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Merged
balhoff merged 1 commit into from
Mar 21, 2022
Merged

Output triples with individuals as subjects. #111

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2 changes: 2 additions & 0 deletions src/main/scala/org/renci/relationgraph/Config.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,8 @@ final case class Config(ontologyFile: String,
outputSubclasses: BoolValue = FalseValue,
reflexiveSubclasses: BoolValue = TrueValue,
equivalenceAsSubclass: BoolValue = TrueValue,
outputClasses: BoolValue = TrueValue,
outputIndividuals: BoolValue = FalseValue,
disableOwlNothing: BoolValue = FalseValue,
verbose: Boolean = false)

Expand Down
95 changes: 56 additions & 39 deletions src/main/scala/org/renci/relationgraph/Main.scala
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Expand Up @@ -62,7 +62,7 @@ object Main extends ZCaseApp[Config] {
_ <- effectBlockingIO(rdfWriter.triple(Triple.create(NodeFactory.createBlankNode("redundant"), RDFType, OWLOntology)))
.when(config.mode == OWLMode)
start <- ZIO.succeed(System.currentTimeMillis())
triplesStream = computeRelations(ontology, indexedWhelk, 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.outputClasses.bool, config.outputIndividuals.bool, config.mode)
_ <- triplesStream.foreach {
case TriplesGroup(triples) => ZIO.effect(triples.foreach(rdfWriter.triple))
}
Expand All @@ -78,18 +78,18 @@ object Main extends ZCaseApp[Config] {
}
}

def computeRelations(ontology: OWLOntology, whelk: IndexedReasonerState, specifiedProperties: Set[AtomicConcept], outputSubclasses: Boolean, reflexiveSubclasses: Boolean, equivalenceAsSubclass: Boolean, mode: Config.OutputMode): UStream[TriplesGroup] = {
def computeRelations(ontology: OWLOntology, whelk: IndexedReasonerState, specifiedProperties: Set[AtomicConcept], outputSubclasses: Boolean, reflexiveSubclasses: Boolean, equivalenceAsSubclass: Boolean, outputClasses: Boolean, outputIndividuals: 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.state, reflexiveSubclasses, equivalenceAsSubclass)))
allClasses(ontology).map(c => ZIO.succeed(processSubclasses(c, whelk.state, reflexiveSubclasses, equivalenceAsSubclass, outputClasses, outputIndividuals)))
} else Stream.empty
val streamZ = for {
queue <- Queue.unbounded[Restriction]
activeRestrictions <- Ref.make(0)
seenRef <- Ref.make(Map.empty[AtomicConcept, Set[AtomicConcept]])
_ <- traverse(specifiedProperties, properties, classes, queue, activeRestrictions, seenRef)
restrictionsStream = Stream.fromQueue(queue).map(r => processRestrictionAndExtendQueue(r, properties, classes, whelk, mode, specifiedProperties.isEmpty, queue, activeRestrictions, seenRef))
restrictionsStream = Stream.fromQueue(queue).map(r => processRestrictionAndExtendQueue(r, properties, classes, whelk, mode, specifiedProperties.isEmpty, outputClasses, outputIndividuals, queue, activeRestrictions, seenRef))
allTasks = classesTasks ++ restrictionsStream
} yield allTasks.mapMParUnordered(JRuntime.getRuntime.availableProcessors)(identity)
Stream.unwrap(streamZ)
Expand Down Expand Up @@ -141,8 +141,8 @@ object Main extends ZCaseApp[Config] {
} yield ()
}

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)
def processRestrictionAndExtendQueue(restriction: Restriction, properties: Hierarchy, classes: Hierarchy, whelk: IndexedReasonerState, mode: Config.OutputMode, descendProperties: Boolean, outputClasses: Boolean, outputIndividuals: Boolean, queue: Queue[Restriction], activeRestrictions: Ref[Int], seenRef: Ref[Map[AtomicConcept, Set[AtomicConcept]]]): UIO[TriplesGroup] = {
val triples = processRestriction(restriction, whelk, mode, outputClasses, outputIndividuals)
for {
directFillerSubclassesRestrictions <- if (triples.redundant.nonEmpty) seenRef.modify { seen =>
val propertyConcept = AtomicConcept(restriction.property.id)
Expand Down Expand Up @@ -170,21 +170,30 @@ object Main extends ZCaseApp[Config] {
} yield triples
}

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)
val target = NodeFactory.createURI(restriction.filler.id)
val outputTriples = mode match {
case RDFMode => subclasses.map(sc => Triple.create(NodeFactory.createURI(sc.id), predicate, target))
case OWLMode => subclasses.flatMap(sc => owlTriples(NodeFactory.createURI(sc.id), predicate, target))
def processRestriction(restriction: Restriction, whelk: IndexedReasonerState, mode: Config.OutputMode, outputClasses: Boolean, outputIndividuals: Boolean): TriplesGroup = {
val subConcepts = queryExistentialSubclasses(restriction, whelk)
val subclasses = if (outputClasses) (subConcepts - Bottom).collect { case AtomicConcept(id) => id } else Set.empty[String]
val instances = if (outputIndividuals) subConcepts.collect { case Nominal(Individual(id)) => id } else Set.empty[String]
val predicate = NodeFactory.createURI(restriction.property.id)
val target = NodeFactory.createURI(restriction.filler.id)
val subclassTriples = subclasses.flatMap { id =>
mode match {
case RDFMode => Set(Triple.create(NodeFactory.createURI(id), predicate, target))
case OWLMode => owlTriples(NodeFactory.createURI(id), predicate, target, RDFSSubClassOf)
}
TriplesGroup(outputTriples)
} else TriplesGroup.empty
}
val instanceTriples = instances.flatMap { id =>
mode match {
case RDFMode => Set(Triple.create(NodeFactory.createURI(id), predicate, target))
case OWLMode => owlTriples(NodeFactory.createURI(id), predicate, target, RDFType)
}
}
val outputTriples = subclassTriples ++ instanceTriples
TriplesGroup(outputTriples)
}

// This is a faster way to compute these than the standard Whelk algorithm
def queryExistentialSubclasses(restriction: Restriction, whelk: IndexedReasonerState): Set[AtomicConcept] = {
def queryExistentialSubclasses(restriction: Restriction, whelk: IndexedReasonerState): Set[Concept] = {
val er = ExistentialRestriction(restriction.property, restriction.filler)
val rs = whelk.reverseRoleHierarchy.getOrElse(er.role, Set.empty)
val cs = whelk.state.closureSubsBySuperclass.getOrElse(er.concept, Set.empty)
Expand All @@ -193,7 +202,7 @@ object Main extends ZCaseApp[Config] {
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
} yield es.iterator).flatten.to(Set)
}

def classHierarchy(reasoner: ReasonerState): Hierarchy = {
Expand Down Expand Up @@ -223,37 +232,45 @@ object Main extends ZCaseApp[Config] {
classHierarchy(whelk)
}

def processSuperclasses(cls: OWLClass, whelk: ReasonerState, reflexiveSubclasses: Boolean, equivalenceAsSubclass: Boolean): TriplesGroup = {
val subject = NodeFactory.createURI(cls.getIRI.toString)
def processSubclasses(cls: OWLClass, whelk: ReasonerState, reflexiveSubclasses: Boolean, equivalenceAsSubclass: Boolean, outputClasses: Boolean, outputIndividuals: Boolean): TriplesGroup = {
val obj = NodeFactory.createURI(cls.getIRI.toString)
val concept = AtomicConcept(cls.getIRI.toString)
val allSuperclasses = (whelk.closureSubsBySubclass.getOrElse(concept, Set.empty) - BuiltIn.Top)
.collect { case ac @ AtomicConcept(_) => ac }
if (allSuperclasses(BuiltIn.Bottom)) TriplesGroup.empty //unsatisfiable
else {
val subConcepts = (whelk.closureSubsBySuperclass.getOrElse(concept, Set.empty) - BuiltIn.Bottom)
val individualsTriples = if (outputIndividuals) {
subConcepts.collect { case Nominal(Individual(id)) =>
Triple.create(NodeFactory.createURI(id), RDFType, obj)
}
} else Set.empty[Triple]
val classesTriples = if (outputClasses) {
val allSubclasses = subConcepts.collect { case ac @ AtomicConcept(_) => ac }
val (equivs, _) = whelk.directlySubsumedBy(concept)
val adjustedEquivs = if (reflexiveSubclasses) equivs + concept else equivs - concept
val equivalentClassTriples = if (equivalenceAsSubclass)
adjustedEquivs.map(c => Triple.create(subject, RDFSSubClassOf, NodeFactory.createURI(c.id)))
else
adjustedEquivs.map(c => Triple.create(subject, OWLEquivalentClass, NodeFactory.createURI(c.id)))
val adjustedSuperclasses = if (reflexiveSubclasses) allSuperclasses + concept else allSuperclasses - concept
val outputTriples = if (equivalenceAsSubclass)
adjustedSuperclasses.map(c => Triple.create(subject, RDFSSubClassOf, NodeFactory.createURI(c.id)))
val unsatisfiable = equivs(BuiltIn.Bottom)
if (unsatisfiable) Set.empty[Triple]
else {
val superclassesMinusEquiv = adjustedSuperclasses -- adjustedEquivs
superclassesMinusEquiv.map(c => Triple.create(subject, RDFSSubClassOf, NodeFactory.createURI(c.id))) ++
equivalentClassTriples
val adjustedEquivs = if (reflexiveSubclasses) equivs + concept else equivs - concept
val equivalentClassTriples = if (equivalenceAsSubclass)
adjustedEquivs.map(c => Triple.create(NodeFactory.createURI(c.id), RDFSSubClassOf, obj))
else
adjustedEquivs.map(c => Triple.create(NodeFactory.createURI(c.id), OWLEquivalentClass, obj))
val adjustedSubclasses = if (reflexiveSubclasses) allSubclasses + concept else allSubclasses - concept
if (equivalenceAsSubclass)
adjustedSubclasses.map(c => Triple.create(NodeFactory.createURI(c.id), RDFSSubClassOf, obj))
else {
val subclassesMinusEquiv = adjustedSubclasses -- adjustedEquivs
subclassesMinusEquiv.map(c => Triple.create(NodeFactory.createURI(c.id), RDFSSubClassOf, obj)) ++ equivalentClassTriples
}
}
TriplesGroup(outputTriples)
}
} else Set.empty[Triple]
val outputTriples = classesTriples ++ individualsTriples
TriplesGroup(outputTriples)
}

def owlTriples(subj: Node, pred: Node, obj: Node): Set[Triple] = {
def owlTriples(subj: Node, pred: Node, obj: Node, relation: Node): Set[Triple] = {
val hash = MessageDigest.getInstance("SHA-256").digest(s"$subj$pred$obj".getBytes(StandardCharsets.UTF_8))
val id = Base64.getEncoder.encodeToString(hash)
val restrictionNode = NodeFactory.createBlankNode(id)
Set(
Triple.create(subj, RDFSSubClassOf, restrictionNode),
Triple.create(subj, relation, restrictionNode),
Triple.create(restrictionNode, RDFType, OWLRestriction),
Triple.create(restrictionNode, OWLOnProperty, pred),
Triple.create(restrictionNode, OWLSomeValuesFrom, obj)
Expand Down
4 changes: 2 additions & 2 deletions src/test/scala/org/renci/relationgraph/TestRelationGraph.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ object TestRelationGraph extends DefaultRunnableSpec {
whelkOntology = Bridge.ontologyToAxioms(ontology)
whelk = Reasoner.assert(whelkOntology)
indexedWhelk = IndexedReasonerState(whelk)
resultsStream = Main.computeRelations(ontology, indexedWhelk, Set.empty, true, false, false, Config.RDFMode)
resultsStream = Main.computeRelations(ontology, indexedWhelk, Set.empty, true, false, false, true, false, Config.RDFMode)
results <- resultsStream.runCollect
triples <- ZIO.fromOption(results.reduceOption((left, right) => TriplesGroup(left.redundant ++ right.redundant)))
TriplesGroup(redundant) = triples
Expand All @@ -45,7 +45,7 @@ object TestRelationGraph extends DefaultRunnableSpec {
whelkOntology = Bridge.ontologyToAxioms(ontology)
whelk = Reasoner.assert(whelkOntology)
indexedWhelk = IndexedReasonerState(whelk)
resultsStream = Main.computeRelations(ontology, indexedWhelk, Set.empty, true, false, false, Config.RDFMode)
resultsStream = Main.computeRelations(ontology, indexedWhelk, Set.empty, true, false, false, true, false, Config.RDFMode)
results <- resultsStream.runCollect
triples <- ZIO.fromOption(results.reduceOption((left, right) => TriplesGroup(left.redundant ++ right.redundant)))
TriplesGroup(redundant) = triples
Expand Down