Refactor: organize packages to reflect the algorithm (#933)

* refactor Main, DSpot and Amplification

* remove global report in main

* refactor DSpot constructor

* remove amplification class

* add new configuration to prettifier

* combine amplify and run in DSpot

* make inputConfiguration private

* change name to DSpotState

* move verbose to DSpotState

* change remaining use of verbose

* clean code

* refactor DSpotState

* first organization

* basically done organization

* fix merge problems

* rename InputConfiguration to UserInput

README-developers.md

@@ -69,14 +69,14 @@ First of all, you have to create an `InputConfiguration`. Only the path to your
 ```java
 // 1. Instantiate `InputConfiguration` and `InputProgram`
 String propertiesFilePath = <pathToYourPropertiesFile>;
-InputConfiguration inputConfiguration = new InputConfiguration(propertiesFilePath);
+InputConfiguration userInput = new InputConfiguration(propertiesFilePath);
 ```
 
 Then you have to build the `InputProgram`, this is done by attaching the `InputProgram` to your `InputConfiguration`:
 
 ```java
 InputProgram program = new InputProgram();
-inputConfiguration.setInputProgram(program);
+userInput.setInputProgram(program);
 ```
 Then, you are ready to construct the `DSpot` object that will allow you to amplify your test.
 There are a lot of constructor available, all of them allow you to custom your `DSpot` object, and so your amplification.
@@ -86,7 +86,7 @@ Following the shortest constructor with all default values of `DSpot`, and the l
 // 2. Instantiate `DSpot` object
 DSpot dspot = new DSpot(InputConfiguration);
 DSpot dspot = new DSpot(
-    InputConfiguration inputConfiguration, // input configuration built at step 1
+    InputConfiguration userInput, // input configuration built at step 1
     int numberOfIterations, // number of time that the main loop will be applied (-i | --iteration option of the CLI)
     List<Amplifier> amplifiers, // list of the amplifiers to be used (-a | --amplifiers option of the CLI)
     TestSelector testSelector // test selector criterion (-s | --test-selector option of the CLI)
@@ -105,4 +105,4 @@ dspot.amplifyAllTests(); // will amplify all test in the test suite.
 
 ## Contributing
 
-DSpot is licensed under LGPLv3. Contributors and pull requests are welcome.
+DSpot is licensed under LGPLv3. Contributors and pull requests are welcome.

dspot-maven/pom.xml

@@ -72,7 +72,7 @@
                 <configuration>
                     <processors>
                         <processor>
-                            eu.stamp_project.utils.DSpotMojoGenerator
+                            eu.stamp_project.dspot.common.miscellaneous.DSpotMojoGenerator
                         </processor>
                     </processors>
                     <withImports>true</withImports>

dspot-prettifier/src/main/java/eu/stamp_project/prettifier/Main.java

@@ -2,23 +2,23 @@
 
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
-import eu.stamp_project.automaticbuilder.AutomaticBuilder;
+import eu.stamp_project.dspot.common.automaticbuilder.AutomaticBuilder;
 import eu.stamp_project.prettifier.code2vec.Code2VecExecutor;
 import eu.stamp_project.prettifier.code2vec.Code2VecParser;
 import eu.stamp_project.prettifier.code2vec.Code2VecWriter;
 import eu.stamp_project.prettifier.context2name.Context2Name;
 import eu.stamp_project.prettifier.minimization.GeneralMinimizer;
 import eu.stamp_project.prettifier.minimization.Minimizer;
 import eu.stamp_project.prettifier.minimization.PitMutantMinimizer;
-import eu.stamp_project.prettifier.options.InputConfiguration;
+import eu.stamp_project.prettifier.options.UserInput;
 import eu.stamp_project.prettifier.output.PrettifiedTestMethods;
 import eu.stamp_project.prettifier.output.report.ReportJSON;
-import eu.stamp_project.test_framework.TestFramework;
-import eu.stamp_project.utils.compilation.DSpotCompiler;
-import eu.stamp_project.utils.configuration.DSpotState;
-import eu.stamp_project.utils.configuration.InitializeDSpot;
-import eu.stamp_project.utils.options.check.Checker;
-import eu.stamp_project.utils.options.check.InputErrorException;
+import eu.stamp_project.dspot.common.test_framework.TestFramework;
+import eu.stamp_project.dspot.common.compilation.DSpotCompiler;
+import eu.stamp_project.dspot.common.configuration.DSpotState;
+import eu.stamp_project.dspot.common.configuration.InitializeDSpot;
+import eu.stamp_project.dspot.common.configuration.check.Checker;
+import eu.stamp_project.dspot.common.configuration.check.InputErrorException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import picocli.CommandLine;
@@ -48,7 +48,7 @@ public class Main {
     public static ReportJSON report = new ReportJSON();
 
     public static void main(String[] args) {
-        InputConfiguration inputConfiguration = new InputConfiguration();
+        UserInput inputConfiguration = new UserInput();
         final CommandLine commandLine = new CommandLine(inputConfiguration);
         commandLine.setUsageHelpWidth(120);
         try {
@@ -80,7 +80,7 @@ public static void main(String[] args) {
         run(inputConfiguration);
     }
 
-    public static void run(InputConfiguration configuration) {
+    public static void run(UserInput configuration) {
         final CtType<?> amplifiedTestClass = loadAmplifiedTestClass(configuration);
         final List<CtMethod<?>> prettifiedAmplifiedTestMethods =
                 run(
@@ -91,7 +91,7 @@ public static void run(InputConfiguration configuration) {
         output(amplifiedTestClass, prettifiedAmplifiedTestMethods, configuration);
     }
 
-    public static CtType<?> loadAmplifiedTestClass(InputConfiguration configuration) {
+    public static CtType<?> loadAmplifiedTestClass(UserInput configuration) {
         Launcher launcher = new Launcher();
         launcher.getEnvironment().setNoClasspath(true);
         launcher.addInputResource(configuration.getPathToAmplifiedTestClass());
@@ -100,7 +100,7 @@ public static CtType<?> loadAmplifiedTestClass(InputConfiguration configuration)
     }
 
     public static List<CtMethod<?>> run(CtType<?> amplifiedTestClass,
-                                        InputConfiguration configuration) {
+                                        UserInput configuration) {
         InitializeDSpot initializeDSpot = new InitializeDSpot();
         final AutomaticBuilder automaticBuilder = configuration.getBuilderEnum().getAutomaticBuilder(configuration);
         final String dependencies = initializeDSpot.completeDependencies(configuration, automaticBuilder);
@@ -127,7 +127,7 @@ public static List<CtMethod<?>> run(CtType<?> amplifiedTestClass,
 
     public static List<CtMethod<?>> applyMinimization(List<CtMethod<?>> amplifiedTestMethodsToBeMinimized,
                                                       CtType<?> amplifiedTestClass,
-                                                      InputConfiguration configuration) {
+                                                      UserInput configuration) {
 
         Main.report.medianNbStatementBefore = Main.getMedian(amplifiedTestMethodsToBeMinimized.stream()
                 .map(ctMethod -> ctMethod.getElements(new TypeFilter<>(CtStatement.class)))
@@ -173,7 +173,7 @@ private static List<CtMethod<?>> applyGivenMinimizer(Minimizer minimizer, List<C
     }
 
     public static void applyCode2Vec(List<CtMethod<?>> amplifiedTestMethodsToBeRenamed,
-                                     InputConfiguration configuration) {
+                                     UserInput configuration) {
         Code2VecWriter writer = new Code2VecWriter(configuration.getPathToRootOfCode2Vec());
         Code2VecParser parser = new Code2VecParser();
         Code2VecExecutor code2VecExecutor = null;
@@ -228,7 +228,7 @@ public static <T extends Number & Comparable<T>> Double getMedian(List<T> list)
 
     public static void output(CtType<?> amplifiedTestClass,
                               List<CtMethod<?>> prettifiedAmplifiedTestMethods,
-                              InputConfiguration configuration) {
+                              UserInput configuration) {
         new PrettifiedTestMethods(configuration.getOutputDirectory())
                 .output(amplifiedTestClass, prettifiedAmplifiedTestMethods);
         Gson gson = new GsonBuilder().setPrettyPrinting().create();

dspot-prettifier/src/main/java/eu/stamp_project/prettifier/RedundantCastRemover.java

@@ -1,6 +1,6 @@
 package eu.stamp_project.prettifier;
 
-import eu.stamp_project.test_framework.TestFramework;
+import eu.stamp_project.dspot.common.test_framework.TestFramework;
 import spoon.reflect.code.CtExpression;
 import spoon.reflect.code.CtInvocation;
 import spoon.reflect.declaration.CtMethod;

dspot-prettifier/src/main/java/eu/stamp_project/prettifier/code2vec/Code2VecExecutor.java

@@ -1,7 +1,6 @@
 package eu.stamp_project.prettifier.code2vec;
 
-import eu.stamp_project.prettifier.options.InputConfiguration;
-import eu.stamp_project.utils.AmplificationHelper;
+import eu.stamp_project.dspot.common.miscellaneous.AmplificationHelper;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

dspot-prettifier/src/main/java/eu/stamp_project/prettifier/code2vec/Code2VecParser.java

@@ -1,6 +1,6 @@
 package eu.stamp_project.prettifier.code2vec;
 
-import eu.stamp_project.utils.AmplificationHelper;
+import eu.stamp_project.dspot.common.miscellaneous.AmplificationHelper;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

dspot-prettifier/src/main/java/eu/stamp_project/prettifier/code2vec/Code2VecWriter.java

@@ -1,8 +1,6 @@
 package eu.stamp_project.prettifier.code2vec;
 
-import eu.stamp_project.prettifier.Main;
-import eu.stamp_project.prettifier.options.InputConfiguration;
-import eu.stamp_project.utils.DSpotUtils;
+import eu.stamp_project.dspot.common.miscellaneous.DSpotUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import spoon.reflect.declaration.CtMethod;

dspot-prettifier/src/main/java/eu/stamp_project/prettifier/minimization/GeneralMinimizer.java

@@ -2,8 +2,8 @@
 
 import eu.stamp_project.prettifier.Main;
 import eu.stamp_project.prettifier.output.report.ReportJSON;
-import eu.stamp_project.test_framework.TestFramework;
-import eu.stamp_project.utils.DSpotUtils;
+import eu.stamp_project.dspot.common.test_framework.TestFramework;
+import eu.stamp_project.dspot.common.miscellaneous.DSpotUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import spoon.reflect.code.*;
@@ -15,7 +15,7 @@
 import java.util.*;
 import java.util.stream.Collectors;
 
-import static eu.stamp_project.test_framework.TestFramework.ASSERTIONS_FILTER;
+import static eu.stamp_project.dspot.common.test_framework.TestFramework.ASSERTIONS_FILTER;
 
 /**
  * Created by Benjamin DANGLOT

dspot-prettifier/src/main/java/eu/stamp_project/prettifier/minimization/PitMutantMinimizer.java

@@ -1,16 +1,15 @@
 package eu.stamp_project.prettifier.minimization;
 
-import eu.stamp_project.automaticbuilder.AutomaticBuilder;
+import eu.stamp_project.dspot.common.automaticbuilder.AutomaticBuilder;
 import eu.stamp_project.prettifier.Main;
 import eu.stamp_project.prettifier.output.report.ReportJSON;
-import eu.stamp_project.test_framework.TestFramework;
-import eu.stamp_project.utils.AmplificationHelper;
-import eu.stamp_project.utils.DSpotUtils;
-import eu.stamp_project.utils.compilation.DSpotCompiler;
-import eu.stamp_project.utils.pit.AbstractParser;
-import eu.stamp_project.utils.pit.AbstractPitResult;
-import eu.stamp_project.utils.pit.PitXMLResultParser;
-import eu.stamp_project.utils.program.InputConfiguration;
+import eu.stamp_project.dspot.common.test_framework.TestFramework;
+import eu.stamp_project.dspot.common.miscellaneous.AmplificationHelper;
+import eu.stamp_project.dspot.common.miscellaneous.DSpotUtils;
+import eu.stamp_project.dspot.common.compilation.DSpotCompiler;
+import eu.stamp_project.dspot.selector.pitmutantscoreselector.AbstractParser;
+import eu.stamp_project.dspot.selector.pitmutantscoreselector.AbstractPitResult;
+import eu.stamp_project.dspot.selector.pitmutantscoreselector.PitXMLResultParser;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import spoon.reflect.code.CtInvocation;

dspot-prettifier/src/main/java/eu/stamp_project/prettifier/options/InputConfiguration.java → dspot-prettifier/src/main/java/eu/stamp_project/prettifier/options/UserInput.java

@@ -1,8 +1,7 @@
 package eu.stamp_project.prettifier.options;
 
-import eu.stamp_project.utils.AmplificationHelper;
-import eu.stamp_project.utils.DSpotUtils;
-import eu.stamp_project.utils.options.check.InputErrorException;
+import eu.stamp_project.dspot.common.miscellaneous.DSpotUtils;
+import eu.stamp_project.dspot.common.configuration.check.InputErrorException;
 import picocli.CommandLine;
 
 /**
@@ -11,9 +10,9 @@
  * on 11/02/19
  */
 @CommandLine.Command(name = "eu.stamp_project.Main", mixinStandardHelpOptions = true)
-public class InputConfiguration extends eu.stamp_project.utils.program.InputConfiguration {
+public class UserInput extends eu.stamp_project.dspot.common.configuration.UserInput {
 
-    public InputConfiguration() {
+    public UserInput() {
 
     }
 
@@ -28,7 +27,7 @@ public String getPathToAmplifiedTestClass() {
         return this.pathToAmplifiedTestClass;
     }
 
-    public InputConfiguration setPathToAmplifiedTestClass(String pathToAmplifiedTestClass) {
+    public UserInput setPathToAmplifiedTestClass(String pathToAmplifiedTestClass) {
         if (!pathToAmplifiedTestClass.endsWith(".java")) {
             // TODO must add this error to the global report
             throw new InputErrorException();
@@ -51,7 +50,7 @@ public String getPathToRootOfCode2Vec() {
         return pathToRootOfCode2Vec;
     }
 
-    public InputConfiguration setPathToRootOfCode2Vec(String pathToRootOfCode2Vec) {
+    public UserInput setPathToRootOfCode2Vec(String pathToRootOfCode2Vec) {
         this.pathToRootOfCode2Vec = DSpotUtils.shouldAddSeparator.apply(pathToRootOfCode2Vec);
         return this;
     }
@@ -67,7 +66,7 @@ public String getRelativePathToModelForCode2Vec() {
         return relativePathToModelForCode2Vec;
     }
 
-    public InputConfiguration setRelativePathToModelForCode2Vec(String relativePathToModelForCode2Vec) {
+    public UserInput setRelativePathToModelForCode2Vec(String relativePathToModelForCode2Vec) {
         this.relativePathToModelForCode2Vec = relativePathToModelForCode2Vec;
         return this;
     }
@@ -78,7 +77,7 @@ public long getTimeToWaitForCode2vecInMillis() {
         return this.timeToWaitForCode2vecInMillis;
     }
 
-    public InputConfiguration setTimeToWaitForCode2vecInMillis(long timeToWaitForCode2vecInMillis) {
+    public UserInput setTimeToWaitForCode2vecInMillis(long timeToWaitForCode2vecInMillis) {
         this.timeToWaitForCode2vecInMillis = timeToWaitForCode2vecInMillis;
         return this;
     }
@@ -91,7 +90,7 @@ public String getPathToRootOfContext2Name() {
         return pathToRootOfContext2Name;
     }
 
-    public InputConfiguration setPathToRootOfContext2Name(String pathToRootOfContext2Name) {
+    public UserInput setPathToRootOfContext2Name(String pathToRootOfContext2Name) {
         this.pathToRootOfContext2Name = DSpotUtils.shouldAddSeparator.apply(pathToRootOfContext2Name);
         return this;
     }
@@ -102,7 +101,7 @@ public String getRelativePathToModelForContext2Name() {
         return relativePathToModelForContext2Name;
     }
 
-    public InputConfiguration setRelativePathToModelForContext2Name(String relativePathToModelForContext2Name) {
+    public UserInput setRelativePathToModelForContext2Name(String relativePathToModelForContext2Name) {
         this.relativePathToModelForContext2Name = relativePathToModelForContext2Name;
         return this;
     }
@@ -113,7 +112,7 @@ public long getTimeToWaitForContext2nameInMillis() {
         return this.timeToWaitForContext2nameInMillis;
     }
 
-    public InputConfiguration setTimeToWaitForContext2nameInMillis(long timeToWaitForContext2nameInMillis) {
+    public UserInput setTimeToWaitForContext2nameInMillis(long timeToWaitForContext2nameInMillis) {
         this.timeToWaitForContext2nameInMillis = timeToWaitForContext2nameInMillis;
         return this;
     }

dspot-prettifier/src/main/java/eu/stamp_project/prettifier/output/PrettifiedTestMethods.java

@@ -1,8 +1,7 @@
 package eu.stamp_project.prettifier.output;
 
-import eu.stamp_project.test_framework.TestFramework;
-import eu.stamp_project.utils.DSpotUtils;
-import eu.stamp_project.utils.program.InputConfiguration;
+import eu.stamp_project.dspot.common.test_framework.TestFramework;
+import eu.stamp_project.dspot.common.miscellaneous.DSpotUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import spoon.reflect.declaration.CtMethod;

dspot-prettifier/src/test/java/eu/stamp_project/AbstractTest.java

@@ -1,10 +1,10 @@
 package eu.stamp_project;
 
-import eu.stamp_project.dspot.amplifier.value.ValueCreator;
-import eu.stamp_project.utils.RandomHelper;
-import eu.stamp_project.utils.configuration.DSpotState;
-import eu.stamp_project.utils.options.AutomaticBuilderEnum;
-import eu.stamp_project.utils.program.InputConfiguration;
+import eu.stamp_project.dspot.amplifier.amplifiers.value.ValueCreator;
+import eu.stamp_project.dspot.amplifier.amplifiers.utils.RandomHelper;
+import eu.stamp_project.dspot.common.configuration.DSpotState;
+import eu.stamp_project.dspot.common.configuration.UserInput;
+import eu.stamp_project.dspot.common.configuration.options.AutomaticBuilderEnum;
 import org.junit.Before;
 
 /**
@@ -18,13 +18,13 @@ public String getPathToPropertiesFile() {
         return "src/test/resources/sample/";
     }
 
-    protected InputConfiguration configuration;
+    protected UserInput configuration;
 
     @Before
     public void setUp() throws Exception {
         RandomHelper.setSeedRandom(72L);
         ValueCreator.count = 0;
-        this.configuration = new InputConfiguration();
+        this.configuration = new UserInput();
         this.configuration.setAbsolutePathToProjectRoot(this.getPathToPropertiesFile());
         this.configuration.setVerbose(true);
         this.configuration.setBuilderEnum(AutomaticBuilderEnum.Maven);

dspot-prettifier/src/test/java/eu/stamp_project/Utils.java

@@ -1,11 +1,10 @@
 package eu.stamp_project;
 
-import eu.stamp_project.automaticbuilder.AutomaticBuilder;
-import eu.stamp_project.test_framework.TestFramework;
-import eu.stamp_project.utils.compilation.DSpotCompiler;
-import eu.stamp_project.utils.configuration.DSpotState;
-import eu.stamp_project.utils.configuration.InitializeDSpot;
-import eu.stamp_project.utils.program.InputConfiguration;
+import eu.stamp_project.dspot.common.automaticbuilder.AutomaticBuilder;
+import eu.stamp_project.dspot.common.configuration.UserInput;
+import eu.stamp_project.dspot.common.test_framework.TestFramework;
+import eu.stamp_project.dspot.common.compilation.DSpotCompiler;
+import eu.stamp_project.dspot.common.configuration.InitializeDSpot;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import spoon.reflect.code.CtLiteral;
@@ -29,9 +28,9 @@ public class Utils {
 
 	public static final Logger LOGGER = LoggerFactory.getLogger(Utils.class);
 
-	private static InputConfiguration configuration;
+	private static UserInput configuration;
 
-	public static void init(InputConfiguration configuration) {
+	public static void init(UserInput configuration) {
 		InitializeDSpot initializeDSpot = new InitializeDSpot();
 		final AutomaticBuilder automaticBuilder = configuration.getBuilderEnum().getAutomaticBuilder(configuration);
 		final String dependencies = initializeDSpot.completeDependencies(configuration, automaticBuilder);

dspot-prettifier/src/test/java/eu/stamp_project/prettifier/RedundantCastRemoverTest.java

@@ -1,6 +1,6 @@
 package eu.stamp_project.prettifier;
 
-import eu.stamp_project.test_framework.TestFramework;
+import eu.stamp_project.dspot.common.test_framework.TestFramework;
 import org.junit.Test;
 import spoon.Launcher;
 import spoon.reflect.declaration.CtMethod;

dspot-prettifier/src/test/java/eu/stamp_project/prettifier/code2vec/Code2VecExecutorTest.java

@@ -1,7 +1,5 @@
 package eu.stamp_project.prettifier.code2vec;
 
-import eu.stamp_project.prettifier.options.InputConfiguration;
-import org.junit.Before;
 import org.junit.Ignore;
 import org.junit.Test;
 

dspot-prettifier/src/test/java/eu/stamp_project/prettifier/code2vec/Code2VecParserTest.java

@@ -1,6 +1,6 @@
 package eu.stamp_project.prettifier.code2vec;
 
-import eu.stamp_project.utils.AmplificationHelper;
+import eu.stamp_project.dspot.common.miscellaneous.AmplificationHelper;
 import org.junit.Test;
 
 import static junit.framework.TestCase.assertEquals;