support code and coverage modifications when aggregating

pitest-aggregator/src/main/java/org/pitest/aggregate/CodeSourceAggregator.java

@@ -1,40 +1,42 @@
 package org.pitest.aggregate;
 
-import java.io.File;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.function.Function;
-import java.util.function.Predicate;
-
 import org.pitest.classinfo.ClassName;
 import org.pitest.classpath.ClassFilter;
 import org.pitest.classpath.ClassPath;
 import org.pitest.classpath.ClassPathRoot;
 import org.pitest.classpath.CodeSource;
-import org.pitest.classpath.DefaultCodeSource;
 import org.pitest.classpath.DirectoryClassPathRoot;
 import org.pitest.classpath.PathFilter;
 import org.pitest.classpath.ProjectClassPaths;
 import org.pitest.functional.FCollection;
 import org.pitest.functional.prelude.Prelude;
 import org.pitest.mutationtest.config.DefaultCodePathPredicate;
 import org.pitest.mutationtest.config.DefaultDependencyPathPredicate;
+import org.pitest.mutationtest.config.SettingsFactory;
 import org.pitest.util.Glob;
 
+import java.io.File;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.function.Function;
+import java.util.function.Predicate;
+
 class CodeSourceAggregator {
 
   private final Collection<File> compiledCodeDirectories;
+  private final SettingsFactory settings;
 
-  CodeSourceAggregator(final Collection<File> compiledCodeDirectories) {
+  CodeSourceAggregator(SettingsFactory settings, Collection<File> compiledCodeDirectories) {
+    this.settings = settings;
     this.compiledCodeDirectories = Collections.unmodifiableCollection(compiledCodeDirectories);
   }
 
   public CodeSource createCodeSource() {
-    return new DefaultCodeSource(createProjectClassPaths());
+    return settings.createCodeSource(createProjectClassPaths());
   }
 
-  private ProjectClassPaths createProjectClassPaths() {
+  public ProjectClassPaths createProjectClassPaths() {
     final ClassPath classPath = new ClassPath(this.compiledCodeDirectories);
     final Predicate<String> classPredicate = createClassPredicate();
     final Predicate<ClassPathRoot> pathPredicate = new DefaultCodePathPredicate();

pitest-aggregator/src/main/java/org/pitest/aggregate/ReportAggregator.java

@@ -11,6 +11,10 @@
 import org.pitest.mutationtest.MutationResult;
 import org.pitest.mutationtest.MutationResultListener;
 import org.pitest.mutationtest.SourceLocator;
+import org.pitest.mutationtest.build.CoverageTransformer;
+import org.pitest.mutationtest.config.PluginServices;
+import org.pitest.mutationtest.config.ReportOptions;
+import org.pitest.mutationtest.config.SettingsFactory;
 import org.pitest.mutationtest.report.html.MutationHtmlReportListener;
 import org.pitest.mutationtest.tooling.SmartSourceLocator;
 import org.pitest.util.Log;
@@ -32,6 +36,8 @@
 import static java.util.Arrays.asList;
 
 public final class ReportAggregator {
+
+  private final SettingsFactory settings;
   private final ResultOutputStrategy       resultOutputStrategy;
   private final DataLoader<BlockCoverage>  blockCoverageLoader;
   private final Set<File> mutationFiles;
@@ -41,13 +47,20 @@ public final class ReportAggregator {
   private final Charset inputCharset;
   private final Charset outputCharset;
 
-  private ReportAggregator(final ResultOutputStrategy resultOutputStrategy, final Set<File> lineCoverageFiles, final Set<File> mutationFiles,
-                           final Set<File> sourceCodeDirs, final Set<File> compiledCodeDirs, Charset inputCharset, Charset outputCharset) {
+  private ReportAggregator(SettingsFactory settings,
+                           ResultOutputStrategy resultOutputStrategy,
+                           Set<File> lineCoverageFiles,
+                           Set<File> mutationFiles,
+                           Set<File> sourceCodeDirs,
+                           Set<File> compiledCodeDirs,
+                           Charset inputCharset,
+                           Charset outputCharset) {
+    this.settings = settings;
     this.resultOutputStrategy = resultOutputStrategy;
     this.blockCoverageLoader = new BlockCoverageDataLoader(lineCoverageFiles);
     this.mutationFiles = mutationFiles;
     this.sourceCodeDirectories = Collections.unmodifiableCollection(new HashSet<>(sourceCodeDirs));
-    this.codeSourceAggregator = new CodeSourceAggregator(new HashSet<>(compiledCodeDirs));
+    this.codeSourceAggregator = new CodeSourceAggregator(settings, new HashSet<>(compiledCodeDirs));
     this.inputCharset = inputCharset;
     this.outputCharset = outputCharset;
   }
@@ -83,7 +96,6 @@ public AggregationResult aggregateReport() throws ReportAggregationException {
   private MutationResultListener createResultListener(SourceLocator sourceLocator, Collection<String> mutatorNames) throws ReportAggregationException {
     final CodeSource codeSource = this.codeSourceAggregator.createCodeSource();
     final ReportCoverage coverageDatabase = calculateCoverage(codeSource);
-    //final Collection<String> mutatorNames = new HashSet<>(FCollection.flatMap(mutationMetaData.getMutations(), resultToMutatorName()));
 
     return new MutationHtmlReportListener(outputCharset, coverageDatabase, this.resultOutputStrategy, mutatorNames, sourceLocator);
   }
@@ -112,12 +124,19 @@ private ReportCoverage calculateCoverage(final CodeSource codeSource) throws Rep
               .collect(Collectors.toList());
       CoverageData cd = new CoverageData(codeSource, new LineMapper(codeSource));
       cd.loadBlockDataOnly(coverageData);
-      return cd;
+
+      return transformCoverage(cd);
+
     } catch (final Exception e) {
       throw new ReportAggregationException(e.getMessage(), e);
     }
   }
 
+  private ReportCoverage transformCoverage(CoverageData cd) {
+    CoverageTransformer transformer = settings.createCoverageTransformer(codeSourceAggregator.createCodeSource());
+    return transformer.transform(cd);
+  }
+
   public static Builder builder() {
     return new Builder();
   }
@@ -247,7 +266,10 @@ public Charset getOutputCharSet() {
 
     public ReportAggregator build() {
       validateState();
-      return new ReportAggregator(this.resultOutputStrategy,
+      final SettingsFactory settings = new SettingsFactory(new ReportOptions(), PluginServices.makeForContextLoader());
+      return new ReportAggregator(
+              settings,
+              this.resultOutputStrategy,
               this.lineCoverageFiles,
               this.mutationResultsFiles,
               this.sourceCodeDirectories,

pitest-aggregator/src/test/java/org/pitest/aggregate/CodeSourceAggregatorTest.java

@@ -11,6 +11,9 @@
 import org.junit.Test;
 import org.pitest.classinfo.ClassName;
 import org.pitest.classpath.CodeSource;
+import org.pitest.mutationtest.config.PluginServices;
+import org.pitest.mutationtest.config.ReportOptions;
+import org.pitest.mutationtest.config.SettingsFactory;
 
 public class CodeSourceAggregatorTest {
 
@@ -23,7 +26,8 @@ public void setup() throws Exception {
         .getParentFile() // pitest
         .getParentFile() // org
         .getParentFile(); // classes
-    this.underTest = new CodeSourceAggregator(Arrays.asList(testDir, mainDir));
+    SettingsFactory f = new SettingsFactory(new ReportOptions(), PluginServices.makeForContextLoader());
+    this.underTest = new CodeSourceAggregator(f, Arrays.asList(testDir, mainDir));
   }
 
   @Test

pitest-aggregator/src/test/java/org/pitest/aggregate/ReportAggregatorBuilderTest.java

@@ -1,5 +1,14 @@
 package org.pitest.aggregate;
 
+import org.hamcrest.Matchers;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.ExpectedException;
+
+import java.io.File;
+import java.nio.charset.Charset;
+import java.util.Arrays;
+
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
@@ -11,20 +20,12 @@
 import static org.pitest.aggregate.TestInvocationHelper.getTestCompiledDirectory;
 import static org.pitest.aggregate.TestInvocationHelper.getTestSourceDirectory;
 
-import java.io.File;
-import java.nio.charset.Charset;
-import java.util.Arrays;
-
-import org.hamcrest.Matchers;
-import org.junit.Rule;
-import org.junit.Test;
-import org.junit.rules.ExpectedException;
-
 public class ReportAggregatorBuilderTest {
 
   private static final String NOT_A_FILE = "is not a file";
   private static final String NOT_A_DIR  = "is not a directory";
   private static final String IS_NULL    = "is null";
+
   @Rule
   public ExpectedException    expected   = ExpectedException.none();
 

pitest-entry/src/main/java/org/pitest/mutationtest/build/intercept/javafeatures/InlinedFinallyBlockFilter.java

@@ -31,7 +31,6 @@
 import java.util.stream.Collectors;
 
 import static java.util.function.Predicate.isEqual;
-
 import static org.pitest.bytecode.analysis.InstructionMatchers.anyInstruction;
 import static org.pitest.bytecode.analysis.InstructionMatchers.isInstruction;
 import static org.pitest.bytecode.analysis.InstructionMatchers.notAnInstruction;