bug: NullPointerException for shadow anonymous classes

.gitignore

@@ -23,6 +23,9 @@ maven-eclipse.xml
 !.idea/codeStyleSettings.xml
 *.iml
 
+# VSCode
+.vscode
+
 # Spoon
 spooned-classes/
 spooned/
@@ -31,3 +34,6 @@ doc/_jekyll/_site/
 
 # Nodejs
 node_modules/
+
+# Gradle
+.gradle

pom.xml

@@ -18,7 +18,7 @@
 
   <artifactId>spoon-core</artifactId>
   <packaging>jar</packaging>
-  <version>8.3.0-SNAPSHOT</version>
+  <version>8.4.0-SNAPSHOT</version>
   <name>Spoon Core</name>
   <description>Spoon is a tool for meta-programming, analysis and transformation of Java programs.</description>
   <url>http://spoon.gforge.inria.fr/</url>

src/main/java/spoon/reflect/factory/TypeFactory.java

@@ -565,6 +565,9 @@ public <T> CtType<T> get(Class<?> cl) {
 				} catch (Throwable e) {
 					throw new SpoonClassNotFoundException("cannot create shadow class: " + cl.getName(), e);
 				}
+				/* if (newShadowClass == null) {
+					return null;
+				} */
 				newShadowClass.setFactory(factory);
 				newShadowClass.accept(new CtScanner() {
 					@Override

src/main/java/spoon/support/compiler/SpoonPom.java

@@ -35,6 +35,7 @@
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -82,7 +83,7 @@ public SpoonPom(String path, SpoonPom parent, MavenLauncher.SOURCE_TYPE sourceTy
 		if (!path.endsWith(".xml") && !path.endsWith(".pom")) {
 			path = Paths.get(path, "pom.xml").toString();
 		}
-		this.pomFile = new File(path);
+		this.pomFile = new File(path).getAbsoluteFile();
 		if (!pomFile.exists()) {
 			throw new IOException("Pom does not exists.");
 		}
@@ -131,9 +132,20 @@ public List<File> getSourceDirectories() {
 			sourcePath = build.getSourceDirectory();
 		}
 		if (sourcePath == null) {
-			sourcePath = Paths.get("src/main/java").toString();
+			sourcePath = getSourceDirectoryFromParent(getParentPom());
+			if (sourcePath == null) {
+				sourcePath = Paths.get("src/main/java").toString();
+			}
+		}
+		sourcePath = extractVariable(sourcePath);
+		Path path = Paths.get(sourcePath);
+
+		String absoluteSourcePath;
+		if (path.isAbsolute()) {
+			absoluteSourcePath = path.toString();
+		} else {
+			absoluteSourcePath = Paths.get(directory.getAbsolutePath(), sourcePath).toString();
 		}
-		String absoluteSourcePath = Paths.get(directory.getAbsolutePath(), sourcePath).toString();
 		File source = new File(absoluteSourcePath);
 		if (source.exists()) {
 			output.add(source);
@@ -148,6 +160,28 @@ public List<File> getSourceDirectories() {
 		return output;
 	}
 
+	/**
+	 * Climbs the pom.xml hierarchy until a model is found in which
+	 * a source directory is declared.
+	 * @return the uninterpolated source directory declared in the nearest ancestor
+	 */
+	private String getSourceDirectoryFromParent(SpoonPom parent) {
+		if (parent == null) {
+			return null;
+		}
+		String sourcePath = null;
+		Build build = parent.model.getBuild();
+		if (build != null) {
+			sourcePath = build.getSourceDirectory();
+			if (sourcePath == null && parent.getParentPom() != null) {
+				return getSourceDirectoryFromParent(parent.getParentPom());
+			}
+		} else if (parent.getParentPom() != null) {
+			return getSourceDirectoryFromParent(parent.getParentPom());
+		}
+		return sourcePath;
+	}
+
 	/**
 	 * Get the list of test directories of the project
 	 * @return the list of test directories
@@ -161,9 +195,20 @@ public List<File> getTestDirectories() {
 			sourcePath = build.getTestSourceDirectory();
 		}
 		if (sourcePath == null) {
-			sourcePath = Paths.get("src/test/java").toString();
+			sourcePath = getTestSourceDirectoryFromParent(getParentPom());
+			if (sourcePath == null) {
+				sourcePath = Paths.get("src/test/java").toString();
+			}
+		}
+		sourcePath = extractVariable(sourcePath);
+		Path path = Paths.get(sourcePath);
+
+		String absoluteSourcePath;
+		if (path.isAbsolute()) {
+			absoluteSourcePath = path.toString();
+		} else {
+			absoluteSourcePath = Paths.get(directory.getAbsolutePath(), sourcePath).toString();
 		}
-		String absoluteSourcePath = Paths.get(directory.getAbsolutePath(), sourcePath).toString();
 		File source = new File(absoluteSourcePath);
 		if (source.exists()) {
 			output.add(source);
@@ -178,6 +223,28 @@ public List<File> getTestDirectories() {
 		return output;
 	}
 
+	/**
+	 * Climbs the pom.xml hierarchy until a model is found in which
+	 * a test source directory is declared.
+	 * @return the uninterpolated test source directory declared in the nearest ancestor
+	 */
+	private String getTestSourceDirectoryFromParent(SpoonPom parent) {
+		if (parent == null) {
+			return null;
+		}
+		String sourcePath = null;
+		Build build = parent.model.getBuild();
+		if (build != null) {
+			sourcePath = build.getTestSourceDirectory();
+			if (sourcePath == null && parent.getParentPom() != null) {
+				return getTestSourceDirectoryFromParent(parent.getParentPom());
+			}
+		} else if (parent.getParentPom() != null) {
+			return getTestSourceDirectoryFromParent(parent.getParentPom());
+		}
+		return sourcePath;
+	}
+
 	/**
 	 * Get the list of classpath files generated by maven
 	 * @return the list of classpath files
@@ -213,29 +280,31 @@ private String extractVariable(String value) {
 	}
 
 	/**
-	 * Get the value of a property
+	 * Get the value of a property. Reference: https://maven.apache.org/ref/3.6.3/maven-model-builder/#Model_Interpolation
 	 * @param key the key of the property
 	 * @return the property value if key exists or null
 	 */
 	private String getProperty(String key) {
-		if ("project.version".equals(key)  || "pom.version".equals(key)) {
+		if ("project.version".equals(key) || "pom.version".equals(key) || "version".equals(key)) {
 			if (model.getVersion() != null) {
 				return model.getVersion();
 			} else if (model.getParent() != null) {
 				return model.getParent().getVersion();
 			}
-		} else if ("project.groupId".equals(key) || "pom.groupId".equals(key)) {
+		} else if ("project.groupId".equals(key) || "pom.groupId".equals(key) || "groupId".equals(key)) {
 			if (model.getGroupId() != null) {
 				return model.getGroupId();
 			} else if (model.getParent() != null) {
 				return model.getParent().getGroupId();
 			}
-		} else if ("project.artifactId".equals(key)  || "pom.artifactId".equals(key)) {
+		} else if ("project.artifactId".equals(key) || "pom.artifactId".equals(key) || "artifactId".equals(key)) {
 			if (model.getArtifactId() != null) {
 				return model.getArtifactId();
 			} else if (model.getParent() != null) {
 				return model.getParent().getArtifactId();
 			}
+		} else if ("project.basedir".equals(key) || "pom.basedir".equals(key) || "basedir".equals(key)) {
+			return pomFile.getParent();
 		}
 		String value = extractVariable(model.getProperties().getProperty(key));
 		if (value == null) {

src/main/java/spoon/support/compiler/jdt/JDTBatchCompiler.java

@@ -91,8 +91,14 @@ public CompilationUnit[] getCompilationUnits() {
 							} else {
 								lastSlash += 1;
 							}
-							//TODO the module name parsed by JDK compiler is in `this.modNames`
-							compilationUnit.module = CharOperation.subarray(modulePath, lastSlash, modulePath.length);
+
+							if (this.module == null) {
+								compilationUnit.module = CharOperation.subarray(modulePath, lastSlash, modulePath.length);
+							} else {
+								//TODO the module name parsed by JDK compiler is in `this.modNames`, consider using that instead?
+								compilationUnit.module = this.module.name();
+							}
+
 							pathToModName.put(String.valueOf(modulePath), compilationUnit.module);
 						}
 					} else {

src/main/java/spoon/support/compiler/jdt/PositionBuilder.java

@@ -7,6 +7,7 @@
  */
 package spoon.support.compiler.jdt;
 
+import org.apache.commons.lang3.ArrayUtils;
 import org.eclipse.jdt.internal.compiler.ast.ASTNode;
 import org.eclipse.jdt.internal.compiler.ast.AbstractMethodDeclaration;
 import org.eclipse.jdt.internal.compiler.ast.AbstractVariableDeclaration;
@@ -46,6 +47,7 @@
 import spoon.support.compiler.jdt.ContextBuilder.CastInfo;
 import spoon.support.reflect.CtExtendedModifier;
 
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
@@ -366,7 +368,12 @@ SourcePosition buildPositionCtElement(CtElement e, ASTNode node) {
 
 			TypeParameter[] typeParameters = methodDeclaration.typeParameters();
 			if (typeParameters != null && typeParameters.length > 0) {
-				modifiersSourceEnd = typeParameters[0].declarationSourceStart - 3;
+				// if there is no space between the modifier and the type parameter vs if there is a space
+				if (contents[typeParameters[0].declarationSourceStart - 2] != ' ') {
+					modifiersSourceEnd = typeParameters[0].declarationSourceStart - 2;
+				} else {
+					modifiersSourceEnd = typeParameters[0].declarationSourceStart - 3;
+				}
 			}
 
 			if (getModifiers(methodDeclaration.modifiers, false, true).isEmpty()) {
@@ -577,10 +584,21 @@ private void setModifiersPosition(CtModifiable e, int start, int end) {
 			if (o2 == -1) {
 				o2 = end;
 			}
+
+			// this is the index into the modifier char array snippet, so must be +o1 if >-1
+			int chevronIndex = ArrayUtils.indexOf(Arrays.copyOfRange(contents, o1, o2), '<');
+			if (chevronIndex != -1) {
+				o2 = o1 + chevronIndex;
+			}
+
 			String modifierName = String.valueOf(contents, o1, o2 - o1);
 			CtExtendedModifier modifier = explicitModifiersByName.remove(modifierName);
 			if (modifier != null) {
-				modifier.setPosition(cf.createSourcePosition(cu, o1, o2 - 1, jdtTreeBuilder.getContextBuilder().getCompilationUnitLineSeparatorPositions()));
+				/* if (chevronIndex > -1) {
+					modifier.setPosition(cf.createSourcePosition(cu, o1, o2, jdtTreeBuilder.getContextBuilder().getCompilationUnitLineSeparatorPositions()));
+				} else { */
+					modifier.setPosition(cf.createSourcePosition(cu, o1, o2 - 1, jdtTreeBuilder.getContextBuilder().getCompilationUnitLineSeparatorPositions()));
+				//}
 			}
 			start = o2;
 		}

src/main/java/spoon/support/reflect/reference/CtReferenceImpl.java

@@ -93,22 +93,22 @@ public boolean equals(Object o) {
 		return false;
 	}
 	private void checkIdentiferForJLSCorrectness(String simplename) {
-	/*
-  * At the level of the Java Virtual Machine, every constructor written in the Java programming language (JLS §8.8)
-  * appears as an instance initialization method that has the special name <init>.
-  * This name is supplied by a compiler. Because the name is not a valid identifier,
-  * it cannot be used directly in a program written in the Java programming language.
-  */
-	//JDTTreeBuilderHelper.computeAnonymousName returns "$numbers$Name" so we have to skip them if they start with numbers
-	//allow empty identifier because they are sometimes used.
+		/*
+		 * At the level of the Java Virtual Machine, every constructor written in the Java programming language (JLS §8.8)
+		 * appears as an instance initialization method that has the special name <init>.
+		 * This name is supplied by a compiler. Because the name is not a valid identifier,
+		 * it cannot be used directly in a program written in the Java programming language.
+		 */
+		//JDTTreeBuilderHelper.computeAnonymousName returns "$numbers$Name" so we have to skip them if they start with numbers
+		//allow empty identifier because they are sometimes used.
 		if (!simplename.matches("<.*>|\\d.*|^.{0}$")) {
 			//split at "<" and ">" because "Iterator<Cache.Entry<K,Store.ValueHolder<V>>>" submits setSimplename ("Cache.Entry<K")
 			String[] splittedSimplename = simplename.split("\\.|<|>");
 			if (checkAllParts(splittedSimplename)) {
 				throw new SpoonException("Not allowed javaletter or keyword in identifier found. See JLS for correct identifier. Identifier: " + simplename);
 			}
+		}
 	}
-}
 	private boolean isKeyword(String simplename) {
 		return keywords.contains(simplename);
 	}
@@ -118,19 +118,25 @@ private boolean checkAllParts(String[] simplenameParts) {
 			simpleName = simpleName.replaceAll("\\[\\]|@", "");
 			if (isKeyword(simpleName) || checkIdentifierChars(simpleName)) {
 				return true;
+			}
 		}
-	}
-	return false;
+		return false;
 	}
 	private boolean checkIdentifierChars(String simplename) {
-		return (!Character.isJavaIdentifierStart(simplename.charAt(0))) || simplename.chars().anyMatch(letter -> !Character.isJavaIdentifierPart(letter));
+		if (simplename.length() == 0) {
+			return false;
+		}
+		return (!Character.isJavaIdentifierStart(simplename.charAt(0)))
+			|| simplename.chars().anyMatch(letter -> !Character.isJavaIdentifierPart(letter)
+		);
 	}
+
 	private static Collection<String> fillWithKeywords() {
-	//removed types because needed as ref: "int","short", "char", "void", "byte","float", "true","false","boolean","double","long","class", "null"
-	return Stream.of("abstract", "continue", "for", "new", "switch", "assert", "default", "if", "package", "synchronized",  "do", "goto", "private",
-	"this", "break",  "implements", "protected", "throw", "else", "import", "public", "throws", "case", "enum", "instanceof", "return",
-	"transient", "catch", "extends", "try", "final", "interface", "static", "finally",  "strictfp", "volatile",
-	"const",  "native", "super", "while", "_")
-	.collect(Collectors.toCollection(HashSet::new));
+		//removed types because needed as ref: "int","short", "char", "void", "byte","float", "true","false","boolean","double","long","class", "null"
+		return Stream.of("abstract", "continue", "for", "new", "switch", "assert", "default", "if", "package", "synchronized",  "do", "goto", "private",
+			"this", "break",  "implements", "protected", "throw", "else", "import", "public", "throws", "case", "enum", "instanceof", "return",
+			"transient", "catch", "extends", "try", "final", "interface", "static", "finally",  "strictfp", "volatile",
+			"const",  "native", "super", "while", "_")
+			.collect(Collectors.toCollection(HashSet::new));
 	}
 }