User JAR file path cannot be added to a custom classpath

[pditommaso]

maven caplet should allow users to include their own jars to the classpath overriding the attribute method.

Currently the sanitize method does not allow that and raises the following exception:

CAPSULE EXCEPTION: Could not resolve item /Users/pditommaso/workspace/nextflow/gradle/wrapper/gradle-wrapper.jar
java.lang.RuntimeException: Could not resolve item /Users/pditommaso/workspace/nextflow/gradle/wrapper/gradle-wrapper.jar
    at Capsule.resolve(Capsule.java:2781)
    at Capsule.buildClassPath(Capsule.java:1858)
    at Capsule.buildJavaProcess(Capsule.java:1744)
    at Capsule.buildProcess0(Capsule.java:1273)
    at Capsule.buildProcess(Capsule.java:1264)
    at Capsule.buildProcess(Capsule.java:1264)
    at Capsule.buildProcess(Capsule.java:1264)
    at Capsule.prelaunch0(Capsule.java:1237)
    at Capsule.prelaunch(Capsule.java:1232)
    at CapsuleLoader.prelaunch(CapsuleLoader.java:45)
    at Capsule.prepareForLaunch(Capsule.java:1146)
    at Capsule.launch(Capsule.java:1091)
    at Capsule.main0(Capsule.java:332)
    at Capsule.main(Capsule.java:311)
Caused by: java.lang.IllegalArgumentException: Path /Users/pditommaso/workspace/nextflow/gradle/wrapper/gradle-wrapper.jar is not local to app cache /Users/pditommaso/.nextflow/capsule/apps/nextflow_0.13.0-SNAPSHOT
    at Capsule.sanitize(Capsule.java:3003)
    at Capsule.resolve(Capsule.java:2768)
    ... 13 more
Unable to initialize nextflow environment

https://groups.google.com/d/msg/capsule-user/1kkx8-Y58R0/E95C17QL4ZoJ

[danthegoodman]

@pron I would like to point out that both paolo and myself have created custom capsules to add to the classpath after a capsule has been created via environment variables or system properties. We use ours to add logging dependencies after capsule creation, and I feel like this is a common enough use case to warrant including it in the core capsule functionality.

That said, would you rather this stay external as custom capsules? Or do you agree with me?

[pron]

Well, I'm not 100% convinced, and when in doubt -- leave it out! (We can always add it later, but taking things out after a 1.0 release is not as simple).

In fact, as you can probably tell, the trend is to remove as much as possible from the core to caplets (I've removed all the Maven stuff). I even entertained the notion of moving all the JVM specific code (classpath etc.) to a caplet (so that core Capsule will just support attributes and buildProcess etc.), but thought that would be too much, as I don't expect people to use Caplet for non-JVM programs...

[danthegoodman]

Sounds good to me 👍

[pditommaso]

Is there a release or a snapshot including this patch?

[pditommaso]

OK. I suppose it's included in the release 1.0-rc2-SNAPSHOT

[pron]

Yep. Note that there will be no 1.0-rc1 release. We will release 1.0 in a couple of weeks.