Merge branch 'version4' into feature/protege-refactoring-reflection

SmartDataAnalytics · Nov 5, 2021 · 73acc7c · 73acc7c
2 parents eef330d + 59fdc95
commit 73acc7c
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diff --git a/binding/owlapi/src/test/java/it/unibz/inf/ontop/owlapi/LeftJoinProfTest.java b/binding/owlapi/src/test/java/it/unibz/inf/ontop/owlapi/LeftJoinProfTest.java
@@ -1,6 +1,7 @@
 package it.unibz.inf.ontop.owlapi;
 
 import com.google.common.collect.ImmutableList;
+import com.google.common.collect.Lists;
 import org.junit.*;
 
 import java.util.Arrays;
@@ -18,7 +19,8 @@ public class LeftJoinProfTest extends AbstractOWLAPITest {
     public static void setUp() throws Exception {
         initOBDA("/test/redundant_join/redundant_join_fk_create.sql",
                 "/test/redundant_join/redundant_join_fk_test.obda",
-                "/test/redundant_join/redundant_join_fk_test.owl");
+                "/test/redundant_join/redundant_join_fk_test.owl",
+                "/test/redundant_join/redundant_join_fk_test.properties");
 
     }
 
@@ -1242,6 +1244,35 @@ public void testNonOptimizableLJAndJoinMix() throws Exception {
         assertTrue(sql.toUpperCase().contains("LEFT"));
     }
 
+    @Test
+    public void testValuesNodeOntologyProperty() throws Exception {
+        String querySelect = "SELECT ?o WHERE {\n" +
+                "?s <http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#conductsLab> ?o\n" +
+                "}";
+
+        checkReturnedValues(querySelect, "o", ImmutableList.of(
+                // From the facts
+                "<http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/Algorithms>",
+                "<http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/DataIntegration>"));
+
+    }
+
+    @Test
+    public void testAggregationMappingProfStudentCountProperty() throws Exception {
+
+        String querySelect =  "PREFIX : <http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#>\n" +
+                "\n" +
+                "SELECT ?v\n" +
+                "WHERE {\n" +
+                "?p a :Teacher ;\n" +
+                "   :nbStudents ?v .\n" +
+                "}" +
+                "ORDER BY ?v\n" ;
+
+        ImmutableList<String> expectedValues = ImmutableList.of("\"12\"^^xsd:integer", "\"13\"^^xsd:integer", "\"21\"^^xsd:integer");
+        checkReturnedValues(querySelect, "v", expectedValues);
+    }
+
     private static boolean containsMoreThanOneOccurrence(String query, String pattern) {
         int firstOccurrenceIndex = query.indexOf(pattern);
         if (firstOccurrenceIndex >= 0) {

diff --git a/binding/owlapi/src/test/java/it/unibz/inf/ontop/owlapi/RedundantJoinFKProfTest.java b/binding/owlapi/src/test/java/it/unibz/inf/ontop/owlapi/RedundantJoinFKProfTest.java
@@ -12,7 +12,8 @@ public class RedundantJoinFKProfTest extends AbstractOWLAPITest {
     public static void setUp() throws Exception {
         initOBDA("/test/redundant_join/redundant_join_fk_create.sql",
                 "/test/redundant_join/redundant_join_fk_test.obda",
-                "/test/redundant_join/redundant_join_fk_test.owl");
+                "/test/redundant_join/redundant_join_fk_test.owl",
+                "/test/redundant_join/redundant_join_fk_test.properties");
     }
 
     @AfterClass

diff --git a/binding/owlapi/src/test/resources/test/redundant_join/redundant_join_fk_test.obda b/binding/owlapi/src/test/resources/test/redundant_join/redundant_join_fk_test.obda
@@ -41,5 +41,9 @@ mappingId	MAPID-course
 target		:course/{course_id} a :Course ; :duration {duration} ; :nbStudents {nb_students} .
 source		SELECT * FROM course;
 
+mappingId	MAPID-prof-student-count
+target		:professor/{prof_id} :nbStudents {count} .
+source		SELECT t.prof_id, sum(c.nb_students) AS count FROM teaching t, course c WHERE t.course_id = c.course_id GROUP BY prof_id
+
 ]]
 
diff --git a/binding/owlapi/src/test/resources/test/redundant_join/redundant_join_fk_test.owl b/binding/owlapi/src/test/resources/test/redundant_join/redundant_join_fk_test.owl
@@ -39,6 +39,13 @@
     </owl:ObjectProperty>
 
 
+    <!-- http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#conductsLab -->
+
+    <owl:ObjectProperty rdf:about="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#conductsLab">
+        <rdfs:domain rdf:resource="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#Teacher"/>
+        <rdfs:range rdf:resource="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#Course"/>
+    </owl:ObjectProperty>
+
 
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
@@ -123,6 +130,63 @@
     <!-- http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#Teacher -->
 
     <owl:Class rdf:about="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#Teacher"/>
+
+
+
+<!--
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Individuals
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/Algorithms -->
+
+    <owl:NamedIndividual rdf:about="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/Algorithms"/>
+
+
+
+<!-- http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/DataIntegration -->
+
+    <owl:NamedIndividual rdf:about="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/DataIntegration"/>
+
+
+
+<!-- http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/Programming -->
+
+    <owl:NamedIndividual rdf:about="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/Programming"/>
+
+
+
+<!-- http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/Mathematics -->
+
+    <owl:NamedIndividual rdf:about="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/Mathematics"/>
+
+
+
+<!-- http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/Painting -->
+
+    <owl:NamedIndividual rdf:about="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/Painting"/>
+
+
+
+<!-- http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#teacher/Jane -->
+
+    <owl:NamedIndividual rdf:about="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#teacher/Jane">
+            <conductsLab rdf:resource="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/Algorithms"/>
+    </owl:NamedIndividual>
+
+
+
+<!-- http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#teacher/Joe -->
+
+    <owl:NamedIndividual rdf:about="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#teacher/Joe">
+            <conductsLab rdf:resource="http://www.semanticweb.org/user/ontologies/2016/8/untitled-ontology-84#course/DataIntegration"/>
+    </owl:NamedIndividual>
 </rdf:RDF>
 
 

diff --git a/binding/owlapi/src/test/resources/test/redundant_join/redundant_join_fk_test.properties b/binding/owlapi/src/test/resources/test/redundant_join/redundant_join_fk_test.properties
@@ -0,0 +1 @@
+ontop.allowRetrievingBlackBoxViewMetadataFromDB = true
diff --git a/binding/rdf4j/src/main/java/it/unibz/inf/ontop/rdf4j/repository/OntopRepository.java b/binding/rdf4j/src/main/java/it/unibz/inf/ontop/rdf4j/repository/OntopRepository.java
@@ -3,6 +3,7 @@
 import it.unibz.inf.ontop.answering.cache.HTTPCacheHeaders;
 import it.unibz.inf.ontop.injection.OntopSystemConfiguration;
 import it.unibz.inf.ontop.rdf4j.repository.impl.OntopVirtualRepository;
+import org.eclipse.rdf4j.repository.RepositoryException;
 
 /**
  * Ontop RDF4J repository
@@ -11,6 +12,9 @@ public interface OntopRepository extends org.eclipse.rdf4j.repository.Repository
 
     HTTPCacheHeaders getHttpCacheHeaders();
 
+    @Override
+    OntopRepositoryConnection getConnection() throws RepositoryException;
+
     static OntopVirtualRepository defaultRepository(OntopSystemConfiguration configuration) {
         return new OntopVirtualRepository(configuration);
     }

diff --git a/...ng/rdf4j/src/main/java/it/unibz/inf/ontop/rdf4j/repository/OntopRepositoryConnection.java b/...ng/rdf4j/src/main/java/it/unibz/inf/ontop/rdf4j/repository/OntopRepositoryConnection.java
@@ -0,0 +1,29 @@
+package it.unibz.inf.ontop.rdf4j.repository;
+
+import com.google.common.collect.ImmutableMultimap;
+import org.eclipse.rdf4j.query.*;
+import org.eclipse.rdf4j.repository.RepositoryException;
+
+public interface OntopRepositoryConnection extends org.eclipse.rdf4j.repository.RepositoryConnection {
+
+    Query prepareQuery(QueryLanguage ql, String query, ImmutableMultimap<String, String> httpHeaders)
+            throws RepositoryException, MalformedQueryException;
+
+    Query prepareQuery(QueryLanguage ql, String queryString, String baseIRI,
+                       ImmutableMultimap<String, String> httpHeaders)
+            throws RepositoryException, MalformedQueryException;
+
+    TupleQuery prepareTupleQuery(QueryLanguage ql, String queryString, String baseIRI,
+                                 ImmutableMultimap<String, String> httpHeaders)
+            throws RepositoryException, MalformedQueryException;
+
+    GraphQuery prepareGraphQuery(QueryLanguage ql, String queryString,
+                                 String baseIRI, ImmutableMultimap<String, String> httpHeaders)
+            throws RepositoryException, MalformedQueryException;
+
+    BooleanQuery prepareBooleanQuery(QueryLanguage ql, String queryString,
+                                     String baseIRI, ImmutableMultimap<String, String> httpHeaders)
+            throws RepositoryException, MalformedQueryException;
+
+    String reformulate(String sparql) throws RepositoryException;
+}
diff --git a/...itory/impl/OntopRepositoryConnection.java → ...y/impl/OntopRepositoryConnectionImpl.java b/...itory/impl/OntopRepositoryConnection.java → ...y/impl/OntopRepositoryConnectionImpl.java
@@ -5,11 +5,11 @@
 import it.unibz.inf.ontop.answering.reformulation.input.RDF4JInputQueryFactory;
 import it.unibz.inf.ontop.answering.reformulation.input.SPARQLQuery;
 import it.unibz.inf.ontop.exception.OntopConnectionException;
-import it.unibz.inf.ontop.exception.OntopInvalidInputQueryException;
 import it.unibz.inf.ontop.exception.OntopReformulationException;
 import it.unibz.inf.ontop.injection.OntopSystemSettings;
 import it.unibz.inf.ontop.rdf4j.query.impl.*;
 import it.unibz.inf.ontop.rdf4j.repository.OntopRepository;
+import it.unibz.inf.ontop.rdf4j.repository.OntopRepositoryConnection;
 import org.eclipse.rdf4j.IsolationLevel;
 import org.eclipse.rdf4j.IsolationLevels;
 import org.eclipse.rdf4j.common.iteration.CloseableIteratorIteration;
@@ -33,10 +33,10 @@
 import java.net.URL;
 import java.util.*;
 
-public class OntopRepositoryConnection implements org.eclipse.rdf4j.repository.RepositoryConnection {
+public class OntopRepositoryConnectionImpl implements OntopRepositoryConnection {
 
     private static final String READ_ONLY_MESSAGE = "Ontop is a read-only system";
-    private static Logger LOGGER = LoggerFactory.getLogger(OntopRepositoryConnection.class);
+    private static Logger LOGGER = LoggerFactory.getLogger(OntopRepositoryConnectionImpl.class);
     private OntopRepository repository;
     private OntopConnection ontopConnection;
     private final RDF4JInputQueryFactory inputQueryFactory;
@@ -47,8 +47,8 @@ public class OntopRepositoryConnection implements org.eclipse.rdf4j.repository.R
     private Map<String, String> namespaces;
 
 
-    OntopRepositoryConnection(OntopRepository rep, OntopConnection connection,
-                              RDF4JInputQueryFactory inputQueryFactory, OntopSystemSettings settings) {
+    OntopRepositoryConnectionImpl(OntopRepository rep, OntopConnection connection,
+                                  RDF4JInputQueryFactory inputQueryFactory, OntopSystemSettings settings) {
         this.repository = rep;
         this.ontopConnection = connection;
         this.inputQueryFactory = inputQueryFactory;
@@ -322,6 +322,7 @@ public BooleanQuery prepareBooleanQuery(QueryLanguage ql, String queryString,
         return prepareBooleanQuery(ql, queryString, baseIRI, ImmutableMultimap.of());
     }
 
+    @Override
     public BooleanQuery prepareBooleanQuery(QueryLanguage ql, String queryString,
                 String baseIRI, ImmutableMultimap<String, String> httpHeaders) throws RepositoryException, MalformedQueryException {
         //Prepares true/false queries.
@@ -351,6 +352,7 @@ public GraphQuery prepareGraphQuery(QueryLanguage ql, String queryString, String
         return prepareGraphQuery(ql, queryString, baseIRI, ImmutableMultimap.of());
     }
 
+    @Override
     public GraphQuery prepareGraphQuery(QueryLanguage ql, String queryString,
                                         String baseIRI, ImmutableMultimap<String, String> httpHeaders)
             throws RepositoryException, MalformedQueryException {
@@ -376,6 +378,7 @@ public Query prepareQuery(QueryLanguage ql, String query)
         return prepareTupleQuery(ql, query, null, ImmutableMultimap.of());
     }
 
+    @Override
     public Query prepareQuery(QueryLanguage ql, String query, ImmutableMultimap<String, String> httpHeaders)
             throws RepositoryException, MalformedQueryException {
         //Prepares a query for evaluation on this repository (optional operation).
@@ -390,6 +393,7 @@ public Query prepareQuery(QueryLanguage ql, String queryString, String baseIRI)
         return prepareQuery(ql, queryString, baseIRI, ImmutableMultimap.of());
     }
 
+    @Override
     public Query prepareQuery(QueryLanguage ql, String queryString, String baseIRI,
                               ImmutableMultimap<String, String> httpHeaders)
             throws RepositoryException, MalformedQueryException {
@@ -426,6 +430,7 @@ public TupleQuery prepareTupleQuery(QueryLanguage ql, String queryString, String
         return prepareTupleQuery(ql, queryString, baseIRI, ImmutableMultimap.of());
     }
 
+    @Override
     public TupleQuery prepareTupleQuery(QueryLanguage ql, String queryString, String baseIRI,
                                         ImmutableMultimap<String, String> httpHeaders)
             throws RepositoryException, MalformedQueryException {
@@ -605,10 +610,15 @@ public <E extends Exception> void remove(
         throw new UnsupportedOperationException(READ_ONLY_MESSAGE);
     }
 
+    @Override
     public String reformulate(String sparql)
-            throws OntopConnectionException, OntopInvalidInputQueryException, OntopReformulationException {
-        SPARQLQuery sparqlQuery = ontopConnection.getInputQueryFactory().createSPARQLQuery(sparql);
-        return ontopConnection.createStatement().getExecutableQuery(sparqlQuery).toString();
+            throws RepositoryException {
+        try {
+            SPARQLQuery sparqlQuery = ontopConnection.getInputQueryFactory().createSPARQLQuery(sparql);
+            return ontopConnection.createStatement().getExecutableQuery(sparqlQuery).toString();
+        } catch (OntopReformulationException | OntopConnectionException e) {
+            throw new RepositoryException(e);
+        }
     }
 
 }
diff --git a/.../rdf4j/src/main/java/it/unibz/inf/ontop/rdf4j/repository/impl/OntopVirtualRepository.java b/.../rdf4j/src/main/java/it/unibz/inf/ontop/rdf4j/repository/impl/OntopVirtualRepository.java
@@ -8,6 +8,7 @@
 import it.unibz.inf.ontop.injection.OntopSystemConfiguration;
 import it.unibz.inf.ontop.injection.OntopSystemSettings;
 import it.unibz.inf.ontop.rdf4j.repository.OntopRepository;
+import it.unibz.inf.ontop.rdf4j.repository.OntopRepositoryConnection;
 import org.eclipse.rdf4j.model.ValueFactory;
 import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
 import org.eclipse.rdf4j.repository.RepositoryException;
@@ -53,7 +54,7 @@ public OntopRepositoryConnection getConnection() throws RepositoryException {
         }
 
         try {
-            return new OntopRepositoryConnection(this, getOntopConnection(), inputQueryFactory, settings);
+            return new OntopRepositoryConnectionImpl(this, getOntopConnection(), inputQueryFactory, settings);
         } catch (Exception e) {
             logger.error("Error creating repo connection: " + e.getMessage());
             throw new RepositoryException(e);

diff --git a/...df4j/src/test/java/it/unibz/inf/ontop/rdf4j/repository/AbstractMultipleOptionalsTest.java b/...df4j/src/test/java/it/unibz/inf/ontop/rdf4j/repository/AbstractMultipleOptionalsTest.java
@@ -59,7 +59,7 @@ public void testThreeOptionals() {
     }
 
     @Test
-    public void testThreeOptionalsWithLimit() {
+    public void testThreeOptionalsWithOrderBy() {
         String query = "PREFIX ex: <http://example.org/>\n" +
                 "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n" +
                 "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n" +

diff --git a/binding/rdf4j/src/test/java/it/unibz/inf/ontop/rdf4j/repository/AbstractRDF4JTest.java b/binding/rdf4j/src/test/java/it/unibz/inf/ontop/rdf4j/repository/AbstractRDF4JTest.java
@@ -4,11 +4,11 @@
 import com.google.common.collect.ImmutableMap;
 import com.google.common.collect.ImmutableSet;
 import it.unibz.inf.ontop.injection.OntopSQLOWLAPIConfiguration;
+import it.unibz.inf.ontop.rdf4j.repository.impl.OntopVirtualRepository;
 import org.eclipse.rdf4j.model.Statement;
 import org.eclipse.rdf4j.model.Value;
 import org.eclipse.rdf4j.query.*;
 import org.eclipse.rdf4j.query.impl.MapBindingSet;
-import org.eclipse.rdf4j.repository.RepositoryConnection;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -31,14 +31,14 @@ public class AbstractRDF4JTest {
     private static final String PASSWORD = "";
     private static final Logger LOGGER = LoggerFactory.getLogger(AbstractRDF4JTest.class);
     private static Connection SQL_CONNECTION;
-    private static RepositoryConnection REPO_CONNECTION;
+    private static OntopRepositoryConnection REPO_CONNECTION;
 
     protected static void initOBDA(String dbScriptRelativePath, String obdaRelativePath) throws SQLException, IOException {
         initOBDA(dbScriptRelativePath, obdaRelativePath, null);
     }
     protected static void initOBDA(String dbScriptRelativePath, String obdaRelativePath,
                                    @Nullable String ontologyRelativePath) throws SQLException, IOException {
-        initOBDA(dbScriptRelativePath, obdaRelativePath, null, null);
+        initOBDA(dbScriptRelativePath, obdaRelativePath, ontologyRelativePath, null);
     }
 
     protected static void initOBDA(String dbScriptRelativePath, String obdaRelativePath,
@@ -95,14 +95,15 @@ protected static void initOBDA(String dbScriptRelativePath, String obdaRelativeP
 
         OntopSQLOWLAPIConfiguration config = builder.build();
 
-        OntopRepository repo = OntopRepository.defaultRepository(config);
+        OntopVirtualRepository repo = OntopRepository.defaultRepository(config);
         repo.init();
         /*
          * Prepare the data connection for querying.
          */
         REPO_CONNECTION = repo.getConnection();
     }
 
+
     protected static void initR2RML(String dbScriptRelativePath, String r2rmlRelativePath) throws SQLException, IOException {
         initR2RML(dbScriptRelativePath, r2rmlRelativePath, null, null);
     }
@@ -149,7 +150,7 @@ protected static void initR2RML(String dbScriptRelativePath, String r2rmlRelativ
 
         OntopSQLOWLAPIConfiguration config = builder.build();
 
-        OntopRepository repo = OntopRepository.defaultRepository(config);
+        OntopVirtualRepository repo = OntopRepository.defaultRepository(config);
         repo.init();
         /*
          * Prepare the data connection for querying.
@@ -196,6 +197,10 @@ protected void runQueryAndCompare(String queryString, ImmutableList<String> expe
         assertEquals(expectedVValues, vValues);
     }
 
+    protected String reformulate(String queryString) {
+        return REPO_CONNECTION.reformulate(queryString);
+    }
+
     protected ImmutableList<String> runQuery(String queryString) {
         return runQuery(queryString, new MapBindingSet());
     }