stack overflow when validating data

[balhoff]

When attempting to validate certain data files, I get a java.lang.StackOverflowError:

Exception in thread "main" java.lang.StackOverflowError
	at cats.data.KleisliFunctions.$anonfun$pure$1(Kleisli.scala:168)
	at cats.data.Kleisli.$anonfun$map$1(Kleisli.scala:19)
	at cats.data.Kleisli.$anonfun$flatMap$1(Kleisli.scala:31)
	at cats.package$$anon$1.flatMap(package.scala:41)
	at cats.data.Kleisli$.$anonfun$shift$1(Kleisli.scala:112)
	at cats.data.Kleisli.$anonfun$flatMap$2(Kleisli.scala:31)
	at cats.package$$anon$1.flatMap(package.scala:41)
	at cats.data.Kleisli.$anonfun$flatMap$1(Kleisli.scala:31)
	at cats.package$$anon$1.flatMap(package.scala:41)
	at cats.data.Kleisli$.$anonfun$shift$1(Kleisli.scala:112)
	at cats.data.Kleisli.$anonfun$flatMap$1(Kleisli.scala:31)
	at cats.package$$anon$1.flatMap(package.scala:41)
(truncated)

The command I am running is:

shaclex --schema go-cam-shapes.shex --schemaFormat SHEXC --shapeMap go-cam-shapes.shapeMap --data Test000-Correct_and_complete_ActivityUnit_model-enriched.ttl --trigger SHAPEMAP --outFile out.shapeMap

The input files are here:

• https://github.com/geneontology/go-shapes/blob/stack-overflow/shapes/go-cam-shapes.shex
• https://github.com/geneontology/go-shapes/blob/stack-overflow/shapes/go-cam-shapes.shapeMap
• https://github.com/geneontology/go-shapes/blob/stack-overflow/scala/test/should_pass/Test000-Correct_and_complete_ActivityUnit_model-enriched.ttl

I am using shaclex built from 83eeedb.

[balhoff]

If I increase the stack size (JAVA_OPTS="-Xmx6G -Xss32m"), I eventually use up the heap instead: java.lang.OutOfMemoryError: GC overhead limit exceeded.

[labra]

Thanks for the report. I reproduced it in my computer and will try to solve it.

By the way, looking at how you use shape maps with SPARQL selectors, I think we should extend them to be able to define prefix declarations. I raised another issue to the spec about that:.

[labra]

I tried the example with the new optimization (#133), and now it works. I published a new release called 0.1.24 which contains that optimization.

[balhoff]

Thanks for the quick fix! I will try it out next week.

[balhoff]

This is working great now, thank you.