JaCoCo Demo Application

This application is to exemplify some issues with JaCoCo and Spring Boot Uber JARs

Steps to reproduce

• JaCoCo version: 0.8.5
• Operating system: Windows
• Tool integration: Agent / CLI
• Complete executable reproducer: https://github.com/tomcruise81/jacoco-demo.git
• Steps: (what exactly are you doing with the above reproducer?)

  git clone https://github.com/tomcruise81/jacoco-demo.git
  cd jacoco-demo
  mvn package
  targetJar=$(ls target/*.jar | sed 's|target/||')
  
  # For Windows, under Git Bash, you may also need to convert Cygwin-type paths to Windows paths
  curDir=$(pwd)
  unameOut="$(uname -s)"
  case "${unameOut}" in
      CYGWIN*)    ;&
      MINGW*)     curDir=$(cygpath -m ${curDir});;
  esac
  
  # Download the appropriate JaCoCo JARs
  curl -k -L https://search.maven.org/remotecontent?filepath=org/jacoco/org.jacoco.cli/0.8.5/org.jacoco.cli-0.8.5-nodeps.jar -o ${curDir}/jacoco-cli.jar
  curl -k -L https://search.maven.org/remotecontent?filepath=org/jacoco/org.jacoco.agent/0.8.5/org.jacoco.agent-0.8.5-runtime.jar -o ${curDir}/jacoco-agent-runtime.jar
  
  # Run JaCoCo
  java -jar ${curDir}/jacoco-cli.jar instrument ${curDir}/target/${targetJar} --dest ${curDir}/instrumented
  java -javaagent:${curDir}/jacoco-agent-runtime.jar=destfile=${curDir}/jacoco.exec,excludes=*,output=file,dumponexit=true -jar ${curDir}/instrumented/${targetJar}

Expected behavior

My expectation is that the pre-instrumented Uber JAR should continue to be runnable and running it with the javaagent enabled should allow code coverage output.

I've had to go about it this way instead of just running the main Uber JAR with the javaagent due to the output of just running with the javaagent being unusable:

java -javaagent:${curDir}/jacoco-agent-runtime.jar=destfile=${curDir}/jacoco.exec,excludes=*,output=file,dumponexit=true -jar ${curDir}/target/${targetJar}
java -jar ${curDir}/jacoco-cli.jar report jacoco.exec --classfiles=${curDir}/target/${targetJar} --html ${curDir}/coverage-html

resulting in:

[INFO] Loading execution data file C:\test\jacoco-demo\jacoco.exec.
Exception in thread "main" java.io.IOException: Error while analyzing C:\test\jacoco-demo\target\jacoco-demo-0.0.1-SNAPSHOT.jar@BOOT-INF/lib/log4j-api-2.12.1.jar@org/apache/logging/log4j/util/Base64Util.class.
        at org.jacoco.cli.internal.core.analysis.Analyzer.analyzerError(Analyzer.java:162)
        at org.jacoco.cli.internal.core.analysis.Analyzer.analyzeClass(Analyzer.java:134)
        at org.jacoco.cli.internal.core.analysis.Analyzer.analyzeClass(Analyzer.java:157)
        at org.jacoco.cli.internal.core.analysis.Analyzer.analyzeAll(Analyzer.java:193)
        at org.jacoco.cli.internal.core.analysis.Analyzer.analyzeZip(Analyzer.java:265)
        at org.jacoco.cli.internal.core.analysis.Analyzer.analyzeAll(Analyzer.java:196)
        at org.jacoco.cli.internal.core.analysis.Analyzer.analyzeZip(Analyzer.java:265)
        at org.jacoco.cli.internal.core.analysis.Analyzer.analyzeAll(Analyzer.java:196)
        at org.jacoco.cli.internal.core.analysis.Analyzer.analyzeAll(Analyzer.java:226)
        at org.jacoco.cli.internal.commands.Report.analyze(Report.java:110)
        at org.jacoco.cli.internal.commands.Report.execute(Report.java:84)
        at org.jacoco.cli.internal.Main.execute(Main.java:90)
        at org.jacoco.cli.internal.Main.main(Main.java:105)
Caused by: java.lang.IllegalStateException: Can't add different class with same name: org/apache/logging/log4j/util/Base64Util
        at org.jacoco.cli.internal.core.analysis.CoverageBuilder.visitCoverage(CoverageBuilder.java:106)
        at org.jacoco.cli.internal.core.analysis.Analyzer$1.visitEnd(Analyzer.java:99)
        at org.jacoco.cli.internal.asm.ClassVisitor.visitEnd(ClassVisitor.java:326)
        at org.jacoco.cli.internal.core.internal.flow.ClassProbesAdapter.visitEnd(ClassProbesAdapter.java:100)
        at org.jacoco.cli.internal.asm.ClassReader.accept(ClassReader.java:692)
        at org.jacoco.cli.internal.asm.ClassReader.accept(ClassReader.java:400)
        at org.jacoco.cli.internal.core.analysis.Analyzer.analyzeClass(Analyzer.java:116)
        at org.jacoco.cli.internal.core.analysis.Analyzer.analyzeClass(Analyzer.java:132)
        ... 11 more

Actual behavior

java -javaagent:${curDir}/jacoco-agent-runtime.jar=destfile=${curDir}/jacoco.exec,excludes=*,output=file,dumponexit=true -jar ${curDir}/instrumented/${targetJar}
Exception in thread "main" java.lang.IllegalStateException: Failed to get nested archive for entry BOOT-INF/lib/spring-boot-starter-actuator-2.2.4.RELEASE.jar
        at org.springframework.boot.loader.archive.JarFileArchive.getNestedArchive(JarFileArchive.java:113)
        at org.springframework.boot.loader.archive.JarFileArchive.getNestedArchives(JarFileArchive.java:87)
        at org.springframework.boot.loader.ExecutableArchiveLauncher.getClassPathArchives(ExecutableArchiveLauncher.java:69)
        at org.springframework.boot.loader.Launcher.launch(Launcher.java:50)
        at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:52)
Caused by: java.io.IOException: Unable to open nested jar file 'BOOT-INF/lib/spring-boot-starter-actuator-2.2.4.RELEASE.jar'
        at org.springframework.boot.loader.jar.JarFile.getNestedJarFile(JarFile.java:261)
        at org.springframework.boot.loader.jar.JarFile.getNestedJarFile(JarFile.java:247)
        at org.springframework.boot.loader.archive.JarFileArchive.getNestedArchive(JarFileArchive.java:109)
        ... 4 more
Caused by: java.lang.IllegalStateException: Unable to open nested entry 'BOOT-INF/lib/spring-boot-starter-actuator-2.2.4.RELEASE.jar'. It has
been compressed and nested jar files must be stored without compression. Please check the mechanism used to create your executable jar file
        at org.springframework.boot.loader.jar.JarFile.createJarFileFromFileEntry(JarFile.java:287)
        at org.springframework.boot.loader.jar.JarFile.createJarFileFromEntry(JarFile.java:269)
        at org.springframework.boot.loader.jar.JarFile.getNestedJarFile(JarFile.java:258)
        ... 6 more

Possible solution

git clone https://github.com/tomcruise81/jacoco-demo.git
cd jacoco-demo

# Download the appropriate JaCoCo JARs
curl -k -L https://search.maven.org/remotecontent?filepath=org/jacoco/org.jacoco.cli/0.8.5/org.jacoco.cli-0.8.5-nodeps.jar -o ${curDir}/jacoco-cli.jar
curl -k -L https://search.maven.org/remotecontent?filepath=org/jacoco/org.jacoco.agent/0.8.5/org.jacoco.agent-0.8.5-runtime.jar -o ${curDir}/jacoco-agent-runtime.jar

# For Windows, under Git Bash, you may also need to convert Cygwin-type paths to Windows paths
curDir=$(pwd)
unameOut="$(uname -s)"
case "${unameOut}" in
    CYGWIN*)    ;&
    MINGW*)     curDir=$(cygpath -m ${curDir});;
esac

# Package the runnable JAR
mvn clean package
uberJar=$(ls target/*.jar | sed 's|target/||')
uberJar=${curDir}/target/${uberJar}

# Package the sources JAR
mvn source:jar
sourcesJar=$(ls target/*-sources.jar | sed 's|target/||')
sourcesJar=${curDir}/target/${sourcesJar}

################################################################
# The purpose of this repo is to determine how to instrument a
# pre-existing Spring Boot Uber JAR. So the setup above is just
# to create the artifacts that are expected to be available for
# this use-case.
################################################################

# Determine the includes list; the sources JAR includes all expected source files, and their corresponding packages
# Instead of including every source file, just include their respective packages
includes=$(zipinfo -2 ${sourcesJar} -x META-INF/** | grep -E '*.java' | awk -F/ 'BEGIN { OFS = FS }; NF { NF -= 1 }; 1' | uniq | sed 's|/|.|g' | awk -v suffix=".*" '{print $0 suffix}' | paste -sd ":" -)

# Run JaCoCo
rm -f jacoco.exec
java -javaagent:${curDir}/jacoco-agent-runtime.jar=destfile=${curDir}/jacoco.exec,includes=${includes},output=file,dumponexit=true -jar ${uberJar}
# The following blows up with "java.lang.IllegalStateException: Can't add different class with same name:..."
# java -jar ${curDir}/jacoco-cli.jar report jacoco.exec --classfiles=${uberJar} --html ${curDir}/coverage-html

# Extract the Uber JAR and explicitly determine which class files to report on as per the includes list (i.e. source packages)
tempClassfilesDir=$(mktemp -d)
unzip ${uberJar} -d ${tempClassfilesDir}
includesFilter=$(echo ${includes} | sed 's/:/|/g')
classfiles=$(zipinfo -2 ${uberJar} | grep -E ${includesFilter} | grep -E '*\.class' | awk -F/ 'BEGIN { OFS = FS }; NF { NF -= 1 }; 1' | uniq | awk -v prefix="--classfiles=${tempClassfilesDir}/" -v suffix="/" '{print prefix $0 suffix}' | paste -sd " " -)

# Extract the source JAR so that source files can be linked during reporting
tempSourcefilesDir=$(mktemp -d)
unzip ${sourcesJar} -d ${tempSourcefilesDir}

# Do the actual reporting
htmlCoverageDir=${curDir}/reports/coverage-html
rm -rf ${htmlCoverageDir}
java -jar ${curDir}/jacoco-cli.jar report jacoco.exec ${classfiles} --sourcefiles=${tempSourcefilesDir} --html ${htmlCoverageDir}

# Cleanup
rm -rf ${tempSourcefilesDir}
rm -rf ${tempClassfilesDir}