Merge pull request #265 from mrnolte/236

Automatic GCI conversion
ease-crc · Jul 26, 2022 · b43026d · b43026d
2 parents d8ab8be + 4e4644a
commit b43026d
Show file tree

Hide file tree

Showing 6 changed files with 103 additions and 3 deletions.
diff --git a/scripts/java/src/main/java/main/CIRunner.java b/scripts/java/src/main/java/main/CIRunner.java
@@ -20,10 +20,13 @@ public class CIRunner implements CommandLineRunner {
 	@Autowired
 	private OntologySaver ontologySaver;
 
+	@Autowired
+	private SubclassNothingRewriter gciRewriter;
+
 
 	@Override
 	public void run(final String... args) throws Exception {
-		final CIRunnable[] toRun = {isDefinedInAdder, versionInfoAdder, collapser, ontologySaver};
+		final CIRunnable[] toRun = {gciRewriter, isDefinedInAdder, versionInfoAdder, collapser, ontologySaver};
 		for (final var next : toRun) {
 			next.run();
 		}

diff --git a/scripts/java/src/main/java/main/ci_runners/Collapser.java b/scripts/java/src/main/java/main/ci_runners/Collapser.java
@@ -10,6 +10,7 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Lazy;
 import org.springframework.stereotype.Component;
 import org.springframework.util.CollectionUtils;
 
@@ -21,6 +22,7 @@
 import java.util.stream.Collectors;
 
 @Component
+@Lazy
 public class Collapser implements CIRunnable {
 
 	/**

diff --git a/scripts/java/src/main/java/main/ci_runners/IsDefinedInAdder.java b/scripts/java/src/main/java/main/ci_runners/IsDefinedInAdder.java
@@ -10,12 +10,14 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
 import org.springframework.stereotype.Component;
 
 import java.util.Collection;
 import java.util.HashSet;
 
 @Component
+@Lazy
 public class IsDefinedInAdder implements CIRunnable {
 
 	/**

diff --git a/scripts/java/src/main/java/main/ci_runners/OntologySaver.java b/scripts/java/src/main/java/main/ci_runners/OntologySaver.java
@@ -7,9 +7,11 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
 import org.springframework.stereotype.Component;
 
 @Component
+@Lazy
 public class OntologySaver implements CIRunnable {
 
 	/**

diff --git a/scripts/java/src/main/java/main/ci_runners/SubclassNothingRewriter.java b/scripts/java/src/main/java/main/ci_runners/SubclassNothingRewriter.java
@@ -0,0 +1,91 @@
+package main.ci_runners;
+
+import main.OntologyManager;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
+import org.springframework.stereotype.Component;
+
+import java.util.Optional;
+
+@Component
+@Lazy
+public class SubclassNothingRewriter implements CIRunnable {
+
+	/**
+	 * {@link Logger} of this class.
+	 */
+	private static final Logger LOGGER = LoggerFactory.getLogger(SubclassNothingRewriter.class);
+	private static final OWLDataFactory df = OWLManager.getOWLDataFactory();
+	private final OntologyManager ontologyManager;
+
+	@Autowired
+	public SubclassNothingRewriter(final OntologyManager ontologyManager) {
+		this.ontologyManager = ontologyManager;
+	}
+
+
+	@Override
+	public void run() {
+		ontologyManager.getOntologyManager().getOntologies().forEach(SubclassNothingRewriter::rewriteGCIs);
+	}
+
+	private static void rewriteGCIs(final OWLOntology ontology) {
+		@SuppressWarnings("OptionalGetWithoutIsPresent") final var iri = ontology.getOntologyID().getOntologyIRI()
+		                                                                         .get();
+		final var gcis = ontology.getGeneralClassAxioms();
+		if (gcis.isEmpty()) {
+			return;
+		}
+		LOGGER.info("Rewriting the following GCIs from ontology {}", iri);
+
+		gcis.forEach(next -> {
+			final Optional<OWLAxiom> rewritten = rewrite(next);
+			if (rewritten.isEmpty()) {
+				return;
+			}
+			LOGGER.info("Rewrote {} to {}", next, rewritten.get());
+			ontology.removeAxiom(next);
+			ontology.add(rewritten.get());
+		});
+
+	}
+
+	@SuppressWarnings("ChainOfInstanceofChecks")
+	private static Optional<OWLAxiom> rewrite(final OWLAxiom gci) {
+		if (gci instanceof OWLSubClassOfAxiom subClassOfAxiom) {
+			if (!subClassOfAxiom.getSuperClass().isOWLNothing()) {
+				return Optional.empty();
+			}
+			if (subClassOfAxiom.getSubClass() instanceof OWLObjectIntersectionOf intersection) {
+				return rewriteIntersectionSubclassNothing(intersection);
+			}
+			if (subClassOfAxiom.getSubClass() instanceof OWLObjectSomeValuesFrom someValuesFrom) {
+				final var rewriting = df.getOWLObjectPropertyRangeAxiom(someValuesFrom.getProperty(),
+				                                                        df.getOWLObjectComplementOf(
+						                                                        someValuesFrom.getFiller()),
+				                                                        gci.getAnnotations());
+				return Optional.of(rewriting);
+			}
+		}
+		return Optional.empty();
+	}
+
+	private static Optional<OWLAxiom> rewriteIntersectionSubclassNothing(final OWLObjectIntersectionOf intersection) {
+		var atomicClass = intersection.operands().filter(AsOWLClass::isOWLClass).findAny();
+		if (atomicClass.isEmpty()) {
+			atomicClass = intersection.operands().findFirst();
+		}
+		if (atomicClass.isEmpty()) {
+			throw new IllegalArgumentException("Corrupted GCI:" + intersection + " subclass of owl:Nothing");
+		}
+
+		final OWLClassExpression finalAtomicClass = atomicClass.get();
+		final var rewriting = df.getOWLSubClassOfAxiom(finalAtomicClass, df.getOWLObjectComplementOf(
+				df.getOWLObjectIntersectionOf(intersection.operands().filter(next -> !next.equals(finalAtomicClass)))));
+		return Optional.of(rewriting);
+	}
+}
diff --git a/scripts/java/src/main/java/main/ci_runners/VersionInfoAdder.java b/scripts/java/src/main/java/main/ci_runners/VersionInfoAdder.java
@@ -8,20 +8,20 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.Lazy;
 import org.springframework.stereotype.Component;
 
 @Component
+@Lazy
 public class VersionInfoAdder implements CIRunnable {
 
-
 	/**
 	 * {@link Logger} of this class.
 	 */
 	private static final Logger LOGGER = LoggerFactory.getLogger(VersionInfoAdder.class);
 
 	private final OntologyManager ontologyManager;
 
-
 	private final String versionInfo;
 
 	@Autowired