Removed extended queries (involving classes MyQueryReasoner and QueryRecord). Executed LightTests successfully.

3 files changed, 57 insertions, 76 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java b/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
index 7220533..54e4837 100644
--- a/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
+++ b/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
@@ -50,7 +50,10 @@ public class AnswerTuple {
                 for(int i = 0; i < arity; ++i) m_tuple[i] = sup.m_tuple[i];
         }
 
-        public static AnswerTuple create(AnswerTuple extendedTuple, int length) {
+        /**
+         * It returns the first argument if its arity equals length, a new AnswerTuple otherwise.
+         */
+        public static AnswerTuple getInstance(AnswerTuple extendedTuple, int length) {
                 if(length == extendedTuple.getArity()) return extendedTuple;
                 else return new AnswerTuple(extendedTuple, length);
         }
diff --git a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
index 1ecd867..8b73abb 100644
--- a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
+++ b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
@@ -22,6 +22,7 @@ public class QueryRecord {
         
         public static final String botQueryText = "SELECT ?X WHERE { ?X <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Nothing> }";
         public static final String SEPARATOR = "----------------------------------------";
+        private static final String RDF_TYPE = "a"; //"rdf:type"; //RDF.type.toString();
         boolean processed = false;
         String stringQueryID = null;
         OWLOntology relevantOntology = null;
@@ -39,18 +40,18 @@ public class QueryRecord {
 
         private QueryRecord() {
         }
-        
-        public QueryRecord(QueryManager manager, String text, int id, int subID) {
-                m_manager = manager;
-                resetInfo(text, id, subID);
-                resetTimer();
-        }
 
 //      private boolean containsAuxPredicate(String str) {
 //              return  str.contains(Namespace.PAGODA_AUX) || str.contains("_AUX") || str.contains("owl#Nothing") ||
 //                              str.contains("internal:def"); 
 //      }
 
+        public QueryRecord(QueryManager manager, String text, int id, int subID) {
+                m_manager = manager;
+                resetInfo(text, id, subID);
+                resetTimer();
+        }
+
         public static Collection<String> collectQueryTexts(Collection<QueryRecord> queryRecords) {
                 Collection<String> texts = new LinkedList<String>();
                 for(QueryRecord record : queryRecords)
@@ -126,56 +127,33 @@ public class QueryRecord {
 
                 RDFoxAnswerTuples rdfoxAnswerTuples = (RDFoxAnswerTuples) answerTuples;
 
-//              if(soundAnswerTuples.size() > 0) {
-//                      int number = 0;
-//                      for(; rdfoxAnswerTuples.isValid(); rdfoxAnswerTuples.moveNext()) {
-//                              ++number;
-//                      }
-//                      Utility.logInfo("The number of answers returned by an upper bound: " + number);
-//                      if(number == soundAnswerTuples.size()) {
-//                              if(gapAnswerTuples != null) gapAnswerTuples.clear();
-//                              else gapAnswerTuples = new HashSet<AnswerTuple>();
-//
-//                              Utility.logInfo("The number of upper bound answers: " + (soundAnswerTuples.size() + gapAnswerTuples.size()));
-//                              return false;
-//                      } else if(number < soundAnswerTuples.size())
-//                              throw new IllegalArgumentException("The upper bound answers must contain all the lower bound ones!");
-//                      rdfoxAnswerTuples.reset();
-//              }
-
-//              boolean justCheck = (rdfoxAnswerTuples.getArity() < getDistinguishedVariables().length);
-//              boolean justCheck = (rdfoxAnswerTuples.getArity() != getDistinguishedVariables().length);
-//              if(justCheck) throw new Error("justCheck!");
-                boolean justCheck = false;
-
                 Set<AnswerTuple> candidateGapAnswerTuples = new HashSet<AnswerTuple>();
-                AnswerTuple tuple, extendedTuple;
+                AnswerTuple tuple;
                 for(; rdfoxAnswerTuples.isValid(); rdfoxAnswerTuples.moveNext()) {
-                        extendedTuple = rdfoxAnswerTuples.getTuple();
-                        if(isBottom() || !extendedTuple.hasAnonymousIndividual()) {
-                                tuple = AnswerTuple.create(extendedTuple, getAnswerVariables().length);
-                                if((!toCheckAux || !tuple.hasAuxPredicate()) && !soundAnswerTuples.contains(tuple)) {
-                                        if(!toCheckAux && justCheck) return false;
-                                        // TODO check
-                                        candidateGapAnswerTuples.add(extendedTuple);
-//                                      candidateGapAnswerTuples.add(tuple);
-                                }
-                        }
+                        tuple = rdfoxAnswerTuples.getTuple();
+                        if(isBottom() || !tuple.hasAnonymousIndividual())
+                                if((!toCheckAux || !tuple.hasAuxPredicate()) && !soundAnswerTuples.contains(tuple))
+                                        candidateGapAnswerTuples.add(tuple);
                 }
 
                 /*** START: debugging ***/
                 if(PagodaProperties.isDebuggingMode()) {
-                        Set<AnswerTuple> projectedAnswerTuples = new HashSet<>();
+                        if(rdfoxAnswerTuples.getArity() != getAnswerVariables().length)
+                                throw new IllegalArgumentException(
+                                                "The arity of answers (" + rdfoxAnswerTuples.getArity() + ") " +
+                                                                "is different from the number of answer variables (" +
+                                                                getAnswerVariables().length + ")");
+
+                        Set<AnswerTuple> namedAnswerTuples = new HashSet<>();
                         rdfoxAnswerTuples.reset();
                         for(; rdfoxAnswerTuples.isValid(); rdfoxAnswerTuples.moveNext()) {
-                                extendedTuple = rdfoxAnswerTuples.getTuple();
-                                if(isBottom() || !extendedTuple.hasAnonymousIndividual()) {
-                                        tuple = AnswerTuple.create(extendedTuple, getAnswerVariables().length);
-                                        projectedAnswerTuples.add(tuple);
-                                }
+                                tuple = rdfoxAnswerTuples.getTuple();
+//                              if(isBottom() || !tuple.hasAnonymousIndividual()) {
+                                namedAnswerTuples.add(tuple);
+//                              }
                         }
                         HashSet<AnswerTuple> difference = new HashSet<>(soundAnswerTuples);
-                        difference.removeAll(projectedAnswerTuples);
+                        difference.removeAll(namedAnswerTuples);
                         if(!difference.isEmpty())
                                 throw new IllegalArgumentException("The upper bound does not contain the lower bound!");
                 }
@@ -218,7 +196,7 @@ public class QueryRecord {
                 if(gapAnswerTuples != null && gapAnswerTuples.isEmpty()) processed = true;
                 return processed;
         }
-        
+
         public String[] getDistinguishedVariables() {
                 return answerVariables[1];
         }
@@ -238,7 +216,7 @@ public class QueryRecord {
         public String getQueryID() {
                 return stringQueryID;
         }
-        
+
         public AnswerTuples getGapAnswers() {
                 return new AnswerTuplesImp(answerVariables[0], gapAnswerTuples);
         }
@@ -355,7 +333,7 @@ public class QueryRecord {
         public void setRelevantOntology(OWLOntology knowledgebase) {
                 relevantOntology = knowledgebase;
         }
-        
+
         public void saveRelevantOntology(String filename) {
                 if(relevantOntology == null) return;
                 OWLOntologyManager manager = relevantOntology.getOWLOntologyManager();
@@ -394,7 +372,7 @@ public class QueryRecord {
                                 Utility.logError("The answer (" + answer + ") cannot be added, because it is not in the upper bound.");
                         gapAnswerTuples.remove(answer);
 
-                        answer = AnswerTuple.create(answer, answerVariables[0].length);
+                        answer = AnswerTuple.getInstance(answer, answerVariables[0].length);
 //                      if (soundAnswerTuples.contains(answer))
 //                              Utility.logError("The answer (" + answer + ") cannot be added, because it is in the lower bound.");
                         soundAnswerTuples.add(answer);
@@ -412,7 +390,7 @@ public class QueryRecord {
         public int getArity() {
                 return answerVariables[0].length;
         }
-        
+
         public void addRelevantClauses(DLClause clause) {
                 relevantClauses.add(clause);
         }
@@ -477,10 +455,10 @@ public class QueryRecord {
         }
         
         public void updateSubID() {
-                ++subID; 
+                ++subID;
                 stringQueryID = String.valueOf(queryID) + "_" + subID;
         }
-        
+
         public DLClause getClause() {
                 if (queryClause != null)
                         return queryClause;
@@ -498,7 +476,7 @@ public class QueryRecord {
         public int getSubID() {
                 return subID;
         }
-        
+
         public boolean hasSameGapAnswers(QueryRecord that) {
                 return gapAnswerTuples.containsAll(that.gapAnswerTuples) && that.gapAnswerTuples.containsAll(gapAnswerTuples);
         }
@@ -539,8 +517,9 @@ public class QueryRecord {
                 return false;
         }
 
+        // TODO remove fully extended query
         public Tuple<String> getExtendedQueryText() {
-//              String[] ret = new String[2];
+//              String[] ret = new String[2];s
                 int index = queryText.toUpperCase().indexOf(" WHERE");
                 String extendedSelect = queryText.substring(0, index);
                 String extendedWhere= queryText.substring(index + 1), fullyExtendedWhere = queryText.substring(index + 1);
@@ -564,10 +543,18 @@ public class QueryRecord {
 //              if (answerVariables[0] != answerVariables[1]) {
                         for (int i = answerVariables[0].length; i < answerVariables[1].length; ++i) {
 //                      for (int i = 0; i < answerVariables[1].length; ++i) {
-                                fullyExtra.append(" . ?").append(answerVariables[1][i]).append(" a <").append(Namespace.PAGODA_ORIGINAL).append(">");
+                                fullyExtra.append(" . ?")
+                                                  .append(answerVariables[1][i])
+                                                  .append(" " + RDF_TYPE + " <")
+                                                  .append(Namespace.PAGODA_ORIGINAL)
+                                                  .append(">");
                                 if ((list = links.get(answerVariables[1][i])) == null || list.size() < 2) ;
                                 else {
-                                        extra.append(" . ?").append(answerVariables[1][i]).append(" a <").append(Namespace.PAGODA_ORIGINAL).append(">");
+                                        extra.append(" . ?")
+                                                 .append(answerVariables[1][i])
+                                                 .append(" " + RDF_TYPE + " <")
+                                                 .append(Namespace.PAGODA_ORIGINAL)
+                                                 .append(">");
                                 }
                         }
 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 2a49e24..cc0e647 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -208,14 +208,10 @@ class MyQueryReasoner extends QueryReasoner {
         private boolean queryUpperStore(BasicQueryEngine upperStore, QueryRecord queryRecord,
                                                                         Tuple<String> extendedQuery, Step step) {
 
-                queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-
-                if(queryRecord.hasNonAnsDistinguishedVariables()) {
-                        if(!queryRecord.processed())
-                                queryUpperBound(upperStore, queryRecord, extendedQuery.get(0), queryRecord.getAnswerVariables());
-                        if(!queryRecord.processed())
-                                queryUpperBound(upperStore, queryRecord, extendedQuery.get(1), queryRecord.getDistinguishedVariables());
-                }
+                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.processed()) {
@@ -245,28 +241,23 @@ class MyQueryReasoner extends QueryReasoner {
 
                 Tuple<String> extendedQueryTexts = queryRecord.getExtendedQueryText();
 
-//              BasicQueryEngine upperStore;
-//              if(queryRecord.isBottom()) upperStore = trackingStore;
-//              upperStore = queryRecord.isBottom() || lazyUpperStore == null ? trackingStore : lazyUpperStore;
-
-                // TODO
-//              if(queryRecord.isBottom() || (lazyUpperStore == null && limitedSkolemUpperStore == null))
-//                      queryUpperStore(trackingStore, queryRecord, extendedQueryTexts);
-//              else {
-
+                Utility.logDebug("Tracking store");
                 if(queryUpperStore(trackingStore, queryRecord, extendedQueryTexts, Step.SIMPLE_UPPER_BOUND))
                         return null;
 
                 if(!queryRecord.isBottom()) {
+                        Utility.logDebug("Lazy store");
                         if(lazyUpperStore != null && queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts, Step.LAZY_UPPER_BOUND))
                                 return null;
+                        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(),
+                        elAnswer = elLowerStore.evaluate(extendedQueryTexts.get(0),
+                                                                                         queryRecord.getAnswerVariables(),
                                                                                          queryRecord.getLowerBoundAnswers());
                         Utility.logDebug(t.duration());
                         queryRecord.updateLowerBoundAnswers(elAnswer);