Closed enoriega closed 3 years ago
kwalcock
commented
3 years ago This stack trace is deceptive, probably because of the reflection involved. It is hiding an array index out of bounds exception which is thrown from LinguisticPolarityEngine line 46. At that point there is a sentence with a token interval [3, 29] but incoming edges only from [0, 28].
val prepc_byed = (evt.tokenInterval filter (tok => deps.getIncomingEdges(tok).map(_._2).contains("advcl_by"))).toSetThis may well have been fixed with https://github.com/clulab/processors/pull/428 which should be in processors 8.2.2, but that's exactly what is supposed to be being used...
MihaiSurdeanu
commented
3 years ago Indeed. This should be fixed there... @enoriega: if you can isolate this a sentence, I will debug this.
kwalcock
commented
3 years ago I know which sentence it is. Will report soon.
On Tue, Jan 5, 2021, 7:32 AM Mihai Surdeanu notifications@github.com wrote:
Indeed. This should be fixed there... @enoriega https://github.com/enoriega: if you can isolate this a sentence, I will debug this.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/clulab/reach/issues/718#issuecomment-754670696, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACCHCOUO5XYJHPNYD3XE54DSYMPGLANCNFSM4VRKD53A .
kwalcock
commented
3 years ago It is this sentence, which is almost the only one in the attached file:
This pleiotropic inflammatory cytokine is produced by T cells, monocytes, macrophages and synovial fibroblasts, and mediates various functions by binding to its receptor IL-6R ( 40 ).AFAICT, the problem is in the processors project, file CoreNLPProcessor.scala, around line 129-130, in which these lines do not pass in a preferredSize when they call CoreNLPUtils.toDirectedGraph, unlike the code in FastNLPProcessor, method parseWithStanford, which might be used as a template.
doc.sentences(offset).setDependencies(GraphMap.UNIVERSAL_BASIC, CoreNLPUtils.toDirectedGraph(basicDeps, in))
doc.sentences(offset).setDependencies(GraphMap.UNIVERSAL_ENHANCED, CoreNLPUtils.toDirectedGraph(enhancedDeps, in))Thanks! I'll take a look soon.
kwalcock
commented
3 years ago @enoriega's keen observational skills are greatly appreciated. Thanks for taking the time to report the problem.
MihaiSurdeanu
commented
3 years ago Solved in processors PR #439, which is in the process of being tested and then merged.
@enoriega: this means that you have to publishLocal processors 8.2.4-SNAPSHOT, and use this version in reach/processors/build.sbt.
MihaiSurdeanu
commented
3 years ago The processors PR has been merged.
kwalcock
commented
3 years ago This has likely been handled with https://github.com/clulab/processors/pull/439.
enoriega
commented
3 years ago I tested again with a freshly cloned processors version 8.2.4-SNAPSHOT and am still getting the same error trace. Could it be that there's still a corner case not covered in processors?
¡¡¡ NxmlReader error !!!
paper: PMC2669449
error:
java.lang.reflect.InvocationTargetException
stack trace:
sun.reflect.GeneratedMethodAccessor23.invoke(Unknown Source)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
scala.reflect.runtime.JavaMirrors$JavaMirror$JavaVanillaMethodMirror2.jinvokeraw(JavaMirrors.scala:398)
scala.reflect.runtime.JavaMirrors$JavaMirror$JavaMethodMirror.jinvoke(JavaMirrors.scala:354)
scala.reflect.runtime.JavaMirrors$JavaMirror$JavaVanillaMethodMirror.apply(JavaMirrors.scala:370)
org.clulab.odin.impl.ActionMirror.$anonfun$reflect$1(ActionMirror.scala:23)
org.clulab.odin.impl.GraphExtractor.findAllIn(Extractor.scala:111)
org.clulab.odin.impl.Extractor.$anonfun$findAllIn$1(Extractor.scala:20)
org.clulab.odin.impl.Extractor.$anonfun$findAllIn$1$adapted(Extractor.scala:19)
scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
scala.collection.immutable.Range.foreach(Range.scala:158)
scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
org.clulab.odin.impl.Extractor.findAllIn(Extractor.scala:19)
org.clulab.odin.impl.Extractor.findAllIn$(Extractor.scala:18)
org.clulab.odin.impl.GraphExtractor.findAllIn(Extractor.scala:99)
org.clulab.odin.ExtractorEngine.$anonfun$extractFrom$2(ExtractorEngine.scala:45)
scala.collection.TraversableLike$WithFilter.$anonfun$flatMap$2(TraversableLike.scala:773)
scala.collection.Iterator.foreach(Iterator.scala:941)
scala.collection.Iterator.foreach$(Iterator.scala:941)
scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
scala.collection.IterableLike.foreach(IterableLike.scala:74)
scala.collection.IterableLike.foreach$(IterableLike.scala:73)
scala.collection.AbstractIterable.foreach(Iterable.scala:56)
scala.collection.TraversableLike$WithFilter.flatMap(TraversableLike.scala:772)
org.clulab.odin.ExtractorEngine.extract$1(ExtractorEngine.scala:43)
org.clulab.odin.ExtractorEngine.loop$1(ExtractorEngine.scala:34)
org.clulab.odin.ExtractorEngine.extractFrom(ExtractorEngine.scala:56)
org.clulab.reach.assembly.sieves.SieveUtils$.$anonfun$assemblyViaRules$4(Sieves.scala:540)
scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
scala.collection.immutable.Map$Map1.foreach(Map.scala:128)
scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
org.clulab.reach.assembly.sieves.SieveUtils$.assemblyViaRules(Sieves.scala:534)
org.clulab.reach.assembly.sieves.PrecedenceSieves.applyPrecedenceRules(Sieves.scala:63)
org.clulab.reach.assembly.sieves.PrecedenceSieves.intrasententialRBPrecedence(Sieves.scala:103)
org.clulab.reach.assembly.Assembler$.$anonfun$applySieves$2(Assembler.scala:146)
org.clulab.reach.assembly.sieves.AssemblySieve$$anon$1.apply(AssemblySieve.scala:32)
org.clulab.reach.assembly.sieves.SieveMixture.apply(AssemblySieve.scala:38)
org.clulab.reach.assembly.sieves.SieveMixture.apply(AssemblySieve.scala:43)
org.clulab.reach.assembly.Assembler$.applySieves(Assembler.scala:158)
org.clulab.reach.assembly.Assembler$.apply(Assembler.scala:116)
org.clulab.reach.ReachCLI.doAssembly(ReachCLI.scala:124)
org.clulab.reach.ReachCLI.outputMentions(ReachCLI.scala:184)
org.clulab.reach.ReachCLI.$anonfun$processPaper$1(ReachCLI.scala:143)
org.clulab.reach.ReachCLI.$anonfun$processPaper$1$adapted(ReachCLI.scala:143)
scala.collection.immutable.List.foreach(List.scala:392)
org.clulab.reach.ReachCLI.processPaper(ReachCLI.scala:143)
org.clulab.reach.ReachCLI.$anonfun$processPapers$3(ReachCLI.scala:90)
org.clulab.reach.ReachCLI.$anonfun$processPapers$3$adapted(ReachCLI.scala:84)
scala.collection.parallel.AugmentedIterableIterator.map2combiner(RemainsIterator.scala:116)
scala.collection.parallel.AugmentedIterableIterator.map2combiner$(RemainsIterator.scala:113)
scala.collection.parallel.immutable.ParVector$ParVectorIterator.map2combiner(ParVector.scala:66)
scala.collection.parallel.ParIterableLike$Map.leaf(ParIterableLike.scala:1056)
scala.collection.parallel.Task.$anonfun$tryLeaf$1(Tasks.scala:53)
scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
scala.util.control.Breaks$$anon$1.catchBreak(Breaks.scala:67)
scala.collection.parallel.Task.tryLeaf(Tasks.scala:56)
scala.collection.parallel.Task.tryLeaf$(Tasks.scala:50)
scala.collection.parallel.ParIterableLike$Map.tryLeaf(ParIterableLike.scala:1053)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.internal(Tasks.scala:160)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.internal$(Tasks.scala:157)
scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.internal(Tasks.scala:440)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.compute(Tasks.scala:150)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask.compute$(Tasks.scala:149)
scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:440)
java.util.concurrent.RecursiveAction.exec(RecursiveAction.java:189)
java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
==========I'll check.
kwalcock
commented
3 years ago It looks like the same error, but has a completely different cause. This line in reach does not check the bounds correctly:
case outOfBounds if outOfBounds == -1 || outOfBounds > words.size => falseCan you please try to fix it? Thank you!
kwalcock
commented
3 years ago Yes, doing so.
kwalcock
commented
3 years ago @enoriega, while it is being tested, approved, and merged, you can use the changes from #719 or the kwalcock-fixes branch.
enoriega
commented
3 years ago Thanks @kwalcock
enoriega
commented
3 years ago I have been running REACH using branch kwalcock-fixes for a while and haven't seen this error. I think it is safe it has been fixed now. Thanks @kwalcock
kwalcock
commented
3 years ago Thanks for the update. We're working on the merge to master and a new release.
When I turn on assembly in the config, sometimes I see an an
NxmlReadererror that I didn't see otherwise. The stack trace points back to some of the assembly methods. I suspect there is an unexpected corner case with this class of files that crashes their processing.The error is not catastrophic, as processing of the other files carries on.
I attach the stack trace of the exception and an nxml file that triggers it for replication purposes.
PMC6797981.nxml.txt
Stack trace: