Release pending changes

.github/workflows/build-and-test.yml

@@ -1,6 +1,16 @@
 name: Build and test
 on: [push]
 
+permissions:
+  # The GITHUB_TOKEN is used to download AppMap service
+  # binaries in addition to cloning the repository; by explicitly
+  # setting permissions, we ensure it has no unnecessary access.
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build-and-check:
     name: Build and check
@@ -9,7 +19,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-java@v4
         with:
-          java-version: '17'
+          java-version: '21'
           distribution: 'temurin'
 
       - name: Setup Gradle
@@ -31,9 +41,21 @@ jobs:
             annotation/build/libs/*.jar
 
   test-suite:
+    services:
+      oracle:
+        image: docker.io/gvenzl/oracle-free:slim-faststart
+        ports:
+          - 1521:1521
+        env:
+          ORACLE_PASSWORD: oracle
+        options: >-
+          --health-cmd healthcheck.sh
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
     strategy:
       matrix:
-        java: ['17', '11', '8']
+        java: ['21', '17', '11', '8']
     runs-on: ubuntu-latest
     name: Run test suite with Java ${{ matrix.java }}
     needs: build-and-check
@@ -106,5 +128,11 @@ jobs:
         env:
           BATS_LIB_PATH: ${{ steps.setup-bats.outputs.lib-path }}
           TERM: xterm
+          # Github token is just to avoid rate limiting when IntelliJ tests
+          # are run and download the AppMap service binaries
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          ORACLE_URL: jdbc:oracle:thin:@localhost:1521
+          ORACLE_USERNAME: system
+          ORACLE_PASSWORD: oracle
         working-directory: ./agent
         run: bin/test_run

.github/workflows/release.yml

@@ -30,7 +30,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-java@v5
         with:
-          java-version: "17"
+          java-version: "21"
           distribution: "temurin"
           cache: gradle
       - name: Setup node

.gitignore

@@ -22,3 +22,6 @@ tmp
 
 # test output
 /.metadata/
+
+# Log files
+*.log

agent/bin/test_install

@@ -9,5 +9,3 @@ for d in build/fixtures/*; do
   ./mvnw package -quiet -DskipTests -Dcheckstyle.skip=true -Dspring-javaformat.skip=true
   cd -
 done
-
-../gradlew testClasses

agent/bin/test_projects

@@ -1,15 +1,23 @@
 #!/usr/bin/env bash
 
-fixture_dir=$PWD/build/fixtures
+set -eo pipefail
+
+AGENT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+
+cd "${AGENT_DIR}"
+
 mkdir -p build/fixtures
 
+# shellcheck source=../test/helper.bash
 source "test/helper.bash"
-export ANNOTATION_JAR="$(find_annotation_jar)"
+ANNOTATION_JAR="$(find_annotation_jar)"
+export ANNOTATION_JAR
 
-function install_petclinic (
+function install_petclinic() {
   local repo="$1"; shift
   local ref=${1:-main}
-  local pkg="$(basename $repo)"
+  local pkg
+  pkg="$(basename "$repo")"
 
   if [[ -d "build/fixtures/${pkg}" ]]; then
     echo "Fixture already exists: ${pkg}"
@@ -43,7 +51,7 @@ function install_petclinic (
 
 
   cd ../../..
-)
+}
 
 function install_scala_test_app {
   if [[ -d "test/scala/play-samples" ]]; then
@@ -53,14 +61,13 @@ function install_scala_test_app {
   cd test/scala
   rm -rf play-samples
   local branch=3.0.x
-  case "${JAVA_VERSION}" in
-    1.8*)
-      branch=2.8.x
-      ;;
-    11.*)
-      branch=2.9.x
-      ;;
-  esac
+  if is_java 17; then
+    branch=3.0.x
+  elif is_java 11; then
+    branch=2.9.x
+  else
+    branch=2.8.x
+  fi
   git clone --no-checkout https://github.com/playframework/play-samples.git --depth 1 --branch $branch
   cd play-samples
   git sparse-checkout set play-scala-rest-api-example
@@ -69,20 +76,16 @@ function install_scala_test_app {
   cd ../../..
 }
 
-case "${JAVA_VERSION}" in
-  1.8*|11.*)
-    install_petclinic "land-of-apps/spring-petclinic" old-java-support
-    ;;
-  17.*)
-    # The spring-petclinic main branch now requires Java 25. This is the last commit that supports Java 17.
-    install_petclinic "spring-projects/spring-petclinic" "3aa79e3944ab1b626288f5d0629e61643ab8fb4a"
-    install_petclinic "spring-petclinic/spring-framework-petclinic"
-    ;;
-  *) # For Java 25+
-    install_petclinic "spring-projects/spring-petclinic" "main"
-    install_petclinic "spring-petclinic/spring-framework-petclinic"
-    ;;
-esac
+if is_java 25; then
+  install_petclinic "spring-projects/spring-petclinic" "main"
+  install_petclinic "spring-petclinic/spring-framework-petclinic"
+elif is_java 17; then
+  # The spring-petclinic main branch now requires Java 25. This is the last commit that supports Java 17.
+  install_petclinic "spring-projects/spring-petclinic" "3aa79e3944ab1b626288f5d0629e61643ab8fb4a"
+  install_petclinic "spring-petclinic/spring-framework-petclinic"
+else
+  install_petclinic "land-of-apps/spring-petclinic" old-java-support
+fi
 
 patch -N -p1 -d build/fixtures/spring-petclinic < test/petclinic/pom.patch
 

agent/bin/test_run

@@ -15,5 +15,5 @@ set -x
 #   * just doing bats -r test doesn't discover a setup_suite.bash file correctly. http_client uses
 #     one, so it needs to be run separately
 
-bats -r test/!(http_client)
-bats -r test/http_client
+bats -r test/!(http_client)/
+bats -r test/http_client/

agent/build.gradle

@@ -14,7 +14,6 @@ plugins {
 }
 
 repositories {
-  jcenter()
   mavenCentral()
 }
 
@@ -52,12 +51,12 @@ dependencies {
   // result, you won't be able to add hooks for anything in those packages.
   implementation 'com.alibaba:fastjson:1.2.83'
   implementation "org.javassist:javassist:${javassistVersion}"
-  implementation 'org.reflections:reflections:0.9.11'
+  implementation 'org.reflections:reflections:0.10.2'
   implementation 'net.bytebuddy:byte-buddy:1.14.10'
-  implementation 'org.apache.commons:commons-lang3:3.10'
+  implementation 'org.apache.commons:commons-lang3:3.20.0'
   implementation 'commons-io:commons-io:2.15.1'
-  implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.13.2'
-  implementation 'com.fasterxml.jackson.core:jackson-databind:2.13.4.2'
+  implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.16.1'
+  implementation 'com.fasterxml.jackson.core:jackson-databind:2.16.1'
   implementation 'org.slf4j:slf4j-nop:1.7.30'
   implementation 'info.picocli:picocli:4.6.1'
   implementation 'org.apache.httpcomponents:httpcore-nio:4.4.15'
@@ -75,6 +74,7 @@ dependencies {
   testImplementation 'org.junit.jupiter:junit-jupiter'
   testImplementation 'org.junit.jupiter:junit-jupiter-params'
   testImplementation 'org.junit.vintage:junit-vintage-engine'
+  testRuntimeOnly 'org.junit.platform:junit-platform-launcher'
 
   testImplementation 'com.github.stefanbirkner:system-rules:1.19.0'
   testImplementation 'com.github.stefanbirkner:system-lambda:1.2.1'
@@ -85,8 +85,7 @@ dependencies {
 }
 
 compileJava {
-    sourceCompatibility = '1.8'
-    targetCompatibility = '1.8'
+    options.release = 8
 }
 
 jar {
@@ -97,11 +96,11 @@ jar {
   }
 }
 
-apply plugin: 'com.github.johnrengelman.shadow'
+apply plugin: 'com.gradleup.shadow'
 
 shadowJar {
-  baseName = 'appmap'
-  classifier = ''
+  archiveBaseName = 'appmap'
+  archiveClassifier = ''
   minimize() {
     // tinylog computes the dependencies it needs at runtime, so don't exclude
     // anything.
@@ -162,6 +161,7 @@ test {
   dependsOn cleanTest
   exclude 'com/appland/appmap/integration/**'
   // systemProperty "appmap.log.level", "debug"
+  jvmArgs '--add-opens', 'java.base/java.lang=ALL-UNNAMED'
 }
 
 task relocateShadowJar(type: ShadowRelocation) {
@@ -179,16 +179,16 @@ tasks.shadowJar.dependsOn tasks.relocateShadowJar
 
 jacocoTestReport {
   reports {
-    xml.enabled false
-    csv.enabled false
-    html.enabled true
+    xml.required = false
+    csv.required = false
+    html.required = true
   }
 }
 
 // extra artifacts used in publishing
 task sourcesJar(type: Jar) {
   from sourceSets.main.allJava
-  classifier = 'sources'
+  archiveClassifier = 'sources'
 }
 
 // for some reason this block generates empty Javadoc
@@ -198,7 +198,7 @@ javadoc {
 }
 
 task mockJavadocJar(type: Jar) {
-  classifier = 'javadoc'
+  archiveClassifier = 'javadoc'
   from javadoc.destinationDir
 }
 
@@ -212,8 +212,8 @@ publishing {
 
       // 1. coordinates (parameterized)
 
-      groupId publishGroupId
-      artifactId publishArtifactId
+      groupId = publishGroupId
+      artifactId = publishArtifactId
 
       // version defined globally
 
@@ -271,4 +271,4 @@ if (project.hasProperty("signingKey")) {
   }
 }
 
-tasks.publishToMavenLocal.dependsOn(check, integrationTest)
+tasks.publishToMavenLocal.dependsOn(check, integrationTest)

agent/src/main/java/com/appland/appmap/Agent.java

@@ -72,8 +72,11 @@ public static void premain(String agentArgs, Instrumentation inst) {
     logger.info("Agent version {}, current time mills: {}",
             implementationVersion, start);
     logger.info("config: {}", AppMapConfig.get());
-    logger.info("System properties: {}", System.getProperties());
-    logger.debug(new Exception(), "whereAmI");
+    logger.debug("System properties: {}", System.getProperties());
+
+    if (Agent.class.getClassLoader() == null) {
+      logger.warn("AppMap agent is running on the bootstrap classpath. This is not a recommended configuration and should only be used for troubleshooting. Git integration will be disabled.");
+    }
 
     addAgentJars(agentArgs, inst);
 
@@ -163,12 +166,18 @@ private static void addAgentJars(String agentArgs, Instrumentation inst) {
     Path agentJarPath = null;
     try {
       Class<Agent> agentClass = Agent.class;
-      URL resourceURL = agentClass.getClassLoader()
-          .getResource(agentClass.getName().replace('.', '/') + ".class");
+      // When the agent is loaded by the bootstrap class loader (e.g., via -Xbootclasspath/a:),
+      // agentClass.getClassLoader() returns null, leading to a NullPointerException. To handle
+      // this, we use Class.getResource() which correctly resolves resources even when the
+      // class is loaded by the bootstrap class loader. The leading '/' in the resource name
+      // is crucial for absolute path resolution when using Class.getResource().
+      URL resourceURL = agentClass.getResource("/" + agentClass.getName().replace('.', '/') + ".class");
+
       // During testing of the agent itself, classes get loaded from a directory, and will have the
       // protocol "file". The rest of the time (i.e. when it's actually deployed), they'll always
-      // come from a jar file.
-      if (resourceURL.getProtocol().equals("jar")) {
+      // come from a jar file. We must also check that resourceURL is not null before using it,
+      // as getResource() can return null if the resource is not found.
+      if (resourceURL != null && resourceURL.getProtocol().equals("jar")) {
         String resourcePath = resourceURL.getPath();
         URL jarURL = new URL(resourcePath.substring(0, resourcePath.indexOf('!')));
         logger.debug("jarURL: {}", jarURL);
@@ -214,13 +223,14 @@ private static void setupRuntime(Path agentJarPath, JarFile agentJar, Instrument
       System.exit(1);
     }
 
-    // Adding the runtime jar to the boot class loader means the classes it
-    // contains will be available everywhere. This avoids issues caused by any
-    // filtering the app's class loader might be doing (e.g. the Scala runtime
-    // when running a Play app).
+    // It's critical to append the runtime JAR to the bootstrap class loader
+    // search path, not the system class loader search path. This ensures that
+    // AppMap's core runtime classes, such as HookFunctions, are available to
+    // all application classes, including those loaded by different class loaders
+    // (e.g., in web servers like Tomcat or other complex environments), which
+    // fixes `NoClassDefFoundError` for `HookFunctions`.
     JarFile runtimeJar = new JarFile(runtimeJarPath.toFile());
-    inst.appendToSystemClassLoaderSearch(runtimeJar);
-    // inst.appendToBootstrapClassLoaderSearch(runtimeJar);
+    inst.appendToBootstrapClassLoaderSearch(runtimeJar);
 
     // HookFunctions can only be referenced after the runtime jar has been
     // appended to the boot class loader.