Replicating a java -jar execution through rJava - r

Question

I have a java file that I would normally execute by doing
java -jar jarname.jar arguments
I want to be able to run this file from R in the most system agnostic way possible. My current pipeline partially relies on rJava do identify JAVA_HOME and run the jar by doing
# path for the example file below
pathToJar = 'pdftk-java.jar'
# start up java session
rJava::.jinit()
# find JAVA_HOME
javaPath = rJava::.jcall( 'java/lang/System', 'S', 'getProperty', 'java.home' )
# get all java files
javaFiles = list.files(javaPath,recursive = TRUE,full.names = TRUE)
# find java command
java = javaFiles[grepl('/java($|\\.exe)',javaFiles)]
# run the jar using system
system(glue::glue('{shQuote(java)} -jar {shQuote(pathToJar)} arguments'))
This does work fine but I was wondering if there was a reliable way to replicate execution of a jar through rJava itself. I want to do this because
I want to avoid any possible system dependent issues when finding the java command from JAVA_HOME
I already started an rJava session just to get the JAVA_HOME. I might as well use it since .jinit isn't undoable
I not that familiar with what calling a jar through -jar does and I am curious. Can it be done in a jar independent way? If not what should I look for in the code to know how to do this.
This is the file in I am working with. Taken from https://gitlab.com/pdftk-java/pdftk/tree/master

Answer 1

Executing JAR file is (essentially) running class file that is embedded inside JAR.
Instead of calling system and executing it as external application, you can do following:
make sure to add your JAR file to CLASSPATH
rJava::.jaddClassPath(pathToJar)
check inside JAR file what is the main class. Look into META-INF/MANIFEST.MF file to identify the main class. (In this case com.gitlab.pdftk_java.pdftk)
instantiate class inside R.
newObj = rJava::.jnew('com/gitlab/pdftk_java/pdftk')
run the class following way: http://www.owsiak.org/running-java-code-in-r/
Update
Running JAR file (calling main method of Main-class) is the same things as calling any other method inside Java based class. Please note that main method takes array of Strings as argument. Take a look here for sample: http://www.owsiak.org/running-jar-file-from-r-using-rjava-without-spawning-new-process/
newObj$main(rJava::.jarray('--version'))
For this specific case if you look at the source code for this class, you'll see that it terminates the session
public static void main(String[] args) {
System.exit(main_noexit(args));
}
This will also terminate your R session. Since all main function does it to call main_noexit then exit, you can replace main with main_noexit in the code above.
newObj$main_noexit(rJava::.jarray('--version'))