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Fix intermittent InterruptedException in ZIO stream termination #357

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Merged
balhoff merged 1 commit into from
Mar 13, 2026
Merged

Fix intermittent InterruptedException in ZIO stream termination #357

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20 changes: 10 additions & 10 deletions core/src/main/scala/org/renci/relationgraph/RelationGraph.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -66,42 +66,42 @@ object RelationGraph extends StrictLogging {
allClasses(ontology).map(c => ZIO.succeed(processSubclasses(c, indexedWhelk.state, outputConfig.reflexiveSubclasses, outputConfig.equivalenceAsSubclass, outputConfig.outputClasses, outputConfig.outputIndividuals)))
} else ZStream.empty
val streamZ = for {
queue <- Queue.unbounded[Restriction]
queue <- Queue.unbounded[Option[Restriction]]
activeRestrictions <- Ref.make(0)
seenRefs <- ZIO.foreach(allProperties)(p => Ref.make(Set.empty[AtomicConcept]).map(p -> _)).map(_.toMap)
_ <- traverse(specifiedProperties, properties, classes, queue, activeRestrictions, seenRefs)
restrictionsStream = ZStream.fromQueue(queue).map(r => processRestrictionAndExtendQueue(r, properties, classes, indexedWhelk, outputConfig.mode, specifiedProperties.isEmpty, outputConfig.outputClasses, outputConfig.outputIndividuals, queue, activeRestrictions, seenRefs))
restrictionsStream = ZStream.fromQueue(queue).collectWhile { case Some(r) => r }.map(r => processRestrictionAndExtendQueue(r, properties, classes, indexedWhelk, outputConfig.mode, specifiedProperties.isEmpty, outputConfig.outputClasses, outputConfig.outputIndividuals, queue, activeRestrictions, seenRefs))
allTasks = ontologyDeclarationStream ++ classesTasks ++ restrictionsStream
} yield allTasks.mapZIOParUnordered(JRuntime.getRuntime.availableProcessors)(identity)
ZStream.unwrap(streamZ)
}

def allClasses(ont: OWLOntology): ZStream[Any, Nothing, OWLClass] = ZStream.fromIterable(ont.getClassesInSignature(Imports.INCLUDED).asScala.to(Set) - OWLThing - OWLNothing)

def traverse(specifiedProperties: Set[AtomicConcept], properties: Hierarchy, classes: Hierarchy, queue: Queue[Restriction], activeRestrictions: Ref[Int], seenRefs: Map[Role, Ref[Set[AtomicConcept]]]): UIO[Unit] = {
def traverse(specifiedProperties: Set[AtomicConcept], properties: Hierarchy, classes: Hierarchy, queue: Queue[Option[Restriction]], activeRestrictions: Ref[Int], seenRefs: Map[Role, Ref[Set[AtomicConcept]]]): UIO[Unit] = {
val descendProperties = specifiedProperties.isEmpty
val queryProperties = if (descendProperties) properties.subclasses.getOrElse(Top, Set.empty) - Bottom else specifiedProperties
if (queryProperties.nonEmpty) ZIO.foreachParDiscard(queryProperties) { subprop =>
traverseProperty(subprop, classes, queue, activeRestrictions, seenRefs)
}
else queue.shutdown
else queue.offer(None).unit
}

def traverseProperty(property: AtomicConcept, classes: Hierarchy, queue: Queue[Restriction], activeRestrictions: Ref[Int], seenRefs: Map[Role, Ref[Set[AtomicConcept]]]): UIO[Unit] = {
def traverseProperty(property: AtomicConcept, classes: Hierarchy, queue: Queue[Option[Restriction]], activeRestrictions: Ref[Int], seenRefs: Map[Role, Ref[Set[AtomicConcept]]]): UIO[Unit] = {
val restrictions = (classes.subclasses.getOrElse(Top, Set.empty) - Bottom).map(filler => Restriction(Role(property.id), filler))
val propSeenRef = seenRefs(Role(property.id))
for {
_ <- propSeenRef.update { seenForThisProperty =>
seenForThisProperty ++ restrictions.map(_.filler)
}
_ <- activeRestrictions.update(current => current + restrictions.size)
_ <- queue.offerAll(restrictions).unit
_ <- queue.offerAll(restrictions.map(Option(_))).unit
active <- activeRestrictions.get
_ <- queue.shutdown.when(active < 1)
_ <- queue.offer(None).when(active < 1).unit
} yield ()
}

def processRestrictionAndExtendQueue(restriction: Restriction, properties: Hierarchy, classes: Hierarchy, whelk: IndexedReasonerState, mode: Config.TriplesMode, descendProperties: Boolean, outputClasses: Boolean, outputIndividuals: Boolean, queue: Queue[Restriction], activeRestrictions: Ref[Int], seenRefs: Map[Role, Ref[Set[AtomicConcept]]]): UIO[TriplesGroup] = {
def processRestrictionAndExtendQueue(restriction: Restriction, properties: Hierarchy, classes: Hierarchy, whelk: IndexedReasonerState, mode: Config.TriplesMode, descendProperties: Boolean, outputClasses: Boolean, outputIndividuals: Boolean, queue: Queue[Option[Restriction]], activeRestrictions: Ref[Int], seenRefs: Map[Role, Ref[Set[AtomicConcept]]]): UIO[TriplesGroup] = {
val triples = processRestriction(restriction, whelk, mode, outputClasses, outputIndividuals)
val continue = triples.redundant.nonEmpty
for {
Expand All @@ -128,9 +128,9 @@ object RelationGraph extends StrictLogging {
} else ZIO.succeed(Set.empty[Restriction])
newRestrictions = directFillerSubclassesRestrictions ++ directSubPropertyRestrictions
_ <- activeRestrictions.update(current => current - 1 + newRestrictions.size)
_ <- queue.offerAll(newRestrictions)
_ <- queue.offerAll(newRestrictions.map(Option(_)))
active <- activeRestrictions.get
_ <- queue.shutdown.when(active < 1)
_ <- queue.offer(None).when(active < 1).unit
} yield triples
}

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