Fix issues #368, #370, #361 (#371)

Fix issue #368 , issue #370 , and issue #361 .
Tests have been added.
One existing test(Issue103) fails, but it was already failing in the
main branch.

src/main/java/org/checkerframework/specimin/JavaParserUtil.java

@@ -16,6 +16,7 @@
 import com.github.javaparser.ast.type.ClassOrInterfaceType;
 import com.github.javaparser.ast.type.Type;
 import com.github.javaparser.resolution.UnsolvedSymbolException;
+import com.github.javaparser.resolution.declarations.ResolvedMethodLikeDeclaration;
 import com.github.javaparser.resolution.types.ResolvedReferenceType;
 import com.github.javaparser.resolution.types.ResolvedType;
 import com.google.common.base.Splitter;
@@ -271,6 +272,18 @@ public static List<String> getReferenceTypesFromCommaSeparatedString(String comm
     return types;
   }
 
+  /**
+   * Returns a package prefix that can be prepended to a class name, for a given method or
+   * constructor declaration.
+   *
+   * @param decl declaration to extract a package prefix from(using getPackageName)
+   * @return empty string if default package, otherwise package name followed by "."
+   */
+  public static String packagePrefix(ResolvedMethodLikeDeclaration decl) {
+    String packageName = decl.getPackageName();
+    return packageName.isEmpty() ? "" : packageName + ".";
+  }
+
   /**
    * Returns true iff the innermost enclosing class/interface is an enum.
    *

src/main/java/org/checkerframework/specimin/SpeciminRunner.java

@@ -1,6 +1,7 @@
 package org.checkerframework.specimin;
 
 import com.github.javaparser.ParseProblemException;
+import com.github.javaparser.ParseResult;
 import com.github.javaparser.ParserConfiguration;
 import com.github.javaparser.StaticJavaParser;
 import com.github.javaparser.ast.CompilationUnit;
@@ -236,7 +237,10 @@ private static void performMinimizationImpl(
     Map<String, String> nonPrimaryClassesToPrimaryClass = new HashMap<>();
     SourceRoot sourceRoot = new SourceRoot(Path.of(root));
     sourceRoot.tryToParse();
-    for (CompilationUnit compilationUnit : sourceRoot.getCompilationUnits()) {
+    // getCompilationUnits does not seem to include all files, causing some to be deleted
+    for (ParseResult<CompilationUnit> res : sourceRoot.getCache()) {
+      CompilationUnit compilationUnit =
+          res.getResult().orElseThrow(() -> new RuntimeException(res.getProblems().toString()));
       Path pathOfCurrentJavaFile =
           compilationUnit.getStorage().get().getPath().toAbsolutePath().normalize();
       String primaryTypeQualifiedName = "";

src/main/java/org/checkerframework/specimin/TargetMemberFinderVisitor.java

@@ -243,7 +243,7 @@ public Visitable visit(ConstructorDeclaration method, Void p) {
       targetMethods.add(resolvedMethod.getQualifiedSignature());
       unfoundMethods.remove(methodName);
       updateUsedClassWithQualifiedClassName(
-          resolvedMethod.getPackageName() + "." + resolvedMethod.getClassName(),
+          JavaParserUtil.packagePrefix(resolvedMethod) + resolvedMethod.getClassName(),
           usedTypeElements,
           nonPrimaryClassesToPrimaryClass);
       if (modularityModel.preserveAllFieldsIfTargetIsConstructor()) {
@@ -341,19 +341,19 @@ public Visitable visit(MethodDeclaration method, Void p) {
       if (parentNode instanceof ObjectCreationExpr) {
         ObjectCreationExpr parentExpression = (ObjectCreationExpr) parentNode;
         ResolvedConstructorDeclaration resolved = parentExpression.resolve();
-        String methodPackage = resolved.getPackageName();
+        String methodPackagePrefix = JavaParserUtil.packagePrefix(resolved);
         String methodClass = resolved.getClassName();
-        usedMembers.add(methodPackage + "." + methodClass + "." + method.getNameAsString() + "()");
+        usedMembers.add(methodPackagePrefix + methodClass + "." + method.getNameAsString() + "()");
         updateUsedClassWithQualifiedClassName(
-            methodPackage + "." + methodClass, usedTypeElements, nonPrimaryClassesToPrimaryClass);
+            methodPackagePrefix + methodClass, usedTypeElements, nonPrimaryClassesToPrimaryClass);
       }
     }
     String methodWithoutAnySpace = methodName.replaceAll("\\s", "");
     if (this.targetMethodNames.contains(methodWithoutAnySpace)) {
       ResolvedMethodDeclaration resolvedMethod = method.resolve();
       updateUsedClassesForInterface(resolvedMethod);
       updateUsedClassWithQualifiedClassName(
-          resolvedMethod.getPackageName() + "." + resolvedMethod.getClassName(),
+          JavaParserUtil.packagePrefix(resolvedMethod) + resolvedMethod.getClassName(),
           usedTypeElements,
           nonPrimaryClassesToPrimaryClass);
 
@@ -518,9 +518,11 @@ public Visitable visit(MethodCallExpr call, Void p) {
                 resolvedYetStuckMethodCall.add(scopeAsString + "." + call.getNameAsString());
                 usedTypeElements.add(scopeAsString);
               } else {
+                String packagePrefix =
+                    getCurrentPackage().isEmpty() ? "" : getCurrentPackage() + ".";
                 resolvedYetStuckMethodCall.add(
-                    getCurrentPackage() + "." + scopeAsString + "." + call.getNameAsString());
-                usedTypeElements.add(getCurrentPackage() + "." + scopeAsString);
+                    packagePrefix + scopeAsString + "." + call.getNameAsString());
+                usedTypeElements.add(packagePrefix + scopeAsString);
               }
             }
           }
@@ -564,7 +566,7 @@ public Visitable visit(MethodCallExpr call, Void p) {
   private void preserveMethodDecl(ResolvedMethodDeclaration decl) {
     usedMembers.add(decl.getQualifiedSignature());
     updateUsedClassWithQualifiedClassName(
-        decl.getPackageName() + "." + decl.getClassName(),
+        JavaParserUtil.packagePrefix(decl) + decl.getClassName(),
         usedTypeElements,
         nonPrimaryClassesToPrimaryClass);
     try {
@@ -624,7 +626,7 @@ public Visitable visit(ObjectCreationExpr newExpr, Void p) {
         ResolvedConstructorDeclaration resolved = newExpr.resolve();
         usedMembers.add(resolved.getQualifiedSignature());
         updateUsedClassWithQualifiedClassName(
-            resolved.getPackageName() + "." + resolved.getClassName(),
+            JavaParserUtil.packagePrefix(resolved) + resolved.getClassName(),
             usedTypeElements,
             nonPrimaryClassesToPrimaryClass);
         for (int i = 0; i < resolved.getNumberOfParams(); ++i) {
@@ -646,7 +648,7 @@ public Visitable visit(ExplicitConstructorInvocationStmt expr, Void p) {
       ResolvedConstructorDeclaration resolved = expr.resolve();
       usedMembers.add(resolved.getQualifiedSignature());
       updateUsedClassWithQualifiedClassName(
-          resolved.getPackageName() + "." + resolved.getClassName(),
+          JavaParserUtil.packagePrefix(resolved) + resolved.getClassName(),
           usedTypeElements,
           nonPrimaryClassesToPrimaryClass);
     }
@@ -850,10 +852,6 @@ public static void updateUsedClassWithQualifiedClassName(
       Set<String> usedTypeElement,
       Map<String, String> nonPrimaryClassesToPrimaryClass) {
 
-    // in case of type variables
-    if (!qualifiedClassName.contains(".")) {
-      return;
-    }
     // strip type variables, if they're present
     if (qualifiedClassName.contains("<")) {
       qualifiedClassName = qualifiedClassName.substring(0, qualifiedClassName.indexOf("<"));
@@ -867,6 +865,10 @@ public static void updateUsedClassWithQualifiedClassName(
           nonPrimaryClassesToPrimaryClass);
     }
 
+    // in case of type variables TODO:investigate side effects of having moved this from earlier
+    if (!qualifiedClassName.contains(".")) {
+      return;
+    }
     String potentialOuterClass =
         qualifiedClassName.substring(0, qualifiedClassName.lastIndexOf("."));
     if (JavaParserUtil.isAClassPath(potentialOuterClass)) {

src/main/java/org/checkerframework/specimin/UnsolvedSymbolVisitor.java

@@ -1588,6 +1588,9 @@ public boolean updatedAddedTargetFilesForPotentialEnum(FieldAccessExpr expr) {
       return false;
     }
     if (resolved.isEnumConstant()) {
+      if (JavaLangUtils.inJdkPackage(resolved.getType().describe())) {
+        return false;
+      }
       String filePathName = qualifiedNameToFilePath(resolved.getType().describe());
       if (!addedTargetFiles.contains(filePathName)) {
         gotException();
@@ -3257,7 +3260,8 @@ public static UnsolvedClassOrInterface getSimpleSyntheticClassFromFullyQualified
               + fullyName);
     }
     String className = fullyQualifiedToSimple(fullyName);
-    String packageName = fullyName.replace("." + className, "");
+    String packageName =
+        fullyName.contains("." + className) ? fullyName.replace("." + className, "") : "";
     return new UnsolvedClassOrInterface(className, packageName);
   }
 

src/test/java/org/checkerframework/specimin/BuiltinEnumTest.java

@@ -0,0 +1,15 @@
+package org.checkerframework.specimin;
+
+import java.io.IOException;
+import org.junit.Test;
+
+/** This test checks if Specimin is able to process Java builtin enum classes. Issue #361 */
+public class BuiltinEnumTest {
+  @Test
+  public void runTest() throws IOException {
+    SpeciminTestExecutor.runTestWithoutJarPaths(
+        "enumbuiltin",
+        new String[] {"com/example/Scheduler.java"},
+        new String[] {"com.example.Scheduler#schedule(Runnable, int)"});
+  }
+}

src/test/java/org/checkerframework/specimin/DefaultPackageTest.java

@@ -0,0 +1,16 @@
+package org.checkerframework.specimin;
+
+import java.io.IOException;
+import org.junit.Test;
+
+/**
+ * This test checks if Specimin correctly preserves things that are used as arguments to enum
+ * constants.
+ */
+public class DefaultPackageTest {
+  @Test
+  public void runTest() throws IOException {
+    SpeciminTestExecutor.runTestWithoutJarPaths(
+        "defaultpackage", new String[] {"A.java"}, new String[] {"A#schedule(Runnable, int)"});
+  }
+}

src/test/java/org/checkerframework/specimin/Issue368Test.java

@@ -0,0 +1,32 @@
+package org.checkerframework.specimin;
+
+import static org.junit.Assert.assertTrue;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
+import org.junit.Test;
+
+/**
+ * This test is the test described in <a
+ * href="https://github.com/njit-jerse/specimin/issues/368">...</a>. The issue caused the original
+ * source file A.java to be deleted, and in addition not appear in the output.
+ */
+public class Issue368Test {
+  @Test
+  public void runTest() throws IOException {
+    Path fileASource = Path.of("src/test/resources/issue368/A_code.java");
+    Path fileAPath = Path.of("src/test/resources/issue368/input/com/example/A.java");
+    Files.copy(fileASource, fileAPath, StandardCopyOption.REPLACE_EXISTING);
+    String fileACode = Files.readString(fileAPath);
+    SpeciminTestExecutor.runTestWithoutJarPaths(
+        "issue368", new String[] {"com/example/B.java"}, new String[] {"com.example.B#test()"});
+
+    try {
+      assertTrue(Files.exists(fileAPath));
+    } finally {
+      Files.writeString(fileAPath, fileACode);
+    }
+  }
+}

src/test/resources/defaultpackage/expected/A.java

@@ -0,0 +1,6 @@
+public class A {
+
+    public static void schedule(Runnable task, int millis) {
+        System.out.println();
+    }
+}

src/test/resources/defaultpackage/input/A.java

@@ -0,0 +1,5 @@
+public class A{//no package declaration
+	public static void schedule(Runnable task, int millis) {
+		System.out.println();
+	}
+}

src/test/resources/enumbuiltin/expected/com/example/Scheduler.java

@@ -0,0 +1,13 @@
+package com.example;
+
+import java.util.concurrent.ScheduledExecutorService;
+import java.util.concurrent.TimeUnit;
+
+public class Scheduler {
+
+    public static final ScheduledExecutorService ses = null;
+
+    public static void schedule(Runnable task, int millis) {
+        ses.schedule(task, millis, TimeUnit.MILLISECONDS);
+    }
+}

src/test/resources/enumbuiltin/input/com/example/Scheduler.java

@@ -0,0 +1,14 @@
+package com.example;
+import static java.util.concurrent.Executors.newSingleThreadScheduledExecutor;
+
+import java.util.concurrent.ScheduledExecutorService;
+import java.util.concurrent.TimeUnit;
+
+public class Scheduler{
+	private Scheduler() {}
+	public static final ScheduledExecutorService ses=newSingleThreadScheduledExecutor(r->new Thread(r,"Scheduler thread"));
+
+	public static void schedule(Runnable task, int millis) {
+		ses.schedule(task,millis,TimeUnit.MILLISECONDS);
+	}
+}

src/test/resources/issue368/A_code.java

@@ -0,0 +1,21 @@
+package com.example;
+import java.io.IOException;
+import java.net.InetAddress;
+import java.net.InetSocketAddress;
+import java.nio.channels.AsynchronousSocketChannel;
+
+public class A{
+	public AsynchronousSocketChannel client;
+	public A(AsynchronousSocketChannel client){
+		this.client=client;
+	}
+	public InetAddress test(){//target method
+		try {
+			if(client.getRemoteAddress() instanceof InetSocketAddress isa)
+				return isa.getAddress();
+		} catch (IOException e) {
+
+		}
+		return null;
+	}
+}

src/test/resources/issue368/expected/com/example/A.java

@@ -0,0 +1,10 @@
+package com.example;
+
+import java.net.InetAddress;
+
+public class A {
+
+    public InetAddress test() {
+        throw new Error();
+    }
+}

src/test/resources/issue368/expected/com/example/B.java

@@ -0,0 +1,10 @@
+package com.example;
+
+import java.net.InetAddress;
+
+public class B extends A {
+
+    public InetAddress test() {
+        return super.test();
+    }
+}

src/test/resources/issue368/input/com/example/A.java

@@ -0,0 +1,21 @@
+package com.example;
+import java.io.IOException;
+import java.net.InetAddress;
+import java.net.InetSocketAddress;
+import java.nio.channels.AsynchronousSocketChannel;
+
+public class A{
+	public AsynchronousSocketChannel client;
+	public A(AsynchronousSocketChannel client){
+		this.client=client;
+	}
+	public InetAddress test(){//target method
+		try {
+			if(client.getRemoteAddress() instanceof InetSocketAddress isa)
+				return isa.getAddress();
+		} catch (IOException e) {
+
+		}
+		return null;
+	}
+}

src/test/resources/issue368/input/com/example/B.java

@@ -0,0 +1,11 @@
+package com.example;
+import java.io.IOException;
+import java.net.InetAddress;
+
+public class B extends A {
+
+    @Override
+    public InetAddress test(){
+        return super.test();
+    }
+}