10 files changed, 103 insertions, 17 deletions

diff --git a/.gitignore b/.gitignore
index e61e937..6c02c6b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,4 +6,6 @@
 /*.log*
 /*.pdf
 test_reports
-.idea
\ No newline at end of file
+.idea
+logs
+statistics
diff --git a/src/resources/log4j.properties b/src/resources/log4j.properties
index 3bfd32e..52688d5 100644
--- a/src/resources/log4j.properties
+++ b/src/resources/log4j.properties
@@ -1,4 +1,4 @@
-log = .
+log = ./logs
 log4j.rootLogger=DEBUG, CONSOLE, FILE_LAST, FILE
 
 log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
diff --git a/src/resources/pagoda.properties b/src/resources/pagoda.properties
index bd387b9..64de225 100644
--- a/src/resources/pagoda.properties
+++ b/src/resources/pagoda.properties
@@ -1,3 +1,5 @@
 debug=true
 useAlwaysSimpleUpperBound=false
-useSkolemUpperBound=true
\ No newline at end of file
+useSkolemUpperBound=true
+
+statisticsDir=/home/alessandro/Dropbox/Oxford/PAGOdA/statistics
\ No newline at end of file
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
index af1b413..479905d 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
@@ -1,5 +1,6 @@
 package uk.ac.ox.cs.pagoda.multistage;
 
+import org.semanticweb.HermiT.model.DLClause;
 import uk.ac.ox.cs.JRDFox.JRDFStoreException;
 import uk.ac.ox.cs.pagoda.constraints.BottomStrategy;
 import uk.ac.ox.cs.pagoda.multistage.treatement.Pick4NegativeConceptNaive;
@@ -9,14 +10,26 @@ 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.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;
 
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
 import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.stream.Collectors;
 
 public class MultiStageQueryEngine extends StageQueryEngine {
 
+    private HashMap<String, List> statistics = new HashMap<>();
+
     public MultiStageQueryEngine(String name, boolean checkValidity) {
         super(name, checkValidity);
     }
@@ -94,6 +107,14 @@ public class MultiStageQueryEngine extends StageQueryEngine {
         return ret;
     }
 
+    @Override
+    public void dispose() {
+        super.dispose();
+
+        if(PagodaProperties.isDebuggingMode())
+            outputStatistics();
+    }
+
     private int materialise(MultiStageUpperProgram program, Treatment treatment, GapByStore4ID gap) {
         if(gap != null)
             treatment.addAdditionalGapTuples();
@@ -169,7 +190,11 @@ public class MultiStageQueryEngine extends StageQueryEngine {
                 subTimer.reset();
                 oldTripleCount = store.getTriplesCount();
 
-                Utility.logInfo("Number of violations: " + violations.size());
+                Utility.logDebug("Number of violations: " + violations.size());
+
+                updateStatistics("violationClauses", violations.stream()
+                                                               .map(Violation::getClause)
+                                                               .collect(Collectors.toList()));
 
                 for(Violation v : violations) {
 
@@ -198,5 +223,21 @@ public class MultiStageQueryEngine extends StageQueryEngine {
         return 0;
     }
 
+    private void updateStatistics(String key, List<DLClause> value) {
+        if(!statistics.containsKey(key))
+            statistics.put(key, new ArrayList<List>());
+        statistics.get(key).add(value.stream().map(DLClause::toString).collect(Collectors.toList()));
+    }
+
+    private void outputStatistics() {
+        Path statisticsPath = PagodaProperties.getDefaultStatisticsDir()
+                                              .resolve(Paths.get("MultiStageQueryEngine-ViolationSequence.json"));
+        try(BufferedWriter writer = Files.newBufferedWriter(statisticsPath)) {
+            QueryRecord.GsonCreator.getInstance().toJson(statistics, writer);
+        } catch(IOException e) {
+            e.printStackTrace();
+        }
+    }
+
 }
 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 727f80d..e6e508a 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -370,7 +370,7 @@ class MyQueryReasoner extends QueryReasoner {
 
         relevantStore.importDataFromABoxOf(relevantSubset);
 
-        int queryDependentMaxTermDepth = 1; // TODO make it dynamic
+        int queryDependentMaxTermDepth = 5; // TODO make it dynamic
         int materialisationTag = relevantStore.materialiseSkolemly(relevantProgram, null,
                                                                    queryDependentMaxTermDepth);
         queryRecord.addProcessingTime(Step.SKOLEM_UPPER_BOUND, t.duration());
@@ -386,6 +386,8 @@ class MyQueryReasoner extends QueryReasoner {
         boolean isFullyProcessed = queryUpperStore(relevantStore, queryRecord,
                                                    queryRecord.getExtendedQueryText(),
                                                    Step.SKOLEM_UPPER_BOUND);
+
+        relevantStore.dispose();
         Utility.logInfo("Semi-Skolemised relevant upper store has been evaluated");
         return isFullyProcessed;
     }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java
index 1e8181f..f823232 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java
@@ -9,6 +9,7 @@ import uk.ac.ox.cs.JRDFox.store.TupleIterator;
 import uk.ac.ox.cs.pagoda.query.AnswerTuple;
 import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
 public class RDFoxAnswerTuples extends AnswerTuples {
 
@@ -35,11 +36,15 @@ public class RDFoxAnswerTuples extends AnswerTuples {
 
         @Override
         public boolean isValid() {
+                if(isDisposed()) throw new DisposedException();
+
                 return multi != 0;
         }
 
         @Override
         public int getArity() {
+                if(isDisposed()) throw new DisposedException();
+
                 try {
                         return m_iter.getArity();
                 } catch (JRDFStoreException e) {
@@ -50,6 +55,8 @@ public class RDFoxAnswerTuples extends AnswerTuples {
 
         @Override
         public void moveNext() {
+                if(isDisposed()) throw new DisposedException();
+
                 try {
                         multi = m_iter.getNext();
                 } catch (JRDFStoreException e) {
@@ -65,11 +72,15 @@ public class RDFoxAnswerTuples extends AnswerTuples {
         
         @Override
         public AnswerTuple getTuple() {
+                if(isDisposed()) throw new DisposedException();
+
                 return new AnswerTuple(m_iter, m_answerVars.length); 
         }
 
         @Override
         public void reset() {
+                if(isDisposed()) throw new DisposedException();
+
                 try {
                         multi = m_iter.open();
                 } catch (JRDFStoreException e) {
@@ -79,17 +90,23 @@ public class RDFoxAnswerTuples extends AnswerTuples {
 
         @Override
         public boolean contains(AnswerTuple t) {
+                if(isDisposed()) throw new DisposedException();
+
                 Utility.logError("Unsupported operation in RDFoxAnswerTuples"); 
                 return false;
         }
 
         @Override
         public void remove() {
+                if(isDisposed()) throw new DisposedException();
+
                 Utility.logError("Unsupported operation in RDFoxAnswerTuples"); 
         }
 
         @Override
         public String[] getAnswerVariables() {
+                if(isDisposed()) throw new DisposedException();
+
                 return m_answerVars;
         }
 
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 ef004c4..44daf7a 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
@@ -87,6 +87,13 @@ public class SkolemTermsManager {
         return individualToDepth_map.keySet().size();
     }
 
+    /**
+     * Just for reading the clause id from <tt>LimitedSkolemisationApproximator</tt>.
+     */
+    int getClauseId(DLClause clause) {
+        return clauseToId_map.get(clause);
+    }
+
     private int mapClauseToId(DLClause clause) {
         if(!clauseToId_map.containsKey(clause)) {
             clauseToId_map.put(clause, termsCounter);
diff --git a/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java b/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
index e07d54f..2c53063 100644
--- a/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
+++ b/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
@@ -5,6 +5,8 @@ import org.apache.log4j.Logger;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.Properties;
 
 public class PagodaProperties {
@@ -13,6 +15,7 @@ public class PagodaProperties {
         public static final boolean DEFAULT_DEBUG = false;
         private static final boolean DEFAULT_USE_ALWAYS_SIMPLE_UPPER_BOUND;
         private static final boolean DEFAULT_USE_SKOLEM_UPPER_BOUND;
+        private static final Path DEFAULT_STATISTICS_DIR;
 
         public static boolean shellModeDefault = false;
         private static boolean debug = DEFAULT_DEBUG;
@@ -20,6 +23,7 @@ public class PagodaProperties {
         static {
                 boolean defaultUseAlwaysSimpleUpperBound = false;
                 boolean defaultUseSkolemUpperBound = true;
+                Path defaultStatisticsDir = null;
 
                 try(InputStream in = PagodaProperties.class.getClassLoader().getResourceAsStream(CONFIG_FILE)) {
                         Properties config = new Properties();
@@ -28,8 +32,12 @@ public class PagodaProperties {
                         Logger logger = Logger.getLogger("PagodaProperties");
                         if(config.containsKey("debug")) {
                                 debug = Boolean.parseBoolean(config.getProperty("debug"));
-//                              logger.info("Debugging mode is enabled (you can disable it from file \"pagoda.properties\")");
                                 logger.info("Debugging mode is enabled");
+
+                                if(config.containsKey("statisticsDir")) {
+                                        defaultStatisticsDir = Paths.get(config.getProperty("statisticsDir"));
+                                        logger.info("The directory where statistics are saved is: \"" + defaultStatisticsDir + "\"");
+                                }
                         }
                         if(config.containsKey("useAlwaysSimpleUpperBound")) {
                                 defaultUseAlwaysSimpleUpperBound =
@@ -40,11 +48,13 @@ public class PagodaProperties {
                                 defaultUseSkolemUpperBound = Boolean.parseBoolean(config.getProperty("useSkolemUpperBound"));
                                 logger.info("The Skolem upper bound is enabled");
                         }
+
                 } catch(IOException e) {
                         e.printStackTrace();
                 }
                 DEFAULT_USE_ALWAYS_SIMPLE_UPPER_BOUND = defaultUseAlwaysSimpleUpperBound;
                 DEFAULT_USE_SKOLEM_UPPER_BOUND = defaultUseSkolemUpperBound;
+                DEFAULT_STATISTICS_DIR = defaultStatisticsDir;
         }
 
         String dataPath = null;
@@ -56,6 +66,8 @@ public class PagodaProperties {
         boolean shellMode = shellModeDefault;
         private boolean useAlwaysSimpleUpperBound = DEFAULT_USE_ALWAYS_SIMPLE_UPPER_BOUND;
         private boolean useSkolemUpperBound = DEFAULT_USE_SKOLEM_UPPER_BOUND;
+        private Path statisticsDir = DEFAULT_STATISTICS_DIR;
+
         public PagodaProperties(String path) {
                 java.util.Properties m_properties = new java.util.Properties();
                 InputStream inputStream = null;
@@ -92,6 +104,10 @@ public class PagodaProperties {
                 return DEFAULT_USE_ALWAYS_SIMPLE_UPPER_BOUND;
         }
 
+        public static Path getDefaultStatisticsDir() {
+                return DEFAULT_STATISTICS_DIR;
+        }
+
         public static boolean getDefaultUseSkolemUpperBound() {
                 return DEFAULT_USE_SKOLEM_UPPER_BOUND;
         }
@@ -167,4 +183,12 @@ public class PagodaProperties {
         public void setUseSkolemUpperBound(boolean flag) {
                 useSkolemUpperBound = flag;
         }
+
+        public Path getStatisticsDir() {
+                return statisticsDir;
+        }
+
+        public void setStatisticsDir(Path statisticsDir) {
+                this.statisticsDir = statisticsDir;
+        }
 }
diff --git a/src/uk/ac/ox/cs/pagoda/util/disposable/Disposable.java b/src/uk/ac/ox/cs/pagoda/util/disposable/Disposable.java
index b208cc3..4015b66 100644
--- a/src/uk/ac/ox/cs/pagoda/util/disposable/Disposable.java
+++ b/src/uk/ac/ox/cs/pagoda/util/disposable/Disposable.java
@@ -25,15 +25,6 @@ public abstract class Disposable {
     }
 
     private class AlreadyDisposedException extends RuntimeException {
-
-        public AlreadyDisposedException() {
-            super();
-        }
-
-        public AlreadyDisposedException(String msg) {
-            super(msg);
-        }
     }
 
-
 }
diff --git a/test/resources/LightTests.xml b/test/resources/LightTests.xml
index e260c25..859e3fa 100644
--- a/test/resources/LightTests.xml
+++ b/test/resources/LightTests.xml
@@ -10,10 +10,10 @@
         </groups>
 
         <classes>
-            <class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaUOBM"/>
+            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaUOBM"/>-->
             <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaLUBM"/>-->
             <!--Fly does not terminate: query-5 looks really hard-->
-            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaFLY"/>-->
+            <class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaFLY"/>
         </classes>
     </test>
 </suite>
\ No newline at end of file