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Fix loophole in disableBottom option. #181

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Jul 1, 2022
Merged

Fix loophole in disableBottom option. #181

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71 changes: 37 additions & 34 deletions modules/core/src/main/scala/org/geneontology/whelk/Reasoner.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ object Reasoner {
val atomicConcepts = distinctConcepts.collect { case a: AtomicConcept => a }
val additionalAxioms = distinctConcepts.flatMap {
case d @ Disjunction(_) => `R⊔`(d)
case c @ Complement(_) => `R¬`(c)
case c @ Complement(_) => `R¬`(c, reasoner.disableBottom)
case _ => Set.empty[ConceptInclusion]
}
val negativeSelfRestrictions = axioms.flatMap(_.subclass.conceptSignature).collect { case sr: SelfRestriction => sr.role -> sr }.toMap
Expand Down Expand Up @@ -190,41 +190,43 @@ object Reasoner {

private[this] val emptySubClassSet: Set[Concept] = Set(Bottom)

private[this] def processConceptInclusion(ci: ConceptInclusion, reasoner: ReasonerState): ReasonerState = {
val ConceptInclusion(subclass, superclass) = ci
val subs = reasoner.closureSubsBySuperclass.getOrElse(superclass, emptySubClassSet)
if (subs(subclass)) reasoner else {
val closureSubsBySuperclass = reasoner.closureSubsBySuperclass.updated(superclass, subs + subclass)
val supers = reasoner.closureSubsBySubclass.getOrElse(subclass, Set.empty)
val closureSubsBySubclass = reasoner.closureSubsBySubclass.updated(subclass, supers + superclass)
val updatedReasoner = `R⊔right`(ci, `R+⟲`(ci, `R-⟲`(ci, `R⊑right`(ci, `R+∃b-right`(ci, `R-∃`(ci, `R+⨅left`(ci, `R+⨅right`(ci, `R-⨅`(ci, `R⊥left`(ci, reasoner.copy(closureSubsBySuperclass = closureSubsBySuperclass, closureSubsBySubclass = closureSubsBySubclass)))))))))))
val newState = ci match {
case ConceptInclusion(Nominal(ind), concept) => reasoner.ruleEngine.processConceptAssertion(ConceptAssertion(concept, ind), updatedReasoner)
case _ => updatedReasoner
}
newState.queueDelegates.keysIterator.foldLeft(newState) { (state, delegateKey) =>
state.queueDelegates(delegateKey).processConceptInclusion(ci, state)
private[this] def processConceptInclusion(ci: ConceptInclusion, reasoner: ReasonerState): ReasonerState =
if (!reasoner.disableBottom || ci.superclass != Bottom) {
val ConceptInclusion(subclass, superclass) = ci
val subs = reasoner.closureSubsBySuperclass.getOrElse(superclass, emptySubClassSet)
if (subs(subclass)) reasoner else {
val closureSubsBySuperclass = reasoner.closureSubsBySuperclass.updated(superclass, subs + subclass)
val supers = reasoner.closureSubsBySubclass.getOrElse(subclass, Set.empty)
val closureSubsBySubclass = reasoner.closureSubsBySubclass.updated(subclass, supers + superclass)
val updatedReasoner = `R⊔right`(ci, `R+⟲`(ci, `R-⟲`(ci, `R⊑right`(ci, `R+∃b-right`(ci, `R-∃`(ci, `R+⨅left`(ci, `R+⨅right`(ci, `R-⨅`(ci, `R⊥left`(ci, reasoner.copy(closureSubsBySuperclass = closureSubsBySuperclass, closureSubsBySubclass = closureSubsBySubclass)))))))))))
val newState = ci match {
case ConceptInclusion(Nominal(ind), concept) => reasoner.ruleEngine.processConceptAssertion(ConceptAssertion(concept, ind), updatedReasoner)
case _ => updatedReasoner
}
newState.queueDelegates.keysIterator.foldLeft(newState) { (state, delegateKey) =>
state.queueDelegates(delegateKey).processConceptInclusion(ci, state)
}
}
}
}
} else reasoner

private[this] def processSubPlus(ci: ConceptInclusion, reasoner: ReasonerState): ReasonerState = {
val ConceptInclusion(subclass, superclass) = ci
val subs = reasoner.closureSubsBySuperclass.getOrElse(superclass, Set.empty)
if (subs(subclass)) reasoner else {
val closureSubsBySuperclass = reasoner.closureSubsBySuperclass.updated(superclass, subs + subclass)
val supers = reasoner.closureSubsBySubclass.getOrElse(subclass, Set.empty)
val closureSubsBySubclass = reasoner.closureSubsBySubclass.updated(subclass, supers + superclass)
val updatedReasoner = `R⊔right`(ci, `R-⟲`(ci, `R⊑right`(ci, `R+∃b-right`(ci, `R+⨅left`(ci, `R+⨅right`(ci, `R⊥left`(ci, reasoner.copy(closureSubsBySuperclass = closureSubsBySuperclass, closureSubsBySubclass = closureSubsBySubclass))))))))
val newState = ci match {
case ConceptInclusion(Nominal(ind), concept) => updatedReasoner.ruleEngine.processConceptAssertion(ConceptAssertion(concept, ind), updatedReasoner)
case _ => updatedReasoner
}
newState.queueDelegates.keysIterator.foldLeft(newState) { (state, delegateKey) =>
state.queueDelegates(delegateKey).processSubPlus(ci, state)
private[this] def processSubPlus(ci: ConceptInclusion, reasoner: ReasonerState): ReasonerState =
if (!reasoner.disableBottom || ci.superclass != Bottom) {
val ConceptInclusion(subclass, superclass) = ci
val subs = reasoner.closureSubsBySuperclass.getOrElse(superclass, Set.empty)
if (subs(subclass)) reasoner else {
val closureSubsBySuperclass = reasoner.closureSubsBySuperclass.updated(superclass, subs + subclass)
val supers = reasoner.closureSubsBySubclass.getOrElse(subclass, Set.empty)
val closureSubsBySubclass = reasoner.closureSubsBySubclass.updated(subclass, supers + superclass)
val updatedReasoner = `R⊔right`(ci, `R-⟲`(ci, `R⊑right`(ci, `R+∃b-right`(ci, `R+⨅left`(ci, `R+⨅right`(ci, `R⊥left`(ci, reasoner.copy(closureSubsBySuperclass = closureSubsBySuperclass, closureSubsBySubclass = closureSubsBySubclass))))))))
val newState = ci match {
case ConceptInclusion(Nominal(ind), concept) => updatedReasoner.ruleEngine.processConceptAssertion(ConceptAssertion(concept, ind), updatedReasoner)
case _ => updatedReasoner
}
newState.queueDelegates.keysIterator.foldLeft(newState) { (state, delegateKey) =>
state.queueDelegates(delegateKey).processSubPlus(ci, state)
}
}
}
}
} else reasoner

private[this] def processLink(link: Link, reasoner: ReasonerState): ReasonerState = {
val Link(subject, role, target) = link
Expand Down Expand Up @@ -526,7 +528,8 @@ object Reasoner {

private[this] def `R⊔`(d: Disjunction): Set[ConceptInclusion] = d.operands.map(o => ConceptInclusion(o, d))

private[this] def `R¬`(c: Complement): Set[ConceptInclusion] = Set(ConceptInclusion(Conjunction(c.concept, c), Bottom))
private[this] def `R¬`(c: Complement, disableBottom: Boolean): Set[ConceptInclusion] =
if (!disableBottom) Set(ConceptInclusion(Conjunction(c.concept, c), Bottom)) else Set.empty

private[this] def saturateRoles(roleInclusions: Set[RoleInclusion]): Map[Role, Set[Role]] = { //FIXME can do this better?
val subToSuper = roleInclusions.groupBy(_.subproperty).map { case (sub, ri) => sub -> ri.map(_.superproperty) }
Expand Down