Merge branch 'version4' of https://github.com/ontop/ontop into version4

# Conflicts: # pom.xml # test/sparql-compliance/pom.xml
SmartDataAnalytics · Feb 25, 2021 · cd626dd · cd626dd
2 parents 2b1d993 + ba049d8
commit cd626dd
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diff --git a/binding/owlapi/pom.xml b/binding/owlapi/pom.xml
@@ -1,70 +1,65 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>it.unibz.inf.ontop</groupId>
- <artifactId>ontop-binding</artifactId>
- <version>4.1.0-beta-1-SNAPSHOT</version>
- <relativePath>..</relativePath>
- </parent>
- <artifactId>ontop-owlapi</artifactId>
- <name>ontop-owlapi</name>
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
- <dependencies>
- <dependency>
- <groupId>ch.qos.logback</groupId>
- <artifactId>logback-classic</artifactId>
- </dependency>
- <dependency>
- <groupId>ch.qos.logback</groupId>
- <artifactId>logback-core</artifactId>
- </dependency>
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-api</artifactId>
- </dependency>
+ <modelVersion>4.0.0</modelVersion>
 
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>${project.groupId}</groupId>
- <artifactId>ontop-system-owlapi</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-api</artifactId>
- </dependency>
- <dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-apibinding</artifactId>
- </dependency>
+ <parent>
+ <groupId>it.unibz.inf.ontop</groupId>
+ <artifactId>ontop-binding</artifactId>
+ <version>4.1.0-beta-1-SNAPSHOT</version>
+ </parent>
 
- <dependency>
- <groupId>${project.groupId}</groupId>
- <artifactId>ontop-system-sql-owlapi</artifactId>
- <scope>test</scope>
- <version>${project.version}</version>
- </dependency>
- <dependency>
- <groupId>org.orbisgis</groupId>
- <artifactId>h2gis-ext</artifactId>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.eclipse.rdf4j</groupId>
- <artifactId>rdf4j-queryparser-sparql</artifactId>
- </dependency>
+ <artifactId>ontop-owlapi</artifactId>
 
+ <dependencies>
+ <dependency>
+ <groupId>ch.qos.logback</groupId>
+ <artifactId>logback-classic</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>ch.qos.logback</groupId>
+ <artifactId>logback-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>${project.groupId}</groupId>
+ <artifactId>ontop-system-owlapi</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>net.sourceforge.owlapi</groupId>
+ <artifactId>owlapi-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>net.sourceforge.owlapi</groupId>
+ <artifactId>owlapi-apibinding</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>${project.groupId}</groupId>
+ <artifactId>ontop-system-sql-owlapi</artifactId>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.orbisgis</groupId>
+ <artifactId>h2gis-ext</artifactId>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.eclipse.rdf4j</groupId>
+ <artifactId>rdf4j-queryparser-sparql</artifactId>
+ </dependency>
  <dependency>
  <groupId>com.google.guava</groupId>
  <artifactId>guava</artifactId>
- </dependency>
+ </dependency>
  </dependencies>
 
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- </properties>
 </project>
diff --git a/binding/owlapi/src/main/java/it/unibz/inf/ontop/owlapi/impl/QuestOWL.java b/binding/owlapi/src/main/java/it/unibz/inf/ontop/owlapi/impl/QuestOWL.java
@@ -228,7 +228,8 @@ public OntopOWLConnection getConnection() throws ReasonerInternalException {
  try {
  OntopConnection conn = queryEngine.getConnection();
  return new DefaultOntopOWLConnection(conn, inputQueryFactory);
- } catch (OntopConnectionException e) {
+ }
+ catch (OntopConnectionException e) {
  // TODO: find a better exception?
  throw new ReasonerInternalException(e);
  }

diff --git a/...lapi/src/main/java/it/unibz/inf/ontop/owlapi/validation/OntopOWLEmptyEntitiesChecker.java b/...lapi/src/main/java/it/unibz/inf/ontop/owlapi/validation/OntopOWLEmptyEntitiesChecker.java
@@ -0,0 +1,189 @@
+package it.unibz.inf.ontop.owlapi.validation;
+
+/*
+ * #%L
+ * ontop-obdalib-core
+ * %%
+ * Copyright (C) 2009 - 2014 Free University of Bozen-Bolzano
+ * %%
+ * 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 it.unibz.inf.ontop.owlapi.connection.OWLConnection;
+import it.unibz.inf.ontop.owlapi.connection.OWLStatement;
+import it.unibz.inf.ontop.owlapi.resultset.TupleOWLResultSet;
+import it.unibz.inf.ontop.spec.ontology.*;
+import org.apache.commons.rdf.api.IRI;
+import org.semanticweb.owlapi.model.OWLException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+import java.util.function.Function;
+import java.util.function.Predicate;
+
+/**
+ * Return empty concepts and roles, based on the mappings. Given an ontology,
+ * which is connected to a database via mappings, generate a suitable set of
+ * queries that test if there are empty concepts, concepts that are no populated
+ * to anything.
+ */
+public class OntopOWLEmptyEntitiesChecker {
+
+ private static final String CLASS_QUERY = "SELECT ?x WHERE {?x a <%s>.} LIMIT 1";
+ private static final String PROPERTY_QUERY = "SELECT * WHERE {?x <%s> ?y.} LIMIT 1";
+
+ private static final Logger LOG = LoggerFactory.getLogger(OntopOWLEmptyEntitiesChecker.class);
+
+ private final ClassifiedTBox onto;
+ private final OWLConnection conn;
+
+ /**
+ * Generate SPARQL queries to check if there are instances for each concept and role in the ontology
+ *
+ * @param tbox the ontology, conn QuestOWL connection
+ */
+ public OntopOWLEmptyEntitiesChecker(ClassifiedTBox tbox, OWLConnection conn) {
+ this.onto = tbox;
+ this.conn = conn;
+ }
+
+ public Iterable<IRI> emptyClasses() {
+ return () -> new FunctionIterator<>(
+ new FilterIterator<>(onto.classes().iterator(), this::isEmpty),
+ OClass::getIRI);
+ }
+
+ public Iterable<IRI> emptyProperties() {
+ return () -> new ChainIterator<>(
+ new FunctionIterator<>(
+ new FilterIterator<>(onto.objectProperties().iterator(), this::isEmpty),
+ ObjectPropertyExpression::getIRI),
+ new FunctionIterator<>(
+ new FilterIterator<>(onto.dataProperties().iterator(), this::isEmpty),
+ DataPropertyExpression::getIRI));
+ }
+
+ private boolean isEmpty(OClass c) {
+ return !c.isTop() && !c.isBottom()
+ && !isResultNonEmpty(String.format(CLASS_QUERY, c.getIRI().getIRIString()), conn);
+ }
+
+ private boolean isEmpty(ObjectPropertyExpression c) {
+ return !c.isTop() && !c.isBottom()
+ && !isResultNonEmpty(String.format(PROPERTY_QUERY, c.getIRI().getIRIString()), conn);
+ }
+
+ private boolean isEmpty(DataPropertyExpression c) {
+ return !c.isTop() && !c.isBottom()
+ && !isResultNonEmpty(String.format(PROPERTY_QUERY, c.getIRI().getIRIString()), conn);
+ }
+
+
+ private static boolean isResultNonEmpty(String query, OWLConnection conn) {
+ try (OWLStatement stm = conn.createStatement();
+ TupleOWLResultSet rs = stm.executeSelectQuery(query)) {
+ return rs.hasNext();
+ }
+ catch (OWLException e) {
+ LOG.debug("Error executing SPARQL query", e);
+ return false;
+ }
+ }
+
+ private static class ChainIterator<E> implements Iterator<E> {
+ private final Iterator<E> first, second;
+
+ ChainIterator(Iterator<E> first, Iterator<E> second) {
+ this.first = first;
+ this.second = second;
+ }
+
+ @Override
+ public boolean hasNext() {
+ return first.hasNext() || second.hasNext();
+ }
+
+ @Override
+ public E next() {
+ return first.hasNext() ? first.next() : second.next();
+ }
+ }
+
+ private static class FunctionIterator<E, F> implements Iterator<F> {
+ private final Iterator<E> iterator;
+ private final Function<E, F> function;
+
+ FunctionIterator(Iterator<E> iterator, Function<E, F> function) {
+ this.iterator = iterator;
+ this.function = function;
+ }
+
+ @Override
+ public boolean hasNext() {
+ return iterator.hasNext();
+ }
+
+ @Override
+ public F next() {
+ return function.apply(iterator.next());
+ }
+ }
+
+ private static class FilterIterator<E> implements Iterator<E> {
+
+ private final Iterator<E> iterator;
+ private final Predicate<E> filter;
+
+ private E next;
+ private boolean atNext;
+
+ FilterIterator(Iterator<E> iterator, Predicate<E> filter) {
+ this.iterator = iterator;
+ this.filter = filter;
+ }
+
+ @Override
+ public boolean hasNext() {
+ if (!atNext)
+ atNext = moveToNext();
+
+ return atNext;
+ }
+
+ @Override
+ public E next() {
+ if (!atNext) {
+ atNext = !moveToNext();
+ if (!atNext)
+ throw new NoSuchElementException();
+ }
+
+ atNext = false;
+ return next;
+ }
+
+ private boolean moveToNext() {
+ while (iterator.hasNext()) {
+ next = iterator.next();
+ if (filter.test(next)) {
+ return true;
+ }
+ }
+ return false;
+ }
+ }
+}
+