[pagoda] Move project to Scala

This commit includes a few changes:
- The repository still uses Maven to manage dependency but it is now a
  Scala project.
- The code has been ported from OWLAPI 3.4.10 to 5.1.20
- A proof of concept program using both RSAComb and PAGOdA has been
  added.

1 files changed, 195 insertions, 0 deletions

diff --git a/src/test/java/uk/ac/ox/cs/jrdfox/Tester.java b/src/test/java/uk/ac/ox/cs/jrdfox/Tester.java
new file mode 100644
index 0000000..94f5401
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/jrdfox/Tester.java
@@ -0,0 +1,195 @@
+package uk.ac.ox.cs.jrdfox;
+
+import java.io.File;
+
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.Prefixes;
+import uk.ac.ox.cs.JRDFox.store.DataStore;
+import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
+import uk.ac.ox.cs.JRDFox.store.Parameters;
+import uk.ac.ox.cs.JRDFox.store.TripleStatus;
+import uk.ac.ox.cs.JRDFox.store.TupleIterator;
+import uk.ac.ox.cs.JRDFox.store.DataStore.StoreType;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxQueryEngine;
+import uk.ac.ox.cs.pagoda.util.Namespace;
+import uk.ac.ox.cs.pagoda.util.Timer;
+
+public class Tester {
+        
+        public static void main(String[] args) throws JRDFStoreException {
+                Tester tester = new Tester();
+                tester.testCrash();
+        }
+        
+        private void evaluate_againstIDs(String queryText) throws JRDFStoreException {
+                int number = 0; 
+                Timer t = new Timer(); 
+                TupleIterator iter = null; 
+                try {
+                        iter = store.compileQuery(queryText, prefixes, parameters, TripleStatus.TUPLE_STATUS_IDB.union(TripleStatus.TUPLE_STATUS_EDB), TripleStatus.TUPLE_STATUS_IDB);
+                        for (long multi = iter.open(); multi != 0; multi = iter.getNext()) 
+                                ++number; 
+                } finally {
+                        if (iter != null) iter.dispose();
+                }
+                System.out.println(number); 
+                System.out.println(t.duration());
+
+        }
+
+        DataStore store; 
+        Prefixes prefixes = new Prefixes(); 
+        Parameters parameters; 
+        
+        public Tester() {
+                try {
+                        store = new DataStore(StoreType.NarrowParallelHead);
+                        store.setNumberOfThreads(RDFoxQueryEngine.matNoOfThreads);
+                        store.initialize();
+                        System.out.println("data store created.");
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+                parameters = new Parameters();
+                parameters.m_allAnswersInRoot = true; 
+                parameters.m_useBushy = true; 
+        }
+        
+        public Tester(String path) {
+                try {
+                        store = new DataStore(new File(path));
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+                parameters = new Parameters(); 
+//              parameters.m_allAnswersInRoot = true; 
+//              parameters.m_useBushy = true;
+        }
+        
+        public void applyReasoning(boolean incremental) {
+                Timer t = new Timer(); 
+                try {
+                        store.applyReasoning(incremental);
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }  
+                System.out.println("reasoning done: " + t.duration()); 
+        }
+        
+        public void dispose() {
+                store.dispose();
+        }
+        
+        public void testCrash() throws JRDFStoreException {
+//              DataStore lowerStore = new DataStore(StoreType.NarrowParallelHead);
+//              lowerStore.setNumberOfThreads(RDFoxQueryEngine.matNoOfThreads);
+//              lowerStore.initialize();
+//              System.out.println("lower data store created.");
+                OWLOntology ontology = OWLHelper.loadOntology("data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl");
+                System.out.println("ontology loaded ... " + ontology.getAxiomCount());
+                
+                store.importTurtleFile(new File("testcase/fly.ttl"));
+                System.out.println("data loaded. " + store.getTriplesCount());
+                
+                store.importRules(new File[] {new File("testcase/lower.dlog")});
+                System.out.println("rules loaded. " + store.getTriplesCount());
+                
+                store.applyReasoning();
+                System.out.println("materialised. " + store.getTriplesCount());
+                
+                store.clearRulesAndMakeFactsExplicit();
+                
+                store.importRules(new File[] {new File("testcase/multi.dlog")});
+                System.out.println("rules loaded. " + store.getTriplesCount());
+                
+                store.applyReasoning();
+                System.out.println("materialised. " + store.getTriplesCount());
+                
+                store.makeFactsExplicit();
+                
+                store.importTurtleFiles(new File[] {new File("testcase/first.ttl")}, UpdateType.ScheduleForAddition);
+                System.out.println("first data loaded. " + store.getTriplesCount());
+                
+                store.applyReasoning(true);
+                System.out.println("incremental reasoning done. " + store.getTriplesCount());
+                
+                store.clearRulesAndMakeFactsExplicit();
+                
+                store.importTurtleFiles(new File[] {new File("testcase/second.ttl")}, UpdateType.ScheduleForAddition);
+                store.importRules(new File[] {new File("testcase/tracking.dlog")}, UpdateType.ScheduleForAddition);
+                store.applyReasoning(true);
+                System.out.println("incremental reasoning done. " + store.getTriplesCount());
+                
+                evaluate_againstIDs("select distinct ?z where { ?x <" + Namespace.RDF_TYPE + "> ?z . }");
+                System.out.println("done."); 
+//              tester.applyReasoning(true);
+//              tester.evaluate_againstIDs("select distinct ?z where { ?x <" + Namespace.RDF_TYPE + "> ?z . }");
+//              System.out.println("done."); 
+                
+                store.dispose();
+//              lowerStore.dispose();
+        }
+        
+        public void test() throws JRDFStoreException {
+                evaluate("PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> " 
+                                + "SELECT distinct ?x WHERE { "
+                                + "?x a benchmark:Person . "
+                                + "?x benchmark:like ?y . "
+                                + "?z a benchmark:Chair . "
+                                + "?z benchmark:isHeadOf <http://www.Department0.University0.edu> . "
+                                + "?z benchmark:like ?y . "
+                                + "?x a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> . "
+                                + "?z a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> . "
+                                + "?y a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> }");
+                
+                evaluate("PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> " 
+                                + "SELECT distinct ?x WHERE { "
+                                + "?x a benchmark:Person . "
+                                + "?x benchmark:like ?y . "
+                                + "?z a benchmark:Chair . "
+                                + "?z benchmark:isHeadOf <http://www.Department0.University0.edu> . "
+                                + "?z benchmark:like ?y . "
+                                + "?z a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> . "
+                                + "?y a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> ."
+                                + "?x a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> }"); 
+
+                evaluate("PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> " 
+                                + "SELECT distinct ?x WHERE { "
+                                + "?x a benchmark:Person . "
+                                + "?x benchmark:like ?y . "
+                                + "?z a benchmark:Chair . "
+                                + "?z benchmark:isHeadOf <http://www.Department0.University0.edu> . "
+                                + "?z benchmark:like ?y . "
+                                + "?y a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> . "
+                                + "?x a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> . "
+                                + "?z a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> }"); 
+                
+                evaluate("PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> " 
+                                + "SELECT distinct ?x WHERE { "
+                                + "?x a benchmark:Person . "
+                                + "?x benchmark:like ?y . "
+                                + "?z a benchmark:Chair . "
+                                + "?z benchmark:isHeadOf <http://www.Department0.University0.edu> . "
+                                + "?z benchmark:like ?y . "
+                                + "?y a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> }"); 
+        }
+        
+        public void evaluate(String query) throws JRDFStoreException {
+                int number = 0; 
+                Timer t = new Timer(); 
+                TupleIterator iter = null; 
+                try {
+                        iter = store.compileQuery(query, prefixes, parameters);
+                        for (long multi = iter.open(); multi != 0; multi = iter.getNext()) 
+                                ++number; 
+                } finally {
+                        if (iter != null) iter.dispose();
+                }
+                System.out.println(number); 
+                System.out.println(t.duration());
+        }
+        
+}