Integration test for extract subset failing in CI

[jamesaoverton]

See #1104 and recent Action results. The integration test here docs/extract.md#subset always passes for me locally, but it's failing 90% of the time on my runs for #1104. I really don't get it. I saw a "zio-fiber" error (?) in relationgraph on one run, but I can't find that message now.

Any ideas?

[jamesaoverton]

I saw that zio error again, this time in a unit test:

testExtractSubset(org.obolibrary.robot.ExtractOperationTest)  Time elapsed: 0.598 sec  <<< ERROR!
Error: Exception in thread "zio-fiber-19" java.lang.InterruptedException: Interrupted by thread "zio-fiber-19"
	at org.renci.relationgraph.RelationGraph.processRestrictionAndExtendQueue(RelationGraph.scala:131)
	at org.renci.relationgraph.RelationGraph.computeRelations.streamZ(RelationGraph.scala:75)

Full logs here: https://github.com/ontodev/robot/actions/runs/7033595317/attempts/1

Any ideas @balhoff?

[balhoff]

@jamesaoverton zio is a concurrency framework I use in relation-graph. But I'm not sure how to debug this; it seems to work fine locally. I don't see errors in the logs you linked.

[jamesaoverton]

@balhoff I fixed my link to point to the first attempt of that run, which failed. I just re-ran it and then it worked.

Yes this is hard to debug, but also really disruptive to development workflows.

[jamesaoverton]

This issue is breaking CI for another (unrelated) PR: https://github.com/ontodev/robot/actions/runs/7107481969/job/19348979228#step:5:21700

I need a solution for this. The best I've got right now is to disable the test, which sucks.

[jamesaoverton]

Hopefully closed by #1174

[jamesaoverton]

I think this is still a problem. A large percentage of my CI runs have been failing, e.g. https://github.com/ontodev/robot/actions/runs/22157649265/job/64065844347#step:5:12256

I never see the problem locally.

Error:  Errors: 
Error:    ExtractOperationTest.testExtractSubset:175 » Interrupted

[jamesaoverton]

@balhoff Can you take another look at this when you have a minute? I'm not sure what the problem is.

[balhoff]

@jamesaoverton I'm trying something in relation-graph. Hopefully I'll come back soon with a solution.