Merge pull request #116 from codellm-devkit/113-call-graph-is-missing…

…-edges-to-implementations-of-interfaces

Fix Issue 113: Call graph is missing edges to implementations of interface classes. Merge to main.

gradle.properties

@@ -1 +1 @@
-version=2.2.0
+version=2.2.1

src/main/java/com/ibm/cldk/SystemDependencyGraph.java

@@ -20,6 +20,8 @@
 import com.ibm.wala.cast.ir.ssa.AstIRFactory;
 import com.ibm.wala.cast.java.translator.jdt.ecj.ECJClassLoaderFactory;
 import com.ibm.wala.classLoader.CallSiteReference;
+import com.ibm.wala.classLoader.JavaLanguage;
+import com.ibm.wala.classLoader.Language;
 import com.ibm.wala.ipa.callgraph.*;
 import com.ibm.wala.ipa.callgraph.AnalysisOptions.ReflectionOptions;
 import com.ibm.wala.ipa.callgraph.impl.Util;
@@ -260,8 +262,9 @@ public static List<Dependency> construct(
         CallGraph callGraph;
         CallGraphBuilder<InstanceKey> builder;
         try {
-            System.setOut(new PrintStream(new NullOutputStream()));
-            System.setErr(new PrintStream(new NullOutputStream()));
+            System.setOut(new PrintStream(NullOutputStream.INSTANCE));
+            System.setErr(new PrintStream(NullOutputStream.INSTANCE));
+//            builder = Util.makeRTABuilder(new JavaLanguage(), options, cache, cha);
             builder = Util.makeRTABuilder(options, cache, cha);
             callGraph = builder.makeCallGraph(options, null);
         } finally {

src/main/java/com/ibm/cldk/utils/AnalysisUtils.java

@@ -198,8 +198,8 @@ public static Iterable<Entrypoint> getEntryPoints(IClassHierarchy cha) {
                 System.exit(1);
                 return Stream.empty();
             }
-        }).filter(method -> method.isPublic() || method.isPrivate() || method.isProtected() || method.isStatic()).map(method -> new DefaultEntrypoint(method, cha)).collect(Collectors.toList());
-
+        }).map(method -> new DefaultEntrypoint(method, cha)).collect(Collectors.toList());
+        // We're assuming that all methods are potential entrypoints. May revisit this later if the assumption is incorrect.
         Log.info("Registered " + entrypoints.size() + " entrypoints.");
         return entrypoints;
     }

src/main/java/com/ibm/cldk/utils/BuildProject.java

@@ -10,10 +10,8 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.text.MessageFormat;
-import java.util.AbstractMap;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
+import java.util.*;
+import java.util.stream.Stream;
 
 
 import static com.ibm.cldk.utils.ProjectDirectoryScanner.classFilesStream;
@@ -159,13 +157,13 @@ public static boolean gradleBuild(String projectPath) {
     }
 
     private static boolean buildProject(String projectPath, String build) {
-        File pomFile = new File(projectPath, "pom.xml");
+        File pomFile = new File(String.valueOf(Paths.get(projectPath).toAbsolutePath()), "pom.xml");
         if (build == null) {
             return true;
         } else if (build.equals("auto")) {
             if (pomFile.exists()) {
                 Log.info("Found pom.xml in the project directory. Using Maven to build the project.");
-                return mavenBuild(projectPath); // Use Maven if pom.xml exists
+                return mavenBuild(Paths.get(projectPath).toAbsolutePath().toString()); // Use Maven if pom.xml exists
             } else {
                 Log.info("Did not find a pom.xml in the project directory. Using Gradle to build the project.");
                 return gradleBuild(projectPath); // Otherwise, use Gradle
@@ -211,7 +209,7 @@ public static boolean downloadLibraryDependencies(String projectPath, String pro
         // created download dir if it does not exist
         String projectRoot = projectRootPom != null ? projectRootPom : projectPath;
 
-        File pomFile = new File(projectRoot, "pom.xml");
+        File pomFile = new File((new File(projectRoot)).getAbsoluteFile(), "pom.xml");
         if (pomFile.exists()) {
             libDownloadPath = Paths.get(projectPath, "target", LIB_DEPS_DOWNLOAD_DIR).toAbsolutePath();
             if (mkLibDepDirs(projectPath))
@@ -231,7 +229,7 @@ public static boolean downloadLibraryDependencies(String projectPath, String pro
                         ));
             }
             Log.info("Found pom.xml in the project directory. Using Maven to download dependencies.");
-            String[] mavenCommand = {MAVEN_CMD, "--no-transfer-progress", "-f", Paths.get(projectRoot, "pom.xml").toString(), "dependency:copy-dependencies", "-DoutputDirectory=" + libDownloadPath.toString()};
+            String[] mavenCommand = {MAVEN_CMD, "--no-transfer-progress", "-f", Paths.get(projectRoot, "pom.xml").toAbsolutePath().toString(), "dependency:copy-dependencies", "-DoutputDirectory=" + libDownloadPath.toString()};
             return buildWithTool(mavenCommand);
         } else if (new File(projectRoot, "build.gradle").exists() || new File(projectRoot, "build.gradle.kts").exists()) {
             libDownloadPath = Paths.get(projectPath, "build", LIB_DEPS_DOWNLOAD_DIR).toAbsolutePath();
@@ -271,8 +269,16 @@ public static void cleanLibraryDependencies() {
         if (libDownloadPath != null) {
             Log.info("Cleaning up library dependency directory: " + libDownloadPath);
             try {
-                Files.walk(libDownloadPath).filter(Files::isRegularFile).map(Path::toFile).forEach(File::delete);
-                Files.delete(libDownloadPath);
+                if (libDownloadPath.toFile().getAbsoluteFile().exists()) {
+                    try (Stream<Path> paths = Files.walk(libDownloadPath)) {
+                        paths.sorted(Comparator.reverseOrder())  // Delete files first, then directories
+                            .map(Path::toFile)
+                            .forEach(file -> {
+                                if (!file.delete())
+                                    Log.warn("Failed to delete: " + file.getAbsolutePath());
+                        });
+                    }
+                }
             } catch (IOException e) {
                 Log.warn("Unable to fully delete library dependency directory: " + e.getMessage());
             }

src/main/java/com/ibm/cldk/utils/ProjectDirectoryScanner.java

@@ -4,13 +4,14 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 public class ProjectDirectoryScanner {
     public static List<Path> classFilesStream(String projectPath) throws IOException {
-        Path projectDir = Paths.get(projectPath);
+        Path projectDir = Paths.get(projectPath).toAbsolutePath();
         Log.info("Finding *.class files in " + projectDir);
         if (Files.exists(projectDir)) {
             try (Stream<Path> paths = Files.walk(projectDir)) {
@@ -37,7 +38,7 @@ public static List<Path> jarFilesStream(String projectPath) throws IOException {
                         .collect(Collectors.toList());
             }
         }
-        return null;
+        return new ArrayList<>();
     }
 
     public static List<Path> sourceFilesStream(String projectPath) throws IOException {

src/test/java/com/ibm/cldk/CodeAnalyzerIntegrationTest.java

@@ -1,10 +1,16 @@
 package com.ibm.cldk;
 
+import com.google.gson.Gson;
+import com.google.gson.JsonArray;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import org.json.JSONArray;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.Assertions;
 import org.testcontainers.containers.BindMode;
 import org.testcontainers.containers.GenericContainer;
+import org.testcontainers.containers.startupcheck.OneShotStartupCheckStrategy;
 import org.testcontainers.junit.jupiter.Container;
 import org.testcontainers.junit.jupiter.Testcontainers;
 import org.testcontainers.utility.MountableFile;
@@ -13,7 +19,9 @@
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.nio.file.Paths;
+import java.time.Duration;
 import java.util.Properties;
+import java.util.stream.StreamSupport;
 
 
 @Testcontainers
@@ -25,7 +33,7 @@ public class CodeAnalyzerIntegrationTest {
      */
     static String codeanalyzerVersion;
     static final String javaVersion = "17";
-
+    static String javaHomePath;
     static {
         // Build project first
         try {
@@ -41,16 +49,14 @@ public class CodeAnalyzerIntegrationTest {
     }
 
     @Container
-    static final GenericContainer<?> container = new GenericContainer<>("openjdk:17-jdk")
+    static final GenericContainer<?> container = new GenericContainer<>("ubuntu:latest")
             .withCreateContainerCmdModifier(cmd -> cmd.withEntrypoint("sh"))
             .withCommand("-c", "while true; do sleep 1; done")
-            .withFileSystemBind(
-                    String.valueOf(Paths.get(System.getProperty("user.dir")).resolve("build/libs")),
-                    "/opt/jars",
-                    BindMode.READ_WRITE)
+            .withCopyFileToContainer(MountableFile.forHostPath(Paths.get(System.getProperty("user.dir")).resolve("build/libs")), "/opt/jars")
             .withCopyFileToContainer(MountableFile.forHostPath(Paths.get(System.getProperty("user.dir")).resolve("build/libs")), "/opt/jars")
             .withCopyFileToContainer(MountableFile.forHostPath(Paths.get(System.getProperty("user.dir")).resolve("src/test/resources/test-applications/mvnw-corrupt-test")), "/test-applications/mvnw-corrupt-test")
             .withCopyFileToContainer(MountableFile.forHostPath(Paths.get(System.getProperty("user.dir")).resolve("src/test/resources/test-applications/plantsbywebsphere")), "/test-applications/plantsbywebsphere")
+            .withCopyFileToContainer(MountableFile.forHostPath(Paths.get(System.getProperty("user.dir")).resolve("src/test/resources/test-applications/call-graph-test")), "/test-applications/call-graph-test")
             .withCopyFileToContainer(MountableFile.forHostPath(Paths.get(System.getProperty("user.dir")).resolve("src/test/resources/test-applications/mvnw-working-test")), "/test-applications/mvnw-working-test");
 
     @Container
@@ -62,8 +68,29 @@ public class CodeAnalyzerIntegrationTest {
             .withCopyFileToContainer(MountableFile.forHostPath(Paths.get(System.getProperty("user.dir")).resolve("src/test/resources/test-applications/mvnw-working-test")), "/test-applications/mvnw-working-test")
             .withCopyFileToContainer(MountableFile.forHostPath(Paths.get(System.getProperty("user.dir")).resolve("src/test/resources/test-applications/daytrader8")), "/test-applications/daytrader8");
 
+    public CodeAnalyzerIntegrationTest() throws IOException, InterruptedException {
+    }
+
     @BeforeAll
     static void setUp() {
+        // Install Java 17 in the base container
+        try {
+            container.execInContainer("apt-get", "update");
+            container.execInContainer("apt-get", "install", "-y", "openjdk-17-jdk");
+
+            // Get JAVA_HOME dynamically
+            var javaHomeResult = container.execInContainer("bash", "-c",
+                    "dirname $(dirname $(readlink -f $(which java)))"
+            );
+            javaHomePath = javaHomeResult.getStdout().trim();
+            Assertions.assertFalse(javaHomePath.isEmpty(), "Failed to determine JAVA_HOME");
+
+        } catch (IOException | InterruptedException e) {
+            throw new RuntimeException(e);
+        }
+
+
+        // Get the version of the codeanalyzer jar
         Properties properties = new Properties();
         try (FileInputStream fis = new FileInputStream(
                 Paths.get(System.getProperty("user.dir"), "gradle.properties").toFile())) {
@@ -92,18 +119,42 @@ void shouldHaveCodeAnalyzerJar() throws Exception {
     @Test
     void shouldBeAbleToRunCodeAnalyzer() throws Exception {
         var runCodeAnalyzerJar = container.execInContainer(
-                "java",
-                "-jar",
-                String.format("/opt/jars/codeanalyzer-%s.jar", codeanalyzerVersion),
-                "--help"
-        );
+                "bash", "-c",
+                String.format("export JAVA_HOME=%s && java -jar /opt/jars/codeanalyzer-%s.jar --help",
+                javaHomePath, codeanalyzerVersion
+        ));
 
         Assertions.assertEquals(0, runCodeAnalyzerJar.getExitCode(),
                 "Command should execute successfully");
         Assertions.assertTrue(runCodeAnalyzerJar.getStdout().length() > 0,
                 "Should have some output");
     }
 
+    @Test
+    void callGraphShouldHaveKnownEdges() throws Exception {
+        var runCodeAnalyzerOnCallGraphTest = container.execInContainer(
+                "bash", "-c",
+                String.format(
+                        "export JAVA_HOME=%s && java -jar /opt/jars/codeanalyzer-%s.jar --input=/test-applications/call-graph-test --analysis-level=2",
+                        javaHomePath, codeanalyzerVersion
+                )
+        );
+
+
+        // Read the output JSON
+        Gson gson = new Gson();
+        JsonObject jsonObject = gson.fromJson(runCodeAnalyzerOnCallGraphTest.getStdout(), JsonObject.class);
+        JsonArray systemDepGraph = jsonObject.getAsJsonArray("system_dependency_graph");
+        Assertions.assertTrue(StreamSupport.stream(systemDepGraph.spliterator(), false)
+                .map(JsonElement::getAsJsonObject)
+                .anyMatch(entry ->
+                        "CALL_DEP".equals(entry.get("type").getAsString()) &&
+                                "1".equals(entry.get("weight").getAsString()) &&
+                                entry.getAsJsonObject("source").get("signature").getAsString().equals("helloString()") &&
+                                entry.getAsJsonObject("target").get("signature").getAsString().equals("log()")
+                ), "Expected edge not found in the system dependency graph");
+    }
+
     @Test
     void corruptMavenShouldNotBuildWithWrapper() throws IOException, InterruptedException {
         // Make executable
@@ -131,42 +182,44 @@ void corruptMavenShouldProduceAnalysisArtifactsWhenMVNCommandIsInPath() throws I
 
     @Test
     void corruptMavenShouldNotTerminateWithErrorWhenMavenIsNotPresentUnlessAnalysisLevel2() throws IOException, InterruptedException {
-        // When javaee level 2, we should get a Runtime Exception
+        // When analysis level 2, we should get a Runtime Exception
         var runCodeAnalyzer = container.execInContainer(
-                "java",
-                "-jar",
-                String.format("/opt/jars/codeanalyzer-%s.jar", codeanalyzerVersion),
-                "--input=/test-applications/mvnw-corrupt-test",
-                "--output=/tmp/",
-                "--analysis-level=2"
+                "bash", "-c",
+                String.format(
+                        "export JAVA_HOME=%s && java -jar /opt/jars/codeanalyzer-%s.jar --input=/test-applications/mvnw-corrupt-test --output=/tmp/ --analysis-level=2",
+                        javaHomePath, codeanalyzerVersion
+                )
         );
+
         Assertions.assertEquals(1, runCodeAnalyzer.getExitCode());
         Assertions.assertTrue(runCodeAnalyzer.getStderr().contains("java.lang.RuntimeException"));
     }
 
     @Test
     void shouldBeAbleToGenerateAnalysisArtifactForDaytrader8() throws Exception {
         var runCodeAnalyzerOnDaytrader8 = mavenContainer.execInContainer(
-                "java",
-                "-jar",
-                String.format("/opt/jars/codeanalyzer-%s.jar", codeanalyzerVersion),
-                "--input=/test-applications/daytrader8",
-                "--analysis-level=1"
+                "bash", "-c",
+                String.format(
+                        "export JAVA_HOME=%s && java -jar /opt/jars/codeanalyzer-%s.jar --input=/test-applications/daytrader8 --analysis-level=1",
+                        javaHomePath, codeanalyzerVersion
+                )
         );
+
         Assertions.assertTrue(runCodeAnalyzerOnDaytrader8.getStdout().contains("\"is_entrypoint_class\": true"), "No entry point classes found");
         Assertions.assertTrue(runCodeAnalyzerOnDaytrader8.getStdout().contains("\"is_entrypoint\": true"), "No entry point methods found");
     }
 
     @Test
     void shouldBeAbleToDetectCRUDOperationsAndQueriesForPlantByWebsphere() throws Exception {
         var runCodeAnalyzerOnPlantsByWebsphere = container.execInContainer(
-                "java",
-                "-jar",
-                String.format("/opt/jars/codeanalyzer-%s.jar", codeanalyzerVersion),
-                "--input=/test-applications/plantsbywebsphere",
-                "--analysis-level=1", "--verbose"
+                "bash", "-c",
+                String.format(
+                        "export JAVA_HOME=%s && java -jar /opt/jars/codeanalyzer-%s.jar --input=/test-applications/plantsbywebsphere --analysis-level=1 --verbose",
+                        javaHomePath, codeanalyzerVersion
+                )
         );
 
+
         String output = runCodeAnalyzerOnPlantsByWebsphere.getStdout();
 
         Assertions.assertTrue(output.contains("\"query_type\": \"NAMED\""), "No entry point classes found");

src/test/resources/generated/.gitignore

@@ -0,0 +1 @@
+*.json

src/test/resources/test-applications/.gitignore

@@ -29,6 +29,9 @@ hs_err_pid*
 .gradle/
 build/
 
+# Don't ignore Gradle wrapper jar file
+!gradle-wrapper.jar
+
 # Ignore Maven target folder
 target/
 

src/test/resources/test-applications/call-graph-test/.gitattributes

@@ -0,0 +1,9 @@
+#
+# https://help.github.com/articles/dealing-with-line-endings/
+#
+# Linux start script should use lf
+/gradlew        text eol=lf
+
+# These are Windows script files and should use crlf
+*.bat           text eol=crlf
+

src/test/resources/test-applications/call-graph-test/.gitignore

@@ -0,0 +1,5 @@
+# Ignore Gradle project-specific cache directory
+.gradle
+
+# Ignore Gradle build output directory
+build

src/test/resources/test-applications/call-graph-test/build.gradle

@@ -0,0 +1,30 @@
+plugins {
+    id 'application'
+}
+
+repositories {
+    mavenCentral()
+}
+
+java {
+    sourceCompatibility = JavaVersion.VERSION_11
+    targetCompatibility = JavaVersion.VERSION_11
+}
+
+if (project.hasProperty('mainClass')) {
+    mainClassName = project.getProperty('mainClass')
+} else {
+    // use a default
+    mainClassName =("org.example.User")
+}
+
+sourceSets {
+    main {
+        java {
+            srcDirs = ["src/main/java"]
+        }
+        resources {
+            srcDirs = ["src/main/resources"]
+        }
+    }
+}

src/test/resources/test-applications/call-graph-test/gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,7 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.12.1-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists