Adapt to changes in the Proof interface of puli

+ some resulting simplifications

elk-distribution/src/main/java/org/semanticweb/elk/owlapi/examples/RetrievingProofsForEntailment.java

@@ -31,6 +31,7 @@
 import java.util.Set;
 
 import org.liveontologies.owlapi.proof.OWLProver;
+import org.liveontologies.puli.DynamicProof;
 import org.liveontologies.puli.Inference;
 import org.liveontologies.puli.Proof;
 import org.semanticweb.elk.owlapi.ElkProverFactory;
@@ -74,34 +75,34 @@ public static void main(String[] args) throws OWLOntologyCreationException {
 		OWLAxiom entailment = getEntailment();
 
 		// Get the inferences used to prove the entailment 
-		Proof<OWLAxiom> inferences = prover.getProof(entailment);
+		DynamicProof<? extends Inference<OWLAxiom>> proof = prover.getProof(entailment);
 
 		// Now we can recursively request inferences and their premises. Print them to std.out in this example.
-		unwindProofs(inferences, entailment);
+		unwindProof(proof, entailment);
 
 		// Terminate the worker threads used by the reasoner.
 		prover.dispose();
 	}
 
-	private static <C> void unwindProofs(Proof<C> inferences, C entailment) {
-		// Start recursive unwinding
-		LinkedList<C> toDo = new LinkedList<C>();
-		Set<C> done = new HashSet<C>();
+	private static void unwindProof(Proof<?> proof, Object entailment) {
+		// Start recursive unwinding of conclusions
+		LinkedList<Object> toDo = new LinkedList<Object>();
+		Set<Object> done = new HashSet<Object>();
 
 		toDo.add(entailment);
 		done.add(entailment);
 
 		for (;;) {
-			C next = toDo.poll();
+			Object next = toDo.poll();
 
 			if (next == null) {
 				break;
 			}
 
-			for (Inference<C> inf : inferences.getInferences(next)) {
+			for (Inference<?> inf : proof.getInferences(next)) {
 				System.out.println(inf);
 				// Recursively unwind premise inferences
-				for (C premise : inf.getPremises()) {
+				for (Object premise : inf.getPremises()) {
 
 					if (done.add(premise)) {
 						toDo.addFirst(premise);

elk-owlapi/src/main/java/org/semanticweb/elk/owlapi/ElkProver.java

@@ -23,6 +23,7 @@
 
 import org.liveontologies.owlapi.proof.OWLProver;
 import org.liveontologies.puli.DynamicProof;
+import org.semanticweb.elk.owlapi.proofs.ElkOwlInference;
 import org.semanticweb.elk.owlapi.proofs.ElkOwlProof;
 import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.reasoner.UnsupportedEntailmentTypeException;
@@ -35,7 +36,7 @@ public ElkProver(ElkReasoner elkReasoner) {
 	}
 
 	@Override
-	public DynamicProof<OWLAxiom> getProof(OWLAxiom entailment)
+	public DynamicProof<ElkOwlInference> getProof(OWLAxiom entailment)
 			throws UnsupportedEntailmentTypeException {
 		return ElkOwlProof.create(getDelegate(), entailment);
 	}

elk-owlapi/src/main/java/org/semanticweb/elk/owlapi/proofs/ElkOwlProof.java

@@ -24,7 +24,8 @@
 import java.util.Collection;
 
 import org.liveontologies.puli.BaseProof;
-import org.liveontologies.puli.GenericDynamicProof;
+import org.liveontologies.puli.DynamicProof;
+import org.liveontologies.puli.Proof;
 import org.liveontologies.puli.Proofs;
 import org.semanticweb.elk.exceptions.ElkException;
 import org.semanticweb.elk.exceptions.ElkRuntimeException;
@@ -36,15 +37,15 @@
 import org.semanticweb.elk.owlapi.ElkConverter;
 import org.semanticweb.elk.owlapi.ElkReasoner;
 import org.semanticweb.elk.owlapi.wrapper.OwlConverter;
-import org.semanticweb.elk.reasoner.entailments.model.EntailmentProof;
+import org.semanticweb.elk.reasoner.entailments.model.EntailmentInference;
 import org.semanticweb.elk.reasoner.query.EntailmentQueryResult;
 import org.semanticweb.elk.reasoner.query.ProperEntailmentQueryResult;
 import org.semanticweb.elk.reasoner.query.UnsupportedIndexingEntailmentQueryResult;
 import org.semanticweb.elk.reasoner.query.UnsupportedQueryTypeEntailmentQueryResult;
 import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.reasoner.UnsupportedEntailmentTypeException;
 
-public class ElkOwlProof extends BaseProof<OWLAxiom, ElkOwlInference>
+public class ElkOwlProof extends BaseProof<ElkOwlInference>
 		implements ElkReasoner.ChangeListener {
 
 	private final ElkReasoner elkReasoner_;
@@ -70,7 +71,7 @@ private ElkOwlProof(ElkReasoner elkReasoner, OWLAxiom elkEntailment) {
 
 	@Override
 	public synchronized Collection<? extends ElkOwlInference> getInferences(
-			OWLAxiom conclusion) {
+			Object conclusion) {
 		ensureSync();
 		return super.getInferences(conclusion);
 	}
@@ -123,7 +124,7 @@ public Void visit(final ProperEntailmentQueryResult properResult)
 						ElkOwlProof.this);
 				final ElkInference.Factory factory = new ElkInferenceOptimizedProducingFactory(
 						producer);
-				final EntailmentProof evidence = properResult
+				final Proof<EntailmentInference> evidence = properResult
 						.getEvidence(false);
 				new ElkProofGenerator(evidence,
 						elkReasoner_.getInternalReasoner(), factory)
@@ -153,9 +154,8 @@ public Void visit(
 
 	};
 
-	public static GenericDynamicProof<OWLAxiom, ElkOwlInference> create(
-			ElkReasoner reasoner, OWLAxiom entailment)
-			throws UnsupportedEntailmentTypeException {
+	public static DynamicProof<ElkOwlInference> create(ElkReasoner reasoner,
+			OWLAxiom entailment) throws UnsupportedEntailmentTypeException {
 		if (reasoner == null) {
 			return Proofs.emptyProof();
 		}

elk-owlapi/src/main/java/org/semanticweb/elk/owlapi/proofs/OwlInternalJustifier.java

@@ -0,0 +1,57 @@
+package org.semanticweb.elk.owlapi.proofs;
+
+/*-
+ * #%L
+ * ELK OWL API Binding
+ * $Id:$
+ * $HeadURL:$
+ * %%
+ * Copyright (C) 2011 - 2017 Department of Computer Science, University of Oxford
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import java.util.Set;
+
+import org.liveontologies.puli.Inference;
+import org.liveontologies.puli.InferenceJustifier;
+import org.semanticweb.elk.owl.interfaces.ElkAxiom;
+import org.semanticweb.elk.owlapi.ElkConverter;
+import org.semanticweb.elk.proofs.InternalJustifier;
+import org.semanticweb.owlapi.model.OWLAxiom;
+
+import com.google.common.base.Function;
+import com.google.common.collect.ImmutableSet;
+import com.google.common.collect.Iterables;
+
+public class OwlInternalJustifier
+		implements InferenceJustifier<Inference<?>, Set<OWLAxiom>>,
+		Function<ElkAxiom, OWLAxiom> {
+
+	private final InferenceJustifier<Inference<?>, Set<? extends ElkAxiom>> internalJustifier_ = new InternalJustifier();
+
+	private final ElkConverter elkConverter_ = ElkConverter.getInstance();
+
+	@Override
+	public Set<OWLAxiom> getJustification(Inference<?> inference) {
+		return ImmutableSet.copyOf(Iterables.transform(
+				internalJustifier_.getJustification(inference), this));
+	}
+
+	@Override
+	public OWLAxiom apply(final ElkAxiom input) {
+		return elkConverter_.convert(input);
+	}
+
+}

elk-owlapi/src/main/java/org/semanticweb/elk/owlapi/proofs/OwlInternalProof.java

@@ -23,11 +23,8 @@
 
 import java.util.Arrays;
 import java.util.Collection;
-import java.util.Set;
 
 import org.liveontologies.puli.Inference;
-import org.liveontologies.puli.InferenceJustifier;
-import org.liveontologies.puli.InferenceJustifiers;
 import org.liveontologies.puli.Inferences;
 import org.liveontologies.puli.Proof;
 import org.semanticweb.elk.exceptions.ElkException;
@@ -41,18 +38,14 @@
 import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.reasoner.UnsupportedEntailmentTypeException;
 
-import com.google.common.base.Function;
-
-public class OwlInternalProof implements Proof<Object>,
-		InferenceJustifier<Object, Set<? extends OWLAxiom>> {
+public class OwlInternalProof implements Proof<Inference<Object>> {
 
 	private final OwlConverter owlConverter_ = OwlConverter.getInstance();
 	private final ElkConverter elkConverter_ = ElkConverter.getInstance();
 
 	private final OWLAxiom goal_;
 	private final Inference<Object> goalInference_;
 	private final InternalProofExtension proof_;
-	private final InferenceJustifier<Object, ? extends Set<? extends OWLAxiom>> justifier_;
 
 	public OwlInternalProof(final Reasoner reasoner, final OWLAxiom goal) {
 		this.goal_ = goal;
@@ -62,13 +55,6 @@ public OwlInternalProof(final Reasoner reasoner, final OWLAxiom goal) {
 		try {
 			this.proof_ = new InternalProofExtension(reasoner,
 					owlConverter_.convert(goal));
-			this.justifier_ = InferenceJustifiers.transform(proof_,
-					new Function<ElkAxiom, OWLAxiom>() {
-						@Override
-						public OWLAxiom apply(final ElkAxiom input) {
-							return elkConverter_.convert(input);
-						}
-					});
 		} catch (final ElkException e) {
 			throw elkConverter_.convert(e);
 		} catch (final ElkRuntimeException e) {
@@ -93,12 +79,6 @@ public Collection<? extends Inference<Object>> getInferences(
 		return proof_.getInferences(conclusion);
 	}
 
-	@Override
-	public Set<? extends OWLAxiom> getJustification(
-			Inference<Object> inference) {
-		return justifier_.getJustification(inference);
-	}
-
 	private class InternalProofExtension extends InternalProof {
 
 		public InternalProofExtension(final Reasoner reasoner,

elk-owlapi/src/test/java/org/semanticweb/elk/owlapi/proofs/OwlInternalProofTest.java

@@ -52,12 +52,22 @@ public class OwlInternalProofTest {
 
 	// @formatter:off
 	static final String[] IGNORE_LIST = {
-			ElkTestUtils.TEST_INPUT_LOCATION + "/query/entailment/AssertionRanges.owl",// Ranges not supported with assertions
-			ElkTestUtils.TEST_INPUT_LOCATION + "/query/entailment/HasValueRanges.owl",// Ranges not supported with ObjectHasValue
-		};
+			ElkTestUtils.TEST_INPUT_LOCATION
+					+ "/query/entailment/AssertionRanges.owl", // Ranges not
+																// supported
+																// with
+																// assertions
+			ElkTestUtils.TEST_INPUT_LOCATION
+					+ "/query/entailment/HasValueRanges.owl",// Ranges not
+																// supported
+																// with
+																// ObjectHasValue
+	};
 	static final String[] IGNORE_COMPLETENESS_LIST = {
-			ElkTestUtils.TEST_INPUT_LOCATION + "/query/entailment/EmptyOntology.owl",// All entailments are tautologies.
-		};
+			ElkTestUtils.TEST_INPUT_LOCATION
+					+ "/query/entailment/EmptyOntology.owl",// All entailments
+															// are tautologies.
+	};
 	// @formatter:on
 
 	static {
@@ -103,7 +113,7 @@ public void testProofCompleteness() throws Exception {
 		Assume.assumeFalse(TestUtils.ignore(manifest_.getInput(),
 				ElkTestUtils.TEST_INPUT_LOCATION, IGNORE_COMPLETENESS_LIST));
 		ProofTestUtils.proofCompletenessTest(prover_, query_,
-				adapter_.getGoal(), adapter_, adapter_, true);
+				adapter_.getGoal(), adapter_, new OwlInternalJustifier(), true);
 	}
 
 	@Config

elk-owlapi/src/test/java/org/semanticweb/elk/owlapi/proofs/ProofTest.java

@@ -34,6 +34,7 @@
 import org.junit.Test;
 import org.liveontologies.owlapi.proof.OWLProver;
 import org.liveontologies.puli.DynamicProof;
+import org.liveontologies.puli.Inference;
 import org.liveontologies.puli.ProofNode;
 import org.liveontologies.puli.ProofNodes;
 import org.liveontologies.puli.ProofStep;
@@ -388,7 +389,8 @@ public void proofListener() throws Exception {
 			final OWLProver prover = OWLAPITestUtils.createProver(
 					OWLAPITestUtils.createReasoner(ontology, bufferringMode));
 			OWLSubClassOfAxiom entailment = factory.getOWLSubClassOfAxiom(a, b);
-			DynamicProof<OWLAxiom> proof = prover.getProof(entailment);
+			DynamicProof<? extends Inference<OWLAxiom>> proof = prover
+					.getProof(entailment);
 			ProofChangeTracker tracker = new ProofChangeTracker();
 			proof.addListener(tracker);
 

elk-owlapi/src/test/java/org/semanticweb/elk/owlapi/proofs/ProofTestUtils.java

@@ -32,6 +32,7 @@
 import java.util.Set;
 
 import org.liveontologies.owlapi.proof.OWLProver;
+import org.liveontologies.puli.Inference;
 import org.liveontologies.puli.InferenceJustifier;
 import org.liveontologies.puli.InferenceJustifiers;
 import org.liveontologies.puli.Proof;
@@ -66,14 +67,14 @@
  */
 public class ProofTestUtils {
 
-	public static <C> void provabilityTest(final Proof<C> proof,
-			final C conclusion) {
+	public static void provabilityTest(final Proof<?> proof,
+			final Object conclusion) {
 		assertTrue(String.format("Conclusion %s not derivable!", conclusion),
 				isDerivable(proof, conclusion));
 	}
 
-	public static <C> boolean isDerivable(final Proof<C> proof,
-			final C conclusion) {
+	public static boolean isDerivable(final Proof<?> proof,
+			final Object conclusion) {
 		return Proofs.isDerivable(proof, conclusion);
 	}
 
@@ -163,25 +164,27 @@ public static void proofCompletenessTest(final OWLProver prover,
 	public static void proofCompletenessTest(final OWLProver prover,
 			final OWLAxiom conclusion, final boolean mustNotBeATautology) {
 		final OWLOntology ontology = prover.getRootOntology();
-		final Proof<OWLAxiom> proof = Proofs.addAssertedInferences(
+		Proof<Inference<OWLAxiom>> proof = Proofs.removeAssertedInferences(
 				prover.getProof(conclusion),
 				ontology.getAxioms(Imports.INCLUDED));
-		final InferenceJustifier<OWLAxiom, ? extends Set<? extends OWLAxiom>> justifier = InferenceJustifiers
+		final InferenceJustifier<Inference<OWLAxiom>, ? extends Set<? extends OWLAxiom>> justifier = InferenceJustifiers
 				.justifyAssertedInferences();
 		proofCompletenessTest(prover, conclusion, conclusion, proof, justifier,
 				mustNotBeATautology);
 	}
 
-	public static <C> void proofCompletenessTest(final OWLProver prover,
-			final OWLAxiom entailment, final C conclusion, final Proof<C> proof,
-			final InferenceJustifier<C, ? extends Set<? extends OWLAxiom>> justifier) {
+	public static <I extends Inference<?>> void proofCompletenessTest(
+			final OWLProver prover, final OWLAxiom entailment,
+			final Object conclusion, final Proof<? extends I> proof,
+			final InferenceJustifier<? super I, ? extends Set<? extends OWLAxiom>> justifier) {
 		proofCompletenessTest(prover, entailment, conclusion, proof, justifier,
 				false);
 	}
 
-	public static <C> void proofCompletenessTest(final OWLProver prover,
-			final OWLAxiom entailment, final C conclusion, final Proof<C> proof,
-			final InferenceJustifier<C, ? extends Set<? extends OWLAxiom>> justifier,
+	public static <I extends Inference<?>> void proofCompletenessTest(
+			final OWLProver prover, final OWLAxiom entailment,
+			final Object conclusion, final Proof<? extends I> proof,
+			final InferenceJustifier<? super I, ? extends Set<? extends OWLAxiom>> justifier,
 			final boolean mustNotBeATautology) {
 
 		final OWLOntology ontology = prover.getRootOntology();

elk-proofs/src/main/java/org/semanticweb/elk/owl/inferences/ElkProof.java

@@ -22,8 +22,7 @@
 package org.semanticweb.elk.owl.inferences;
 
 import org.liveontologies.puli.Proof;
-import org.semanticweb.elk.owl.interfaces.ElkAxiom;
 
-public interface ElkProof extends Proof<ElkAxiom> {
+public interface ElkProof extends Proof<ElkInference> {
 
 }