12 files changed, 132 insertions, 17 deletions

diff --git a/pom.xml b/pom.xml
index 0a9f1c7..3b9a94a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -172,11 +172,11 @@
                         <artifactId>jrdfox</artifactId>
                         <version>1.0</version>
                 </dependency>
-                <!--<dependency>-->
-                        <!--<groupId>commons-lang</groupId>-->
-                        <!--<artifactId>commons-lang</artifactId>-->
-                        <!--<version>2.1</version>-->
-                <!--</dependency>-->
+                <dependency>
+                        <groupId>commons-lang</groupId>
+                        <artifactId>commons-lang</artifactId>
+                        <version>2.1</version>
+                </dependency>
                 <!--<dependency>-->
                         <!--<groupId>org.codehaus.plexus</groupId>-->
                         <!--<artifactId>plexus-utils</artifactId>-->
diff --git a/src/uk/ac/ox/cs/pagoda/Pagoda.java b/src/uk/ac/ox/cs/pagoda/Pagoda.java
index aeb85a7..f5dce15 100644
--- a/src/uk/ac/ox/cs/pagoda/Pagoda.java
+++ b/src/uk/ac/ox/cs/pagoda/Pagoda.java
@@ -177,6 +177,12 @@ public class Pagoda implements Runnable {
             return this;
         }
 
+        public PagodaBuilder skolem(Boolean isEnabled) {
+            if(instance == null) return null;
+            instance.properties.setUseSkolemUpperBound(isEnabled);
+            return this;
+        }
+
         public Pagoda build() {
             Pagoda builtInstance = instance;
             instance = null;
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
index 479905d..2471c80 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
@@ -10,6 +10,7 @@ import uk.ac.ox.cs.pagoda.query.GapByStore4ID;
 import uk.ac.ox.cs.pagoda.query.QueryRecord;
 import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
 import uk.ac.ox.cs.pagoda.rules.Program;
+import uk.ac.ox.cs.pagoda.rules.approximators.SkolemTermsManager;
 import uk.ac.ox.cs.pagoda.util.PagodaProperties;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
@@ -216,6 +217,9 @@ public class MultiStageQueryEngine extends StageQueryEngine {
                 Utility.logDebug(name + " store after adding facts for violations: " + (tripleCount =
                         store.getTriplesCount()) + " (" + (tripleCount - oldTripleCount) + " new)");
                 Utility.logDebug("Time to add triples for violations: " + subTimer.duration());
+
+                Utility.logDebug("Number of Skolem individuals: " + SkolemTermsManager.getInstance()
+                                                                                      .getSkolemIndividualsCount());
             }
         } catch(JRDFStoreException e) {
             e.printStackTrace();
diff --git a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
index 7f02741..5878a57 100644
--- a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
+++ b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
@@ -2,6 +2,7 @@ package uk.ac.ox.cs.pagoda.query;
 
 import com.google.gson.*;
 import com.google.gson.reflect.TypeToken;
+import org.apache.commons.lang.WordUtils;
 import org.semanticweb.HermiT.model.*;
 import org.semanticweb.owlapi.model.*;
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
@@ -713,7 +714,12 @@ public class QueryRecord extends Disposable {
         FRAGMENT_REFINEMENT,
         SUMMARISATION,
         DEPENDENCY,
-        FULL_REASONING
+        FULL_REASONING;
+
+        @Override
+        public String toString() {
+            return WordUtils.capitalizeFully(super.toString(), new char[]{'_'}).replace("_", "");
+        }
     }
 
     /**
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index e6e508a..e689de6 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -19,7 +19,6 @@ import uk.ac.ox.cs.pagoda.tracking.QueryTracker;
 import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoder;
 import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderDisjVar1;
 import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderWithGap;
-import uk.ac.ox.cs.pagoda.util.PagodaProperties;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
 import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
@@ -192,7 +191,7 @@ class MyQueryReasoner extends QueryReasoner {
         OWLOntology relevantOntologySubset = extractRelevantOntologySubset(queryRecord);
 //        queryRecord.saveRelevantOntology("./fragment_query" + queryRecord.getQueryID() + ".owl");
 
-        if(PagodaProperties.getDefaultUseSkolemUpperBound() &&
+        if(properties.getUseSkolemUpperBound() &&
                 querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord))
             return;
 
@@ -297,7 +296,7 @@ class MyQueryReasoner extends QueryReasoner {
 
         Tuple<String> extendedQueryTexts = queryRecord.getExtendedQueryText();
 
-        if(PagodaProperties.getDefaultUseAlwaysSimpleUpperBound() || lazyUpperStore == null) {
+        if(properties.getUseAlwaysSimpleUpperBound() || lazyUpperStore == null) {
             Utility.logDebug("Tracking store");
             if(queryUpperStore(trackingStore, queryRecord, extendedQueryTexts, Step.SIMPLE_UPPER_BOUND))
                 return true;
@@ -369,8 +368,10 @@ class MyQueryReasoner extends QueryReasoner {
                 new MultiStageQueryEngine("Relevant-store", true); // checkValidity is true
 
         relevantStore.importDataFromABoxOf(relevantSubset);
+        String relevantOriginalMarkProgram = OWLHelper.getOriginalMarkProgram(relevantSubset);
 
         int queryDependentMaxTermDepth = 5; // TODO make it dynamic
+        relevantStore.materialise("Mark original individuals", relevantOriginalMarkProgram);
         int materialisationTag = relevantStore.materialiseSkolemly(relevantProgram, null,
                                                                    queryDependentMaxTermDepth);
         queryRecord.addProcessingTime(Step.SKOLEM_UPPER_BOUND, t.duration());
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
index eab6a1b..3a057ec 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
@@ -193,6 +193,7 @@ public abstract class QueryReasoner extends Disposable {
                 if(!record.isProcessed())
                     evaluate(record);
                 Utility.logInfo("Total time to answer this query: " + t.duration());
+                Utility.logInfo("Difficulty of this query: " + record.getDifficulty());
                 if(!fullReasoner && !record.isProcessed()) {
                     Utility.logInfo("The query has not been fully answered in " + t.duration() + " seconds.");
                     continue;
diff --git a/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java b/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
index 44daf7a..a78aabe 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
@@ -83,7 +83,7 @@ public class SkolemTermsManager {
     /**
      * Get the number of individuals generated by this manager.
      */
-    public int getNumberOfSkolemisedIndividual() {
+    public int getSkolemIndividualsCount() {
         return individualToDepth_map.keySet().size();
     }
 
diff --git a/src/uk/ac/ox/cs/pagoda/util/tuples/Tuple.java b/src/uk/ac/ox/cs/pagoda/util/tuples/Tuple.java
index 9139a5d..0a5983c 100644
--- a/src/uk/ac/ox/cs/pagoda/util/tuples/Tuple.java
+++ b/src/uk/ac/ox/cs/pagoda/util/tuples/Tuple.java
@@ -46,4 +46,9 @@ public class Tuple<T> implements Iterable<T> {
     public int hashCode() {
         return elements.hashCode() + getClass().hashCode();
     }
+
+    @Override
+    public String toString() {
+        return elements.toString();
+    }
 }
diff --git a/test/resources/ComparisonTests.xml b/test/resources/ComparisonTests.xml
new file mode 100644
index 0000000..0095724
--- /dev/null
+++ b/test/resources/ComparisonTests.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd" >
+
+<!--
+Compare different configurations of the system.
+
+Actually it is not a great idea to test performances in this way,
+because all the different configurations are executed on the same JVM.
+-->
+
+<suite name="ComparisonTests">
+    <test name="comparison">
+        <groups>
+            <run>
+                <include name="comparison"/>
+            </run>
+        </groups>
+        <classes>
+            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaUOBM"/>-->
+            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaLUBM"/>-->
+            <class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaFLY"/>
+        </classes>
+    </test>
+</suite>
\ No newline at end of file
diff --git a/test/resources/LightTests.xml b/test/resources/LightTests.xml
index 859e3fa..8d9a700 100644
--- a/test/resources/LightTests.xml
+++ b/test/resources/LightTests.xml
@@ -5,10 +5,10 @@
     <test name="light">
         <groups>
             <run>
-                <include name="light"/>
+                <!--<include name="light"/>-->
+                <include name="justExecute"/>
             </run>
         </groups>
-
         <classes>
             <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaUOBM"/>-->
             <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaLUBM"/>-->
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
index 4fdccf8..42827a0 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
@@ -4,6 +4,7 @@ import org.testng.annotations.Test;
 import uk.ac.ox.cs.pagoda.Pagoda;
 import uk.ac.ox.cs.pagoda.query.CheckAnswers;
 import uk.ac.ox.cs.pagoda.util.TestUtil;
+import uk.ac.ox.cs.pagoda.util.Timer;
 
 import java.io.File;
 import java.io.IOException;
@@ -20,8 +21,8 @@ public class TestPagodaFLY {
                 Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-fly-with-GJ-FC-individuals.json");
 
                 Pagoda pagoda = Pagoda.builder()
-                                                          .ontology(TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"))
-                                              .query(TestUtil.combinePaths(ontoDir, "fly/queries/fly.sparql"))
+                                                          .ontology(Paths.get(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"))
+                                                          .query(Paths.get(ontoDir, "fly/queries/fly.sparql"))
                                                           .answer(answers)
                                                           .classify(false)
                                                           .hermit(true)
@@ -39,9 +40,10 @@ public class TestPagodaFLY {
                 Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-fly-rolledup.json");
 
                 Pagoda pagoda = Pagoda.builder()
-                                                          .ontology(TestUtil.combinePaths(ontoDir, "fly/fly_rolledUp.owl"))
-                                                          .query(TestUtil.combinePaths(ontoDir, "fly/queries/fly_rolledUp.sparql"))
+                                                          .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
+                                                          .query(Paths.get(ontoDir, "fly/queries/fly_rolledUp.sparql"))
                                                           .answer(answers)
+                                                          .answer(Paths.get("/home/alessandro/Desktop/answers.json"))
                                                           .classify(false)
                                                           .hermit(true)
                                                           .build();
@@ -49,4 +51,54 @@ public class TestPagodaFLY {
                 pagoda.run();
                 CheckAnswers.assertSameAnswers(answers, givenAnswers);
         }
+
+        @Test(groups = {"light", "justExecute"})
+        public void justExecute_newQueries() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+                Pagoda pagoda = Pagoda.builder()
+                                .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
+//                                                        .ontology(Paths.get(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"))
+                                .query(Paths.get(ontoDir, "fly/queries/new_queries.sparql"))
+//                                                        .answer(Paths.get("/home/alessandro/Desktop/answers.json"))
+                                .classify(false)
+                                .hermit(true)
+                                .skolem(false)
+                                .build();
+
+                pagoda.run();
+        }
+
+        @Test(groups = {"light", "comparison"})
+        public void compare_newQueries() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+                Timer timer = new Timer();
+                Pagoda.builder()
+                          .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
+                          .query(Paths.get(ontoDir, "fly/queries/new_queries.sparql"))
+                          .classify(false)
+                          .hermit(true)
+                                .skolem(true) // <----<< Skolem upper bound is ENABLED <<<
+                                .build()
+                                .run();
+                double t1 = timer.duration();
+
+                timer.reset();
+
+                Pagoda.builder()
+                          .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
+                          .query(Paths.get(ontoDir, "fly/queries/new_queries.sparql"))
+                          .classify(false)
+                          .hermit(true)
+                                .skolem(false) // <----<< Skolem upper bound is DISABLED <<<
+                                .build()
+                                .run();
+                double t2 = timer.duration();
+
+                if(t1 < t2)
+                        TestUtil.logInfo("Overall reasoning with Skolem upper bound was " + (int) (t2 / t1 * 100 - 100) + "x faster!");
+                else
+                        TestUtil.logInfo("Overall reasoning with Skolem upper bound was " + (int) (t1 / t2 * 100 - 100) + "x slower...");
+        }
 }
diff --git a/test/uk/ac/ox/cs/pagoda/util/TestUtil.java b/test/uk/ac/ox/cs/pagoda/util/TestUtil.java
index c3909d5..fdd242a 100644
--- a/test/uk/ac/ox/cs/pagoda/util/TestUtil.java
+++ b/test/uk/ac/ox/cs/pagoda/util/TestUtil.java
@@ -22,7 +22,7 @@ import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
 public class TestUtil {
 
     public static final String CONFIG_FILE = "test.properties";
-
+    private static final Logger LOGGER = Logger.getLogger("Tester");
     private static boolean isConfigLoaded = false;
     private static Properties config;
 
@@ -71,4 +71,20 @@ public class TestUtil {
         return Paths.get(givenAnswersURL.getPath());
     }
 
+    public static void logInfo(Object msg) {
+        LOGGER.info(msg);
+    }
+
+    public static void logDebug(Object msg) {
+        LOGGER.debug(msg);
+    }
+
+    public static void logError(Object msg) {
+        LOGGER.error(msg);
+    }
+
+    public static void logError(Object msg, Throwable t) {
+        LOGGER.error(msg, t);
+    }
+
 }