Fix Issue 113: call graph is missing edges to implementations of interfaces. Merge to v1.X.X.

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

@@ -153,7 +153,7 @@ 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());
 
         Log.info("Registered " + entrypoints.size() + " entrypoints.");
         return entrypoints;

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

@@ -4,6 +4,7 @@
 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;
@@ -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

@@ -1,23 +1,28 @@
 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;
 
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
-import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.text.MessageFormat;
+import java.time.Duration;
 import java.util.Properties;
+import java.util.stream.StreamSupport;
 
-import static org.junit.jupiter.api.Assertions.assertThrows;
 
 @Testcontainers
 @SuppressWarnings("resource")
@@ -28,7 +33,7 @@ public class CodeAnalyzerIntegrationTest {
      */
     static String codeanalyzerVersion;
     static final String javaVersion = "17";
-
+    static String javaHomePath;
     static {
         // Build project first
         try {
@@ -44,15 +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
@@ -61,11 +65,32 @@ public class CodeAnalyzerIntegrationTest {
             .withCommand("-c", "while true; do sleep 1; done")
             .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/mvnw-working-test")), "/test-applications/mvnw-working-test");
+            .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())) {
@@ -94,18 +119,36 @@ 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 whatIsInTheTestAppFolder = container.execInContainer("ls", "/test-applications/call-graph-test");
+        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.assertEquals(4, StreamSupport.stream(systemDepGraph.spliterator(), false).count(),
+                "Expected exactly 4 entries in the system dependency graph");
+    }
+
     @Test
     void corruptMavenShouldNotBuildWithWrapper() throws IOException, InterruptedException {
         // Make executable
@@ -129,19 +172,19 @@ void corruptMavenShouldProduceAnalysisArtifactsWhenMVNCommandIsInPath() throws I
         Assertions.assertTrue(runCodeAnalyzer.getStdout().contains("[ERROR]\tCannot run program \"/test-applications/mvnw-corrupt-test/mvnw\"") && runCodeAnalyzer.getStdout().contains("/mvn."));
         // We should correctly identify the build tool used in the mvn command from the system path.
         Assertions.assertTrue(runCodeAnalyzer.getStdout().contains("[INFO]\tBuilding the project using /usr/bin/mvn."));
-        }
+    }
 
     @Test
     void corruptMavenShouldNotTerminateWithErrorWhenMavenIsNotPresentUnlessAnalysisLevel2() throws IOException, InterruptedException {
         // 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"));
     }

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

@@ -38,6 +38,8 @@ target/
 *.iws
 *.ipr
 
+!gradle-wrapper.jar
+
 # Ignore Eclipse files
 .settings/
 *.classpath

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