cli', name: 'commons-cli', version: '1.2'
+    implementation 'commons-cli:commons-cli:1.2'
 }

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
-#Sun Mar 05 18:43:08 UTC 2017
+#Wed Nov 28 12:06:22 EET 2018
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-3.4.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-3.4.1-all.zip