JAXB problems in Java 9

[johngrimes]

There appears to be some problems with JAXB in Java 9.

Take a look at these CI build results, which contains the results of trying to validate a resource using the hapi-fhir-cli on Mac OS X with Java 9:

https://jenkins.brew.sh/job/Homebrew%20Core%20Pull%20Requests/17367/

I did a bit of Googling, and found that these APIs may have now been moved to Java EE, and the fix may be to include them as explicit dependencies.

https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j

[jamesagnew]

Hi @johngrimes ,

I'm definitely not opposed to fixing this by adding the dependencies they suggest... but I'm actually confused at why this is even an issue. As far as I know we have nothing in the tool that uses JAXB.

Is there a stack trace or any kind of error being outputted that hints at where JAXB is getting used?

BTW- this is super cool. I'm a Homebrew user myself and I had no idea you had created a cask for the CLI. :) Any objections if I link to it from the HAPI FHIR website?

[johngrimes]

Well, hopefully I can decommission my repo shortly. Once we fix this error, the pull request to have it merged into hombrew-core should be accepted, and people will be able to brew install hapi-fhir-cli without the brew tap johngrimes/hapi-fhir-cli step.

Here is the stack trace:

Testing hapi-fhir-cli
/usr/bin/sandbox-exec -f /tmp/homebrew20180128-96235-1xoaicq.sb /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby -W0 -I /usr/local/Homebrew/Library/Homebrew -- /usr/local/Homebrew/Library/Homebrew/test.rb /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/hapi-fhir-cli.rb --verbose
==> /usr/local/Cellar/hapi-fhir-cli/3.2.0/bin/hapi-fhir-cli validate -n /tmp/hapi-fhir-cli-test-20180128-96236-xv7z18/TestResource.json
Picked up _JAVA_OPTIONS:  -Duser.home=/Users/brew/Library/Caches/Homebrew/java_cache
------------------------------------------------------------
? HAPI FHIR 3.2.0 - Command Line Tool
------------------------------------------------------------
Max configured JVM memory (Xmx): 1.8GB
Detected Java version: 9.0.1
------------------------------------------------------------
02:38:24 INFO  ca.uhn.fhir.cli.ValidateCommand - Reading file '/tmp/hapi-fhir-cli-test-20180128-96236-xv7z18/TestResource.json' using encoding UTF-8
02:38:24 INFO  ca.uhn.fhir.cli.ValidateCommand - Fully read - Size is 5KB
02:38:24 INFO  ca.uhn.fhir.context.FhirContext - Creating new FHIR context for FHIR version [DSTU3]
02:38:26 INFO  ca.uhn.fhir.util.XmlUtil - FHIR XML procesing will use StAX implementation 'null' version 'null'
02:38:26 WARN  c.u.fhir.parser.LenientErrorHandler - Unknown element 'comment' found while parsing
Exception in thread "main" java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
	at com.phloc.schematron.svrl.SVRLReader.readXML(SVRLReader.java:73)
	at com.phloc.schematron.xslt.AbstractSchematronXSLTResource.applySchematronValidationToSVRL(AbstractSchematronXSLTResource.java:171)
	at com.phloc.schematron.SchematronHelper.applySchematron(SchematronHelper.java:126)
	at ca.uhn.fhir.validation.schematron.SchematronBaseValidator.validateResource(SchematronBaseValidator.java:79)
	at ca.uhn.fhir.validation.FhirValidator.validateWithResult(FhirValidator.java:231)
	at ca.uhn.fhir.cli.ValidateCommand.run(ValidateCommand.java:135)
	at ca.uhn.fhir.cli.App.main(App.java:189)
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.JAXBException
	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
	at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:185)
	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:496)
	... 7 more
Error: hapi-fhir-cli: failed
Failed executing: /usr/local/Cellar/hapi-fhir-cli/3.2.0/bin/hapi-fhir-cli validate -n /tmp/hapi-fhir-cli-test-20180128-96236-xv7z18/TestResource.json
/usr/local/Homebrew/Library/Homebrew/formula.rb:1792:in `block in system'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1730:in `open'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1730:in `system'
/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/hapi-fhir-cli.rb:157:in `block in <class:HapiFhirCli>'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1636:in `block (3 levels) in run_test'
/usr/local/Homebrew/Library/Homebrew/utils.rb:549:in `with_env'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1635:in `block (2 levels) in run_test'
/usr/local/Homebrew/Library/Homebrew/formula.rb:835:in `with_logging'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1634:in `block in run_test'
/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:14:in `block in mktemp'
/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:74:in `block in run'
/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:74:in `chdir'
/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:74:in `run'
/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:13:in `mktemp'
/usr/local/Homebrew/Library/Homebrew/formula.rb:1628:in `run_test'
/usr/local/Homebrew/Library/Homebrew/test.rb:28:in `block in <main>'
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/timeout.rb:91:in `block in timeout'
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/timeout.rb:33:in `block in catch'
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/timeout.rb:33:in `catch'
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/timeout.rb:33:in `catch'
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/timeout.rb:106:in `timeout'
/usr/local/Homebrew/Library/Homebrew/test.rb:27:in `<main>'

[jamesagnew]

Ahhhh, it's Phloc's fault. Well then. :)

Fix incoming.