MutAPK 2.0.0 - Merge from develop

Author: caev03

.classpath

@@ -1,30 +1,39 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry including="**/*.java" kind="src" output="target/classes" path="src">
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
 		<attributes>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
 		<attributes>
-			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" path="target/generated-sources/annotations">
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
-			<attribute name="ignore_optional_problems" value="true"/>
-			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="m2e-apt" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="lib" path="extra/commons-io-2.4.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

.gitignore

@@ -1,5 +1,6 @@
 target/
 temp/
+test/mutants
 pom.xml.tag
 pom.xml.releaseBackup
 pom.xml.versionsBackup
@@ -12,7 +13,8 @@ test/temp/
 test/mutantes/
 .vscode/
 .settings/
+.classpath
 
 # Avoid ignoring Maven wrapper jar file (.jar files are usually ignored)
 !/.mvn/wrapper/maven-wrapper.jar
-/target/
+/target/

.project

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>MutAPK</name>
+	<name>MutAPK2</name>
 	<comment></comment>
 	<projects>
 	</projects>

.settings/org.eclipse.jdt.apt.core.prefs

@@ -1,15 +1,6 @@
 eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
 org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
-org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
 org.eclipse.jdt.core.compiler.compliance=1.7
-org.eclipse.jdt.core.compiler.debug.lineNumber=generate
-org.eclipse.jdt.core.compiler.debug.localVariable=generate
-org.eclipse.jdt.core.compiler.debug.sourceFile=generate
-org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.processAnnotations=disabled
 org.eclipse.jdt.core.compiler.release=disabled
 org.eclipse.jdt.core.compiler.source=1.7

.settings/org.eclipse.jdt.core.prefs

@@ -23,14 +23,37 @@ cd MutAPK
 mvn clean
 mvn package
 ```
-The generated runnable jar can be found in: ``MutAPK/target/MutAPK-0.0.1.jar``
+The generated runnable jar can be found in: ``MutAPK/target/MutAPK-2.0.0.jar``
 
 # Usage
-To run MutAPK use the following command, specifying the required arguments:
+To run MutAPK use the following command, specifying the path to the config file:
 ```
-java -jar MutAPK-0.0.1.jar <APKPath> <AppPackage> <Output> <ExtraComponentFolder> <operatorsDir> <multithread> <amountMutants>?
+java -jar MutAPK-2.0.0.jar <pathToJSONConfigFile>
 ```
-### Arguments
+
+### JSON Configuration File
+
+MutAPK uses a JSON file to define the values to be used during execution, an example of this file can be found in ```./src/main/resources/parameters.json```. Following is the structure of the JSON file:
+
+```json
+{
+    "apkPath": "./apk/com.evancharlton.mileage_3110.apk",
+    "appName": "com.evancharlton.mileage",
+    "mutantsFolder": "./mutants", 
+    "operatorsDir": "./",
+    "multithreadExec": "true",
+    "extraPath": "./extra",
+    "selectionStrategy": "all",
+    "selectionParameters":{
+        "amountMutants":"34",
+        "perOperator":"false",
+        "confidenceLevel":"85",
+        "marginError":"10",
+        "baseAPKPath":"./"
+    }
+}
+```
+
 Provide the following list of required arguments when running MutAPK:
 1. ``APK path``: relative path of the apk to mutate;
 2. ``AppPackage``: App main package name;

README.md

@@ -1,21 +1,13 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
-	<groupId>MutAPK</groupId>
+	<groupId>edu.uniandes.thesoftwaredesignlab</groupId>
 	<artifactId>MutAPK</artifactId>
-	<version>0.0.1</version>
+	<version>2.0.0</version>
 	<name>MutAPK</name>
 	<description>Android Application Mutation Testion over APK files</description>
 	<build>
-		<sourceDirectory>src</sourceDirectory>
-		<resources>
-			<resource>
-				<directory>src</directory>
-				<excludes>
-					<exclude>**/*.java</exclude>
-				</excludes>
-			</resource>
-		</resources>
 		<plugins>
 			<plugin>
 				<artifactId>maven-compiler-plugin</artifactId>
@@ -41,7 +33,7 @@
 								<!-- add Main-Class to manifest file -->
 								<transformer
 									implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
-									<mainClass>uniandes.tsdl.mutapk.MutAPK</mainClass>
+									<mainClass>edu.uniandes.tsdl.mutapk.MutAPK</mainClass>
 								</transformer>
 							</transformers>
 							<filters>
@@ -62,6 +54,27 @@
 		</plugins>
 	</build>
 	<dependencies>
+		<dependency>
+			<groupId>org.bouncycastle</groupId>
+			<artifactId>bcprov-jdk15on</artifactId>
+			<version>1.53</version>
+		</dependency>
+		<dependency>
+			<groupId>com.googlecode.json-simple</groupId>
+			<artifactId>json-simple</artifactId>
+			<version>1.1.1</version>
+		</dependency>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.12</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-math3</artifactId>
+			<version>3.0</version>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.directory.studio</groupId>
 			<artifactId>org.apache.commons.io</artifactId>
@@ -113,9 +126,10 @@
 			<version>3.5.2</version>
 		</dependency>
 		<dependency>
-		    <groupId>org.smali</groupId>
-		    <artifactId>dexlib2</artifactId>
-		    <version>2.2.3</version>
+			<groupId>org.smali</groupId>
+			<artifactId>dexlib2</artifactId>
+			<version>2.2.3</version>
 		</dependency>
 	</dependencies>
+
 </project>