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authorRncLsn <rnc.lsn@gmail.com>2015-05-19 18:22:26 +0100
committerRncLsn <rnc.lsn@gmail.com>2015-05-19 18:22:26 +0100
commit612729386b645b120f8397a007cd8421986af0ad (patch)
treef5d15c839092c1dd65e951aa98f4256bfa391a0b /src/uk/ac/ox/cs
parent5d54af2638a53721b414a41356a93686a9616272 (diff)
downloadACQuA-612729386b645b120f8397a007cd8421986af0ad.tar.gz
ACQuA-612729386b645b120f8397a007cd8421986af0ad.zip
Changes in the upper store querying (mainly in MyQueryReasoner).
Diffstat (limited to 'src/uk/ac/ox/cs')
-rw-r--r--src/uk/ac/ox/cs/pagoda/Pagoda.java1
-rw-r--r--src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java4
-rw-r--r--src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java94
-rw-r--r--src/uk/ac/ox/cs/pagoda/query/QueryRecord.java479
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java66
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java102
-rw-r--r--src/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java9
-rw-r--r--src/uk/ac/ox/cs/pagoda/util/tuples/TupleBuilder.java4
8 files changed, 383 insertions, 376 deletions
diff --git a/src/uk/ac/ox/cs/pagoda/Pagoda.java b/src/uk/ac/ox/cs/pagoda/Pagoda.java
index 4ad7678..04920c4 100644
--- a/src/uk/ac/ox/cs/pagoda/Pagoda.java
+++ b/src/uk/ac/ox/cs/pagoda/Pagoda.java
@@ -30,6 +30,7 @@ public class Pagoda implements Runnable {
30 30
31 public static void main(String... args) { 31 public static void main(String... args) {
32 32
33 // TODO treat the mandatory options as simple args
33 Options options = new Options(); 34 Options options = new Options();
34 options.addOption(Option.builder(OPTION_ONTOLOGY) 35 options.addOption(Option.builder(OPTION_ONTOLOGY)
35 .argName(OPTION_ONTOLOGY) 36 .argName(OPTION_ONTOLOGY)
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
index fefb8b2..00e7e2b 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
@@ -109,9 +109,9 @@ public abstract class Pick4NegativeConcept implements Treatment {
109 for (int j = 0; j < answerTupleID.getArity(); j++) { 109 for (int j = 0; j < answerTupleID.getArity(); j++) {
110 String rawTerm = tripleManager.getRawTerm(answerTupleID.getTerm(j)); 110 String rawTerm = tripleManager.getRawTerm(answerTupleID.getTerm(j));
111 Individual individual = Individual.create(rawTerm.substring(1, rawTerm.length()-1)); 111 Individual individual = Individual.create(rawTerm.substring(1, rawTerm.length()-1));
112 tupleBuilder.add(individual); 112 tupleBuilder.append(individual);
113 } 113 }
114 violationTuples.add(tupleBuilder.create()); 114 violationTuples.add(tupleBuilder.build());
115 } 115 }
116 116
117 for (DLClause clause : program.convertExist(constraint, violation.getClause(), violationTuples)) { 117 for (DLClause clause : program.convertExist(constraint, violation.getClause(), violationTuples)) {
diff --git a/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java b/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
index cd86282..7220533 100644
--- a/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
+++ b/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
@@ -22,10 +22,11 @@ import java.util.regex.Pattern;
22public class AnswerTuple { 22public class AnswerTuple {
23 23
24 public static final String SEPARATOR = "\t"; 24 public static final String SEPARATOR = "\t";
25 static final Pattern owlLiteralRegex =
26 Pattern.compile("^\"(?<lexicalForm>[^@]+(@(?<langTag>.+))?)\"(^^<(?<dataType>.+)>)?$");
27 String m_str = null;
28 GroundTerm[] m_tuple;
25 29
26 String m_str = null;
27 GroundTerm[] m_tuple;
28
29 public AnswerTuple(TupleIterator iter, int arity) { 30 public AnswerTuple(TupleIterator iter, int arity) {
30 m_tuple = new GroundTerm[arity]; 31 m_tuple = new GroundTerm[arity];
31 try { 32 try {
@@ -33,24 +34,29 @@ public class AnswerTuple {
33 m_tuple[i] = iter.getGroundTerm(i); 34 m_tuple[i] = iter.getGroundTerm(i);
34 } catch (JRDFStoreException e) { 35 } catch (JRDFStoreException e) {
35 e.printStackTrace(); 36 e.printStackTrace();
36 } 37 }
37 } 38 }
38 39
39 public AnswerTuple(GroundTerm[] terms) { 40 public AnswerTuple(GroundTerm[] terms) {
40 m_tuple = terms; 41 m_tuple = terms;
41 }
42
43 private AnswerTuple(AnswerTuple sup, int arity) {
44 m_tuple = new GroundTerm[arity];
45 for (int i = 0; i < arity; ++i) m_tuple[i] = sup.m_tuple[i];
46 } 42 }
47 43
48// private AnswerTuple(String m_str) { 44// private AnswerTuple(String m_str) {
49// this.m_str = m_str; 45// this.m_str = m_str;
50// } 46// }
47
48 private AnswerTuple(AnswerTuple sup, int arity) {
49 m_tuple = new GroundTerm[arity];
50 for(int i = 0; i < arity; ++i) m_tuple[i] = sup.m_tuple[i];
51 }
52
53 public static AnswerTuple create(AnswerTuple extendedTuple, int length) {
54 if(length == extendedTuple.getArity()) return extendedTuple;
55 else return new AnswerTuple(extendedTuple, length);
56 }
51 57
52 public int getArity() { 58 public int getArity() {
53 return m_tuple.length; 59 return m_tuple.length;
54 } 60 }
55 61
56 public int hashCode() { 62 public int hashCode() {
@@ -60,7 +66,7 @@ public class AnswerTuple {
60 code = code * 1997 + m_tuple[i].hashCode(); 66 code = code * 1997 + m_tuple[i].hashCode();
61 return code; 67 return code;
62 } 68 }
63 69
64 public boolean equals(Object obj) { 70 public boolean equals(Object obj) {
65 if (!(obj instanceof AnswerTuple)) return false; 71 if (!(obj instanceof AnswerTuple)) return false;
66 AnswerTuple that = (AnswerTuple) obj; 72 AnswerTuple that = (AnswerTuple) obj;
@@ -73,8 +79,8 @@ public class AnswerTuple {
73 } 79 }
74 80
75 public String toString() { 81 public String toString() {
76 if (m_str != null) return m_str; 82 if(m_str != null) return m_str;
77 StringBuilder sb = new StringBuilder(); 83 StringBuilder sb = new StringBuilder();
78 for (int i = 0; i < m_tuple.length; ++i) { 84 for (int i = 0; i < m_tuple.length; ++i) {
79 if (sb.length() != 0) sb.append(SEPARATOR); 85 if (sb.length() != 0) sb.append(SEPARATOR);
80 if (m_tuple[i] instanceof uk.ac.ox.cs.JRDFox.model.Individual) 86 if (m_tuple[i] instanceof uk.ac.ox.cs.JRDFox.model.Individual)
@@ -83,64 +89,58 @@ public class AnswerTuple {
83 sb.append(m_tuple[i].toString()); 89 sb.append(m_tuple[i].toString());
84 } 90 }
85 else { 91 else {
86 Literal l = (Literal) m_tuple[i]; 92 Literal l = (Literal) m_tuple[i];
87 sb.append('"').append(l.getLexicalForm()).append("\""); 93 sb.append('"').append(l.getLexicalForm()).append("\"");
88 if (!l.getDatatype().equals(Datatype.XSD_STRING) && !l.getDatatype().equals(Datatype.RDF_PLAIN_LITERAL)) 94 if (!l.getDatatype().equals(Datatype.XSD_STRING) && !l.getDatatype().equals(Datatype.RDF_PLAIN_LITERAL))
89 sb.append("^^<").append(l.getDatatype().getIRI()).append(">"); 95 sb.append("^^<").append(l.getDatatype().getIRI()).append(">");
90 } 96 }
91 } 97 }
92 return m_str = sb.toString(); 98 return m_str = sb.toString();
93 } 99 }
94 100
95 public GroundTerm getGroundTerm(int i) { 101 public GroundTerm getGroundTerm(int i) {
96 return m_tuple[i]; 102 return m_tuple[i];
97 } 103 }
98 104
99 public Map<Variable, Term> getAssignment(String[] vars) { 105 public Map<Variable, Term> getAssignment(String[] vars) {
100 Map<Variable, Term> map = new HashMap<Variable, Term>(); 106 Map<Variable, Term> map = new HashMap<Variable, Term>();
101 int index = 0; 107 int index = 0;
102 Term t; 108 Term t;
103 for (String var: vars) { 109 for (String var: vars) {
104 if (m_tuple[index] instanceof uk.ac.ox.cs.JRDFox.model.Individual) 110 if(m_tuple[index] instanceof uk.ac.ox.cs.JRDFox.model.Individual)
105 t = Individual.create((((uk.ac.ox.cs.JRDFox.model.Individual) m_tuple[index]).getIRI())); 111 t = Individual.create((((uk.ac.ox.cs.JRDFox.model.Individual) m_tuple[index]).getIRI()));
106 else { 112 else {
107 uk.ac.ox.cs.JRDFox.model.Literal l = (uk.ac.ox.cs.JRDFox.model.Literal) m_tuple[index]; 113 uk.ac.ox.cs.JRDFox.model.Literal l = (uk.ac.ox.cs.JRDFox.model.Literal) m_tuple[index];
108 t = Constant.create(l.getLexicalForm(), l.getDatatype().getIRI()); 114 t = Constant.create(l.getLexicalForm(), l.getDatatype().getIRI());
109 } 115 }
110 map.put(Variable.create(var), t); 116 map.put(Variable.create(var), t);
111 ++index; 117 ++index;
112 } 118 }
113 return map; 119 return map;
114 } 120 }
115 121
116 public boolean hasAuxPredicate() { 122 public boolean hasAuxPredicate() {
117 String iri; 123 String iri;
118 for (int i = 0; i < m_tuple.length; ++i) 124 for (int i = 0; i < m_tuple.length; ++i)
119 if ((m_tuple[i] instanceof uk.ac.ox.cs.JRDFox.model.Individual)) { 125 if ((m_tuple[i] instanceof uk.ac.ox.cs.JRDFox.model.Individual)) {
120 iri = ((uk.ac.ox.cs.JRDFox.model.Individual) m_tuple[i]).getIRI(); 126 iri = ((uk.ac.ox.cs.JRDFox.model.Individual) m_tuple[i]).getIRI();
121 if ( iri.startsWith(Namespace.PAGODA_AUX) || iri.contains("_AUX") || iri.contains("_neg") || iri.contains("internal:def")) 127 if(iri.startsWith(Namespace.PAGODA_AUX) || iri.contains("_AUX") || iri.contains("_neg") || iri.contains("internal:def"))
122 return true; 128 return true;
123 } 129 }
124 return false; 130 return false;
125 } 131 }
126 132
127 public boolean hasAnonyIndividual() { 133 public boolean hasAnonymousIndividual() {
128 String iri; 134 String iri;
129 for (int i = 0; i < m_tuple.length; ++i) 135 for(int i = 0; i < m_tuple.length; ++i)
130 if ((m_tuple[i] instanceof uk.ac.ox.cs.JRDFox.model.Individual)) { 136 if((m_tuple[i] instanceof uk.ac.ox.cs.JRDFox.model.Individual)) {
131 iri = ((uk.ac.ox.cs.JRDFox.model.Individual) m_tuple[i]).getIRI(); 137 iri = ((uk.ac.ox.cs.JRDFox.model.Individual) m_tuple[i]).getIRI();
132 if (iri.startsWith(Namespace.PAGODA_ANONY) || iri.startsWith(Namespace.KARMA_ANONY)) 138 if(iri.startsWith(Namespace.PAGODA_ANONY) || iri.startsWith(Namespace.KARMA_ANONY))
133 return true; 139 return true;
134 } 140 }
135 return false; 141 return false;
136 } 142 }
137 143
138 public static AnswerTuple create(AnswerTuple extendedTuple, int length) {
139 if (length == extendedTuple.getArity()) return extendedTuple;
140 else return new AnswerTuple(extendedTuple, length);
141 }
142
143
144 public static class AnswerTupleSerializer implements JsonSerializer<AnswerTuple> { 144 public static class AnswerTupleSerializer implements JsonSerializer<AnswerTuple> {
145 145
146 public JsonElement serialize(AnswerTuple src, Type typeOfSrc, JsonSerializationContext context) { 146 public JsonElement serialize(AnswerTuple src, Type typeOfSrc, JsonSerializationContext context) {
@@ -149,8 +149,6 @@ public class AnswerTuple {
149 149
150 } 150 }
151 151
152 static final Pattern owlLiteralRegex = Pattern.compile("^\"(?<lexicalForm>[^@]+(@(?<langTag>.+))?)\"(^^<(?<dataType>.+)>)?$");
153
154 public static class AnswerTupleDeserializer implements JsonDeserializer<AnswerTuple> { 152 public static class AnswerTupleDeserializer implements JsonDeserializer<AnswerTuple> {
155 public AnswerTuple deserialize(JsonElement json, Type typeOfT, JsonDeserializationContext context) 153 public AnswerTuple deserialize(JsonElement json, Type typeOfT, JsonDeserializationContext context)
156 throws JsonParseException { 154 throws JsonParseException {
diff --git a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
index 15b2c01..4998a19 100644
--- a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
+++ b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
@@ -10,6 +10,8 @@ import uk.ac.ox.cs.pagoda.rules.GeneralProgram;
10import uk.ac.ox.cs.pagoda.util.ConjunctiveQueryHelper; 10import uk.ac.ox.cs.pagoda.util.ConjunctiveQueryHelper;
11import uk.ac.ox.cs.pagoda.util.Namespace; 11import uk.ac.ox.cs.pagoda.util.Namespace;
12import uk.ac.ox.cs.pagoda.util.Utility; 12import uk.ac.ox.cs.pagoda.util.Utility;
13import uk.ac.ox.cs.pagoda.util.tuples.Tuple;
14import uk.ac.ox.cs.pagoda.util.tuples.TupleBuilder;
13 15
14import java.io.*; 16import java.io.*;
15import java.lang.reflect.Type; 17import java.lang.reflect.Type;
@@ -18,199 +20,204 @@ import java.util.*;
18public class QueryRecord { 20public class QueryRecord {
19 21
20 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> }"; 22 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> }";
21 23 public static final String SEPARATOR = "----------------------------------------";
24 boolean processed = false;
25 String stringQueryID = null;
26 OWLOntology relevantOntology = null;
27 Set<DLClause> relevantClauses = new HashSet<DLClause>();
28 double[] timer;
29 int subID;
30 DLClause queryClause = null;
22 private Step difficulty; 31 private Step difficulty;
23 32 private String queryText;
24 private String queryText; 33 private int queryID = -1;
25 private int queryID = -1;
26
27 private String[][] answerVariables = null; 34 private String[][] answerVariables = null;
28 private Set<AnswerTuple> soundAnswerTuples = new HashSet<AnswerTuple>(); 35 private Set<AnswerTuple> soundAnswerTuples = new HashSet<AnswerTuple>();
29 private Set<AnswerTuple> gapAnswerTuples = null; 36 private Set<AnswerTuple> gapAnswerTuples = null;
30
31 private QueryManager m_manager; 37 private QueryManager m_manager;
38
39 private QueryRecord() {
40 }
32 41
33 public QueryRecord(QueryManager manager, String text, int id, int subID) { 42 public QueryRecord(QueryManager manager, String text, int id, int subID) {
34 m_manager =manager; 43 m_manager = manager;
35 resetInfo(text, id, subID); 44 resetInfo(text, id, subID);
36 resetTimer(); 45 resetTimer();
37 } 46 }
38 47
48// private boolean containsAuxPredicate(String str) {
49// return str.contains(Namespace.PAGODA_AUX) || str.contains("_AUX") || str.contains("owl#Nothing") ||
50// str.contains("internal:def");
51// }
52
53 public static Collection<String> collectQueryTexts(Collection<QueryRecord> queryRecords) {
54 Collection<String> texts = new LinkedList<String>();
55 for(QueryRecord record : queryRecords)
56 texts.add(record.queryText);
57 return texts;
58 }
59
39 public void resetInfo(String text, int id, int subid) { 60 public void resetInfo(String text, int id, int subid) {
40 queryID = id; 61 queryID = id;
41 subID = subid; 62 subID = subid;
42 stringQueryID = id + (subID == 0 ? "" : "_" + subID); 63 stringQueryID = id + (subID == 0 ? "" : "_" + subID);
43 m_manager.remove(queryText); 64 m_manager.remove(queryText);
44 m_manager.put(text, this); 65 m_manager.put(text, this);
45 queryClause = null; 66 queryClause = null;
46 answerVariables = ConjunctiveQueryHelper.getAnswerVariables(text); 67 answerVariables = ConjunctiveQueryHelper.getAnswerVariables(text);
47 queryText = text; // .replace("_:", "?"); 68 queryText = text; // .replace("_:", "?");
48 } 69 }
49 70
50 public void resetTimer() { 71 public void resetTimer() {
51 int length = Step.values().length; 72 int length = Step.values().length;
52 timer = new double[length]; 73 timer = new double[length];
53 for (int i = 0; i < length; ++i) timer[i] = 0; 74 for(int i = 0; i < length; ++i) timer[i] = 0;
54 } 75 }
55 76
56 public AnswerTuples getAnswers() { 77 public AnswerTuples getAnswers() {
57 if (processed()) 78 if(processed())
58 return getLowerBoundAnswers(); 79 return getLowerBoundAnswers();
59 80
60 return getUpperBoundAnswers(); 81 return getUpperBoundAnswers();
61 } 82 }
62 83
63 public AnswerTuples getLowerBoundAnswers() { 84 public AnswerTuples getLowerBoundAnswers() {
64 return new AnswerTuplesImp(answerVariables[0], soundAnswerTuples); 85 return new AnswerTuplesImp(answerVariables[0], soundAnswerTuples);
65 } 86 }
66 87
67 public AnswerTuples getUpperBoundAnswers() { 88 public AnswerTuples getUpperBoundAnswers() {
68 return new AnswerTuplesImp(answerVariables[0], soundAnswerTuples, gapAnswerTuples); 89 return new AnswerTuplesImp(answerVariables[0], soundAnswerTuples, gapAnswerTuples);
69 } 90 }
70 91
71 public boolean updateLowerBoundAnswers(AnswerTuples answerTuples) { 92 public boolean updateLowerBoundAnswers(AnswerTuples answerTuples) {
72 if (answerTuples == null) return false; 93 if(answerTuples == null) return false;
73 boolean update = false; 94 boolean update = false;
74 for (AnswerTuple tuple; answerTuples.isValid(); answerTuples.moveNext()) { 95 for(AnswerTuple tuple; answerTuples.isValid(); answerTuples.moveNext()) {
75 tuple = answerTuples.getTuple(); 96 tuple = answerTuples.getTuple();
76 if (!soundAnswerTuples.contains(tuple) && (gapAnswerTuples == null || gapAnswerTuples.contains(tuple))) { 97 if(!soundAnswerTuples.contains(tuple) && (gapAnswerTuples == null || gapAnswerTuples.contains(tuple))) {
77 soundAnswerTuples.add(tuple); 98 soundAnswerTuples.add(tuple);
78 if (gapAnswerTuples != null) 99 if(gapAnswerTuples != null)
79 gapAnswerTuples.remove(tuple); 100 gapAnswerTuples.remove(tuple);
80 update = true; 101 update = true;
81 } 102 }
82 // TODO could be wrong, but if possible add the check
83// else if (! gapAnswerTuples.contains(tuple)) {
84// throw new IllegalArgumentException("The lower bound answers must be contained in the upper ones!");
85// }
86 } 103 }
87 Utility.logInfo("The number of answers in the lower bound: " + soundAnswerTuples.size()); 104 Utility.logInfo("The number of answers in the lower bound: " + soundAnswerTuples.size());
88 105
89 return update; 106 return update;
90 } 107 }
91 108
92 public boolean updateUpperBoundAnswers(AnswerTuples answerTuples) { 109 public boolean updateUpperBoundAnswers(AnswerTuples answerTuples) {
93 return updateUpperBoundAnswers(answerTuples, false); 110 return updateUpperBoundAnswers(answerTuples, false);
94 } 111 }
95 112
96 public boolean updateUpperBoundAnswers(AnswerTuples answerTuples, boolean toCheckAux) { 113 public boolean updateUpperBoundAnswers(AnswerTuples answerTuples, boolean toCheckAux) {
97 RDFoxAnswerTuples rdfAnswerTuples; 114 RDFoxAnswerTuples rdfAnswerTuples;
98 if (answerTuples instanceof RDFoxAnswerTuples) 115 if(answerTuples instanceof RDFoxAnswerTuples)
99 rdfAnswerTuples = (RDFoxAnswerTuples) answerTuples; 116 rdfAnswerTuples = (RDFoxAnswerTuples) answerTuples;
100 else { 117 else {
101 Utility.logError("The upper bound must be computed by RDFox!"); 118 Utility.logError("The upper bound must be computed by RDFox!");
102 return false; 119 return false;
103 } 120 }
104 121
105 if (soundAnswerTuples.size() > 0) { 122 if(soundAnswerTuples.size() > 0) {
106 int number = 0; 123 int number = 0;
107 for (; answerTuples.isValid(); answerTuples.moveNext()) { 124 for(; rdfAnswerTuples.isValid(); rdfAnswerTuples.moveNext()) {
108 ++number; 125 ++number;
109 } 126 }
110 Utility.logInfo("The number of answers returned by an upper bound: " + number); 127 Utility.logInfo("The number of answers returned by an upper bound: " + number);
111 if (number <= soundAnswerTuples.size()) { 128 if(number == soundAnswerTuples.size()) {
112 if (gapAnswerTuples != null) gapAnswerTuples.clear(); 129 if(gapAnswerTuples != null) gapAnswerTuples.clear();
113 else gapAnswerTuples = new HashSet<AnswerTuple>(); 130 else gapAnswerTuples = new HashSet<AnswerTuple>();
114 131
115 Utility.logInfo("The number of upper bound answers: " + (soundAnswerTuples.size() + gapAnswerTuples.size())); 132 Utility.logInfo("The number of upper bound answers: " + (soundAnswerTuples.size() + gapAnswerTuples.size()));
116 return false; 133 return false;
117 } 134 } else if(number < soundAnswerTuples.size())
118 else if (number < soundAnswerTuples.size())
119 throw new IllegalArgumentException("The upper bound answers must contain all the lower bound ones!"); 135 throw new IllegalArgumentException("The upper bound answers must contain all the lower bound ones!");
120 answerTuples.reset(); 136 rdfAnswerTuples.reset();
121 } 137 }
122 138
123 boolean justCheck = (answerTuples.getArity() != answerVariables[1].length); 139 boolean justCheck = (rdfAnswerTuples.getArity() != answerVariables[1].length);
124 140
125 Set<AnswerTuple> tupleSet = new HashSet<AnswerTuple>(); 141 Set<AnswerTuple> tupleSet = new HashSet<AnswerTuple>();
126 AnswerTuple tuple, extendedTuple; 142 AnswerTuple tuple, extendedTuple;
127 for (; answerTuples.isValid(); answerTuples.moveNext()) { 143 for(; rdfAnswerTuples.isValid(); rdfAnswerTuples.moveNext()) {
128 extendedTuple = rdfAnswerTuples.getTuple(); 144 extendedTuple = rdfAnswerTuples.getTuple();
129 if (isBottom() || !extendedTuple.hasAnonyIndividual()) { 145 if(isBottom() || !extendedTuple.hasAnonymousIndividual()) {
130 tuple = AnswerTuple.create(extendedTuple, answerVariables[0].length); 146 tuple = AnswerTuple.create(extendedTuple, answerVariables[0].length);
131 if ((!toCheckAux || !tuple.hasAuxPredicate()) && !soundAnswerTuples.contains(tuple)) { 147 if((!toCheckAux || !tuple.hasAuxPredicate()) && !soundAnswerTuples.contains(tuple)) {
132 if (!toCheckAux && justCheck) return false; 148 if(!toCheckAux && justCheck) return false;
133 tupleSet.add(extendedTuple); 149 // TODO check
150// tupleSet.add(extendedTuple);
151 tupleSet.add(tuple);
134 } 152 }
135 } 153 }
136 } 154 }
137 155
138 if (gapAnswerTuples == null) { 156 if(gapAnswerTuples == null) {
139 gapAnswerTuples = tupleSet; 157 gapAnswerTuples = tupleSet;
140 158
141 Utility.logInfo("The number of answers in the upper bound: " + (soundAnswerTuples.size() + gapAnswerTuples.size())); 159 Utility.logInfo("The number of answers in the upper bound: " + (soundAnswerTuples.size() + gapAnswerTuples.size()));
142 return true; 160 return true;
143 } 161 }
144 162
145 boolean update = false; 163 boolean update = false;
146 for (Iterator<AnswerTuple> iter = gapAnswerTuples.iterator(); iter.hasNext(); ) { 164 for(Iterator<AnswerTuple> iter = gapAnswerTuples.iterator(); iter.hasNext(); ) {
147 tuple = iter.next(); 165 tuple = iter.next();
148 if (!tupleSet.contains(tuple)) { 166 if(!tupleSet.contains(tuple)) {
149 iter.remove(); 167 iter.remove();
150 update = true; 168 update = true;
151 } 169 }
152 } 170 }
153 171
154 Utility.logInfo("The number of answers in the upper bound: " + (soundAnswerTuples.size() + gapAnswerTuples.size())); 172 Utility.logInfo("The number of answers in the upper bound: " + (soundAnswerTuples.size() + gapAnswerTuples.size()));
155 173
156 return update; 174 return update;
157 } 175 }
158 176
159// private boolean containsAuxPredicate(String str) {
160// return str.contains(Namespace.PAGODA_AUX) || str.contains("_AUX") || str.contains("owl#Nothing") ||
161// str.contains("internal:def");
162// }
163
164 boolean processed = false;
165
166 public void markAsProcessed() { 177 public void markAsProcessed() {
167 processed = true; 178 processed = true;
168 } 179 }
169 180
170 public boolean processed() { 181 public boolean processed() {
171 if (gapAnswerTuples != null && gapAnswerTuples.isEmpty()) processed = true; 182 if(gapAnswerTuples != null && gapAnswerTuples.isEmpty()) processed = true;
172 return processed; 183 return processed;
173 } 184 }
174 185
175 public String[] getDistinguishedVariables() { 186 public String[] getDistinguishedVariables() {
176 return answerVariables[1]; 187 return answerVariables[1];
177 } 188 }
178 189
179 public String[] getAnswerVariables() { 190 public String[] getAnswerVariables() {
180 return answerVariables[0]; 191 return answerVariables[0];
181 } 192 }
182 193
183 public String[][] getVariables() { 194 public String[][] getVariables() {
184 return answerVariables; 195 return answerVariables;
185 } 196 }
186 197
187 public String getQueryText() { 198 public String getQueryText() {
188 return queryText; 199 return queryText;
189 } 200 }
190 201
191 String stringQueryID = null;
192
193 public String getQueryID() { 202 public String getQueryID() {
194 return stringQueryID; 203 return stringQueryID;
195 } 204 }
196 205
197 public AnswerTuples getGapAnswers() { 206 public AnswerTuples getGapAnswers() {
198 return new AnswerTuplesImp(answerVariables[0], gapAnswerTuples); 207 return new AnswerTuplesImp(answerVariables[0], gapAnswerTuples);
199 } 208 }
200 209
201 public String toString() { 210 public String toString() {
202 return queryText; 211 return queryText;
203 } 212 }
204
205 public static final String SEPARATOR = "----------------------------------------";
206 213
207 public void outputAnswers(BufferedWriter writer) throws IOException { 214 public void outputAnswers(BufferedWriter writer) throws IOException {
208 215
209 int answerCounter = soundAnswerTuples.size(); 216 int answerCounter = soundAnswerTuples.size();
210 if (!processed()) answerCounter += gapAnswerTuples.size(); 217 if(!processed()) answerCounter += gapAnswerTuples.size();
211 218
212 Utility.logInfo("The number of answer tuples: " + answerCounter); 219 Utility.logInfo("The number of answer tuples: " + answerCounter);
213 220
214 if (writer != null) { 221 if (writer != null) {
215 writer.write("-------------- Query " + queryID + " ---------------------"); 222 writer.write("-------------- Query " + queryID + " ---------------------");
216 writer.newLine(); 223 writer.newLine();
@@ -242,7 +249,7 @@ public class QueryRecord {
242// writer.write(SEPARATOR); 249// writer.write(SEPARATOR);
243 writer.newLine(); 250 writer.newLine();
244 } 251 }
245 252
246 } 253 }
247 254
248 public void outputAnswerStatistics() { 255 public void outputAnswerStatistics() {
@@ -276,51 +283,48 @@ public class QueryRecord {
276// jsonAnswers.put(Integer.toString(queryID), jsonAnswer); 283// jsonAnswers.put(Integer.toString(queryID), jsonAnswer);
277// } 284// }
278 } 285 }
279 286
280 public void outputTimes() { 287 public void outputTimes() {
281 for (Step step: Step.values()) { 288 for (Step step: Step.values()) {
282 Utility.logDebug("time for " + step + ": " + timer[step.ordinal()]); 289 Utility.logDebug("time for " + step + ": " + timer[step.ordinal()]);
283 } 290 }
284 } 291 }
285 292
286 public String outputSoundAnswerTuple() { 293 public String outputSoundAnswerTuple() {
287 StringBuilder builder = new StringBuilder(); 294 StringBuilder builder = new StringBuilder();
288 for (AnswerTuple tuple: soundAnswerTuples) 295 for (AnswerTuple tuple: soundAnswerTuples)
289 builder.append(tuple.toString()).append(Utility.LINE_SEPARATOR); 296 builder.append(tuple.toString()).append(Utility.LINE_SEPARATOR);
290 return builder.toString(); 297 return builder.toString();
291 } 298 }
292 299
293 public String outputGapAnswerTuple() { 300 public String outputGapAnswerTuple() {
294 StringBuilder builder = new StringBuilder(); 301 StringBuilder builder = new StringBuilder();
295 for (AnswerTuple tuple: gapAnswerTuples) 302 for(AnswerTuple tuple : gapAnswerTuples)
296 builder.append(tuple.toString()).append(Utility.LINE_SEPARATOR); 303 builder.append(tuple.toString()).append(Utility.LINE_SEPARATOR);
297 return builder.toString(); 304 return builder.toString();
298 }
299
300 public void setDifficulty(Step step) {
301 this.difficulty = step;
302 } 305 }
303 306
304 public Step getDifficulty() { 307 public Step getDifficulty() {
305 return difficulty; 308 return difficulty;
306 } 309 }
307 310
308 OWLOntology relevantOntology = null; 311 public void setDifficulty(Step step) {
309 Set<DLClause> relevantClauses = new HashSet<DLClause>(); 312 this.difficulty = step;
310
311 public void setRelevantOntology(OWLOntology knowledgebase) {
312 relevantOntology = knowledgebase;
313 } 313 }
314 314
315 public OWLOntology getRelevantOntology() { 315 public OWLOntology getRelevantOntology() {
316 return relevantOntology; 316 return relevantOntology;
317 } 317 }
318 318
319 public void setRelevantOntology(OWLOntology knowledgebase) {
320 relevantOntology = knowledgebase;
321 }
322
319 public void saveRelevantOntology(String filename) { 323 public void saveRelevantOntology(String filename) {
320 if (relevantOntology == null) return ; 324 if(relevantOntology == null) return;
321 OWLOntologyManager manager = relevantOntology.getOWLOntologyManager(); 325 OWLOntologyManager manager = relevantOntology.getOWLOntologyManager();
322 try { 326 try {
323 FileOutputStream outputStream = new FileOutputStream(filename); 327 FileOutputStream outputStream = new FileOutputStream(filename);
324 manager.saveOntology(relevantOntology, outputStream); 328 manager.saveOntology(relevantOntology, outputStream);
325 outputStream.close(); 329 outputStream.close();
326 } catch (OWLOntologyStorageException e) { 330 } catch (OWLOntologyStorageException e) {
@@ -333,12 +337,11 @@ public class QueryRecord {
333 } 337 }
334 338
335 public void saveRelevantClause() { 339 public void saveRelevantClause() {
336 if (relevantClauses == null) return ; 340 if(relevantClauses == null) return;
337 GeneralProgram p = new GeneralProgram(relevantClauses, relevantOntology); 341 GeneralProgram p = new GeneralProgram(relevantClauses, relevantOntology);
338 p.save(); 342 p.save();
339 } 343 }
340 344
341
342 public void removeUpperBoundAnswers(Collection<AnswerTuple> answers) { 345 public void removeUpperBoundAnswers(Collection<AnswerTuple> answers) {
343 for (AnswerTuple answer: answers) { 346 for (AnswerTuple answer: answers) {
344// if (soundAnswerTuples.contains(answer)) 347// if (soundAnswerTuples.contains(answer))
@@ -349,50 +352,37 @@ public class QueryRecord {
349 } 352 }
350 } 353 }
351 354
352
353 public void addLowerBoundAnswers(Collection<AnswerTuple> answers) { 355 public void addLowerBoundAnswers(Collection<AnswerTuple> answers) {
354 for (AnswerTuple answer: answers) { 356 for (AnswerTuple answer: answers) {
355 if (!gapAnswerTuples.contains(answer)) 357 if (!gapAnswerTuples.contains(answer))
356 Utility.logError("The answer (" + answer + ") cannot be added, because it is not in the upper bound."); 358 Utility.logError("The answer (" + answer + ") cannot be added, because it is not in the upper bound.");
357 gapAnswerTuples.remove(answer); 359 gapAnswerTuples.remove(answer);
358 360
359 answer = AnswerTuple.create(answer, answerVariables[0].length); 361 answer = AnswerTuple.create(answer, answerVariables[0].length);
360// if (soundAnswerTuples.contains(answer)) 362// if (soundAnswerTuples.contains(answer))
361// Utility.logError("The answer (" + answer + ") cannot be added, because it is in the lower bound."); 363// Utility.logError("The answer (" + answer + ") cannot be added, because it is in the lower bound.");
362 soundAnswerTuples.add(answer); 364 soundAnswerTuples.add(answer);
363 } 365 }
364 } 366 }
365 367
366 public int getNoOfSoundAnswers() { 368 public int getNoOfSoundAnswers() {
367 return soundAnswerTuples.size(); 369 return soundAnswerTuples.size();
368 } 370 }
369
370 public enum Step {LowerBound, UpperBound, ELLowerBound,
371 Fragment, FragmentRefinement, Summarisation, Dependency, FullReasoning}
372
373 double[] timer;
374 371
375 public void addProcessingTime(Step step, double time) { 372 public void addProcessingTime(Step step, double time) {
376 timer[step.ordinal()] += time; 373 timer[step.ordinal()] += time;
377 } 374 }
378 375
379 public int getArity() { 376 public int getArity() {
380 return answerVariables[0].length; 377 return answerVariables[0].length;
381 } 378 }
382 379
383 public static Collection<String> collectQueryTexts(Collection<QueryRecord> queryRecords) {
384 Collection<String> texts = new LinkedList<String>();
385 for (QueryRecord record: queryRecords)
386 texts.add(record.queryText);
387 return texts;
388 }
389
390 public void addRelevantClauses(DLClause clause) { 380 public void addRelevantClauses(DLClause clause) {
391 relevantClauses.add(clause); 381 relevantClauses.add(clause);
392 } 382 }
393 383
394 public Set<DLClause> getRelevantClauses() { 384 public Set<DLClause> getRelevantClauses() {
395 return relevantClauses; 385 return relevantClauses;
396 } 386 }
397 387
398 public void clearClauses() { 388 public void clearClauses() {
@@ -403,36 +393,40 @@ public class QueryRecord {
403 for (DLClause clause: relevantClauses) 393 for (DLClause clause: relevantClauses)
404 if (clause.getHeadLength() > 1) 394 if (clause.getHeadLength() > 1)
405 return false; 395 return false;
406 return true; 396 return true;
407 } 397 }
408 398
409 public void saveABoxInTurtle(String filename) { 399 public void saveABoxInTurtle(String filename) {
410 try { 400 try {
411 BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename))); 401 BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename)));
412 OWLIndividual a, b; 402 OWLIndividual a, b;
413 StringBuilder builder = new StringBuilder(); 403 StringBuilder builder = new StringBuilder();
414 for (OWLAxiom axiom: relevantOntology.getABoxAxioms(true)) { 404 for (OWLAxiom axiom: relevantOntology.getABoxAxioms(true)) {
415 if (axiom instanceof OWLClassAssertionAxiom) { 405 if (axiom instanceof OWLClassAssertionAxiom) {
416 OWLClassAssertionAxiom classAssertion = (OWLClassAssertionAxiom) axiom; 406 OWLClassAssertionAxiom classAssertion = (OWLClassAssertionAxiom) axiom;
417 OWLClass c = (OWLClass) classAssertion.getClassExpression(); 407 OWLClass c = (OWLClass) classAssertion.getClassExpression();
418 a = classAssertion.getIndividual(); 408 a = classAssertion.getIndividual();
419 builder.append(a.toString()).append(" <").append(Namespace.RDF_TYPE).append("> ").append(c.toString()); 409 builder.append(a.toString())
410 .append(" <")
411 .append(Namespace.RDF_TYPE)
412 .append("> ")
413 .append(c.toString());
420 } 414 }
421 else if (axiom instanceof OWLObjectPropertyAssertionAxiom) { 415 else if (axiom instanceof OWLObjectPropertyAssertionAxiom) {
422 OWLObjectPropertyAssertionAxiom propertyAssertion = (OWLObjectPropertyAssertionAxiom) axiom; 416 OWLObjectPropertyAssertionAxiom propertyAssertion = (OWLObjectPropertyAssertionAxiom) axiom;
423 OWLObjectProperty p = (OWLObjectProperty) propertyAssertion.getProperty(); 417 OWLObjectProperty p = (OWLObjectProperty) propertyAssertion.getProperty();
424 a = propertyAssertion.getSubject(); 418 a = propertyAssertion.getSubject();
425 b = propertyAssertion.getObject(); 419 b = propertyAssertion.getObject();
426 builder.append(a.toString()).append(" ").append(p.toString()).append(" ").append(b.toString()); 420 builder.append(a.toString()).append(" ").append(p.toString()).append(" ").append(b.toString());
427 } 421 }
428 else if (axiom instanceof OWLDataPropertyAssertionAxiom) { 422 else if (axiom instanceof OWLDataPropertyAssertionAxiom) {
429 OWLDataPropertyAssertionAxiom propertyAssertion = (OWLDataPropertyAssertionAxiom) axiom; 423 OWLDataPropertyAssertionAxiom propertyAssertion = (OWLDataPropertyAssertionAxiom) axiom;
430 OWLDataProperty p = (OWLDataProperty) propertyAssertion.getProperty(); 424 OWLDataProperty p = (OWLDataProperty) propertyAssertion.getProperty();
431 a = propertyAssertion.getSubject(); 425 a = propertyAssertion.getSubject();
432 OWLLiteral l = propertyAssertion.getObject(); 426 OWLLiteral l = propertyAssertion.getObject();
433 builder.append(a.toString()).append(" ").append(p.toString()).append(" ").append(l.toString()); 427 builder.append(a.toString()).append(" ").append(p.toString()).append(" ").append(l.toString());
434 } 428 }
435 429
436 writer.write(builder.toString()); 430 writer.write(builder.toString());
437 writer.write(" ."); 431 writer.write(" .");
438 writer.newLine(); 432 writer.newLine();
@@ -442,23 +436,19 @@ public class QueryRecord {
442 } catch (IOException e) { 436 } catch (IOException e) {
443 e.printStackTrace(); 437 e.printStackTrace();
444 } finally { 438 } finally {
445 439
446 } 440 }
447 } 441 }
448
449 int subID;
450 442
451 public void updateSubID() { 443 public void updateSubID() {
452 ++subID; 444 ++subID;
453 stringQueryID = String.valueOf(queryID) + "_" + subID; 445 stringQueryID = String.valueOf(queryID) + "_" + subID;
454 } 446 }
455 447
456 DLClause queryClause = null;
457
458 public DLClause getClause() { 448 public DLClause getClause() {
459 if (queryClause != null) 449 if (queryClause != null)
460 return queryClause; 450 return queryClause;
461 return queryClause = DLClauseHelper.getQuery(queryText, null); 451 return queryClause = DLClauseHelper.getQuery(queryText, null);
462 } 452 }
463 453
464 public boolean isBottom() { 454 public boolean isBottom() {
@@ -468,19 +458,19 @@ public class QueryRecord {
468 public int getNoOfCompleteAnswers() { 458 public int getNoOfCompleteAnswers() {
469 return soundAnswerTuples.size() + gapAnswerTuples.size(); 459 return soundAnswerTuples.size() + gapAnswerTuples.size();
470 } 460 }
471 461
472 public int getSubID() { 462 public int getSubID() {
473 return subID; 463 return subID;
474 } 464 }
475 465
476 public boolean hasSameGapAnswers(QueryRecord that) { 466 public boolean hasSameGapAnswers(QueryRecord that) {
477 return gapAnswerTuples.containsAll(that.gapAnswerTuples) && that.gapAnswerTuples.containsAll(gapAnswerTuples); 467 return gapAnswerTuples.containsAll(that.gapAnswerTuples) && that.gapAnswerTuples.containsAll(gapAnswerTuples);
478 } 468 }
479 469
480 public void dispose() { 470 public void dispose() {
481 m_manager.remove(queryText); 471 m_manager.remove(queryText);
482 if (gapAnswerTuples != null) gapAnswerTuples = null; 472 if(gapAnswerTuples != null) gapAnswerTuples = null;
483 if (soundAnswerTuples != null) soundAnswerTuples = null; 473 if(soundAnswerTuples != null) soundAnswerTuples = null;
484 if (relevantClauses != null) relevantClauses.clear(); 474 if (relevantClauses != null) relevantClauses.clear();
485 if (relevantOntology != null) 475 if (relevantOntology != null)
486 relevantOntology.getOWLOntologyManager().removeOntology(relevantOntology); 476 relevantOntology.getOWLOntologyManager().removeOntology(relevantOntology);
@@ -488,53 +478,53 @@ public class QueryRecord {
488 } 478 }
489 479
490 public boolean canBeEncodedIntoAtom() { 480 public boolean canBeEncodedIntoAtom() {
491 // FIXME 481 // FIXME
492 return true; 482 return true;
493// return false; 483// return false;
494 } 484 }
495 485
496 public boolean isPredicate(AnswerTuple a, int i) { 486 public boolean isPredicate(AnswerTuple a, int i) {
497 Atom[] atoms = getClause().getBodyAtoms(); 487 Atom[] atoms = getClause().getBodyAtoms();
498 Variable v = Variable.create(answerVariables[1][i]); 488 Variable v = Variable.create(answerVariables[1][i]);
499 String iri; 489 String iri;
500 for (Atom atom: atoms) { 490 for(Atom atom : atoms) {
501 DLPredicate p = atom.getDLPredicate(); 491 DLPredicate p = atom.getDLPredicate();
502 if (p instanceof AtomicConcept) { 492 if (p instanceof AtomicConcept) {
503 if (((AtomicConcept) p).getIRI().equals(v.toString())) return true; 493 if(((AtomicConcept) p).getIRI().equals(v.toString())) return true;
504 } 494 }
505 else if (p instanceof AtomicRole) { 495 else if (p instanceof AtomicRole) {
506 iri = ((AtomicRole) p).getIRI(); 496 iri = ((AtomicRole) p).getIRI();
507 if (iri.equals(v.toString())) return true; 497 if (iri.equals(v.toString())) return true;
508 if (iri.startsWith("?")) 498 if(iri.startsWith("?"))
509 iri = a.getGroundTerm(i).toString(); 499 iri = a.getGroundTerm(i).toString();
510 if (iri.equals(Namespace.RDF_TYPE) && atom.getArgument(1).equals(v)) return true; 500 if(iri.equals(Namespace.RDF_TYPE) && atom.getArgument(1).equals(v)) return true;
511 } 501 }
512 } 502 }
513 return false; 503 return false;
514 } 504 }
515 505
516 public String[] getExtendedQueryText() { 506 public Tuple<String> getExtendedQueryText() {
517 String[] ret = new String[2]; 507// String[] ret = new String[2];
518 int index = queryText.toUpperCase().indexOf(" WHERE"); 508 int index = queryText.toUpperCase().indexOf(" WHERE");
519 String extendedSelect = queryText.substring(0, index); 509 String extendedSelect = queryText.substring(0, index);
520 String extendedWhere= queryText.substring(index + 1), fullyExtendedWhere = queryText.substring(index + 1); 510 String extendedWhere= queryText.substring(index + 1), fullyExtendedWhere = queryText.substring(index + 1);
521 511
522 String sub, obj; 512 String sub, obj;
523 Map<String, Set<String>> links = new HashMap<String, Set<String>>(); 513 Map<String, Set<String>> links = new HashMap<String, Set<String>>();
524 Set<String> list; 514 Set<String> list;
525 for (Atom atom: getClause().getBodyAtoms()) 515 for (Atom atom: getClause().getBodyAtoms())
526 if (atom.getDLPredicate() instanceof AtomicRole && atom.getArgument(0) instanceof Variable && atom.getArgument(1) instanceof Variable) { 516 if (atom.getDLPredicate() instanceof AtomicRole && atom.getArgument(0) instanceof Variable && atom.getArgument(1) instanceof Variable) {
527 sub = atom.getArgumentVariable(0).getName(); 517 sub = atom.getArgumentVariable(0).getName();
528 obj = atom.getArgumentVariable(1).getName(); 518 obj = atom.getArgumentVariable(1).getName();
529 if ((list = links.get(sub)) == null) 519 if((list = links.get(sub)) == null)
530 links.put(sub, list = new HashSet<String>()); 520 links.put(sub, list = new HashSet<String>());
531 list.add(obj); 521 list.add(obj);
532 if ((list = links.get(obj)) == null) 522 if((list = links.get(obj)) == null)
533 links.put(obj, list = new HashSet<String>()); 523 links.put(obj, list = new HashSet<String>());
534 list.add(sub); 524 list.add(sub);
535 } 525 }
536 526
537 StringBuilder extra = new StringBuilder(), fullyExtra = new StringBuilder(); 527 StringBuilder extra = new StringBuilder(), fullyExtra = new StringBuilder();
538// if (answerVariables[0] != answerVariables[1]) { 528// if (answerVariables[0] != answerVariables[1]) {
539 for (int i = answerVariables[0].length; i < answerVariables[1].length; ++i) { 529 for (int i = answerVariables[0].length; i < answerVariables[1].length; ++i) {
540// for (int i = 0; i < answerVariables[1].length; ++i) { 530// for (int i = 0; i < answerVariables[1].length; ++i) {
@@ -542,21 +532,22 @@ public class QueryRecord {
542 if ((list = links.get(answerVariables[1][i])) == null || list.size() < 2) ; 532 if ((list = links.get(answerVariables[1][i])) == null || list.size() < 2) ;
543 else { 533 else {
544 extra.append(" . ?").append(answerVariables[1][i]).append(" a <").append(Namespace.PAGODA_ORIGINAL).append(">"); 534 extra.append(" . ?").append(answerVariables[1][i]).append(" a <").append(Namespace.PAGODA_ORIGINAL).append(">");
545 } 535 }
546 } 536 }
547 537
548 if (extra.length() > 0) { 538 if(extra.length() > 0) {
549 extra.append(" }"); 539 extra.append(" }");
550 extendedWhere = extendedWhere.replace(" }", extendedWhere.contains(". }") ? extra.substring(2) : extra.toString()); 540 extendedWhere = extendedWhere.replace(" }", extendedWhere.contains(". }") ? extra.substring(2) : extra.toString());
551 } 541 }
552 542
553 if (fullyExtra.length() > 0) { 543 if(fullyExtra.length() > 0) {
554 fullyExtra.append(" }"); 544 fullyExtra.append(" }");
555 fullyExtendedWhere = fullyExtendedWhere.replace(" }", fullyExtendedWhere.contains(". }") ? fullyExtra.substring(2) : fullyExtra.toString()); 545 fullyExtendedWhere = fullyExtendedWhere.replace(" }", fullyExtendedWhere.contains(". }") ? fullyExtra.substring(2) : fullyExtra.toString());
556 } 546 }
557// } 547// }
558 548
559 ret[0] = extendedSelect + " " + fullyExtendedWhere; 549 TupleBuilder result = new TupleBuilder();
550 result.append(extendedSelect + " " + fullyExtendedWhere);
560 551
561 extra.setLength(0); 552 extra.setLength(0);
562 if (answerVariables[0] != answerVariables[1]) { 553 if (answerVariables[0] != answerVariables[1]) {
@@ -564,9 +555,9 @@ public class QueryRecord {
564 extra.append(" ?").append(answerVariables[1][i]); 555 extra.append(" ?").append(answerVariables[1][i]);
565 extendedSelect = extendedSelect + extra.toString(); 556 extendedSelect = extendedSelect + extra.toString();
566 } 557 }
567 ret[1] = extendedSelect + " " + extendedWhere; 558 result.append(extendedSelect + " " + extendedWhere);
568 559
569 return ret; 560 return result.build();
570 } 561 }
571 562
572 public boolean hasNonAnsDistinguishedVariables() { 563 public boolean hasNonAnsDistinguishedVariables() {
@@ -574,6 +565,31 @@ public class QueryRecord {
574 } 565 }
575 566
576 /** 567 /**
568 * Two <tt>QueryRecords</tt> are equal iff
569 * they have the same <tt>queryText</tt>,
570 * <tt>soundAnswerTuples</tt>
571 * and <tt>gapAnswerTuples</tt>.
572 */
573 @Override
574 public boolean equals(Object o) {
575 if(!o.getClass().equals(getClass())) return false;
576 QueryRecord that = (QueryRecord) o;
577 return this.queryText.equals(that.queryText)
578 && soundAnswerTuples.equals(that.soundAnswerTuples)
579 && gapAnswerTuples.equals(that.gapAnswerTuples);
580 }
581
582 @Override
583 public int hashCode() {
584 return Objects.hash(queryText, soundAnswerTuples, gapAnswerTuples);
585 }
586
587 public enum Step {
588 LowerBound, UpperBound, ELLowerBound,
589 Fragment, FragmentRefinement, Summarisation, Dependency, FullReasoning
590 }
591
592 /**
577 * A Json serializer, which considers the main attributes. 593 * A Json serializer, which considers the main attributes.
578 */ 594 */
579 public static class QueryRecordSerializer implements JsonSerializer<QueryRecord> { 595 public static class QueryRecordSerializer implements JsonSerializer<QueryRecord> {
@@ -592,8 +608,6 @@ public class QueryRecord {
592 } 608 }
593 } 609 }
594 610
595 private QueryRecord() { }
596
597 /** 611 /**
598 * A Json deserializer, compliant to the output of the serializer defined above. 612 * A Json deserializer, compliant to the output of the serializer defined above.
599 */ 613 */
@@ -628,25 +642,8 @@ public class QueryRecord {
628 } 642 }
629 643
630 /** 644 /**
631 * Two <tt>QueryRecords</tt> are equal iff 645 * Provides an instance (singleton) of Gson, having a specific configuration.
632 * they have the same <tt>queryText</tt>,
633 * <tt>soundAnswerTuples</tt>
634 * and <tt>gapAnswerTuples</tt>.
635 * */ 646 * */
636 @Override
637 public boolean equals(Object o) {
638 if(!o.getClass().equals(getClass())) return false;
639 QueryRecord that = (QueryRecord) o;
640 return this.queryText.equals(that.queryText)
641 && soundAnswerTuples.equals(that.soundAnswerTuples)
642 && gapAnswerTuples.equals(that.gapAnswerTuples);
643 }
644
645 @Override
646 public int hashCode() {
647 return Objects.hash(queryText, soundAnswerTuples, gapAnswerTuples);
648 }
649
650 public static class GsonCreator { 647 public static class GsonCreator {
651 648
652 private static Gson gson; 649 private static Gson gson;
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
index 0d24a02..6da86ac 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
@@ -2,7 +2,6 @@ package uk.ac.ox.cs.pagoda.reasoner;
2 2
3import org.semanticweb.karma2.profile.ELHOProfile; 3import org.semanticweb.karma2.profile.ELHOProfile;
4import org.semanticweb.owlapi.model.OWLOntology; 4import org.semanticweb.owlapi.model.OWLOntology;
5
6import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine; 5import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
7import uk.ac.ox.cs.pagoda.owl.EqualitiesEliminator; 6import uk.ac.ox.cs.pagoda.owl.EqualitiesEliminator;
8import uk.ac.ox.cs.pagoda.owl.OWLHelper; 7import uk.ac.ox.cs.pagoda.owl.OWLHelper;
@@ -26,59 +25,60 @@ public class ELHOUQueryReasoner extends QueryReasoner {
26 KarmaQueryEngine elLowerStore = null; 25 KarmaQueryEngine elLowerStore = null;
27 26
28 boolean multiStageTag, equalityTag; 27 boolean multiStageTag, equalityTag;
29 28 String originalMarkProgram;
29 private Timer t = new Timer();
30
30 public ELHOUQueryReasoner(boolean multiStageTag, boolean considerEqualities) { 31 public ELHOUQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
31 this.multiStageTag = multiStageTag; 32 this.multiStageTag = multiStageTag;
32 this.equalityTag = considerEqualities; 33 this.equalityTag = considerEqualities;
33 rlLowerStore = new BasicQueryEngine("rl-lower-bound"); 34 rlLowerStore = new BasicQueryEngine("rl-lower-bound");
34 elLowerStore = new KarmaQueryEngine("el-lower-bound"); 35 elLowerStore = new KarmaQueryEngine("el-lower-bound");
35 36
36 if (!multiStageTag) 37 if(!multiStageTag)
37 rlUpperStore = new BasicQueryEngine("rl-upper-bound"); 38 rlUpperStore = new BasicQueryEngine("rl-upper-bound");
38 else 39 else
39 rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false); 40 rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false);
40 } 41 }
41
42 private Timer t = new Timer();
43 42
44 @Override 43 @Override
45 public void evaluate(QueryRecord queryRecord) { 44 public void evaluate(QueryRecord queryRecord) {
46 AnswerTuples rlAnswer = null; 45 AnswerTuples rlAnswer = null;
47 t.reset(); 46 t.reset();
48 try { 47 try {
49 rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables()); 48 rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
50 queryRecord.updateLowerBoundAnswers(rlAnswer); 49 queryRecord.updateLowerBoundAnswers(rlAnswer);
51 } finally { 50 } finally {
52 if (rlAnswer != null) rlAnswer.dispose(); 51 if(rlAnswer != null) rlAnswer.dispose();
53 } 52 }
54 queryRecord.addProcessingTime(Step.LowerBound, t.duration()); 53 queryRecord.addProcessingTime(Step.LowerBound, t.duration());
55 54
56 String extendedQueryText = queryRecord.getExtendedQueryText()[0]; 55 String extendedQueryText = queryRecord.getExtendedQueryText().get(0);
57 String[] toQuery = queryRecord.getQueryText().equals(extendedQueryText) ? 56 String[] toQuery = queryRecord.getQueryText().equals(extendedQueryText) ?
58 new String[] {queryRecord.getQueryText()} : 57 new String[]{queryRecord.getQueryText()} :
59 new String[] {queryRecord.getQueryText(), extendedQueryText}; 58 new String[] {queryRecord.getQueryText(), extendedQueryText};
60 59
61 for (String queryText: toQuery) { 60 for (String queryText: toQuery) {
62 rlAnswer = null; 61 rlAnswer = null;
63 t.reset(); 62 t.reset();
64 try { 63 try {
65 rlAnswer = rlUpperStore.evaluate(queryText, queryRecord.getAnswerVariables()); 64 rlAnswer = rlUpperStore.evaluate(queryText, queryRecord.getAnswerVariables());
66 queryRecord.updateUpperBoundAnswers(rlAnswer); 65 queryRecord.updateUpperBoundAnswers(rlAnswer);
67 } finally { 66 } finally {
68 if (rlAnswer != null) rlAnswer.dispose(); 67 if(rlAnswer != null) rlAnswer.dispose();
69 } 68 }
70 queryRecord.addProcessingTime(Step.UpperBound, t.duration()); 69 queryRecord.addProcessingTime(Step.UpperBound, t.duration());
71 70
72 if (queryRecord.processed()) { 71 if (queryRecord.processed()) {
73 queryRecord.setDifficulty(Step.UpperBound); 72 queryRecord.setDifficulty(Step.UpperBound);
74 return ; 73 return;
75 } 74 }
76 } 75 }
77 76
78 AnswerTuples elAnswer = null; 77 AnswerTuples elAnswer = null;
79 t.reset(); 78 t.reset();
80 try { 79 try {
81 elAnswer = elLowerStore.evaluate(extendedQueryText, queryRecord.getAnswerVariables(), queryRecord.getLowerBoundAnswers()); 80 elAnswer =
81 elLowerStore.evaluate(extendedQueryText, queryRecord.getAnswerVariables(), queryRecord.getLowerBoundAnswers());
82 queryRecord.updateLowerBoundAnswers(elAnswer); 82 queryRecord.updateLowerBoundAnswers(elAnswer);
83 } finally { 83 } finally {
84 if (elAnswer != null) elAnswer.dispose(); 84 if (elAnswer != null) elAnswer.dispose();
@@ -88,19 +88,19 @@ public class ELHOUQueryReasoner extends QueryReasoner {
88 88
89 @Override 89 @Override
90 public void evaluateUpper(QueryRecord queryRecord) { 90 public void evaluateUpper(QueryRecord queryRecord) {
91 AnswerTuples rlAnswer = null; 91 AnswerTuples rlAnswer = null;
92 try { 92 try {
93 rlAnswer = rlUpperStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables()); 93 rlAnswer = rlUpperStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
94 queryRecord.updateUpperBoundAnswers(rlAnswer, true); 94 queryRecord.updateUpperBoundAnswers(rlAnswer, true);
95 } finally { 95 } finally {
96 if (rlAnswer != null) rlAnswer.dispose(); 96 if(rlAnswer != null) rlAnswer.dispose();
97 } 97 }
98 } 98 }
99 99
100 @Override 100 @Override
101 public void dispose() { 101 public void dispose() {
102 if (elLowerStore != null) elLowerStore.dispose(); 102 if (elLowerStore != null) elLowerStore.dispose();
103 if (rlUpperStore != null) rlUpperStore.dispose(); 103 if(rlUpperStore != null) rlUpperStore.dispose();
104 super.dispose(); 104 super.dispose();
105 } 105 }
106 106
@@ -110,19 +110,17 @@ public class ELHOUQueryReasoner extends QueryReasoner {
110 EqualitiesEliminator eliminator = new EqualitiesEliminator(o); 110 EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
111 o = eliminator.getOutputOntology(); 111 o = eliminator.getOutputOntology();
112 eliminator.save(); 112 eliminator.save();
113 } 113 }
114
115 OWLOntology ontology = o;
116 program = new DatalogProgram(ontology, properties.getToClassify());
114 117
115 OWLOntology ontology = o;
116 program = new DatalogProgram(ontology, properties.getToClassify());
117
118 importData(program.getAdditionalDataFile()); 118 importData(program.getAdditionalDataFile());
119 119
120 elho_ontology = new ELHOProfile().getFragment(ontology); 120 elho_ontology = new ELHOProfile().getFragment(ontology);
121 elLowerStore.processOntology(elho_ontology); 121 elLowerStore.processOntology(elho_ontology);
122 originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology); 122 originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
123 } 123 }
124
125 String originalMarkProgram;
126 124
127 @Override 125 @Override
128 public boolean preprocess() { 126 public boolean preprocess() {
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index dfbcb4d..b10e2d1 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -20,28 +20,25 @@ import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderDisjVar1;
20import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderWithGap; 20import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderWithGap;
21import uk.ac.ox.cs.pagoda.util.Timer; 21import uk.ac.ox.cs.pagoda.util.Timer;
22import uk.ac.ox.cs.pagoda.util.Utility; 22import uk.ac.ox.cs.pagoda.util.Utility;
23import uk.ac.ox.cs.pagoda.util.tuples.Tuple;
23 24
24import java.util.Collection; 25import java.util.Collection;
25import java.util.HashMap; 26import java.util.HashMap;
26 27
27public class MyQueryReasoner extends QueryReasoner { 28public class MyQueryReasoner extends QueryReasoner {
28 29
29 OWLOntology ontology; 30 OWLOntology ontology;
31 DatalogProgram program;
30 32
31// String additonalDataFile; 33// String additonalDataFile;
32
33 DatalogProgram program;
34
35 BasicQueryEngine rlLowerStore = null; 34 BasicQueryEngine rlLowerStore = null;
36 BasicQueryEngine lazyUpperStore = null; 35 BasicQueryEngine lazyUpperStore = null;
37 BasicQueryEngine limitedSkolemUpperStore; 36 BasicQueryEngine limitedSkolemUpperStore;
38// boolean[] namedIndividuals_lazyUpper;
39
40 OWLOntology elho_ontology; 37 OWLOntology elho_ontology;
38// boolean[] namedIndividuals_lazyUpper;
41 KarmaQueryEngine elLowerStore = null; 39 KarmaQueryEngine elLowerStore = null;
42
43 BasicQueryEngine trackingStore = null; 40 BasicQueryEngine trackingStore = null;
44// boolean[] namedIndividuals_tracking; 41 // boolean[] namedIndividuals_tracking;
45 TrackingRuleEncoder encoder; 42 TrackingRuleEncoder encoder;
46 private boolean equalityTag; 43 private boolean equalityTag;
47 private boolean multiStageTag; 44 private boolean multiStageTag;
@@ -53,7 +50,6 @@ public class MyQueryReasoner extends QueryReasoner {
53 public MyQueryReasoner() { 50 public MyQueryReasoner() {
54 setup(true, true); 51 setup(true, true);
55 } 52 }
56
57 public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) { 53 public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
58 setup(multiStageTag, considerEqualities); 54 setup(multiStageTag, considerEqualities);
59 } 55 }
@@ -65,7 +61,7 @@ public class MyQueryReasoner extends QueryReasoner {
65 else 61 else
66 return new BasicQueryEngine(name); 62 return new BasicQueryEngine(name);
67 } 63 }
68 64
69 public void setup(boolean multiStageTag, boolean considerEqualities) { 65 public void setup(boolean multiStageTag, boolean considerEqualities) {
70 satisfiable = SatisfiabilityStatus.UNCHECKED; 66 satisfiable = SatisfiabilityStatus.UNCHECKED;
71 this.multiStageTag = multiStageTag; 67 this.multiStageTag = multiStageTag;
@@ -115,7 +111,7 @@ public class MyQueryReasoner extends QueryReasoner {
115 public Collection<String> getPredicatesWithGap() { 111 public Collection<String> getPredicatesWithGap() {
116 return predicatesWithGap; 112 return predicatesWithGap;
117 } 113 }
118 114
119 @Override 115 @Override
120 public boolean preprocess() { 116 public boolean preprocess() {
121 t.reset(); 117 t.reset();
@@ -192,18 +188,40 @@ public class MyQueryReasoner extends QueryReasoner {
192 188
193 return true; 189 return true;
194 } 190 }
195 191
196 @Override 192 @Override
197 public boolean isConsistent() { 193 public boolean isConsistent() {
198 if(satisfiable == SatisfiabilityStatus.UNCHECKED) { 194 if(satisfiable == SatisfiabilityStatus.UNCHECKED) {
199 satisfiable = consistency.check() ? SatisfiabilityStatus.SATISFIABLE : SatisfiabilityStatus.UNSATISFIABLE; 195 satisfiable = consistency.check() ? SatisfiabilityStatus.SATISFIABLE : SatisfiabilityStatus.UNSATISFIABLE;
200 Utility.logInfo("time for satisfiability checking: " + t.duration()); 196 Utility.logInfo("time for satisfiability checking: " + t.duration());
201 } 197 }
202 return satisfiable == SatisfiabilityStatus.SATISFIABLE ? true : false; 198 return satisfiable == SatisfiabilityStatus.SATISFIABLE;
199 }
200
201 // TODO why the following???
202 private void queryUpperStore(BasicQueryEngine upperStore, QueryRecord queryRecord, Tuple<String> extendedQuery) {
203
204// Utility.logInfo("1");
205// queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
206//
207// boolean conditionA = !queryRecord.processed() && !queryRecord.getQueryText().equals(extendedQuery.get(0));
208// boolean conditionB = !queryRecord.processed() && queryRecord.hasNonAnsDistinguishedVariables();
209//
210// if(conditionA ^ conditionB)
211// throw new Error("It really happened! I thought it was impossible");
212//
213// if (conditionA) {
214// Utility.logInfo("2");
215 queryUpperBound(upperStore, queryRecord, extendedQuery.get(0), queryRecord.getAnswerVariables());
216// }
217// if (conditionB) {
218// Utility.logInfo("3");
219// queryUpperBound(upperStore, queryRecord, extendedQuery.get(1), queryRecord.getDistinguishedVariables());
220// }
203 } 221 }
204 222
205 /** 223 /**
206 * Returns the relevant part of the ontology, while computing the bound answers. 224 * Returns the part of the ontology relevant for Hermit, while computing the bound answers.
207 * */ 225 * */
208 private OWLOntology relevantPart(QueryRecord queryRecord) { 226 private OWLOntology relevantPart(QueryRecord queryRecord) {
209 AnswerTuples rlAnswer = null, elAnswer = null; 227 AnswerTuples rlAnswer = null, elAnswer = null;
@@ -219,28 +237,23 @@ public class MyQueryReasoner extends QueryReasoner {
219 queryRecord.addProcessingTime(Step.LowerBound, t.duration()); 237 queryRecord.addProcessingTime(Step.LowerBound, t.duration());
220 238
221 t.reset(); 239 t.reset();
222 BasicQueryEngine upperStore = queryRecord.isBottom() || lazyUpperStore == null ? trackingStore : lazyUpperStore;
223 240
224 String[] extendedQuery = queryRecord.getExtendedQueryText(); 241 Tuple<String> extendedQueryTexts = queryRecord.getExtendedQueryText();
225 242
226 // TODO why the following??? 243// BasicQueryEngine upperStore;
227 queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables()); 244// if(queryRecord.isBottom()) upperStore = trackingStore;
245// upperStore = queryRecord.isBottom() || lazyUpperStore == null ? trackingStore : lazyUpperStore;
228 246
229 if (!queryRecord.processed() && !queryRecord.getQueryText().equals(extendedQuery[0])) { 247 // TODO
230 queryUpperBound(upperStore, queryRecord, extendedQuery[0], queryRecord.getAnswerVariables()); 248// if(queryRecord.isBottom() || (lazyUpperStore == null && limitedSkolemUpperStore == null))
231 } 249// queryUpperStore(trackingStore, queryRecord, extendedQueryTexts);
232 if (!queryRecord.processed() && queryRecord.hasNonAnsDistinguishedVariables()) { 250// else {
233 queryUpperBound(upperStore, queryRecord, extendedQuery[1], queryRecord.getDistinguishedVariables());
234 }
235
236// Utility.logDebug(toJsonKeyValuePair("upperBound", queryRecord));
237 251
238 // TODO test intersection and new upper bound 252 queryUpperStore(trackingStore, queryRecord, extendedQueryTexts);
239 if (!queryRecord.isBottom() && lazyUpperStore != null) { 253 if(!(queryRecord.isBottom() || (lazyUpperStore == null && limitedSkolemUpperStore == null))) {
240 queryUpperBound(trackingStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables()); 254 if(lazyUpperStore != null) queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts);
241 } 255 if(limitedSkolemUpperStore != null)
242 if (!queryRecord.isBottom() && limitedSkolemUpperStore != null) { 256 queryUpperStore(limitedSkolemUpperStore, queryRecord, extendedQueryTexts);
243 queryUpperBound(limitedSkolemUpperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
244 } 257 }
245 258
246 queryRecord.addProcessingTime(Step.UpperBound, t.duration()); 259 queryRecord.addProcessingTime(Step.UpperBound, t.duration());
@@ -251,7 +264,8 @@ public class MyQueryReasoner extends QueryReasoner {
251 264
252 t.reset(); 265 t.reset();
253 try { 266 try {
254 elAnswer = elLowerStore.evaluate(extendedQuery[0], queryRecord.getAnswerVariables(), queryRecord.getLowerBoundAnswers()); 267 elAnswer = elLowerStore.evaluate(extendedQueryTexts.get(0), queryRecord.getAnswerVariables(),
268 queryRecord.getLowerBoundAnswers());
255 Utility.logDebug(t.duration()); 269 Utility.logDebug(t.duration());
256 queryRecord.updateLowerBoundAnswers(elAnswer); 270 queryRecord.updateLowerBoundAnswers(elAnswer);
257 } finally { 271 } finally {
@@ -268,7 +282,7 @@ public class MyQueryReasoner extends QueryReasoner {
268 282
269 QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord); 283 QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord);
270 284
271 OWLOntology knowledgebase; 285 OWLOntology knowledgeBase;
272 t.reset(); 286 t.reset();
273// if (program.getGeneral().isHorn()) { 287// if (program.getGeneral().isHorn()) {
274// knowledgebase = tracker.extract(lazyUpperStore, consistency.getQueryRecords(), true); 288// knowledgebase = tracker.extract(lazyUpperStore, consistency.getQueryRecords(), true);
@@ -276,14 +290,14 @@ public class MyQueryReasoner extends QueryReasoner {
276// return knowledgebase; 290// return knowledgebase;
277// } 291// }
278// else { 292// else {
279 knowledgebase = tracker.extract(trackingStore, consistency.getQueryRecords(), true); 293 knowledgeBase = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
280 queryRecord.addProcessingTime(Step.Fragment, t.duration()); 294 queryRecord.addProcessingTime(Step.Fragment, t.duration());
281// } 295// }
282 296
283 if(knowledgebase.isEmpty() || queryRecord.isBottom()) 297 if(knowledgeBase.isEmpty() || queryRecord.isBottom())
284 return knowledgebase; 298 return knowledgeBase;
285 299
286 if(program.getGeneral().isHorn()) return knowledgebase; 300 if(program.getGeneral().isHorn()) return knowledgeBase;
287 301
288// t.reset(); 302// t.reset();
289// if (queryRecord.isHorn() && lazyUpperStore != null) { 303// if (queryRecord.isHorn() && lazyUpperStore != null) {
@@ -298,7 +312,7 @@ public class MyQueryReasoner extends QueryReasoner {
298// if (knowledgebase == null) 312// if (knowledgebase == null)
299// queryRecord.setDifficulty(Step.FragmentRefinement); 313// queryRecord.setDifficulty(Step.FragmentRefinement);
300 314
301 return knowledgebase; 315 return knowledgeBase;
302 } 316 }
303 317
304 private String toJsonKeyValuePair(String key, Object value) { 318 private String toJsonKeyValuePair(String key, Object value) {
@@ -307,8 +321,6 @@ public class MyQueryReasoner extends QueryReasoner {
307 return QueryRecord.GsonCreator.getInstance().toJson(map); 321 return QueryRecord.GsonCreator.getInstance().toJson(map);
308 } 322 }
309 323
310// int counter = 0;
311
312 private void queryUpperBound(BasicQueryEngine upperStore, QueryRecord queryRecord, String queryText, String[] answerVariables) { 324 private void queryUpperBound(BasicQueryEngine upperStore, QueryRecord queryRecord, String queryText, String[] answerVariables) {
313 AnswerTuples rlAnswer = null; 325 AnswerTuples rlAnswer = null;
314 try { 326 try {
@@ -317,11 +329,13 @@ public class MyQueryReasoner extends QueryReasoner {
317 Utility.logDebug(t.duration()); 329 Utility.logDebug(t.duration());
318 queryRecord.updateUpperBoundAnswers(rlAnswer); 330 queryRecord.updateUpperBoundAnswers(rlAnswer);
319 } finally { 331 } finally {
320 if (rlAnswer != null) rlAnswer.dispose(); 332 if(rlAnswer != null) rlAnswer.dispose();
321 rlAnswer = null; 333 rlAnswer = null;
322 } 334 }
323 } 335 }
324 336
337// int counter = 0;
338
325 @Override 339 @Override
326 public void evaluate(QueryRecord queryRecord) { 340 public void evaluate(QueryRecord queryRecord) {
327 OWLOntology knowledgeBase = relevantPart(queryRecord); 341 OWLOntology knowledgeBase = relevantPart(queryRecord);
@@ -349,6 +363,7 @@ public class MyQueryReasoner extends QueryReasoner {
349 363
350 @Override 364 @Override
351 public void evaluateUpper(QueryRecord queryRecord) { 365 public void evaluateUpper(QueryRecord queryRecord) {
366 // TODO add new upper store
352 AnswerTuples rlAnswer = null; 367 AnswerTuples rlAnswer = null;
353 boolean useFull = queryRecord.isBottom() || lazyUpperStore == null; 368 boolean useFull = queryRecord.isBottom() || lazyUpperStore == null;
354 try { 369 try {
@@ -359,7 +374,7 @@ public class MyQueryReasoner extends QueryReasoner {
359 if(rlAnswer != null) rlAnswer.dispose(); 374 if(rlAnswer != null) rlAnswer.dispose();
360 } 375 }
361 } 376 }
362 377
363 @Override 378 @Override
364 public void dispose() { 379 public void dispose() {
365 if (encoder != null) encoder.dispose(); 380 if (encoder != null) encoder.dispose();
@@ -367,6 +382,7 @@ public class MyQueryReasoner extends QueryReasoner {
367 if (lazyUpperStore != null) lazyUpperStore.dispose(); 382 if (lazyUpperStore != null) lazyUpperStore.dispose();
368 if (elLowerStore != null) elLowerStore.dispose(); 383 if (elLowerStore != null) elLowerStore.dispose();
369 if (trackingStore != null) trackingStore.dispose(); 384 if (trackingStore != null) trackingStore.dispose();
385 if(limitedSkolemUpperStore != null) limitedSkolemUpperStore.dispose();
370 super.dispose(); 386 super.dispose();
371 } 387 }
372 388
diff --git a/src/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java b/src/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java
index ba58e23..20ae53b 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java
@@ -20,11 +20,10 @@ import java.util.*;
20public class LimitedSkolemisationApproximator implements TupleDependentApproximator { 20public class LimitedSkolemisationApproximator implements TupleDependentApproximator {
21 21
22 private static final Atom[] EMPTY_BODY = new Atom[0]; 22 private static final Atom[] EMPTY_BODY = new Atom[0];
23 23 private static final Variable X = Variable.create("X");
24 private final int maxTermDepth; 24 private final int maxTermDepth;
25 private final TupleDependentApproximator alternativeApproximator; 25 private final TupleDependentApproximator alternativeApproximator;
26 private final SkolemTermsManager skolemTermsManager; 26 private final SkolemTermsManager skolemTermsManager;
27
28 private Map<AnswerTupleID, Integer> mapIndividualsToDepth; 27 private Map<AnswerTupleID, Integer> mapIndividualsToDepth;
29 28
30 public LimitedSkolemisationApproximator(int maxTermDepth) { 29 public LimitedSkolemisationApproximator(int maxTermDepth) {
@@ -67,8 +66,6 @@ public class LimitedSkolemisationApproximator implements TupleDependentApproxima
67 return result; 66 return result;
68 } 67 }
69 68
70 private static final Variable X = Variable.create("X");
71
72 private Collection<DLClause> getGroundSkolemisation(DLClause clause, 69 private Collection<DLClause> getGroundSkolemisation(DLClause clause,
73 DLClause originalClause, 70 DLClause originalClause,
74 Tuple<Individual> violationTuple) { 71 Tuple<Individual> violationTuple) {
@@ -78,8 +75,8 @@ public class LimitedSkolemisationApproximator implements TupleDependentApproxima
78 // TODO check: strong assumption, the first tuples are the common ones 75 // TODO check: strong assumption, the first tuples are the common ones
79 TupleBuilder<Individual> commonIndividualsBuilder = new TupleBuilder<>(); 76 TupleBuilder<Individual> commonIndividualsBuilder = new TupleBuilder<>();
80 for (int i = 0; i < commonVars.length; i++) 77 for (int i = 0; i < commonVars.length; i++)
81 commonIndividualsBuilder.add(violationTuple.get(i)); 78 commonIndividualsBuilder.append(violationTuple.get(i));
82 Tuple<Individual> commonIndividuals = commonIndividualsBuilder.create(); 79 Tuple<Individual> commonIndividuals = commonIndividualsBuilder.build();
83 80
84 Atom headAtom = clause.getHeadAtom(0); 81 Atom headAtom = clause.getHeadAtom(0);
85 82
diff --git a/src/uk/ac/ox/cs/pagoda/util/tuples/TupleBuilder.java b/src/uk/ac/ox/cs/pagoda/util/tuples/TupleBuilder.java
index aacd15e..ee2b74d 100644
--- a/src/uk/ac/ox/cs/pagoda/util/tuples/TupleBuilder.java
+++ b/src/uk/ac/ox/cs/pagoda/util/tuples/TupleBuilder.java
@@ -10,12 +10,12 @@ public class TupleBuilder<T> {
10 10
11 private boolean building = true; 11 private boolean building = true;
12 12
13 public boolean add(T t) { 13 public boolean append(T t) {
14 if(building) tuple.elements.add(t); 14 if(building) tuple.elements.add(t);
15 return building; 15 return building;
16 } 16 }
17 17
18 public Tuple<T> create() { 18 public Tuple<T> build() {
19 if(building) { 19 if(building) {
20 building = false; 20 building = false;
21 return tuple; 21 return tuple;
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-05 14:18:53 +0000