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Avoid slowdown for existential fillers with large numbers of subclasses. #64

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Merged
balhoff merged 2 commits into from
Nov 7, 2021
Merged

Avoid slowdown for existential fillers with large numbers of subclasses. #64

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e26dae5
Avoid slowdown for existential fillers with large numbers of subclasses.
balhoff Nov 7, 2021
644ec6a
Update test.
balhoff Nov 7, 2021
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48 changes: 36 additions & 12 deletions src/main/scala/org/renci/relationgraph/Main.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ import zio._
import zio.blocking._
import zio.stream._

import java.io.{File, FileOutputStream, OutputStream}
import java.io.{File, FileOutputStream}
import java.lang.{Runtime => JRuntime}
import java.nio.charset.StandardCharsets
import java.security.MessageDigest
Expand Down Expand Up @@ -46,12 +46,13 @@ object Main extends ZCaseApp[Config] {
whelkOntology = Bridge.ontologyToAxioms(ontology)
_ <- ZIO.succeed(scribe.info("Running reasoner"))
whelk = Reasoner.assert(whelkOntology)
indexedWhelk = IndexedReasonerState(whelk)
_ <- ZIO.succeed(scribe.info("Done running reasoner"))
_ <- ZIO.fail(new Exception("Ontology is incoherent; please correct unsatisfiable classes.")).when(isIncoherent(whelk))
_ <- effectBlockingIO(rdfWriter.triple(Triple.create(NodeFactory.createBlankNode("redundant"), RDFType, OWLOntology)))
.when(config.mode == OWLMode)
start <- ZIO.succeed(System.currentTimeMillis())
triplesStream = computeRelations(ontology, whelk, specifiedProperties, config.outputSubclasses.bool, config.reflexiveSubclasses.bool, config.equivalenceAsSubclass.bool, config.mode)
triplesStream = computeRelations(ontology, indexedWhelk, specifiedProperties, config.outputSubclasses.bool, config.reflexiveSubclasses.bool, config.equivalenceAsSubclass.bool, config.mode)
_ <- triplesStream.foreach {
case TriplesGroup(triples) => ZIO.effect(triples.foreach(rdfWriter.triple))
}
Expand All @@ -62,11 +63,11 @@ object Main extends ZCaseApp[Config] {
program.exitCode
}

def computeRelations(ontology: OWLOntology, whelk: ReasonerState, specifiedProperties: Set[AtomicConcept], outputSubclasses: Boolean, reflexiveSubclasses: Boolean, equivalenceAsSubclass: Boolean, mode: Config.OutputMode): UStream[TriplesGroup] = {
val classes = classHierarchy(whelk)
def computeRelations(ontology: OWLOntology, whelk: IndexedReasonerState, specifiedProperties: Set[AtomicConcept], outputSubclasses: Boolean, reflexiveSubclasses: Boolean, equivalenceAsSubclass: Boolean, mode: Config.OutputMode): UStream[TriplesGroup] = {
val classes = classHierarchy(whelk.state)
val properties = propertyHierarchy(ontology)
val classesTasks = if (outputSubclasses) {
allClasses(ontology).map(c => ZIO.succeed(processSuperclasses(c, whelk, reflexiveSubclasses, equivalenceAsSubclass)))
allClasses(ontology).map(c => ZIO.succeed(processSuperclasses(c, whelk.state, reflexiveSubclasses, equivalenceAsSubclass)))
} else Stream.empty
val streamZ = for {
queue <- Queue.unbounded[Restriction]
Expand Down Expand Up @@ -124,7 +125,7 @@ object Main extends ZCaseApp[Config] {
} yield ()
}

def processRestrictionAndExtendQueue(restriction: Restriction, properties: Hierarchy, classes: Hierarchy, whelk: ReasonerState, mode: Config.OutputMode, descendProperties: Boolean, queue: Queue[Restriction], activeRestrictions: Ref[Int], seenRef: Ref[Map[AtomicConcept, Set[AtomicConcept]]]): UIO[TriplesGroup] = {
def processRestrictionAndExtendQueue(restriction: Restriction, properties: Hierarchy, classes: Hierarchy, whelk: IndexedReasonerState, mode: Config.OutputMode, descendProperties: Boolean, queue: Queue[Restriction], activeRestrictions: Ref[Int], seenRef: Ref[Map[AtomicConcept, Set[AtomicConcept]]]): UIO[TriplesGroup] = {
val triples = processRestriction(restriction, whelk, mode)
for {
directFillerSubclassesRestrictions <- if (triples.redundant.nonEmpty) seenRef.modify { seen =>
Expand Down Expand Up @@ -153,7 +154,7 @@ object Main extends ZCaseApp[Config] {
} yield triples
}

def processRestriction(restriction: Restriction, whelk: ReasonerState, mode: Config.OutputMode): TriplesGroup = {
def processRestriction(restriction: Restriction, whelk: IndexedReasonerState, mode: Config.OutputMode): TriplesGroup = {
val subclasses = queryExistentialSubclasses(restriction, whelk)
if (subclasses.nonEmpty) {
val predicate = NodeFactory.createURI(restriction.property.id)
Expand All @@ -166,12 +167,17 @@ object Main extends ZCaseApp[Config] {
} else TriplesGroup.empty
}

def queryExistentialSubclasses(restriction: Restriction, whelk: ReasonerState): Set[AtomicConcept] = {
val queryConcept = AtomicConcept(s"${restriction.property.id}${restriction.filler.id}")
// This is a faster way to compute these than the standard Whelk algorithm
def queryExistentialSubclasses(restriction: Restriction, whelk: IndexedReasonerState): Set[AtomicConcept] = {
val er = ExistentialRestriction(restriction.property, restriction.filler)
val axioms = Set(ConceptInclusion(queryConcept, er), ConceptInclusion(er, queryConcept))
val updatedWhelk = Reasoner.assert(axioms, whelk)
updatedWhelk.closureSubsBySuperclass(queryConcept).collect { case x: AtomicConcept => x } - queryConcept - Bottom
val rs = whelk.reverseRoleHierarchy.getOrElse(er.role, Set.empty)
val cs = whelk.state.closureSubsBySuperclass.getOrElse(er.concept, Set.empty)
val validTargets = cs.intersect(whelk.allTargets)
(for {
target <- validTargets
(r, es) <- whelk.linksByTargetList.getOrElse(target, Map.empty)
if rs(r)
} yield es.iterator).flatten.to(Set).collect { case x: AtomicConcept => x } - Bottom
}

def classHierarchy(reasoner: ReasonerState): Hierarchy = {
Expand Down Expand Up @@ -253,4 +259,22 @@ object Main extends ZCaseApp[Config] {

}

final case class IndexedReasonerState(state: ReasonerState) {

val negativeExistentials: Set[ExistentialRestriction] = state.negExistsMapByConcept.flatMap(_._2).to(Set)

val reverseRoleHierarchy: Map[Role, Set[Role]] = (for {
(r, ss) <- state.hier.toList
s <- ss
} yield {
s -> r
}).groupMapReduce(_._1)(e => Set(e._2))(_ ++ _)

val allTargets: Set[Concept] = state.linksByTarget.keySet

val linksByTargetList: Map[Concept, List[(Role, List[Concept])]] =
state.linksByTarget.view.mapValues(_.to(List)).toMap

}

}
5 changes: 3 additions & 2 deletions src/test/scala/org/renci/relationgraph/TestRelationGraph.scala
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Expand Up @@ -2,7 +2,7 @@ package org.renci.relationgraph

import org.apache.jena.graph.{Node, NodeFactory, Triple}
import org.geneontology.whelk.{Bridge, Reasoner}
import org.renci.relationgraph.Main.TriplesGroup
import org.renci.relationgraph.Main.{IndexedReasonerState, TriplesGroup}
import org.semanticweb.owlapi.apibinding.OWLManager
import zio._
import zio.test.Assertion._
Expand All @@ -23,7 +23,8 @@ object TestRelationGraph extends DefaultRunnableSpec {
ontology <- ZIO.effect(manager.loadOntologyFromOntologyDocument(this.getClass.getResourceAsStream("materialize_test.ofn")))
whelkOntology = Bridge.ontologyToAxioms(ontology)
whelk = Reasoner.assert(whelkOntology)
resultsStream = Main.computeRelations(ontology, whelk, Set.empty, true, false, false, Config.RDFMode)
indexedWhelk = IndexedReasonerState(whelk)
resultsStream = Main.computeRelations(ontology, indexedWhelk, Set.empty, true, false, false, Config.RDFMode)
results <- resultsStream.runCollect
triples <- ZIO.fromOption(results.reduceOption((left, right) => TriplesGroup(left.redundant ++ right.redundant)))
TriplesGroup(redundant) = triples
Expand Down