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-rw-r--r--src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java6
-rw-r--r--src/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java3
-rw-r--r--src/uk/ac/ox/cs/pagoda/multistage/TwoStageApplication.java7
-rw-r--r--src/uk/ac/ox/cs/pagoda/query/GapByTriple.java12
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java32
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java12
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java2
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java2
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java17
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java9
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java32
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java6
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java39
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java14
-rw-r--r--src/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java4
-rw-r--r--src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java69
-rw-r--r--src/uk/ac/ox/cs/pagoda/util/Properties.java133
17 files changed, 217 insertions, 182 deletions
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
index b74fe7d..b77c264 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
@@ -18,6 +18,9 @@ public class MultiStageQueryEngine extends StageQueryEngine {
18 super(name, checkValidity); 18 super(name, checkValidity);
19 } 19 }
20 20
21 /**
22 * c-chase
23 */
21 @Override 24 @Override
22 public void materialiseFoldedly(DatalogProgram dProgram, GapByStore4ID gap) { 25 public void materialiseFoldedly(DatalogProgram dProgram, GapByStore4ID gap) {
23 materialise("lower program", dProgram.getLower().toString()); 26 materialise("lower program", dProgram.getLower().toString());
@@ -27,6 +30,9 @@ public class MultiStageQueryEngine extends StageQueryEngine {
27 materialise(program, treatment, gap); 30 materialise(program, treatment, gap);
28 } 31 }
29 32
33 /**
34 * c-chase^f
35 */
30 @Override 36 @Override
31 public int materialiseRestrictedly(DatalogProgram dProgram, GapByStore4ID gap) { 37 public int materialiseRestrictedly(DatalogProgram dProgram, GapByStore4ID gap) {
32 if (gap != null) 38 if (gap != null)
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java
index caa26fa..4239ccc 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java
@@ -245,6 +245,7 @@ public abstract class MultiStageUpperProgram {
245 if (tuples != null) tuples.dispose(); 245 if (tuples != null) tuples.dispose();
246 } 246 }
247 247
248 tuples = null;
248 try { 249 try {
249 tuples = engine.internal_evaluateNotExpanded(SparqlHelper.getSPARQLQuery(atoms, x, y)); 250 tuples = engine.internal_evaluateNotExpanded(SparqlHelper.getSPARQLQuery(atoms, x, y));
250 for (long multi = tuples.open(); multi != 0; multi = tuples.getNext()) 251 for (long multi = tuples.open(); multi != 0; multi = tuples.getNext())
@@ -279,7 +280,7 @@ public abstract class MultiStageUpperProgram {
279 TupleIterator tuples = null; 280 TupleIterator tuples = null;
280 try { 281 try {
281 tuples = engine.internal_evaluateNotExpanded(headQuery); 282 tuples = engine.internal_evaluateNotExpanded(headQuery);
282 for (; tuples.isValid(); tuples.getNext()) 283 for (long multi = tuples.open(); multi != 0; multi = tuples.getNext())
283 headAnswers.add(new AnswerTupleID(tuples)); 284 headAnswers.add(new AnswerTupleID(tuples));
284 } catch (JRDFStoreException e) { 285 } catch (JRDFStoreException e) {
285 e.printStackTrace(); 286 e.printStackTrace();
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/TwoStageApplication.java b/src/uk/ac/ox/cs/pagoda/multistage/TwoStageApplication.java
index e52213b..f08bfbd 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/TwoStageApplication.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/TwoStageApplication.java
@@ -149,8 +149,8 @@ abstract class TwoStageApplication {
149 // TODO Auto-generated catch block 149 // TODO Auto-generated catch block
150 e.printStackTrace(); 150 e.printStackTrace();
151 } finally { 151 } finally {
152 if (tuples != null) 152 if (tuples != null) tuples.dispose();
153 tuples.dispose(); 153 tuples = null;
154 } 154 }
155 } 155 }
156 } 156 }
@@ -209,8 +209,7 @@ abstract class TwoStageApplication {
209 // TODO Auto-generated catch block 209 // TODO Auto-generated catch block
210 e.printStackTrace(); 210 e.printStackTrace();
211 } finally { 211 } finally {
212 if (tuples != null) 212 if (tuples != null) tuples.dispose();
213 tuples.dispose();
214 } 213 }
215 return ret; 214 return ret;
216 } 215 }
diff --git a/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java b/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java
index 1a94f07..a1c1b0e 100644
--- a/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java
+++ b/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java
@@ -53,7 +53,7 @@ public class GapByTriple extends GapTupleIterator<String> {
53 53
54 @Override 54 @Override
55 public boolean hasNext() { 55 public boolean hasNext() {
56 TupleIterator iter; 56 TupleIterator iter = null;
57 boolean inGap; 57 boolean inGap;
58 StringBuffer queryBuffer = new StringBuffer(); 58 StringBuffer queryBuffer = new StringBuffer();
59 try { 59 try {
@@ -75,9 +75,13 @@ public class GapByTriple extends GapTupleIterator<String> {
75 queryBuffer.setLength(0); 75 queryBuffer.setLength(0);
76 queryBuffer.append("SELECT WHERE { ").append(sub).append(" ").append(predicate).append(" ").append(obj).append(" }"); 76 queryBuffer.append("SELECT WHERE { ").append(sub).append(" ").append(predicate).append(" ").append(obj).append(" }");
77 77
78 iter = lowerStore.compileQuery(queryBuffer.toString(), prefixes, parameters); 78 try {
79 inGap = iter.open() != 0; 79 iter = lowerStore.compileQuery(queryBuffer.toString(), prefixes, parameters);
80 iter.dispose(); 80 inGap = iter.open() != 0;
81 } finally {
82 if (iter != null) iter.dispose();
83 iter = null;
84 }
81 if (inGap) 85 if (inGap)
82 return true; 86 return true;
83 } 87 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
index a222645..7d3e40c 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
@@ -43,7 +43,15 @@ public class ConsistencyManager {
43 43
44 boolean checkRLLowerBound() { 44 boolean checkRLLowerBound() {
45 fullQueryRecord = m_queryManager.create(QueryRecord.botQueryText, 0); 45 fullQueryRecord = m_queryManager.create(QueryRecord.botQueryText, 0);
46 fullQueryRecord.updateLowerBoundAnswers(m_reasoner.rlLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables())); 46 AnswerTuples iter = null;
47
48 try {
49 iter = m_reasoner.rlLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
50 fullQueryRecord.updateLowerBoundAnswers(iter);
51 } finally {
52 iter.dispose();
53 }
54
47 if (fullQueryRecord.getNoOfSoundAnswers() > 0) { 55 if (fullQueryRecord.getNoOfSoundAnswers() > 0) {
48 Utility.logInfo("Answers to bottom in the lower bound: ", fullQueryRecord.outputSoundAnswerTuple()); 56 Utility.logInfo("Answers to bottom in the lower bound: ", fullQueryRecord.outputSoundAnswerTuple());
49 return unsatisfiability(t.duration()); 57 return unsatisfiability(t.duration());
@@ -81,8 +89,15 @@ public class ConsistencyManager {
81// if (!checkRLLowerBound()) return false; 89// if (!checkRLLowerBound()) return false;
82// if (!checkELLowerBound()) return false; 90// if (!checkELLowerBound()) return false;
83// if (checkLazyUpper()) return true; 91// if (checkLazyUpper()) return true;
92 AnswerTuples iter = null;
93
94 try {
95 iter = m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
96 fullQueryRecord.updateUpperBoundAnswers(iter);
97 } finally {
98 if (iter != null) iter.dispose();
99 }
84 100
85 fullQueryRecord.updateUpperBoundAnswers(m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()));
86 if (fullQueryRecord.getNoOfCompleteAnswers() == 0) 101 if (fullQueryRecord.getNoOfCompleteAnswers() == 0)
87 return satisfiability(t.duration()); 102 return satisfiability(t.duration());
88 103
@@ -101,7 +116,7 @@ public class ConsistencyManager {
101 for (QueryRecord r: getQueryRecords()) { 116 for (QueryRecord r: getQueryRecords()) {
102 // TODO to be removed ... 117 // TODO to be removed ...
103// r.saveRelevantOntology("bottom" + r.getQueryID() + ".owl"); 118// r.saveRelevantOntology("bottom" + r.getQueryID() + ".owl");
104 checker = new HermitSummaryFilter(r); // m_reasoner.factory.getSummarisedReasoner(r); 119 checker = new HermitSummaryFilter(r, true); // m_reasoner.factory.getSummarisedReasoner(r);
105 satisfiability = checker.isConsistent(); 120 satisfiability = checker.isConsistent();
106 checker.dispose(); 121 checker.dispose();
107 if (!satisfiability) return unsatisfiability(t.duration()); 122 if (!satisfiability) return unsatisfiability(t.duration());
@@ -143,8 +158,15 @@ public class ConsistencyManager {
143 QueryRecord[] tempQueryRecords = new QueryRecord[number - 1]; 158 QueryRecord[] tempQueryRecords = new QueryRecord[number - 1];
144 QueryRecord record; 159 QueryRecord record;
145 for (int i = 0; i < number - 1; ++i) { 160 for (int i = 0; i < number - 1; ++i) {
146 tempQueryRecords[i] = record = m_queryManager.create(QueryRecord.botQueryText.replace("Nothing", "Nothing" + (i + 1)), 0, i + 1); 161 tempQueryRecords[i] = record = m_queryManager.create(QueryRecord.botQueryText.replace("Nothing", "Nothing" + (i + 1)), 0, i + 1);
147 record.updateUpperBoundAnswers(m_reasoner.trackingStore.evaluate(record.getQueryText(), record.getAnswerVariables())); 162 AnswerTuples iter = null;
163 try {
164 iter = m_reasoner.trackingStore.evaluate(record.getQueryText(), record.getAnswerVariables());
165 record.updateUpperBoundAnswers(iter);
166 } finally {
167 if (iter != null) iter.dispose();
168 iter = null;
169 }
148 } 170 }
149 171
150 int bottomNumber = 0; 172 int bottomNumber = 0;
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java
index 67dc4fc..9c335f3 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java
@@ -3,6 +3,7 @@ package uk.ac.ox.cs.pagoda.reasoner;
3import org.semanticweb.owlapi.model.OWLOntologyCreationException; 3import org.semanticweb.owlapi.model.OWLOntologyCreationException;
4import org.semanticweb.owlapi.model.OWLOntologyManager; 4import org.semanticweb.owlapi.model.OWLOntologyManager;
5 5
6import uk.ac.ox.cs.pagoda.query.AnswerTuples;
6import uk.ac.ox.cs.pagoda.query.QueryRecord; 7import uk.ac.ox.cs.pagoda.query.QueryRecord;
7import uk.ac.ox.cs.pagoda.reasoner.full.Checker; 8import uk.ac.ox.cs.pagoda.reasoner.full.Checker;
8import uk.ac.ox.cs.pagoda.summary.HermitSummaryFilter; 9import uk.ac.ox.cs.pagoda.summary.HermitSummaryFilter;
@@ -32,8 +33,15 @@ public class ConsistencyManager2 extends ConsistencyManager {
32// if (!checkRLLowerBound()) return false; 33// if (!checkRLLowerBound()) return false;
33// if (!checkELLowerBound()) return false; 34// if (!checkELLowerBound()) return false;
34 if (checkLazyUpper()) return true; 35 if (checkLazyUpper()) return true;
36 AnswerTuples iter = null;
37
38 try {
39 iter = m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
40 fullQueryRecord.updateUpperBoundAnswers(iter);
41 } finally {
42 if (iter != null) iter.dispose();
43 }
35 44
36 fullQueryRecord.updateUpperBoundAnswers(m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()));
37 if (fullQueryRecord.getNoOfCompleteAnswers() == 0) 45 if (fullQueryRecord.getNoOfCompleteAnswers() == 0)
38 return satisfiability(t.duration()); 46 return satisfiability(t.duration());
39 47
@@ -43,7 +51,7 @@ public class ConsistencyManager2 extends ConsistencyManager {
43 e.printStackTrace(); 51 e.printStackTrace();
44 } 52 }
45 53
46 Checker checker = new HermitSummaryFilter(fullQueryRecord); // m_reasoner.factory.getSummarisedReasoner(fullQueryRecord); 54 Checker checker = new HermitSummaryFilter(fullQueryRecord, true); // m_reasoner.factory.getSummarisedReasoner(fullQueryRecord);
47// fullQueryRecord.saveRelevantOntology("fragment_bottom.owl"); 55// fullQueryRecord.saveRelevantOntology("fragment_bottom.owl");
48 boolean satisfiable = checker.isConsistent(); 56 boolean satisfiable = checker.isConsistent();
49 checker.dispose(); 57 checker.dispose();
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
index 4ebe5f2..ab57ccf 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
@@ -54,7 +54,7 @@ public class ELHOQueryReasoner extends QueryReasoner {
54 54
55 @Override 55 @Override
56 public void loadOntology(OWLOntology ontology) { 56 public void loadOntology(OWLOntology ontology) {
57 program = new LowerDatalogProgram(!forSemFacet); 57 program = new LowerDatalogProgram(properties.getToClassify());
58 program.load(ontology, new UnaryBottom()); 58 program.load(ontology, new UnaryBottom());
59 program.transform(); 59 program.transform();
60 60
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
index 62d238b..0d24a02 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
@@ -113,7 +113,7 @@ public class ELHOUQueryReasoner extends QueryReasoner {
113 } 113 }
114 114
115 OWLOntology ontology = o; 115 OWLOntology ontology = o;
116 program = new DatalogProgram(ontology, !forSemFacet); 116 program = new DatalogProgram(ontology, properties.getToClassify());
117 117
118 importData(program.getAdditionalDataFile()); 118 importData(program.getAdditionalDataFile());
119 119
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java b/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
index ba6a4d4..447a92d 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
@@ -7,6 +7,7 @@ import org.semanticweb.owlapi.model.OWLOntology;
7import uk.ac.ox.cs.pagoda.constraints.BottomStrategy; 7import uk.ac.ox.cs.pagoda.constraints.BottomStrategy;
8import uk.ac.ox.cs.pagoda.constraints.UpperUnaryBottom; 8import uk.ac.ox.cs.pagoda.constraints.UpperUnaryBottom;
9import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine; 9import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
10import uk.ac.ox.cs.pagoda.query.AnswerTuples;
10import uk.ac.ox.cs.pagoda.query.QueryRecord; 11import uk.ac.ox.cs.pagoda.query.QueryRecord;
11import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine; 12import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
12import uk.ac.ox.cs.pagoda.rules.GeneralProgram; 13import uk.ac.ox.cs.pagoda.rules.GeneralProgram;
@@ -47,7 +48,13 @@ public class IterativeRefinement {
47 return m_record.getRelevantOntology(); 48 return m_record.getRelevantOntology();
48 } 49 }
49 50
50 update = m_record.updateUpperBoundAnswers(tEngine.evaluate(m_record.getQueryText())); 51 AnswerTuples ans = null;
52 try {
53 ans = tEngine.evaluate(m_record.getQueryText());
54 update = m_record.updateUpperBoundAnswers(ans);
55 } finally {
56 if (ans != null) ans.dispose();
57 }
51 } finally { 58 } finally {
52 tEngine.dispose(); 59 tEngine.dispose();
53 } 60 }
@@ -78,7 +85,13 @@ public class IterativeRefinement {
78 return m_record.getRelevantOntology(); 85 return m_record.getRelevantOntology();
79 } 86 }
80 87
81 update = m_record.updateUpperBoundAnswers(tEngine.evaluate(m_record.getQueryText())); 88 AnswerTuples ans = null;
89 try {
90 ans = tEngine.evaluate(m_record.getQueryText());
91 update = m_record.updateUpperBoundAnswers(ans);
92 } finally {
93 if (ans != null) ans.dispose();
94 }
82 } finally { 95 } finally {
83 tEngine.dispose(); 96 tEngine.dispose();
84 } 97 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 2c2feae..875dcdd 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -85,7 +85,7 @@ public class MyQueryReasoner extends QueryReasoner {
85 } 85 }
86 86
87 ontology = o; 87 ontology = o;
88 program = new DatalogProgram(ontology, !forSemFacet); 88 program = new DatalogProgram(ontology, properties.getToClassify());
89// program.getLower().save(); 89// program.getLower().save();
90// program.getUpper().save(); 90// program.getUpper().save();
91// program.getGeneral().save(); 91// program.getGeneral().save();
@@ -275,11 +275,10 @@ public class MyQueryReasoner extends QueryReasoner {
275 rlAnswer = upperStore.evaluate(queryText, answerVariables); 275 rlAnswer = upperStore.evaluate(queryText, answerVariables);
276 Utility.logDebug(t.duration()); 276 Utility.logDebug(t.duration());
277 queryRecord.updateUpperBoundAnswers(rlAnswer); 277 queryRecord.updateUpperBoundAnswers(rlAnswer);
278 rlAnswer.dispose();
279 } finally { 278 } finally {
280 if (rlAnswer != null) rlAnswer.dispose(); 279 if (rlAnswer != null) rlAnswer.dispose();
280 rlAnswer = null;
281 } 281 }
282 rlAnswer = null;
283 } 282 }
284 283
285 @Override 284 @Override
@@ -296,11 +295,11 @@ public class MyQueryReasoner extends QueryReasoner {
296// queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl"); 295// queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl");
297 296
298 Timer t = new Timer(); 297 Timer t = new Timer();
299 Checker summarisedChecker = new HermitSummaryFilter(queryRecord); 298 Checker summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT());
300 int validNumber = summarisedChecker.check(queryRecord.getGapAnswers()); 299 int validNumber = summarisedChecker.check(queryRecord.getGapAnswers());
301 summarisedChecker.dispose(); 300 summarisedChecker.dispose();
302 Utility.logDebug("Total time for full reasoner: " + t.duration()); 301 Utility.logDebug("Total time for full reasoner: " + t.duration());
303 if (!forSemFacet || validNumber == 0) { 302 if (validNumber == 0) {
304 queryRecord.markAsProcessed(); 303 queryRecord.markAsProcessed();
305 Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty()); 304 Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
306 } 305 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
index 0c009a2..a484444 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
@@ -14,23 +14,41 @@ import uk.ac.ox.cs.pagoda.owl.OWLHelper;
14import uk.ac.ox.cs.pagoda.query.AnswerTuples; 14import uk.ac.ox.cs.pagoda.query.AnswerTuples;
15import uk.ac.ox.cs.pagoda.query.QueryManager; 15import uk.ac.ox.cs.pagoda.query.QueryManager;
16import uk.ac.ox.cs.pagoda.query.QueryRecord; 16import uk.ac.ox.cs.pagoda.query.QueryRecord;
17import uk.ac.ox.cs.pagoda.util.Properties;
17import uk.ac.ox.cs.pagoda.util.Timer; 18import uk.ac.ox.cs.pagoda.util.Timer;
18import uk.ac.ox.cs.pagoda.util.Utility; 19import uk.ac.ox.cs.pagoda.util.Utility;
19 20
20public abstract class QueryReasoner { 21public abstract class QueryReasoner {
21 22
22 protected boolean forSemFacet = false; 23// protected boolean forSemFacet = false;
23 24 Properties properties;
25
24 public static enum Type { Full, RLU, ELHOU }; 26 public static enum Type { Full, RLU, ELHOU };
25 27
26 public static QueryReasoner getInstanceForSemFacet(OWLOntology o) { 28 public static QueryReasoner getInstance(Properties p) {
27 QueryReasoner reasoner = getInstance(Type.Full, o, true, true); 29 OWLOntology ontology = OWLHelper.loadOntology(p.getOntologyPath());
28 reasoner.forSemFacet = true; 30 QueryReasoner pagoda = getInstance(ontology, p);
29 return reasoner; 31 pagoda.properties = p;
32 pagoda.loadOntology(ontology);
33 pagoda.importData(p.getDataPath());
34 if (pagoda.preprocess()) {
35 System.out.println("The ontology is consistent!");
36 return pagoda;
37 }
38 else {
39 System.out.println("The ontology is inconsistent!");
40 pagoda.dispose();
41 return null;
42 }
30 } 43 }
31 44
32
33 public static QueryReasoner getInstance(OWLOntology o) { 45 public static QueryReasoner getInstance(OWLOntology o) {
46 QueryReasoner pagoda = getInstance(Type.Full, o, true, true);
47 pagoda.properties = new Properties();
48 return pagoda;
49 }
50
51 private static QueryReasoner getInstance(OWLOntology o, Properties p) {
34 return getInstance(Type.Full, o, true, true); 52 return getInstance(Type.Full, o, true, true);
35 } 53 }
36 54
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java b/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
index 6f5d363..97925fc 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
@@ -43,6 +43,7 @@ public class HermitChecker implements Checker {
43 protected OWLOntology ontology; 43 protected OWLOntology ontology;
44 protected QueryRecord record; 44 protected QueryRecord record;
45 protected QueryGraph qGraph = null; 45 protected QueryGraph qGraph = null;
46 boolean toCheck = true;
46 47
47 public HermitChecker(Checker checker) { 48 public HermitChecker(Checker checker) {
48 if (checker instanceof HermitChecker) { 49 if (checker instanceof HermitChecker) {
@@ -58,12 +59,13 @@ public class HermitChecker implements Checker {
58 hermit = new Reasoner(ontology); 59 hermit = new Reasoner(ontology);
59 } 60 }
60 61
61 public HermitChecker(OWLOntology ontology, QueryRecord record) { 62 public HermitChecker(OWLOntology ontology, QueryRecord record, boolean toCheck) {
62 this.ontology = ontology; 63 this.ontology = ontology;
63 queryText = record.getQueryText(); 64 queryText = record.getQueryText();
64 answerVariable = record.getVariables(); 65 answerVariable = record.getVariables();
65 queryClause = record.getClause(); 66 queryClause = record.getClause();
66// this.record = record; 67// this.record = record;
68 this.toCheck = toCheck;
67 } 69 }
68 70
69 public HermitChecker(OWLOntology ontology, String queryText) { 71 public HermitChecker(OWLOntology ontology, String queryText) {
@@ -198,6 +200,8 @@ public class HermitChecker implements Checker {
198 200
199 @Override 201 @Override
200 public boolean check(AnswerTuple answerTuple) { 202 public boolean check(AnswerTuple answerTuple) {
203 if (!toCheck) return false;
204
201 if (hermit == null) initialiseReasoner(); 205 if (hermit == null) initialiseReasoner();
202 if (tag != 0) return tag == 1; 206 if (tag != 0) return tag == 1;
203 ++counter; 207 ++counter;
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
index 3207ff1..11588ce 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
@@ -47,8 +47,8 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
47 getDataStore().clearRulesAndMakeFactsExplicit(); 47 getDataStore().clearRulesAndMakeFactsExplicit();
48 } catch (JRDFStoreException e) { 48 } catch (JRDFStoreException e) {
49 e.printStackTrace(); 49 e.printStackTrace();
50 gap.clear();
51 } finally { 50 } finally {
51 gap.clear();
52 } 52 }
53 } 53 }
54 else 54 else
@@ -149,9 +149,14 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
149 if (instanceTuples != null) instanceTuples.dispose(); 149 if (instanceTuples != null) instanceTuples.dispose();
150 } 150 }
151 } 151 }
152 } catch (JRDFStoreException e) {
153 e.printStackTrace();
154 } finally {
155 if (predicateTuples != null) predicateTuples.dispose();
156 predicateTuples = null;
157 }
152 158
153 predicateTuples.dispose(); 159 try {
154
155 predicateTuples = getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X ?Y ?Z }", prefixes, parameters); 160 predicateTuples = getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X ?Y ?Z }", prefixes, parameters);
156 for (long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) { 161 for (long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) {
157 predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0)); 162 predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0));
@@ -172,6 +177,7 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
172 e.printStackTrace(); 177 e.printStackTrace();
173 } finally { 178 } finally {
174 if (predicateTuples != null) predicateTuples.dispose(); 179 if (predicateTuples != null) predicateTuples.dispose();
180 predicateTuples = null;
175 } 181 }
176 182
177 Utility.redirectCurrentOut(filename); 183 Utility.redirectCurrentOut(filename);
@@ -184,13 +190,13 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
184 190
185 public TupleIterator internal_evaluateAgainstIDBs(String queryText) throws JRDFStoreException { 191 public TupleIterator internal_evaluateAgainstIDBs(String queryText) throws JRDFStoreException {
186 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters, TripleStatus.TUPLE_STATUS_IDB.union(TripleStatus.TUPLE_STATUS_EDB), TripleStatus.TUPLE_STATUS_IDB); 192 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters, TripleStatus.TUPLE_STATUS_IDB.union(TripleStatus.TUPLE_STATUS_EDB), TripleStatus.TUPLE_STATUS_IDB);
187 iter.open(); 193// iter.open();
188 return iter; 194 return iter;
189 } 195 }
190 196
191 public TupleIterator internal_evaluate(String queryText) throws JRDFStoreException { 197 public TupleIterator internal_evaluate(String queryText) throws JRDFStoreException {
192 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters); 198 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters);
193 iter.open(); 199// iter.open();
194 return iter; 200 return iter;
195 } 201 }
196 202
@@ -201,7 +207,7 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
201 public TupleIterator internal_evaluateNotExpanded(String queryText) throws JRDFStoreException { 207 public TupleIterator internal_evaluateNotExpanded(String queryText) throws JRDFStoreException {
202 parameters.m_expandEquality = false; 208 parameters.m_expandEquality = false;
203 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters); 209 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters);
204 iter.open(); 210// iter.open();
205 parameters.m_expandEquality = true; 211 parameters.m_expandEquality = true;
206 return iter; 212 return iter;
207 } 213 }
@@ -346,19 +352,22 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
346 for (int[] t: collection) 352 for (int[] t: collection)
347 store.addTriplesByResourceIDs(t, ut); 353 store.addTriplesByResourceIDs(t, ut);
348 354
349 iter = internal_evaluateAgainstIDBs("select ?x ?y ?z where { ?x ?y ?z . }"); 355 try {
350 for (long multi = iter.open(); multi != 0; multi = iter.getNext()) { 356 iter = internal_evaluateAgainstIDBs("select ?x ?y ?z where { ?x ?y ?z . }");
351 int[] triple = new int[3]; 357 for (long multi = iter.open(); multi != 0; multi = iter.getNext()) {
352 for (int i = 0; i < 3; ++i) 358 int[] triple = new int[3];
353 triple[i] = iter.getResourceID(i); 359 for (int i = 0; i < 3; ++i)
354 store.addTriplesByResourceIDs(triple, ut); 360 triple[i] = iter.getResourceID(i);
361 store.addTriplesByResourceIDs(triple, ut);
362 }
363 } finally {
364 if (iter != null) iter.dispose();
365 iter = null;
355 } 366 }
356 store.applyReasoning(true); 367 store.applyReasoning(true);
357 } catch (JRDFStoreException e) { 368 } catch (JRDFStoreException e) {
358 e.printStackTrace(); 369 e.printStackTrace();
359 } finally { 370 }
360 if (iter != null) iter.dispose();
361 }
362 Utility.logInfo("Time for deletion: " + timer.duration()); 371 Utility.logInfo("Time for deletion: " + timer.duration());
363 } 372 }
364 373
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
index 2280b12..c2065dc 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
@@ -2,12 +2,9 @@ package uk.ac.ox.cs.pagoda.reasoner.light;
2 2
3import java.util.Collection; 3import java.util.Collection;
4import java.util.HashMap; 4import java.util.HashMap;
5import java.util.HashSet;
6import java.util.LinkedList; 5import java.util.LinkedList;
7import java.util.Map; 6import java.util.Map;
8import java.util.Queue; 7import java.util.Queue;
9import java.util.Set;
10
11import org.semanticweb.HermiT.model.AnnotatedEquality; 8import org.semanticweb.HermiT.model.AnnotatedEquality;
12import org.semanticweb.HermiT.model.Atom; 9import org.semanticweb.HermiT.model.Atom;
13import org.semanticweb.HermiT.model.AtomicConcept; 10import org.semanticweb.HermiT.model.AtomicConcept;
@@ -37,7 +34,7 @@ public class RDFoxTripleManager {
37 34
38 DataStore m_store; 35 DataStore m_store;
39 Dictionary m_dict; 36 Dictionary m_dict;
40 Set<Atom> triplesByTerm = new HashSet<Atom>(); 37// Set<Atom> triplesByTerm = new HashSet<Atom>();
41 38
42 public RDFoxTripleManager(DataStore store, boolean incrementally) { 39 public RDFoxTripleManager(DataStore store, boolean incrementally) {
43 m_store = store; 40 m_store = store;
@@ -63,7 +60,16 @@ public class RDFoxTripleManager {
63 } 60 }
64 61
65 public void addTripleByID(int[] tuple) { 62 public void addTripleByID(int[] tuple) {
63// System.out.println(getRawTerm(tuple[0]) + " " + getRawTerm(tuple[1]) + " " + getRawTerm(tuple[2]) + " .");
66 try { 64 try {
65// Resource[] rsc = new Resource[3];
66// m_dict.getResources(tuple, 0, 3, rsc);
67//
68// GroundTerm[] terms = new GroundTerm[3];
69// for (int i = 0; i < 3; ++i)
70// terms[i] = uk.ac.ox.cs.JRDFox.model.Individual.create(rsc[i].m_lexicalForm);
71// m_store.addTriples(terms, m_incrementally);
72
67 m_store.addTriplesByResourceIDs(tuple, m_incrementally); 73 m_store.addTriplesByResourceIDs(tuple, m_incrementally);
68 } catch (JRDFStoreException e) { 74 } catch (JRDFStoreException e) {
69 e.printStackTrace(); 75 e.printStackTrace();
diff --git a/src/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java b/src/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java
index a57d188..a0ecce8 100644
--- a/src/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java
+++ b/src/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java
@@ -34,9 +34,9 @@ public class HermitSummaryFilter implements Checker {
34 34
35 Endomorph endomorphismChecker = null; 35 Endomorph endomorphismChecker = null;
36 36
37 public HermitSummaryFilter(QueryRecord record) { 37 public HermitSummaryFilter(QueryRecord record, boolean toCallHermiT) {
38 m_record = record; 38 m_record = record;
39 HermitChecker hermitChecker = new HermitChecker(record.getRelevantOntology(), record); 39 HermitChecker hermitChecker = new HermitChecker(record.getRelevantOntology(), record, toCallHermiT);
40 endomorphismChecker = new Endomorph(record, hermitChecker); 40 endomorphismChecker = new Endomorph(record, hermitChecker);
41 hermitChecker.setDependencyGraph(endomorphismChecker.getDependencyGraph()); 41 hermitChecker.setDependencyGraph(endomorphismChecker.getDependencyGraph());
42 } 42 }
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java b/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java
index 0e19e30..f836212 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java
+++ b/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java
@@ -35,6 +35,7 @@ import uk.ac.ox.cs.JRDFox.model.Datatype;
35import uk.ac.ox.cs.JRDFox.store.DataStore; 35import uk.ac.ox.cs.JRDFox.store.DataStore;
36import uk.ac.ox.cs.JRDFox.store.Resource; 36import uk.ac.ox.cs.JRDFox.store.Resource;
37import uk.ac.ox.cs.JRDFox.store.TupleIterator; 37import uk.ac.ox.cs.JRDFox.store.TupleIterator;
38import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
38 39
39public class QueryTracker { 40public class QueryTracker {
40 41
@@ -80,7 +81,7 @@ public class QueryTracker {
80 Timer t1 = new Timer(); 81 Timer t1 = new Timer();
81 oldTripleCount = store.getTriplesCount(); 82 oldTripleCount = store.getTriplesCount();
82 // store.addRules(new String[] {m_encoder.getTrackingProgram()}); 83 // store.addRules(new String[] {m_encoder.getTrackingProgram()});
83 store.importRules(m_encoder.getTrackingProgram()); 84 store.importRules(m_encoder.getTrackingProgram(), UpdateType.ScheduleForAddition);
84 store.applyReasoning(incrementally); 85 store.applyReasoning(incrementally);
85 tripleCount = store.getTriplesCount(); 86 tripleCount = store.getTriplesCount();
86 87
@@ -93,8 +94,7 @@ public class QueryTracker {
93 + t1.duration() + " seconds."); 94 + t1.duration() + " seconds.");
94 } catch (JRDFStoreException e) { 95 } catch (JRDFStoreException e) {
95 e.printStackTrace(); 96 e.printStackTrace();
96 } 97 }
97
98 extractAxioms(trackingStore); 98 extractAxioms(trackingStore);
99 99
100 trackingStore.clearRulesAndIDBFacts(m_encoder.getAddedData()); 100 trackingStore.clearRulesAndIDBFacts(m_encoder.getAddedData());
@@ -145,8 +145,7 @@ public class QueryTracker {
145 } catch (JRDFStoreException e) { 145 } catch (JRDFStoreException e) {
146 e.printStackTrace(); 146 e.printStackTrace();
147 } finally { 147 } finally {
148 if (answers != null) 148 if (answers != null) answers.dispose();
149 answers.dispose();
150 } 149 }
151 150
152 Utility.logTrace("Extracted TBox axioms: "); 151 Utility.logTrace("Extracted TBox axioms: ");
@@ -190,7 +189,6 @@ public class QueryTracker {
190 } 189 }
191 } 190 }
192 } catch (JRDFStoreException e) { 191 } catch (JRDFStoreException e) {
193 // TODO Auto-generated catch block
194 e.printStackTrace(); 192 e.printStackTrace();
195 } finally { 193 } finally {
196 if (trackingAnswers != null) trackingAnswers.dispose(); 194 if (trackingAnswers != null) trackingAnswers.dispose();
@@ -329,9 +327,7 @@ public class QueryTracker {
329 continue; 327 continue;
330 TupleIterator answers = null, lowerAnswers = null; 328 TupleIterator answers = null, lowerAnswers = null;
331 Set<String> lower = new HashSet<String>(); 329 Set<String> lower = new HashSet<String>();
332 OWLClass cls = factory 330 OWLClass cls = factory.getOWLClass(IRI.create(clsIRI.startsWith("<") ? OWLHelper.removeAngles(clsIRI) : clsIRI));
333 .getOWLClass(IRI.create(clsIRI.startsWith("<") ? OWLHelper
334 .removeAngles(clsIRI) : clsIRI));
335 try { 331 try {
336 answers = trackingStore.internal_evaluateAgainstIDBs(getSPARQLQuery4Unary(trackingIRI)); 332 answers = trackingStore.internal_evaluateAgainstIDBs(getSPARQLQuery4Unary(trackingIRI));
337 answers.open(); 333 answers.open();
@@ -359,10 +355,8 @@ public class QueryTracker {
359 } catch (JRDFStoreException e) { 355 } catch (JRDFStoreException e) {
360 e.printStackTrace(); 356 e.printStackTrace();
361 } finally { 357 } finally {
362 if (answers != null) 358 if (answers != null) answers.dispose();
363 answers.dispose(); 359 if (lowerAnswers != null) lowerAnswers.dispose();
364 if (lowerAnswers != null)
365 lowerAnswers.dispose();
366 lower.clear(); 360 lower.clear();
367 } 361 }
368 Utility.logDebug("class: " + clsIRI + " " + count); 362 Utility.logDebug("class: " + clsIRI + " " + count);
@@ -370,53 +364,37 @@ public class QueryTracker {
370 return aboxAxiomCounter; 364 return aboxAxiomCounter;
371 } 365 }
372 366
373 private void getDerivedPredicates(BasicQueryEngine trackingStore, 367 private void getDerivedPredicates(BasicQueryEngine trackingStore, Set<String> unaryPredicates, Set<String> binaryPredicates) {
374 Set<String> unaryPredicates, Set<String> binaryPredicates) {
375
376 TupleIterator derivedTuples = null; 368 TupleIterator derivedTuples = null;
377 String selectedPredicate = OWLHelper.addAngles(m_encoder.getSelectedPredicate()); 369 String selectedPredicate = OWLHelper.addAngles(m_encoder.getSelectedPredicate());
378 try { 370 try {
379 derivedTuples = trackingStore 371 derivedTuples = trackingStore.internal_evaluateAgainstIDBs("select distinct ?z where { ?x <" + Namespace.RDF_TYPE + "> ?z . }");
380 .internal_evaluateAgainstIDBs("select distinct ?z where { ?x <"
381 + Namespace.RDF_TYPE + "> ?z . }");
382 for (long multi = derivedTuples.open(); multi != 0; multi = derivedTuples.getNext()) { 372 for (long multi = derivedTuples.open(); multi != 0; multi = derivedTuples.getNext()) {
383 String p = RDFoxTripleManager.getQuotedTerm(derivedTuples.getResource(0)); 373 String p = RDFoxTripleManager.getQuotedTerm(derivedTuples.getResource(0));
384 if (p.equals(selectedPredicate)) 374 if (p.equals(selectedPredicate)) ;
385 ; 375 else if (m_encoder.isAuxPredicate(p)) ;
386 else if (m_encoder.isAuxPredicate(p)) 376 else unaryPredicates.add(p);
387 ;
388 else
389 unaryPredicates.add(p);
390 } 377 }
391 } catch (JRDFStoreException e) { 378 } catch (JRDFStoreException e) {
392 e.printStackTrace(); 379 e.printStackTrace();
393 } finally { 380 } finally {
394 if (derivedTuples != null) 381 if (derivedTuples != null) derivedTuples.dispose();
395 derivedTuples.dispose();
396 } 382 }
397 383
398 derivedTuples = null; 384 derivedTuples = null;
399 try { 385 try {
400 derivedTuples = trackingStore 386 derivedTuples = trackingStore.internal_evaluateAgainstIDBs("select distinct ?y where { ?x ?y ?z . }");
401 .internal_evaluateAgainstIDBs("select distinct ?y where { ?x ?y ?z . }");
402 for (long multi = derivedTuples.open(); multi != 0; multi = derivedTuples.getNext()) { 387 for (long multi = derivedTuples.open(); multi != 0; multi = derivedTuples.getNext()) {
403 String p = RDFoxTripleManager.getQuotedTerm(derivedTuples.getResource(0)); 388 String p = RDFoxTripleManager.getQuotedTerm(derivedTuples.getResource(0));
404 if (p.equals(Namespace.RDF_TYPE_ABBR) 389 if (p.equals(Namespace.RDF_TYPE_ABBR) || p.equals(Namespace.RDF_TYPE_QUOTED)) ;
405 || p.equals(Namespace.RDF_TYPE_QUOTED)) 390 else if (p.equals(Namespace.EQUALITY_ABBR) || p.equals(Namespace.EQUALITY_QUOTED)) ;
406 ; 391 else if (m_encoder.isAuxPredicate(p)) ;
407 else if (p.equals(Namespace.EQUALITY_ABBR) 392 else binaryPredicates.add(p);
408 || p.equals(Namespace.EQUALITY_QUOTED))
409 ;
410 else if (m_encoder.isAuxPredicate(p))
411 ;
412 else
413 binaryPredicates.add(p);
414 } 393 }
415 } catch (JRDFStoreException e) { 394 } catch (JRDFStoreException e) {
416 e.printStackTrace(); 395 e.printStackTrace();
417 } finally { 396 } finally {
418 if (derivedTuples != null) 397 if (derivedTuples != null) derivedTuples.dispose();
419 derivedTuples.dispose();
420 } 398 }
421 } 399 }
422 400
@@ -428,8 +406,7 @@ public class QueryTracker {
428 toAddedRecords.add(botQueryRecord); 406 toAddedRecords.add(botQueryRecord);
429 407
430 for (QueryRecord botQueryRecord : toAddedRecords) { 408 for (QueryRecord botQueryRecord : toAddedRecords) {
431 m_manager.addAxioms(m_record.getRelevantOntology(), botQueryRecord 409 m_manager.addAxioms(m_record.getRelevantOntology(), botQueryRecord.getRelevantOntology().getAxioms());
432 .getRelevantOntology().getAxioms());
433 for (DLClause clause : botQueryRecord.getRelevantClauses()) 410 for (DLClause clause : botQueryRecord.getRelevantClauses())
434 m_record.addRelevantClauses(clause); 411 m_record.addRelevantClauses(clause);
435 } 412 }
@@ -456,16 +433,14 @@ public class QueryTracker {
456 433
457 private String getSPARQLQuery4Unary(String p) { 434 private String getSPARQLQuery4Unary(String p) {
458 StringBuilder builder = new StringBuilder(); 435 StringBuilder builder = new StringBuilder();
459 builder.append("select ?x where { ?x <") 436 builder.append("select ?x where { ?x <").append(Namespace.RDF_TYPE).append("> ");
460 .append(Namespace.RDF_TYPE).append("> ");
461 builder.append(p).append(" . }"); 437 builder.append(p).append(" . }");
462 return builder.toString(); 438 return builder.toString();
463 } 439 }
464 440
465 private String getSPARQLQuery4Binary(String p) { 441 private String getSPARQLQuery4Binary(String p) {
466 StringBuilder builder = new StringBuilder(); 442 StringBuilder builder = new StringBuilder();
467 builder.append("select ?x ?y where { ?x ").append(p) 443 builder.append("select ?x ?y where { ?x ").append(p).append(" ?y . }");
468 .append(" ?y . }");
469 return builder.toString(); 444 return builder.toString();
470 } 445 }
471 446
diff --git a/src/uk/ac/ox/cs/pagoda/util/Properties.java b/src/uk/ac/ox/cs/pagoda/util/Properties.java
index 551f94f..b687b53 100644
--- a/src/uk/ac/ox/cs/pagoda/util/Properties.java
+++ b/src/uk/ac/ox/cs/pagoda/util/Properties.java
@@ -1,95 +1,66 @@
1package uk.ac.ox.cs.pagoda.util; 1package uk.ac.ox.cs.pagoda.util;
2 2
3import java.io.BufferedReader;
4import java.io.FileInputStream; 3import java.io.FileInputStream;
5import java.io.IOException; 4import java.io.IOException;
6import java.io.InputStreamReader; 5import java.io.InputStream;
7import java.util.HashMap;
8 6
9public class Properties { 7public class Properties {
10
11 public static final String FILE_SEPARATOR = ";";
12 8
13// switches 9 String dataPath = null;
14// public static final String reuseGapFile = "REUSE_GAP"; 10 public String getDataPath() { return dataPath; }
15 public static final String toTrackProofs = "TO_TRACK"; 11 public void setDataPath(String path) { dataPath = path; }
16 public static final String checkAnswers = "TO_CHECK_ANSWERS";
17 public static final String redirectSysOut = "TO_REDIRECT_SYS_OUT";
18 public static final String considerEqualities = "TO_CONSIDER_EQUALITIES";
19
20// parameters
21 public static final String testcase = "TEST_CASE";
22 public static final String typeOfLowerBounds = "TYPE_LOWER_BOUNDS";
23 public static final String FULL_REASONER = "OWLREASONER";
24
25// file locations
26 public static final String ontologyFile = "LOWER_T_FILE";
27 public static final String importedData = "IMPORT";
28 public static final String queryFile = "QUERY_FILE";
29
30// auxiliary files
31// public static final String auxiliaryDirectory = "AUXILIARY_DIRECTORY";
32// public static final String queryAnswerGapFile = "GAP_FILE";
33// public static final String lowerAnswerFile = "LOWER_ANSWER_FILE";
34// public static final String upperAnswerFile = "UPPER_ANSWER_FILE";
35// public static final String boundsGapFile = "BOUNDS_GAP_FILE";
36// public static final String fragmentFile = "FRAGMENT_FILE";
37 12
38 public static final String correspondence = "CORRESPONDENCE"; 13 String ontologyPath;
39 14 public String getOntologyPath() { return ontologyPath; }
40 private HashMap<String, String> param = new HashMap<String, String>(); 15 public void setOntologyPath(String path) { ontologyPath = path; }
41
42 public static final String on = String.valueOf(true);
43 public static final String off = String.valueOf(false);
44
45 public void reset() {
46 param.clear();
47// param.put(reuseGapFile, on);
48 param.put(toTrackProofs, on);
49 param.put(checkAnswers, on);
50 param.put(redirectSysOut, off);
51 param.put(considerEqualities, off);
52 }
53
54 public Properties() {
55 reset();
56 }
57
58 public void addImportedFile(String additionalDataFile) {
59 if (additionalDataFile == null) return ;
60 String files = param.get(importedData);
61 StringBuilder sb = new StringBuilder();
62 if (files != null)
63 sb.append(files).append(FILE_SEPARATOR);
64 sb.append(additionalDataFile);
65 param.put(importedData, sb.toString());
66 }
67 16
68 public void load(String file) throws IOException { 17 String queryPath = null;
69 BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(file))); 18 public String getQueryPath() { return queryPath; }
70 String line; 19 public void setQueryPath(String path) { queryPath = path; }
71 String tokens[]; 20
72 while ((line = Utility.readLine(reader)) != null) { 21 String answerPath = null;
73 if (line.isEmpty() || line.startsWith("#")) 22 public String getAnswerPath() { return answerPath; }
74 continue; 23 public void setAnswerPath(String path) { answerPath = path; }
24
25 boolean toClassify = true;
26 public boolean getToClassify() { return toClassify; }
27 public void setToClassify(boolean flag) { toClassify = flag; }
28
29 boolean toCallHermiT = true;
30 public boolean getToCallHermiT() { return toCallHermiT; }
31 public void setToCallHermiT(boolean flag) { toCallHermiT = flag; }
32
33 public static boolean ShellModeDefault = false;
34
35 boolean shellMode = ShellModeDefault;
36 public boolean getShellMode() { return shellMode; }
37 public void setShellMode(boolean flag) { shellMode = flag; }
38
39 public Properties(String path) {
40 java.util.Properties m_properties = new java.util.Properties();
41 InputStream inputStream = null;
42 try {
43 inputStream = new FileInputStream(path);
44 m_properties.load(inputStream);
75 45
76 tokens = line.split("="); 46 setOntologyPath(m_properties.getProperty("ONTOLOGY"));
77 if (tokens[1].equals("on")) 47 setDataPath(m_properties.getProperty("DATA"));
78 set(tokens[0], String.valueOf(true)); 48 setQueryPath(m_properties.getProperty("QUERY"));
79 else if (tokens[1].equals("off")) 49 setAnswerPath(m_properties.getProperty("ANSWER"));
80 set(tokens[0], String.valueOf(false)); 50 setToClassify(Boolean.parseBoolean(m_properties.getProperty("TO_CLASSIFY")));
81 else 51 setToCallHermiT(Boolean.parseBoolean(m_properties.getProperty("CALL_HERMIT")));
82 set(tokens[0], tokens[1]); 52
53 } catch (IOException e) {
54 e.printStackTrace();
55 } finally {
56 if (inputStream != null)
57 try {
58 inputStream.close();
59 } catch (IOException e) {
60 e.printStackTrace();
61 }
83 } 62 }
84 reader.close();
85 }
86
87 public String get(String key) {
88 return param.get(key);
89 }
90
91 public void set(String key, String value) {
92 param.put(key, value);
93 } 63 }
64 public Properties() { }
94 65
95} 66}
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-06 06:22:11 +0000