Merge pull request #37 from jscancella/mutationTesting

refs #18 - pitest

build.gradle

@@ -1,25 +1,27 @@
 plugins {
   id 'java'
 
-  //these have to be in the main project for now see - https://discuss.gradle.org/t/how-do-i-include-buildscript-block-from-external-gradle-script/7016/2
+  //these have to be in the main project for now see:
+  //https://discuss.gradle.org/t/how-do-i-include-buildscript-block-from-external-gradle-script/7016/2
   id "com.github.kt3k.coveralls" version "2.9.0" 
   id "de.aaschmid.cpd" version "3.1"
   id "org.owasp.dependencycheck" version "5.3.0"
-//  id "com.dorongold.task-tree" version "1.5"
   id "org.ajoberstar.grgit" version "4.0.1"
   id "jp.skypencil.spotbugs.snom" version "0.5.1"
 //  id "com.github.spotbugs" version "3.0.0"
   id "com.jfrog.bintray" version "1.8.4"
+  id 'info.solidsoft.pitest' version '1.4.7'
 }
 apply from: 'eclipse.gradle'
 apply from: 'bintray.gradle'
-//apply from: 'maven-central.gradle'
 apply from: 'code-quality.gradle'
 apply from: 'message-bundle.gradle'
 
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
 
+project.group = "com.github.jscancella"
+
 if(project.version == "unspecified"){
   String now = new Date().format( 'MMM-dd-yyyy_HH-mm-ss' )
   project.version = "1.0.0-${now}-SNAPSHOT"
@@ -54,12 +56,18 @@ test {
   //testLogging.showStandardStreams = true
 }
 
-/*tasks.withType(com.github.spotbugs.SpotBugsTask) {
-  reports {
-      xml.enabled = false
-      html.enabled = true
-  }
-}*/
+pitest {
+	//turn on to figure out why BagitProfileTest is failing
+	//verbose = true
+    //it adds dependency to org.pitest:pitest-junit5-plugin and also sets "testPlugin" to "junit5"
+    junit5PluginVersion = '0.12'
+    targetClasses = ['com.github.jscancella.*']
+	excludedTestClasses = ['com.github.jscancella.conformance.profile.BagitProfileTest'] //breaks due to testing all fields
+	useClasspathFile = true
+	threads = 4
+    outputFormats = ['XML', 'HTML']
+    timestampedReports = false
+}
 
 import org.ajoberstar.grgit.*
 task cloneConformanceSuite(){

code-quality.gradle

@@ -36,10 +36,8 @@ jacocoTestReport.dependsOn test //ensure the tests have run before generating a
 check.dependsOn integrationTest //run the integration tests
 check.dependsOn jacocoTestReport //run the code coverage reports
 check.dependsOn javadoc //ensure javadocs are generated correctly
-
-//ignore some of the code quality checks for tests since you can't always follow the best practices when testing
-//spotbugsIntegrationTest.enabled = false
-//spotbugsTest.enabled = false
+check.dependsOn spotbugsMain //run the spotbugs on the main source code
+check.dependsOn pmdMain //run pmd and cpd on the main source code 
 
 pmdIntegrationTest.enabled = false
 pmdTest.enabled = false

src/integration/java/com/github/jscancella/BagitSuiteComplanceTest.java

@@ -163,14 +163,19 @@ public void testReadWriteProducesSameBag() throws Exception{
     Path newBagDir;
 
     for(final Path bagDir : visitor.getValidTestCases()){
-      newBagDir = folder.resolve("readWriteProducesSameBag");
-      bag = Bag.read(bagDir);
-      bag.write(newBagDir);
-
-      testTagFileContents(bag, newBagDir);
-
-      testBagsStructureAreEqual(bagDir, newBagDir);
-      delete(newBagDir);
+      try {
+        newBagDir = folder.resolve("readWriteProducesSameBag");
+        bag = Bag.read(bagDir);
+        bag.write(newBagDir);
+
+        testTagFileContents(bag, newBagDir);
+
+        testBagsStructureAreEqual(bagDir, newBagDir);
+        delete(newBagDir);
+      }
+      catch(Exception e) {
+        Assertions.fail("Read write equivialence fail on bag " + bagDir, e);
+      }
     }
   }
 

src/main/java/com/github/jscancella/domain/Bag.java

@@ -179,8 +179,7 @@ public String toString() {
 
   @Override
   public int hashCode() {
-    return Objects.hash(version) + Objects.hash(fileEncoding) + Objects.hash(payLoadManifests) + 
-        Objects.hash(tagManifests) + Objects.hash(itemsToFetch) + Objects.hash(metadata);
+    return Objects.hash(version, fileEncoding, payLoadManifests, tagManifests, itemsToFetch, metadata);
   }
 
   @Override

src/main/java/com/github/jscancella/domain/BagBuilder.java

@@ -18,6 +18,7 @@
 import com.github.jscancella.domain.Metadata.MetadataBuilder;
 import com.github.jscancella.domain.internal.PathPair;
 import com.github.jscancella.exceptions.InvalidBagStateException;
+import com.github.jscancella.exceptions.NoSuchBagitAlgorithmException;
 import com.github.jscancella.hash.BagitChecksumNameMapping;
 
 /**
@@ -116,6 +117,7 @@ public BagBuilder addAlgorithm(final String bagitAlgorithmName) {
     }
     else {
       logger.error(messages.getString("algorithm_not_supported"), bagitAlgorithmName, bagitAlgorithmName);
+      throw new NoSuchBagitAlgorithmException("Algorithm [" + bagitAlgorithmName + "] is not supported!");
     }
     return this;
   }
@@ -153,7 +155,7 @@ public BagBuilder bagLocation(final Path dir) {
 
   /**
    * Write the bag out to a physical location (on disk)
-   * @return this builder so as to chain commands
+   * @return The bag that was created
    * @throws IOException if there is a problem reading a file
    */
   public Bag write() throws IOException{
@@ -172,24 +174,27 @@ private Set<Manifest> createTagManifests() throws IOException{
 
     for(final String name : bagitAlgorithmNames) {
       final ManifestBuilder builder = new ManifestBuilder(name);
+
       for(final Path tagFile : tagFiles) {
-        builder.addFile(tagFile, rootDir);
+        builder.addFile(tagFile, rootDir.relativize(rootDir));
       }
 
       manifests.add(builder.build());
     }
 
     return manifests;
   }
-
+  
   @SuppressWarnings("PMD.AvoidInstantiatingObjectsInLoops")
   private Set<Manifest> createPayloadManifests() throws IOException{
     final Set<Manifest> manifests = new HashSet<>();
 
     for(final String name : bagitAlgorithmNames) {
       final ManifestBuilder builder = new ManifestBuilder(name);
       for(final PathPair pair : payloadFiles) {        
-        builder.addFile(pair.payloadFile, rootDir.resolve(pair.relativeLocation));
+        final Path fullPathToNewLocation = rootDir.resolve(pair.getRelativeLocation());
+        final Path relativeToBaseDir = rootDir.relativize(fullPathToNewLocation);
+        builder.addFile(pair.getPayloadFile(), relativeToBaseDir);
       }
 
       manifests.add(builder.build());

src/main/java/com/github/jscancella/domain/FetchItem.java

@@ -50,7 +50,7 @@ private String internalToString() {
       builder.append(length).append(' ');
     }
 
-    builder.append(path);
+    builder.append(path.toString().replace('\\', '/'));
 
     return builder.toString();
   }
@@ -86,7 +86,7 @@ public Path getPath() {
 
   @Override
   public int hashCode() {
-    return Objects.hash(uri) + Objects.hash(length) + Objects.hash(path);
+    return Objects.hash(uri, length, path);
   }
 
   @Override

src/main/java/com/github/jscancella/domain/Manifest.java

@@ -46,7 +46,7 @@ public String toString() {
 
   @Override
   public int hashCode() {
-    return Objects.hash(bagitAlgorithmName) + entries.hashCode();
+    return Objects.hash(bagitAlgorithmName, entries);
   }
 
   @Override
@@ -109,7 +109,9 @@ public ManifestBuilder addEntry(final ManifestEntry entry) {
      */
     public ManifestBuilder addFile(final Path file, final Path relative) throws IOException {
       if(Files.isDirectory(file)) {
-        Files.walkFileTree(file, new ManifestBuilderVistor(entries, file, hasher));
+        final ManifestBuilderVistor vistor = new ManifestBuilderVistor(file, hasher);
+        Files.walkFileTree(file, vistor);
+        entries.addAll(vistor.getEntries());
       }
       else {
         final Path physicalLocation = file.toAbsolutePath();
@@ -128,5 +130,9 @@ public ManifestBuilder addFile(final Path file, final Path relative) throws IOEx
     public Manifest build() {
       return new Manifest(algorithmName, entries);
     }
+
+    public String getAlgorithmName(){
+      return algorithmName;
+    }
   }
 }

src/main/java/com/github/jscancella/domain/ManifestEntry.java

@@ -52,7 +52,7 @@ public String toString(){
 
   @Override
   public int hashCode(){
-    return Objects.hash(this.physicalLocation) + Objects.hash(this.relativeLocation) + Objects.hash(this.checksum);
+    return Objects.hash(this.physicalLocation, this.relativeLocation, this.checksum);
   }
 
   @Override

src/main/java/com/github/jscancella/domain/Metadata.java

@@ -23,13 +23,17 @@ public class Metadata {
   private Metadata(final Map<String, List<String>> map, final List<SimpleImmutableEntry<String, String>> list) {
     this.map = Collections.unmodifiableMap(map);
     this.list = Collections.unmodifiableList(list);
-    cachedString = String.join(",", list.stream().map(o -> o.toString()).collect(Collectors.toList()));
+    cachedString = buildString();
+  }
+
+  private String buildString() {
+    return String.join(",", list.stream().map(o -> o.toString()).collect(Collectors.toList()));
   }
 
   @Override
   public String toString() {
     if(cachedString == null) {
-      cachedString = String.join(",", list.stream().map(o -> o.toString()).collect(Collectors.toList()));
+      cachedString = buildString();
     }
     return cachedString;
   }
@@ -68,7 +72,7 @@ public List<SimpleImmutableEntry<String, String>> getList(){
    * @return the list of values for that label
    */
   public List<String> get(final String key){
-    return map.get(key.toUpperCase());
+    return map.getOrDefault(key.toUpperCase(), Collections.EMPTY_LIST);
   }
 
   /**

src/main/java/com/github/jscancella/domain/Version.java

@@ -73,7 +73,7 @@ public int compareTo(final Version other) {
 
   @Override
   public int hashCode() {
-    return Objects.hash(major) + Objects.hash(minor);
+    return Objects.hash(major, minor);
   }
 
   @Override

src/main/java/com/github/jscancella/domain/internal/ManifestBuilderVistor.java

@@ -6,6 +6,7 @@
 import java.nio.file.Paths;
 import java.nio.file.SimpleFileVisitor;
 import java.nio.file.attribute.BasicFileAttributes;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.ResourceBundle;
 
@@ -29,13 +30,12 @@ public final class ManifestBuilderVistor extends SimpleFileVisitor<Path> {
   /**
    * Create a manifest from the starting point
    * 
-   * @param entries the {@link ManifestEntry} that corresponds to a particular file
    * @param startingPoint The place to use when creating a relative path
    * @param hasher the hashing implementation
    */
-  public ManifestBuilderVistor(final List<ManifestEntry> entries, final Path startingPoint, final Hasher hasher) {
+  public ManifestBuilderVistor(final Path startingPoint, final Hasher hasher) {
     super();
-    this.entries = entries;
+    this.entries =  new ArrayList<>();
     this.startingPoint = Paths.get(startingPoint.toAbsolutePath().toString());
     this.hasher = hasher;
   }

src/main/java/com/github/jscancella/domain/internal/PathPair.java

@@ -4,8 +4,8 @@
 
 public final class PathPair {
 
-  public final Path payloadFile;
-  public final String relativeLocation;
+  private final Path payloadFile;
+  private final String relativeLocation;
 
   public PathPair(final Path payloadFile, final String relativeLocation) {
     this.payloadFile = payloadFile;

src/main/java/com/github/jscancella/hash/Hasher.java

@@ -32,9 +32,8 @@ public interface Hasher {
    * <b>NOT THREAD SAFE</b> 
    * 
    * @param bytes the bytes with which to update the checksum
-   * @param length the number of bytes to update from the array
    */
-  void update(final byte[] bytes, final int length);
+  void update(final byte[] bytes);
 
   /**
    * @return the checksum of the streamed file. If no file has been streamed, returns a default hash.

src/main/java/com/github/jscancella/hash/StandardHasher.java

@@ -56,26 +56,6 @@ public String hash(final Path path) throws IOException{
     updateMessageDigest(path, messageDigestInstance);
     return formatMessageDigest(messageDigestInstance);
   }
-
-  @Override
-  public void update(final byte[] bytes, final int length){
-    messageDigestInstance.update(bytes, 0, length);
-  }
-
-  @Override
-  public String getHash(){
-    return formatMessageDigest(messageDigestInstance);
-  }
-
-  @Override
-  public void reset(){
-    messageDigestInstance.reset();
-  }
-
-  @Override
-  public String getBagitAlgorithmName(){
-    return BAGIT_ALGORITHM_NAME;
-  }
 
   private static void updateMessageDigest(final Path path, final MessageDigest messageDigest) throws IOException{
     try(InputStream inputStream = new BufferedInputStream(Files.newInputStream(path, StandardOpenOption.READ))){
@@ -98,7 +78,27 @@ private static String formatMessageDigest(final MessageDigest messageDigest){
       return formatter.toString();
     }
   }
+
+  @Override
+  public String getHash(){
+    return formatMessageDigest(messageDigestInstance);
+  }
+
+  @Override
+  public void update(final byte[] bytes){
+    messageDigestInstance.update(bytes);
+  }
+
+  @Override
+  public void reset(){
+    messageDigestInstance.reset();
+  }
 
+  @Override
+  public String getBagitAlgorithmName(){
+    return BAGIT_ALGORITHM_NAME;
+  }
+
   @Override
   public void initialize() throws NoSuchAlgorithmException{
     messageDigestInstance = MessageDigest.getInstance(MESSAGE_DIGEST_NAME);

src/main/java/com/github/jscancella/writer/internal/FetchWriter.java

@@ -46,7 +46,7 @@ public static Path writeFetchFile(final List<FetchItem> itemsToFetch, final Path
     return fetchFilePath;
   }
 
-  private static String formatFetchLine(final FetchItem fetchItem, final Path bagitRootDir){
+  static String formatFetchLine(final FetchItem fetchItem, final Path bagitRootDir){
     final StringBuilder fetchLineBuilder = new StringBuilder();
     fetchLineBuilder.append(fetchItem.getUri()).append(' ');
 

src/main/java/com/github/jscancella/writer/internal/ManifestWriter.java

@@ -75,7 +75,7 @@ private static Set<Path> writeManifests(
 
       try(BufferedWriter writer = Files.newBufferedWriter(manifestPath, charsetName,
           StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.CREATE)){
-        for(final ManifestEntry entry : manifest.getEntries()){
+        for(final ManifestEntry entry : manifest.getEntries()){          
           // there are 2 spaces between the checksum and the path so that the manifests
           // are compatible with the md5sum tools available on most unix systems.
           // This may cause problems on windows due to it being text mode, in which case

src/test/java/com/github/jscancella/conformance/internal/BagProfileCheckerTest.java

@@ -9,7 +9,6 @@
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 
-import com.github.jscancella.TempFolderTest;
 import com.github.jscancella.conformance.exceptions.BagitVersionIsNotAcceptableException;
 import com.github.jscancella.conformance.exceptions.FetchFileNotAllowedException;
 import com.github.jscancella.conformance.exceptions.MetatdataValueIsNotAcceptableException;
@@ -19,7 +18,7 @@
 import com.github.jscancella.conformance.exceptions.RequiredTagFileNotPresentException;
 import com.github.jscancella.domain.Bag;
 
-public class BagProfileCheckerTest extends TempFolderTest {
+public class BagProfileCheckerTest{
   private static final Path profileJson = new File("src/test/resources/bagitProfiles/allOptionalFieldsProfile_v1.2.0.json").toPath();
 
   @Test