Disposable.

1 files changed, 332 insertions, 330 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 618fb70..8445713 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -21,362 +21,364 @@ import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderDisjVar1;
 import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderWithGap;
 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 uk.ac.ox.cs.pagoda.util.tuples.Tuple;
 
 import java.util.Collection;
 
 class MyQueryReasoner extends QueryReasoner {
 
-        OWLOntology ontology;
-        DatalogProgram program;
-
-//      String additonalDataFile; 
-        BasicQueryEngine rlLowerStore = null;
-        BasicQueryEngine lazyUpperStore = null;
-        //      BasicQueryEngine limitedSkolemUpperStore;
-        OWLOntology elho_ontology;
-//      boolean[] namedIndividuals_lazyUpper; 
-        KarmaQueryEngine elLowerStore = null;
-        BasicQueryEngine trackingStore = null;
-        //      boolean[] namedIndividuals_tracking;
-        TrackingRuleEncoder encoder;
-        private boolean equalityTag;
-        private boolean multiStageTag;
-        private Timer t = new Timer();
-        private Collection<String> predicatesWithGap = null;
-        private SatisfiabilityStatus satisfiable;
-        private ConsistencyManager consistency = new ConsistencyManager(this);
-        private boolean useUpperStores = false;
-        public MyQueryReasoner() {
-                setup(true, true);
-        }
-        public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
-                setup(multiStageTag, considerEqualities);
-        }
-
-        private BasicQueryEngine getUpperStore(String name, boolean checkValidity) {
-                if (multiStageTag)
-                        return new MultiStageQueryEngine(name, checkValidity);
-//                      return new TwoStageQueryEngine(name, checkValidity);
-                else
-                        return new BasicQueryEngine(name);
-        }
-
-        public void setup(boolean multiStageTag, boolean considerEqualities) {
-                satisfiable = SatisfiabilityStatus.UNCHECKED;
-                this.multiStageTag = multiStageTag;
-                this.equalityTag = considerEqualities;
-
-                rlLowerStore = new BasicQueryEngine("rl-lower-bound");
-                elLowerStore = new KarmaQueryEngine("elho-lower-bound");
-
-                trackingStore = getUpperStore("tracking", false);
-        }
-        
-        protected void internal_importDataFile(String name, String datafile) {
-//              addDataFile(datafile);
-                rlLowerStore.importRDFData(name, datafile);
-                if (lazyUpperStore != null)
-                        lazyUpperStore.importRDFData(name, datafile);
-                elLowerStore.importRDFData(name, datafile);
-                trackingStore.importRDFData(name, datafile);
-        }
-
-        @Override
-        public void loadOntology(OWLOntology o) {
-                if(!equalityTag) {
-                        EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
-                        o = eliminator.getOutputOntology();
-                        eliminator.save();
-                }
-
-                ontology = o;
-                program = new DatalogProgram(ontology, properties.getToClassify());
+    OWLOntology ontology;
+    DatalogProgram program;
+
+    //  String additonalDataFile;
+    BasicQueryEngine rlLowerStore = null;
+    BasicQueryEngine lazyUpperStore = null;
+    MultiStageQueryEngine limitedSkolemUpperStore;
+    OWLOntology elho_ontology;
+    //  boolean[] namedIndividuals_lazyUpper;
+    KarmaQueryEngine elLowerStore = null;
+    BasicQueryEngine trackingStore = null;
+    //  boolean[] namedIndividuals_tracking;
+    TrackingRuleEncoder encoder;
+    private boolean equalityTag;
+    private boolean multiStageTag;
+    private Timer t = new Timer();
+    private Collection<String> predicatesWithGap = null;
+    private SatisfiabilityStatus satisfiable;
+    private ConsistencyManager consistency = new ConsistencyManager(this);
+    private boolean useUpperStores = false;
+
+    public MyQueryReasoner() {
+        setup(true, true);
+    }
+
+    public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
+        setup(multiStageTag, considerEqualities);
+    }
+
+    public void setup(boolean multiStageTag, boolean considerEqualities) {
+        if(isDisposed()) throw new DisposedException();
+        satisfiable = SatisfiabilityStatus.UNCHECKED;
+        this.multiStageTag = multiStageTag;
+        this.equalityTag = considerEqualities;
+
+        rlLowerStore = new BasicQueryEngine("rl-lower-bound");
+        elLowerStore = new KarmaQueryEngine("elho-lower-bound");
+
+        trackingStore = getUpperStore("tracking", false);
+    }
+
+    @Override
+    public void loadOntology(OWLOntology o) {
+        if(isDisposed()) throw new DisposedException();
+        if(!equalityTag) {
+            EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
+            o = eliminator.getOutputOntology();
+            eliminator.save();
+        }
+
+        ontology = o;
+        program = new DatalogProgram(ontology, properties.getToClassify());
 //              program.getLower().save();
 //              program.getUpper().save();
 //              program.getGeneral().save();
 
-                useUpperStores = multiStageTag && !program.getGeneral().isHorn();
-                if(useUpperStores) {
-                        lazyUpperStore = getUpperStore("lazy-upper-bound", true);
-//                      limitedSkolemUpperStore = getUpperStore("limited-skolem-upper-bound", true);
-                }
+        useUpperStores = multiStageTag && !program.getGeneral().isHorn();
+        if(useUpperStores) {
+            lazyUpperStore = getUpperStore("lazy-upper-bound", true);
+            limitedSkolemUpperStore = new MultiStageQueryEngine("limited-skolem-upper-bound", true);
+        }
 
-                importData(program.getAdditionalDataFile());
+        importData(program.getAdditionalDataFile());
 
-                elho_ontology = new ELHOProfile().getFragment(ontology);
-                elLowerStore.processOntology(elho_ontology);
-        }
+        elho_ontology = new ELHOProfile().getFragment(ontology);
+        elLowerStore.processOntology(elho_ontology);
+    }
 
-        public Collection<String> getPredicatesWithGap() {
-                return predicatesWithGap;
-        }
+    public Collection<String> getPredicatesWithGap() {
+        if(isDisposed()) throw new DisposedException();
+        return predicatesWithGap;
+    }
 
-        @Override
-        public boolean preprocess() {
-                t.reset();
-                Utility.logInfo("Preprocessing... checking satisfiability... ");
+    @Override
+    public boolean preprocess() {
+        if(isDisposed()) throw new DisposedException();
+        t.reset();
+        Utility.logInfo("Preprocessing... checking satisfiability... ");
 
-                String name = "data", datafile = importedData.toString();
-                rlLowerStore.importRDFData(name, datafile);
-                rlLowerStore.materialise("lower program", program.getLower().toString());
+        String name = "data", datafile = importedData.toString();
+        rlLowerStore.importRDFData(name, datafile);
+        rlLowerStore.materialise("lower program", program.getLower().toString());
 //              program.getLower().save();
-                if(!consistency.checkRLLowerBound()) return false;
-                Utility.logInfo("The number of sameAs assertions in RL lower store: " + rlLowerStore.getSameAsNumber());
-
-                String originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
-
-                elLowerStore.importRDFData(name, datafile);
-                elLowerStore.materialise("saturate named individuals", originalMarkProgram);
-                elLowerStore.materialise("lower program", program.getLower().toString());
-                elLowerStore.initialiseKarma();
-                if(!consistency.checkELLowerBound()) return false;
-
-                if(lazyUpperStore != null) {
-                        lazyUpperStore.importRDFData(name, datafile);
-                        lazyUpperStore.materialise("saturate named individuals", originalMarkProgram);
-                        int tag = lazyUpperStore.materialiseRestrictedly(program, null);
-                        if(tag != 1) {
-                                lazyUpperStore.dispose();
-                                lazyUpperStore = null;
-                        }
-                        if(tag == -1) return false;
-                }
-                if(consistency.checkUpper(lazyUpperStore)) {
-                        satisfiable = SatisfiabilityStatus.SATISFIABLE;
-                        Utility.logInfo("time for satisfiability checking: " + t.duration());
-                }
-
-//              if(limitedSkolemUpperStore != null) {
-//                      limitedSkolemUpperStore.importRDFData(name, datafile);
-//                      limitedSkolemUpperStore.materialise("saturate named individuals", originalMarkProgram);
-//                      int tag = limitedSkolemUpperStore.materialiseSkolemly(program, null);
-//                      if(tag != 1) {
-//                              limitedSkolemUpperStore.dispose();
-//                              limitedSkolemUpperStore = null;
-//                      }
-//                      if(tag == -1) return false;
-//              }
-//              if(satisfiable == SatisfiabilityStatus.UNCHECKED && consistency.checkUpper(limitedSkolemUpperStore)) {
-//                      satisfiable = SatisfiabilityStatus.SATISFIABLE;
-//                      Utility.logInfo("time for satisfiability checking: " + t.duration());
-//              }
-
-                trackingStore.importRDFData(name, datafile);
-                trackingStore.materialise("saturate named individuals", originalMarkProgram);
+        if(!consistency.checkRLLowerBound()) return false;
+        Utility.logInfo("The number of sameAs assertions in RL lower store: " + rlLowerStore.getSameAsNumber());
+
+        String originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
+
+        elLowerStore.importRDFData(name, datafile);
+        elLowerStore.materialise("saturate named individuals", originalMarkProgram);
+        elLowerStore.materialise("lower program", program.getLower().toString());
+        elLowerStore.initialiseKarma();
+        if(!consistency.checkELLowerBound()) return false;
+
+        if(lazyUpperStore != null) {
+            lazyUpperStore.importRDFData(name, datafile);
+            lazyUpperStore.materialise("saturate named individuals", originalMarkProgram);
+            int tag = lazyUpperStore.materialiseRestrictedly(program, null);
+            if(tag != 1) {
+                lazyUpperStore.dispose();
+                lazyUpperStore = null;
+            }
+            if(tag == -1) return false;
+        }
+        if(consistency.checkUpper(lazyUpperStore)) {
+            satisfiable = SatisfiabilityStatus.SATISFIABLE;
+            Utility.logInfo("time for satisfiability checking: " + t.duration());
+        }
+
+        if(limitedSkolemUpperStore != null) {
+            limitedSkolemUpperStore.importRDFData(name, datafile);
+            limitedSkolemUpperStore.materialise("saturate named individuals", originalMarkProgram);
+            int tag = limitedSkolemUpperStore.materialiseSkolemly(program, null);
+            if(tag != 1) {
+                limitedSkolemUpperStore.dispose();
+                limitedSkolemUpperStore = null;
+            }
+            if(tag == -1) return false;
+        }
+        if(satisfiable == SatisfiabilityStatus.UNCHECKED && consistency.checkUpper(limitedSkolemUpperStore)) {
+            satisfiable = SatisfiabilityStatus.SATISFIABLE;
+            Utility.logInfo("time for satisfiability checking: " + t.duration());
+        }
+
+        trackingStore.importRDFData(name, datafile);
+        trackingStore.materialise("saturate named individuals", originalMarkProgram);
 
 //              materialiseFullUpper();
-//              GapByStore4ID gap = new GapByStore4ID(trackingStore); 
-                GapByStore4ID gap = new GapByStore4ID2(trackingStore, rlLowerStore);
-                trackingStore.materialiseFoldedly(program, gap);
-                predicatesWithGap = gap.getPredicatesWithGap();
-                gap.clear();
-
-                if(program.getGeneral().isHorn())
-                        encoder = new TrackingRuleEncoderWithGap(program.getUpper(), trackingStore);
-                else
-                        encoder = new TrackingRuleEncoderDisjVar1(program.getUpper(), trackingStore);
+//              GapByStore4ID gap = new GapByStore4ID(trackingStore);
+        GapByStore4ID gap = new GapByStore4ID2(trackingStore, rlLowerStore);
+        trackingStore.materialiseFoldedly(program, gap);
+        predicatesWithGap = gap.getPredicatesWithGap();
+        gap.clear();
+
+        if(program.getGeneral().isHorn())
+            encoder = new TrackingRuleEncoderWithGap(program.getUpper(), trackingStore);
+        else
+            encoder = new TrackingRuleEncoderDisjVar1(program.getUpper(), trackingStore);
 //                      encoder = new TrackingRuleEncoderDisj1(program.getUpper(), trackingStore);
 //                      encoder = new TrackingRuleEncoderDisjVar2(program.getUpper(), trackingStore);
 //                      encoder = new TrackingRuleEncoderDisj2(program.getUpper(), trackingStore);
 
-                program.deleteABoxTurtleFile();
-
-                if(!isConsistent())
-                        return false;
-
-                consistency.extractBottomFragment();
-                consistency.dispose();
-
-                return true;
-        }
-        
-        @Override
-        public boolean isConsistent() {
-                if(satisfiable == SatisfiabilityStatus.UNCHECKED) {
-                        satisfiable = consistency.check() ? SatisfiabilityStatus.SATISFIABLE : SatisfiabilityStatus.UNSATISFIABLE;
-                        Utility.logInfo("time for satisfiability checking: " + t.duration());
-                }
-                return satisfiable == SatisfiabilityStatus.SATISFIABLE;
-        }
-
-        /**
-         * It deals with blanks nodes differently from variables
-         * according to SPARQL semantics for OWL2 Entailment Regime.
-         * <p>
-         * In particular variables are matched only against named individuals,
-         * and blank nodes against named and anonymous individuals.
-         */
-        private boolean queryUpperStore(BasicQueryEngine upperStore, QueryRecord queryRecord,
-                                                                        Tuple<String> extendedQuery, Step step) {
-
-                if(queryRecord.hasNonAnsDistinguishedVariables())
-                        queryUpperBound(upperStore, queryRecord, extendedQuery.get(0), queryRecord.getAnswerVariables());
-                else
-                        queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-
-                queryRecord.addProcessingTime(step, t.duration());
-                if(queryRecord.isProcessed()) {
-                        queryRecord.setDifficulty(step);
-                        return true;
-                }
-                return false;
-        }
-
-        /**
-         * Returns the part of the ontology relevant for Hermit, while computing the bound answers.
-         * */
-        private boolean queryBounds(QueryRecord queryRecord) {
-                AnswerTuples rlAnswer = null, elAnswer = null;
-
-                t.reset();
-                try {
-                        rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-                        Utility.logDebug(t.duration());
-                        queryRecord.updateLowerBoundAnswers(rlAnswer);
-                } finally {
-                        if (rlAnswer != null) rlAnswer.dispose();
-                }
-                queryRecord.addProcessingTime(Step.LOWER_BOUND, t.duration());
-
-                t.reset();
-
-                Tuple<String> extendedQueryTexts = queryRecord.getExtendedQueryText();
-
-                Utility.logDebug("Tracking store");
-                if(queryUpperStore(trackingStore, queryRecord, extendedQueryTexts, Step.SIMPLE_UPPER_BOUND))
-                        return true;
-
-                if(!queryRecord.isBottom()) {
-                        Utility.logDebug("Lazy store");
-                        if(lazyUpperStore != null && queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts, Step.LAZY_UPPER_BOUND))
-                                return true;
+        if(!isConsistent())
+            return false;
+
+        consistency.extractBottomFragment();
+        consistency.dispose();
+
+        program.dispose();
+
+        return true;
+    }
+
+    @Override
+    public boolean isConsistent() {
+        if(isDisposed()) throw new DisposedException();
+        if(satisfiable == SatisfiabilityStatus.UNCHECKED) {
+            satisfiable = consistency.check() ? SatisfiabilityStatus.SATISFIABLE : SatisfiabilityStatus.UNSATISFIABLE;
+            Utility.logInfo("time for satisfiability checking: " + t.duration());
+        }
+        return satisfiable == SatisfiabilityStatus.SATISFIABLE;
+    }
+
+    @Override
+    public void evaluate(QueryRecord queryRecord) {
+        if(isDisposed()) throw new DisposedException();
+        if(queryBounds(queryRecord))
+            return;
+
+        OWLOntology relevantOntologySubset = extractRelevantOntologySubset(queryRecord);
+
+        int aBoxCount = relevantOntologySubset.getABoxAxioms(true).size();
+        Utility.logInfo("Relevant ontology subset: ABox_axioms=" + aBoxCount + " TBox_axioms=" + (relevantOntologySubset
+                .getAxiomCount() - aBoxCount));
+//              queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl");
+
+        if(querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord))
+            return;
+
+        Timer t = new Timer();
+        Checker summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT());
+        summarisedChecker.check(queryRecord.getGapAnswers());
+        summarisedChecker.dispose();
+        Utility.logDebug("Total time for full reasoner: " + t.duration());
+        queryRecord.markAsProcessed();
+        Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
+    }
+
+    @Override
+    public void evaluateUpper(QueryRecord queryRecord) {
+        if(isDisposed()) throw new DisposedException();
+        // TODO add new upper store
+        AnswerTuples rlAnswer = null;
+        boolean useFull = queryRecord.isBottom() || lazyUpperStore == null;
+        try {
+            rlAnswer =
+                    (useFull ? trackingStore : lazyUpperStore).evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+            queryRecord.updateUpperBoundAnswers(rlAnswer, true);
+        } finally {
+            if(rlAnswer != null) rlAnswer.dispose();
+        }
+    }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+
+        if(encoder != null) encoder.dispose();
+        if(rlLowerStore != null) rlLowerStore.dispose();
+        if(lazyUpperStore != null) lazyUpperStore.dispose();
+        if(elLowerStore != null) elLowerStore.dispose();
+        if(trackingStore != null) trackingStore.dispose();
+        if(limitedSkolemUpperStore != null) limitedSkolemUpperStore.dispose();
+
+    }
+
+    private BasicQueryEngine getUpperStore(String name, boolean checkValidity) {
+        if(multiStageTag)
+            return new MultiStageQueryEngine(name, checkValidity);
+//                      return new TwoStageQueryEngine(name, checkValidity);
+        else
+            return new BasicQueryEngine(name);
+    }
+
+    protected void internal_importDataFile(String name, String datafile) {
+//              addDataFile(datafile);
+        rlLowerStore.importRDFData(name, datafile);
+        if(lazyUpperStore != null)
+            lazyUpperStore.importRDFData(name, datafile);
+        elLowerStore.importRDFData(name, datafile);
+        trackingStore.importRDFData(name, datafile);
+    }
+
+    /**
+     * It deals with blanks nodes differently from variables
+     * according to SPARQL semantics for OWL2 Entailment Regime.
+     * <p>
+     * In particular variables are matched only against named individuals,
+     * and blank nodes against named and anonymous individuals.
+     */
+    private boolean queryUpperStore(BasicQueryEngine upperStore, QueryRecord queryRecord,
+                                    Tuple<String> extendedQuery, Step step) {
+
+        if(queryRecord.hasNonAnsDistinguishedVariables())
+            queryUpperBound(upperStore, queryRecord, extendedQuery.get(0), queryRecord.getAnswerVariables());
+        else
+            queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+
+        queryRecord.addProcessingTime(step, t.duration());
+        if(queryRecord.isProcessed()) {
+            queryRecord.setDifficulty(step);
+            return true;
+        }
+        return false;
+    }
+
+    /**
+     * Returns the part of the ontology relevant for Hermit, while computing the bound answers.
+     */
+    private boolean queryBounds(QueryRecord queryRecord) {
+        AnswerTuples rlAnswer = null, elAnswer = null;
+
+        t.reset();
+        try {
+            rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+            Utility.logDebug(t.duration());
+            queryRecord.updateLowerBoundAnswers(rlAnswer);
+        } finally {
+            if(rlAnswer != null) rlAnswer.dispose();
+        }
+        queryRecord.addProcessingTime(Step.LOWER_BOUND, t.duration());
+
+        t.reset();
+
+        Tuple<String> extendedQueryTexts = queryRecord.getExtendedQueryText();
+
+        Utility.logDebug("Tracking store");
+        if(queryUpperStore(trackingStore, queryRecord, extendedQueryTexts, Step.SIMPLE_UPPER_BOUND))
+            return true;
+
+        if(!queryRecord.isBottom()) {
+            Utility.logDebug("Lazy store");
+            if(lazyUpperStore != null && queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts, Step.LAZY_UPPER_BOUND))
+                return true;
 //                      Utility.logDebug("Skolem store");
 //                      if(limitedSkolemUpperStore != null && queryUpperStore(limitedSkolemUpperStore, queryRecord, extendedQueryTexts, Step.L_SKOLEM_UPPER_BOUND))
 //                              return null;
-                }
-
-                t.reset();
-                try {
-                        elAnswer = elLowerStore.evaluate(extendedQueryTexts.get(0),
-                                                                                         queryRecord.getAnswerVariables(),
-                                                                                         queryRecord.getLowerBoundAnswers());
-                        Utility.logDebug(t.duration());
-                        queryRecord.updateLowerBoundAnswers(elAnswer);
-                } finally {
-                        if (elAnswer != null) elAnswer.dispose();
-                }
-                queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
-
-                if(queryRecord.isProcessed()) {
-                        queryRecord.setDifficulty(Step.EL_LOWER_BOUND);
-                        return true;
-                }
-
-                return false;
-        }
-
-        private OWLOntology extractRelevantOntologySubset(QueryRecord queryRecord) {
-                t.reset();
-
-                QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord);
-                OWLOntology relevantOntologySubset = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
-
-                queryRecord.addProcessingTime(Step.FRAGMENT, t.duration());
-
-                return relevantOntologySubset;
-        }
-
-        private void queryUpperBound(BasicQueryEngine upperStore, QueryRecord queryRecord, String queryText, String[] answerVariables) {
-                AnswerTuples rlAnswer = null;
-                try {
-                        Utility.logDebug(queryText);
-                        rlAnswer = upperStore.evaluate(queryText, answerVariables);
-                        Utility.logDebug(t.duration());
-                        queryRecord.updateUpperBoundAnswers(rlAnswer);
-                } finally {
-                        if(rlAnswer != null) rlAnswer.dispose();
-                }
-        }
-
-        @Override
-        public void evaluate(QueryRecord queryRecord) {
-                if(queryBounds(queryRecord))
-                        return;
-
-                OWLOntology relevantOntologySubset = extractRelevantOntologySubset(queryRecord);
-
-                int aBoxCount = relevantOntologySubset.getABoxAxioms(true).size();
-                Utility.logInfo("Relevant ontology subset: ABox_axioms=" + aBoxCount + " TBox_axioms=" + (relevantOntologySubset
-                                .getAxiomCount() - aBoxCount));
-//              queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl");
-
-                if(querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord))
-                        return;
-
-                Timer t = new Timer();
-                Checker summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT());
-                summarisedChecker.check(queryRecord.getGapAnswers());
-                summarisedChecker.dispose();
-                Utility.logDebug("Total time for full reasoner: " + t.duration());
-                queryRecord.markAsProcessed();
-                Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
-        }
-
-        private boolean querySkolemisedRelevantSubset(OWLOntology relevantSubset, QueryRecord queryRecord) {
-                MultiStageQueryEngine relevantStore =
-                                new MultiStageQueryEngine("Relevant-store", true); // checkValidity is true
-                DatalogProgram relevantProgram = new DatalogProgram(relevantSubset, false); // toClassify is false
-
-//        relevantStore.importRDFData("data", importedData.toString()); // 2 answers more
-                relevantStore.importDataFromABoxOf(relevantSubset);
-
-                int materialisationResult = relevantStore.materialiseSkolemly(relevantProgram, null);
-                if(materialisationResult != 1)
-                        throw new RuntimeException("Skolemised materialisation error"); // TODO check consistency
+        }
+
+        t.reset();
+        try {
+            elAnswer = elLowerStore.evaluate(extendedQueryTexts.get(0),
+                                             queryRecord.getAnswerVariables(),
+                                             queryRecord.getLowerBoundAnswers());
+            Utility.logDebug(t.duration());
+            queryRecord.updateLowerBoundAnswers(elAnswer);
+        } finally {
+            if(elAnswer != null) elAnswer.dispose();
+        }
+        queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
+
+        if(queryRecord.isProcessed()) {
+            queryRecord.setDifficulty(Step.EL_LOWER_BOUND);
+            return true;
+        }
+
+        return false;
+    }
+
+    private OWLOntology extractRelevantOntologySubset(QueryRecord queryRecord) {
+        t.reset();
+
+        QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord);
+        OWLOntology relevantOntologySubset = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
+
+        queryRecord.addProcessingTime(Step.FRAGMENT, t.duration());
+
+        return relevantOntologySubset;
+    }
+
+    private void queryUpperBound(BasicQueryEngine upperStore, QueryRecord queryRecord, String queryText, String[] answerVariables) {
+        AnswerTuples rlAnswer = null;
+        try {
+            Utility.logDebug(queryText);
+            rlAnswer = upperStore.evaluate(queryText, answerVariables);
+            Utility.logDebug(t.duration());
+            queryRecord.updateUpperBoundAnswers(rlAnswer);
+        } finally {
+            if(rlAnswer != null) rlAnswer.dispose();
+        }
+    }
+
+    private boolean querySkolemisedRelevantSubset(OWLOntology relevantSubset, QueryRecord queryRecord) {
+        DatalogProgram relevantProgram = new DatalogProgram(relevantSubset, false); // toClassify is false
+
+        MultiStageQueryEngine relevantStore =
+                new MultiStageQueryEngine("Relevant-store", true); // checkValidity is true
+//        relevantStore.importRDFData("data", relevantProgram.getAdditionalDataFile()); // tried, doesn't work
+        relevantStore.importDataFromABoxOf(relevantSubset);
+
+        int materialisationResult = relevantStore.materialiseSkolemly(relevantProgram, null);
+//        int materialisationResult = relevantStore.materialiseRestrictedly(relevantProgram, null); // DOESN'T WORK!!!
+        if(materialisationResult != 1)
+            throw new RuntimeException("Skolemised materialisation error"); // TODO check consistency
 //        relevantStore.materialiseRestrictedly(relevantProgram, null); // it has been tried
 
-                return queryUpperStore(relevantStore, queryRecord, queryRecord.getExtendedQueryText(), Step.L_SKOLEM_UPPER_BOUND);
-
-                // the following has been tried
-//        Tuple<String> extendedQueryText = queryRecord.getExtendedQueryText();
-//        if(queryRecord.hasNonAnsDistinguishedVariables()) {
-//            queryUpperBound(relevantStore, queryRecord, extendedQueryText.get(0), queryRecord.getAnswerVariables());
-//            queryUpperBound(relevantStore, queryRecord, extendedQueryText.get(1), queryRecord.getDistinguishedVariables());
-//        }
-//        else
-//            queryUpperBound(relevantStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-//
-//              return queryRecord.isProcessed();
-
-        }
-
-        @Override
-        public void evaluateUpper(QueryRecord queryRecord) {
-                // TODO add new upper store
-                AnswerTuples rlAnswer = null;
-                boolean useFull = queryRecord.isBottom() || lazyUpperStore == null;
-                try {
-                        rlAnswer =
-                                        (useFull ? trackingStore : lazyUpperStore).evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-                        queryRecord.updateUpperBoundAnswers(rlAnswer, true);
-                } finally {
-                        if(rlAnswer != null) rlAnswer.dispose();
-                }
-        }
-
-        @Override
-        public void dispose() {
-                if (encoder != null) encoder.dispose();
-                if (rlLowerStore != null) rlLowerStore.dispose();
-                if (lazyUpperStore != null) lazyUpperStore.dispose();
-                if (elLowerStore != null) elLowerStore.dispose();
-                if (trackingStore != null) trackingStore.dispose();
-
-//              if(limitedSkolemUpperStore != null) limitedSkolemUpperStore.dispose();
-                super.dispose();
-        }
-
-        enum SatisfiabilityStatus {SATISFIABLE, UNSATISFIABLE, UNCHECKED}
+        return queryUpperStore(relevantStore, queryRecord, queryRecord.getExtendedQueryText(), Step.L_SKOLEM_UPPER_BOUND);
+
+//        return queryUpperStore(limitedSkolemUpperStore, queryRecord, queryRecord.getExtendedQueryText(), Step.L_SKOLEM_UPPER_BOUND);
+    }
+
+    enum SatisfiabilityStatus {SATISFIABLE, UNSATISFIABLE, UNCHECKED}
 
 }