Today's Status:

• Installed required files to update the system to use Java 12.
• Trying to solve errors that occurring during the IGB build process. (i.e. Attempt to compile the entire project)

Update:
Shamika Gajanan Kulkarni, Jay Chamma and I were trying to build the IGB but the build was failing for Heatmap module and build for other modules after that was skipped. We are facing this exception:
An exception has occurred in the compiler (1.8.0-internal_bootstrap). Please file a bug at the Java Developer Connection (http://java.sun.com/webapps/bugreport) after checking the Bug Parade for duplicates. Include your program and the following diagnostic in your report. Thank you.
java.lang.NullPointerException
at com.sun.tools.javac.file.Locations.getPathEntries(Locations.java:149)
at com.sun.tools.javac.file.Locations.getPathEntries(Locations.java:134)
at com.sun.tools.javac.file.Locations.access$000(Locations.java:71)
at com.sun.tools.javac.file.Locations$BootClassPathLocationHandler.computePath(Locations.java:617)
at com.sun.tools.javac.file.Locations$BootClassPathLocationHandler.lazy(Locations.java:643)
at com.sun.tools.javac.file.Locations$BootClassPathLocationHandler.getLocation(Locations.java:577)
at com.sun.tools.javac.file.Locations.getLocation(Locations.java:678)
at com.sun.tools.javac.file.JavacFileManager.getLocation(JavacFileManager.java:803)
at com.sun.tools.javac.file.JavacFileManager.list(JavacFileManager.java:617)
at com.sun.tools.javac.jvm.ClassReader.fillIn(ClassReader.java:2747)
at com.sun.tools.javac.jvm.ClassReader.complete(ClassReader.java:2444)
at com.sun.tools.javac.jvm.ClassReader.access$000(ClassReader.java:76)
at com.sun.tools.javac.jvm.ClassReader$1.complete(ClassReader.java:240)
at com.sun.tools.javac.code.Symbol.complete(Symbol.java:574)
at com.sun.tools.javac.comp.Enter.visitTopLevel(Enter.java:300)
at com.sun.tools.javac.tree.JCTree$JCCompilationUnit.accept(JCTree.java:518)
at com.sun.tools.javac.comp.Enter.classEnter(Enter.java:258)
at com.sun.tools.javac.comp.Enter.classEnter(Enter.java:272)
at com.sun.tools.javac.comp.Enter.complete(Enter.java:486)
at com.sun.tools.javac.comp.Enter.main(Enter.java:471)
at com.sun.tools.javac.main.JavaCompiler.enterTrees(JavaCompiler.java:982)
at com.sun.tools.javac.main.JavaCompiler.compile(JavaCompiler.java:855)
at com.sun.tools.javac.main.Main.compile(Main.java:523)
at com.sun.tools.javac.main.Main.compile(Main.java:381)
at com.sun.tools.javac.main.Main.compile(Main.java:370)
at com.google.errorprone.ErrorProneCompiler.run(ErrorProneCompiler.java:220)
at com.google.errorprone.ErrorProneCompiler.run(ErrorProneCompiler.java:158)
at com.google.errorprone.ErrorProneCompiler.compile(ErrorProneCompiler.java:87)
at org.codehaus.plexus.compiler.javac.errorprone.JavacCompilerWithErrorProne$CompilerInvoker.compile(JavacCompilerWithErrorProne.java:219)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:567)
at org.codehaus.plexus.compiler.javac.errorprone.JavacCompilerWithErrorProne.performCompile(JavacCompilerWithErrorProne.java:91)
at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:1134)
at org.apache.maven.plugin.compiler.CompilerMojo.execute(CompilerMojo.java:187)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:137)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:210)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:156)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:148)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:117)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:81)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:56)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:305)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:192)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:105)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:956)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:192)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:567)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:282)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:225)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:406)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:347)

When we tried to search for solutions, we found out https://bugs.openjdk.java.net/browse/JDK-8199449 link which says the exception is because of multiple JDK versions on the system. Jay Chamma had multiple versions on his system. Whereas, my system doesn't have any other version of JDK than JDK 12.0.2 still the build process was throwing the same exception for me. We are still trying to dig deeper on that part. Meanwhile, Dr. [~aloraine] if you have any suggestions for us then please let us know.

Suggestions:

• Inspect the POM for the heatmap module. Check to see if it "hard-codes" the JDK to be used during compilation.
• Check to see if other modules can build. Due to how the application is structured, you may be able to remove heatmap module from the application simply by commenting it out - it depends on which other modules are depending on it. Removing the heatmap module and then attempting to build the application may help determine if you are running into a heatmap module-specific problem or if the same problem would be encountered elsewhere.

attn: Prutha Kulkarni, Jay Chamma, Shamika Gajanan Kulkarni

Dr. [~aloraine], we tried out your suggestion but it looks like the problem is not plugin specific.
We are now trying to check if there is a way to change

<code:xml>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
</code>

these versions to use the latest version. When we tried to change it directly to the latest version it is saying:
javac (with error-prone): invalid target release: 12.0.2
Usage: javac (with error-prone) <options> <source files>

We are trying to find a solution for this error now.

Helpful link:
https://maven.apache.org/plugins/maven-compiler-plugin/examples/set-compiler-source-and-target.html

Please read "NOTE" part when you visit the link. It says:
Note: Merely setting the target option does not guarantee that your code actually runs on a JRE with the specified version. The pitfall is unintended usage of APIs that only exist in later JREs which would make your code fail at runtime with a linkage error. To avoid this issue, you can either configure the compiler's boot classpath to match the target JRE or use the Animal Sniffer Maven Plugin to verify your code doesn't use unintended APIs. In the same way, setting the source option does not guarantee that your code actually compiles on a JDK with the specified version. To compile your code with a specific JDK version, different than the one used to launch Maven, refer to the Compile Using A Different JDK example.

cc: Jay Chamma, Shamika Gajanan Kulkarni

Compile using a different JDK:
https://maven.apache.org/plugins/maven-compiler-plugin/examples/compile-using-different-jdk.html
NOTE: You can find the settings.xml on the local maven repository on your system which is .m2 directory. If its not there then your can create a new one.

Animal Sniffer Plugin:
http://www.mojohaus.org/animal-sniffer/animal-sniffer-maven-plugin/

cc: Shamika Gajanan Kulkarni, Jay Chamma

Findings:
I tried to use maven toolchain plugin which lets you specify any jdk version which you would want to use in order to compile the code.
links:
https://maven.apache.org/guides/mini/guide-using-toolchains.html#:~:text=The%20maven%2Dtoolchains%2Dplugin%20is,as%20shown%20in%20the%20pom.
https://www.baeldung.com/maven-java-version

after making changes to the main POM in order to configure the compiler settings, I was getting javac: invalid flag: --release
I found a link which tells you to provide jdk folder path to the toolchain plugin and not the bin folder path inside jdk folder.
https://stackoverflow.com/questions/53571709/maven-with-jdk11-javac-invalid-flag-release
I tried this out and still I was getting the same error.
I believe using maven toolchain plugin in order to run the code on java 12 is the best option as many people have multiple versions of jdk accidentally installed on their system while updating the java and not clicking on replace option. This way, people won't need to explicitly change their JAVA_HOME for IGB run specifically as we are going to be using toolchain configuration to let the compiler know which version to use for compilation. I will have to dig a little deeper on this tomorrow with the help of Jay Chamma or Shamika Gajanan Kulkarni or anybody if they are available.

A quick follow-up:

• The IGB installer includes a copy of the JRE and JDK, thus ensuring that IGB can run no matter what java version the user has previously installed on their computer. This IGB-specific JRE is supposed to be contained in IGB's installation directory, ideally ensuring that no other applications will be affected.

Updates:

• Like I mentioned in the scrum meeting, we built JRE bundles for all OS.
• I uploaded those bundles into the downloads section of the "JRE Bundles Install4j" repo.
• Updated the docker file in order to build a new docker image which uses Java 12 configuration.
• Changed image in the pipeline configuration file of my branch.
• Tried to build the pipeline but still facing the same problem of compiler i.e. a NULLPointerException is getting thrown when we try to build the IGB.
  pipeline build failed three times:
  https://bitbucket.org/pkulka10/igb_prutha/addon/pipelines/home#!/

Next Steps:

• We might need to change the main POM.xml in order to configure maven compiler plugin to use latest jdk version so that it will use proper elements in order to run the IGB.
• Like I mentioned earlier, we might need to find an alternative using maven toolchain plugin on local system first and if it succeeds then we can replicate the same using docker.

NOTE: javaws i.e. java web start support is removed in java versions after the Java SE 11(18.9LTS) release:
https://askubuntu.com/questions/1137698/installing-java-web-start-java-12
that is why we had to comment out "update-alternatives --install "/usr/bin/javaws" "javaws" "/usr/lib/jvm/jdk/bin/javaws" 1 && \" line from the docker file after which the image built properly.

cc: [~aloraine], Shamika Gajanan Kulkarni, Noor Zahara

Updates:

• We tried changing the main POM in following ways:
  1. We added the maven toolchain plugin to use jdk 12
  2. We added a new profile inside the pom to use jdk 12
  3. Changed maven compiler configuration parameter settings to add desired version of the jdk.
  Still we are not able to compile the code as the build is still failing and again the problem is not module specific.
  instead of using

<maven.compiler.source>1.8</maven.compiler.source> 
<maven.compiler.target>1.8</maven.compiler.target>

in the pom, we need to add maven.compiler.release tag for java version 9+ but adding this doesn't resolve the problem and it again says invalid release tag. We seem to be stuck on this and don't know how to proceed. I really am sorry that I couldn't complete the investigation before the last day.
could you please guide the next person who picks this up by providing the next steps?
Thanks.

cc: [~aloraine], Shamika Gajanan Kulkarni

Thank you a thousand times for all the careful and thoughtful work you did, and the kindness you showed to everybody. Bon voyage Prutha Kulkarni!

Special thanks to you Dr. [~aloraine] for giving me an opportunity to work for the lab and for always being so supportive.