Rewritten ontology loading of class RLPlusOntology. Now query-dependent skolemisation works.

1 files changed, 47 insertions, 44 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java b/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
index 767d379..d961223 100644
--- a/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
+++ b/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
@@ -1,5 +1,6 @@
 package uk.ac.ox.cs.pagoda.approx;
 
+import org.apache.commons.io.FilenameUtils;
 import org.semanticweb.HermiT.Configuration;
 import org.semanticweb.HermiT.model.DLClause;
 import org.semanticweb.HermiT.model.DLOntology;
@@ -19,25 +20,22 @@ import java.nio.file.Paths;
 import java.util.*;
 
 public class RLPlusOntology implements KnowledgeBase {
-        
+
+        private static final String DEFAULT_ONTOLOGY_FILE_EXTENSION = "owl";
         OWLOntologyManager manager;
         OWLDataFactory factory;
         String ontologyIRI;
         String corrFileName = null;
         String outputPath, aBoxPath;
-        
         OWLOntology inputOntology = null;
         OWLOntology tBox = null;
         OWLOntology aBox = null;
         OWLOntology restOntology = null;
         OWLOntology outputOntology = null; //RL ontology
-        
         DLOntology dlOntology = null;
         int rlCounter = 0;
-        
-        LinkedList<Clause> clauses; 
+        LinkedList<Clause> clauses;
         Map<OWLAxiom, OWLAxiom> correspondence;
-        
         BottomStrategy botStrategy;
         Random random = new Random(19900114);
         private Map<OWLClassExpression, Integer> subCounter = null;
@@ -45,7 +43,7 @@ public class RLPlusOntology implements KnowledgeBase {
 
         // FIXME multiple anonymous ontologies
         @Override
-        public void load(OWLOntology o, uk.ac.ox.cs.pagoda.constraints.BottomStrategy bottomStrategy) {
+        public void load(OWLOntology ontology, uk.ac.ox.cs.pagoda.constraints.BottomStrategy bottomStrategy) {
                 if (bottomStrategy instanceof UnaryBottom)
                         botStrategy = BottomStrategy.UNARY;
                 else if (bottomStrategy instanceof NullaryBottom)
@@ -55,55 +53,60 @@ public class RLPlusOntology implements KnowledgeBase {
 
                 if(corrFileName == null)
                         corrFileName = "rlplus.crr";
-                manager = o.getOWLOntologyManager();
+                manager = ontology.getOWLOntologyManager();
 //              manager = OWLManager.createOWLOntologyManager();
                 factory = manager.getOWLDataFactory();
-                inputOntology = o;
+                inputOntology = ontology;
 
                 try {
-                        String path = OWLHelper.getOntologyPath(inputOntology);
-                        String name = path.substring(path.lastIndexOf(Utility.JAVA_FILE_SEPARATOR));
-                        String originalExtension = name.lastIndexOf(".") >= 0 ? name.substring(name.lastIndexOf(".")) : "";
-
-                        if (inputOntology.getOntologyID().getOntologyIRI() == null)
-                                ontologyIRI = "http://www.example.org/anonymous-ontology" + originalExtension;
+                        IRI ontologyIri;
+                        if(ontology.isAnonymous()) {
+                                String anonymousOntologySuffix = Long.toString(System.currentTimeMillis());
+                                ontologyIri = IRI.create("http://www.example.org/", "anonymous-ontology-"
+                                                + anonymousOntologySuffix + "." + DEFAULT_ONTOLOGY_FILE_EXTENSION);
+                        }
                         else
-                                ontologyIRI = inputOntology.getOntologyID().getOntologyIRI().toString();
-
-                        String tOntoIRI = ontologyIRI;
-                        if (!tOntoIRI.endsWith(originalExtension)) tOntoIRI += originalExtension;
-
-                        String rlOntologyIRI = originalExtension.isEmpty() ? tOntoIRI + "-RL.owl" : tOntoIRI.replaceFirst(originalExtension, "-RL.owl");
-                        String rlDocumentIRI = (outputPath = Paths.get(Utility.getGlobalTempDirAbsolutePath(), "RL.owl").toString());
-                        outputOntology = manager.createOntology(IRI.create(rlOntologyIRI));
-                        manager.setOntologyDocumentIRI(outputOntology, IRI.create(Utility.toFileIRI(rlDocumentIRI)));
-
-                        String tBoxOntologyIRI, aBoxOntologyIRI;
-                        tBoxOntologyIRI =
-                                        originalExtension.isEmpty() ? tOntoIRI + "-TBox.owl" : tOntoIRI.replaceFirst(originalExtension, "-TBox.owl");
-                        aBoxOntologyIRI = originalExtension.isEmpty() ? tOntoIRI + "-ABox.owl" : tOntoIRI.replaceFirst(originalExtension, "-ABox.owl");
-
-                        String tBoxDocumentIRI = Paths.get(Utility.getGlobalTempDirAbsolutePath(), "TBox.owl").toString();
-                        String aBoxDocumentIRI = (aBoxPath = Paths.get(Utility.getGlobalTempDirAbsolutePath(), "ABox.owl").toString());
-                        tBox = manager.createOntology(IRI.create(tBoxOntologyIRI));
-                        aBox = manager.createOntology(IRI.create(aBoxOntologyIRI));
-                        manager.setOntologyDocumentIRI(tBox, IRI.create(Utility.toFileIRI(tBoxDocumentIRI)));
-                        manager.setOntologyDocumentIRI(aBox, IRI.create(Utility.toFileIRI(aBoxDocumentIRI)));
+                                ontologyIri = inputOntology.getOntologyID().getOntologyIRI();
+
+                        String ontologyIriPrefix = ontologyIri.getNamespace();
+                        ontologyIRI = ontologyIri.toString();
+                        String ontologyIriFragment = ontologyIri.getFragment();
+                        String originalFileName = FilenameUtils.removeExtension(ontologyIriFragment);
+                        String originalExtension = FilenameUtils.getExtension(ontologyIriFragment);
+                        if(originalExtension.isEmpty()) originalExtension = DEFAULT_ONTOLOGY_FILE_EXTENSION;
+
+
+                        IRI rlOntologyIRI = IRI.create(ontologyIriPrefix, originalFileName + "-RL." + originalExtension);
+                        outputPath = Paths.get(Utility.getGlobalTempDirAbsolutePath(),
+                                                                   originalFileName + "-RL." + originalExtension).toString();
+                        IRI rlDocumentIRI = IRI.create(outputPath);
+                        outputOntology = manager.createOntology(rlOntologyIRI);
+                        manager.setOntologyDocumentIRI(outputOntology, rlDocumentIRI);
+
+                        String tBoxOntologyFragment = originalFileName + "-TBox." + originalExtension;
+                        IRI tBoxOntologyIRI = IRI.create(ontologyIriPrefix, tBoxOntologyFragment);
+                        IRI tBoxDocumentIRI =
+                                        IRI.create("file://" + Paths.get(Utility.getGlobalTempDirAbsolutePath(), tBoxOntologyFragment));
+
+                        String aBoxOntologyFragment = originalFileName + "-ABox." + originalExtension;
+                        IRI aBoxOntologyIRI = IRI.create(ontologyIriPrefix, aBoxOntologyFragment);
+                        aBoxPath = Paths.get(Utility.getGlobalTempDirAbsolutePath()) + aBoxOntologyFragment;
+                        IRI aBoxDocumentIRI =
+                                        IRI.create("file://" + Paths.get(Utility.getGlobalTempDirAbsolutePath(), aBoxOntologyFragment));
+
+                        tBox = manager.createOntology(tBoxOntologyIRI);
+                        aBox = manager.createOntology(aBoxOntologyIRI);
+                        manager.setOntologyDocumentIRI(tBox, tBoxDocumentIRI);
+                        manager.setOntologyDocumentIRI(aBox, aBoxDocumentIRI);
 
                         FileOutputStream aBoxOut = new FileOutputStream(aBoxPath);
                         manager.saveOntology(aBox, aBoxOut);
                         aBoxOut.close();
 
                         restOntology = manager.createOntology();
-                }
-                catch (OWLOntologyCreationException e) {
-                        e.printStackTrace();
-                } catch (OWLOntologyStorageException e) {
-                        // TODO Auto-generated catch block
-                        e.printStackTrace();
-                } catch (IOException e) {
-                        // TODO Auto-generated catch block
+                } catch(OWLOntologyCreationException | OWLOntologyStorageException | IOException e) {
                         e.printStackTrace();
+                        System.exit(1);
                 }
         }