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PathwayCommons / factoid-converters

Web services for Factoid project to convert between JSON, BioPAX, SBGN data formats
http://biopax.baderlab.org/factoid-converters/
MIT License
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Failing tests (x-to-SBGN) for certain Java versions #32

Closed jvwong closed 1 year ago

jvwong commented 1 year ago

Initial observation is that two of the factoid.web -> ControllerT -> testXToSbgn tests are failing, blocking gradle builds.

I could get the tests passing with openjdk13 with some warnings, but not 8, 11, 17 and our github actions specifies 8, 11 so now any recent builds fail. The relevant error I've pasted below: 

java.security.PrivilegedActionException: null.
...
Caused by: java.lang.NoSuchMethodException: sun.misc.Unsafe.defineClass...

Some discussions suggest adding org.glassfish.jaxb:jaxb-runtime which seemed to allow the tests to pass.

jvwong commented 1 year ago

The gradle.build has org.biopax.paxtools:sbgn-converter:5.2.1-SNAPSHOT

The GitHub Actions workflow (daily?) cron paused itself about 11 months ago because of inactivity. The Docker image we use was built >1 year ago, and it seems OK as it uses openjdk-13-alpine.

IgorRodchenkov commented 1 year ago

Which branch shall we work in? Does that "unstable" branch still make any sense?..

IgorRodchenkov commented 1 year ago

We should require min java 11 and build only with jdk19 these days (some dependencies are old, needs work).

jvwong commented 1 year ago

Which branch shall we work in? Does that "unstable" branch still make any sense?..

No idea what's in those branches - @metincansiper ?

metincansiper commented 1 year ago

There are some changes in unstable branch that we may consider merging into master branch later. I think you can work in master branch for the time being.

IgorRodchenkov commented 1 year ago

I fixed in master (not sure what other branches do...)