build(hermit): bump HermiT v1.3.8.1 -> v1.4.5.519

This commit contains a "hacky" fix for KARMA2 to access some (now
private) field in the OWLAxioms class. The code is now using Java
Reflections to turn a private field public and gain access to internal
resources.

5 files changed, 42 insertions, 13 deletions

diff --git a/src/main/java/org/semanticweb/karma2/clausifier/OntologyProcesser.java b/src/main/java/org/semanticweb/karma2/clausifier/OntologyProcesser.java
index 5ff339e..8e97a2f 100644
--- a/src/main/java/org/semanticweb/karma2/clausifier/OntologyProcesser.java
+++ b/src/main/java/org/semanticweb/karma2/clausifier/OntologyProcesser.java
@@ -12,6 +12,7 @@ import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Set;
+import java.lang.reflect.*;
 
 import org.semanticweb.HermiT.model.Atom;
 import org.semanticweb.HermiT.model.AtomicConcept;
@@ -196,21 +197,46 @@ public class OntologyProcesser {
         public void clausify(OWLDataFactory factory,String ontologyIRI,OWLAxioms axioms,OWLAxiomsExpressivity axiomsExpressivity, File dataFile, File ruleFile) {
         Set<DLClause> dlClauses=new LinkedHashSet<DLClause>();
         Set<Atom> positiveFacts=new HashSet<Atom>();
-        for (OWLObjectPropertyExpression[] inclusion : axioms.m_simpleObjectPropertyInclusions) {
-            Atom subRoleAtom=getRoleAtom(inclusion[0],X,Y);
-            Atom superRoleAtom=getRoleAtom(inclusion[1],X,Y);
+        /* Quick fix (using Java reflexions) to access some fields that became private in later versions.
+         * TODO: find how to properly do this... don't be that guy!
+         */
+        Field f_simpleObjectPropertyInclusions;
+        Field f_conceptInclusions;
+        Field f_facts;
+        Collection<List<OWLObjectPropertyExpression>> m_simpleObjectPropertyInclusions;
+        Collection<List<OWLClassExpression>> m_conceptInclusions;
+        Collection<OWLIndividualAxiom> m_facts;
+        try {
+            f_simpleObjectPropertyInclusions = axioms.getClass().getDeclaredField("m_simpleObjectPropertyInclusions");
+            f_simpleObjectPropertyInclusions.setAccessible(true);
+            f_conceptInclusions = axioms.getClass().getDeclaredField("m_conceptInclusions");
+            f_conceptInclusions.setAccessible(true);
+            f_facts = axioms.getClass().getDeclaredField("m_facts");
+            f_facts.setAccessible(true);
+            m_simpleObjectPropertyInclusions = (Collection<List<OWLObjectPropertyExpression>>) f_simpleObjectPropertyInclusions.get(axioms);
+            m_conceptInclusions = (Collection<List<OWLClassExpression>>) f_conceptInclusions.get(axioms);
+            m_facts = (Collection<OWLIndividualAxiom>) f_facts.get(axioms);
+        } catch (java.lang.NoSuchFieldException e) {
+            return;
+        } catch (java.lang.IllegalAccessException e) {
+            return;
+        }
+
+        for (List<OWLObjectPropertyExpression> inclusion : m_simpleObjectPropertyInclusions) {
+            Atom subRoleAtom=getRoleAtom(inclusion.get(0),X,Y);
+            Atom superRoleAtom=getRoleAtom(inclusion.get(1),X,Y);
             DLClause dlClause=DLClause.create(new Atom[] { superRoleAtom },new Atom[] { subRoleAtom });
             dlClauses.add(dlClause);
         }
         NormalizedDatalogAxiomClausifier clausifier=new NormalizedDatalogAxiomClausifier(positiveFacts,factory);
-        for (OWLClassExpression[] inclusion : axioms.m_conceptInclusions) {
+        for (List<OWLClassExpression> inclusion : m_conceptInclusions) {
             for (OWLClassExpression description : inclusion)
                 description.accept(clausifier);
             for(DLClause dlClause :clausifier.getDLClause())
                 dlClauses.add(dlClause.getSafeVersion(AtomicConcept.THING));
         }
         DatalogFactClausifier factClausifier=new DatalogFactClausifier(positiveFacts);
-        for (OWLIndividualAxiom fact : axioms.m_facts)
+        for (OWLIndividualAxiom fact :  m_facts)
             fact.accept(factClausifier);
         writeDataFile(positiveFacts, dataFile);
         writeRules(dlClauses, ruleFile);
diff --git a/src/main/java/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
index ac62488..ebf1960 100644
--- a/src/main/java/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
@@ -1,5 +1,6 @@
 package uk.ac.ox.cs.pagoda.reasoner;
 
+import org.semanticweb.HermiT.Configuration;
 import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.owlapi.model.*;
 import uk.ac.ox.cs.JRDFox.model.Individual;
@@ -63,7 +64,7 @@ class HermiTReasoner extends QueryReasoner {
         factory = onto.getOWLOntologyManager().getOWLDataFactory();
         roller = new QueryRoller(factory);
 
-        hermit = new Reasoner(onto);
+        hermit = new Reasoner(new Configuration(), onto);
         return isConsistent();
     }
 
diff --git a/src/main/java/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
index 3f3c22d..fb7e062 100644
--- a/src/main/java/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
@@ -1,5 +1,6 @@
 package uk.ac.ox.cs.pagoda.reasoner.full;
 
+import org.semanticweb.HermiT.Configuration;
 import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.HermiT.model.DLClause;
 import org.semanticweb.HermiT.model.Term;
@@ -57,7 +58,7 @@ public class HermitChecker extends Checker {
 //                      record = other.record;
         }
 
-        hermit = new Reasoner(ontology);
+        hermit = new Reasoner(new Configuration(), ontology);
     }
 
     public HermitChecker(OWLOntology ontology, QueryRecord record, boolean toCheck) {
@@ -174,12 +175,12 @@ public class HermitChecker extends Checker {
             addTopAndBotTuple(topAxioms, botAxioms);
             manager.addAxioms(ontology, topAxioms);
             manager.addAxioms(ontology, botAxioms);
-            hermit = new Reasoner(ontology);
+            hermit = new Reasoner(new Configuration(), ontology);
             boolean topValid = true;
             if(!hermit.isConsistent() || topAnswerTuple != null && (topValid = check(topAnswerTuple))) {
                 hermit.dispose();
                 manager.removeAxioms(ontology, topAxioms);
-                hermit = new Reasoner(ontology);
+                hermit = new Reasoner(new Configuration(), ontology);
             }
             else {
                 if(!topValid) tag = -1;
@@ -187,7 +188,7 @@ public class HermitChecker extends Checker {
             }
         }
         else
-            hermit = new Reasoner(ontology);
+            hermit = new Reasoner(new Configuration(), ontology);
     }
 
     private void addTopAndBotTuple(Set<OWLAxiom> topAxioms, Set<OWLAxiom> botAxioms) {
diff --git a/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
index a2676e8..2610652 100644
--- a/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
@@ -1,6 +1,7 @@
 package uk.ac.ox.cs.pagoda.rules;
 
 import org.apache.commons.io.FilenameUtils;
+import org.semanticweb.HermiT.Configuration;
 import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.HermiT.model.*;
 import org.semanticweb.owlapi.model.*;
@@ -149,7 +150,7 @@ class ClassifyThread extends Thread {
         public void run() {
                 ontology = m_program.getOntology();
                 try {
-                        hermitReasoner = new Reasoner(ontology);
+                        hermitReasoner = new Reasoner(new Configuration(), ontology);
                         Timer t = new Timer(); 
                         hermitReasoner.classifyClasses();
                         Utility.logInfo("HermiT classification done: " + t.duration());
@@ -235,4 +236,4 @@ class ClassifyThread extends Thread {
         private Atom getAtom(OWLClass c) {
                 return Atom.create(AtomicConcept.create(c.toStringID()), X);
         }
-}
\ No newline at end of file
+}
diff --git a/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java
index de06f52..22eb9ec 100644
--- a/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java
@@ -273,7 +273,7 @@ protected PredicateDependency dependencyGraph;
                 Utility.logInfo("The number of data property range axioms that are ignored: " + noOfDataPropertyRangeAxioms + "(" + noOfAxioms + ")");
 
         DLOntology dlOntology = (DLOntology) clausifier.preprocessAndClausify(filteredOntology, null)[1];
-        dlClauses = dlOntology.getDLClauses();
+        dlClauses = new HashSet<DLClause>(dlOntology.getDLClauses());
         positiveFacts = dlOntology.getPositiveFacts();
         }