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authorRncLsn <rnc.lsn@gmail.com>2015-05-28 17:11:35 +0100
committerRncLsn <rnc.lsn@gmail.com>2015-05-28 17:11:35 +0100
commitde3749532d060f26c966a81c03f9a5d846c33d06 (patch)
tree6cc5ba2837dc3c167b100f5e8be4e8c16da7be98 /src/uk
parent4298cdef8e551325cd16b4e24ae6699c44b60751 (diff)
downloadACQuA-de3749532d060f26c966a81c03f9a5d846c33d06.tar.gz
ACQuA-de3749532d060f26c966a81c03f9a5d846c33d06.zip
Merged updates from upstream.
Diffstat (limited to 'src/uk')
-rw-r--r--src/uk/ac/ox/cs/pagoda/endomorph/Clique.java5
-rw-r--r--src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndMultiThreadPlan.java85
-rw-r--r--src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndPlan.java74
-rw-r--r--src/uk/ac/ox/cs/pagoda/endomorph/plan/PlainPlan.java6
-rw-r--r--src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java120
-rw-r--r--src/uk/ac/ox/cs/pagoda/query/GapByStore4ID2.java141
-rw-r--r--src/uk/ac/ox/cs/pagoda/query/GapByTriple.java40
-rw-r--r--src/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java6
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java5
-rw-r--r--src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java154
-rw-r--r--src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java2
-rw-r--r--src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java38
-rw-r--r--src/uk/ac/ox/cs/pagoda/util/Utility.java104
13 files changed, 453 insertions, 327 deletions
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/Clique.java b/src/uk/ac/ox/cs/pagoda/endomorph/Clique.java
index 1c269ea..9b0d88e 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/Clique.java
+++ b/src/uk/ac/ox/cs/pagoda/endomorph/Clique.java
@@ -1,11 +1,11 @@
1package uk.ac.ox.cs.pagoda.endomorph; 1package uk.ac.ox.cs.pagoda.endomorph;
2 2
3import uk.ac.ox.cs.pagoda.summary.NodeTuple;
4
3import java.util.Collection; 5import java.util.Collection;
4import java.util.HashSet; 6import java.util.HashSet;
5import java.util.Set; 7import java.util.Set;
6 8
7import uk.ac.ox.cs.pagoda.summary.NodeTuple;
8
9public class Clique { 9public class Clique {
10 NodeTuple representative; 10 NodeTuple representative;
11 Set<NodeTuple> nodeTuples = null; 11 Set<NodeTuple> nodeTuples = null;
@@ -13,6 +13,7 @@ public class Clique {
13 public Clique(NodeTuple u) { 13 public Clique(NodeTuple u) {
14 nodeTuples = new HashSet<NodeTuple>(); 14 nodeTuples = new HashSet<NodeTuple>();
15 representative = u; 15 representative = u;
16 nodeTuples.add(u);
16 } 17 }
17 18
18 public boolean addNodeTuple(NodeTuple nodeTuple) { 19 public boolean addNodeTuple(NodeTuple nodeTuple) {
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndMultiThreadPlan.java b/src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndMultiThreadPlan.java
index 8c7ce6a..862fdc8 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndMultiThreadPlan.java
+++ b/src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndMultiThreadPlan.java
@@ -1,88 +1,81 @@
1package uk.ac.ox.cs.pagoda.endomorph.plan; 1package uk.ac.ox.cs.pagoda.endomorph.plan;
2 2
3import java.util.Collection;
4import java.util.Collections;
5import java.util.LinkedList;
6import java.util.Map;
7import java.util.Set;
8import java.util.concurrent.ConcurrentHashMap;
9import java.util.concurrent.ConcurrentLinkedDeque;
10import java.util.concurrent.atomic.AtomicInteger;
11
12import uk.ac.ox.cs.pagoda.endomorph.DependencyGraph;
13import uk.ac.ox.cs.pagoda.endomorph.Clique; 3import uk.ac.ox.cs.pagoda.endomorph.Clique;
4import uk.ac.ox.cs.pagoda.endomorph.DependencyGraph;
14import uk.ac.ox.cs.pagoda.query.AnswerTuple; 5import uk.ac.ox.cs.pagoda.query.AnswerTuple;
15import uk.ac.ox.cs.pagoda.reasoner.full.Checker; 6import uk.ac.ox.cs.pagoda.reasoner.full.Checker;
16import uk.ac.ox.cs.pagoda.reasoner.full.HermitChecker; 7import uk.ac.ox.cs.pagoda.reasoner.full.HermitChecker;
17import uk.ac.ox.cs.pagoda.util.Utility; 8import uk.ac.ox.cs.pagoda.util.Utility;
18 9
10import java.util.*;
11import java.util.concurrent.ConcurrentHashMap;
12import java.util.concurrent.ConcurrentLinkedDeque;
13import java.util.concurrent.atomic.AtomicInteger;
14
19public class OpenEndMultiThreadPlan implements CheckPlan { 15public class OpenEndMultiThreadPlan implements CheckPlan {
20 16
21 Checker checker; 17 Checker checker;
22 DependencyGraph dGraph; 18 DependencyGraph dGraph;
23 19 // Clique[] topo;
20// AtomicInteger open, end;
21 ConcurrentLinkedDeque<Clique> topo;
22 Set<Clique> validated, falsified;
23 AtomicInteger counter = new AtomicInteger();
24
24 public OpenEndMultiThreadPlan(Checker checker, DependencyGraph dGraph) { 25 public OpenEndMultiThreadPlan(Checker checker, DependencyGraph dGraph) {
25 this.checker = checker; 26 this.checker = checker;
26 this.dGraph = dGraph; 27 this.dGraph = dGraph;
27 } 28 }
28 29
29// Clique[] topo;
30// AtomicInteger open, end;
31 ConcurrentLinkedDeque<Clique> topo;
32
33 Set<Clique> validated, falsified;
34
35 @Override 30 @Override
36 public int check() { 31 public int check() {
37 Collection<Clique> cliques = dGraph.getTopologicalOrder(); 32 Collection<Clique> cliques = dGraph.getTopologicalOrder();
38// topo = new LinkedBlockingDeque<Clique>(cliques); 33// topo = new LinkedBlockingDeque<Clique>(cliques);
39 topo = new ConcurrentLinkedDeque<Clique>(cliques); 34 topo = new ConcurrentLinkedDeque<Clique>(cliques);
40 35
41// topo = new Clique[cliques.size()]; 36// topo = new Clique[cliques.size()];
42// int index = 0; 37// int index = 0;
43// for (Clique clique: cliques) topo[index++] = clique; 38// for (Clique clique: cliques) topo[index++] = clique;
44// open = new AtomicInteger(); 39// open = new AtomicInteger();
45// end = new AtomicInteger(cliques.size() - 1); 40// end = new AtomicInteger(cliques.size() - 1);
46 41
47// validated = Collections.synchronizedSet(new HashSet<Clique>()); 42// validated = Collections.synchronizedSet(new HashSet<Clique>());
48// falsified = Collections.synchronizedSet(new HashSet<Clique>()); 43// falsified = Collections.synchronizedSet(new HashSet<Clique>());
49 validated = Collections.newSetFromMap(new ConcurrentHashMap<Clique, Boolean>()); 44 validated = Collections.newSetFromMap(new ConcurrentHashMap<Clique, Boolean>());
50 falsified = Collections.newSetFromMap(new ConcurrentHashMap<Clique, Boolean>()); 45 falsified = Collections.newSetFromMap(new ConcurrentHashMap<Clique, Boolean>());
51 46
52 int numOfThreads = 10; 47 int numOfThreads = 10;
53 Collection<Thread> threads = new LinkedList<Thread>(); 48 Collection<Thread> threads = new LinkedList<Thread>();
54 for (int i = 0; i < numOfThreads; ++i) 49 for(int i = 0; i < numOfThreads; ++i)
55 threads.add(new Thread(new SubThread(new HermitChecker(checker), i))); 50 threads.add(new Thread(new SubThread(new HermitChecker(checker), i)));
56 51
57 for (Thread thread: threads) thread.start(); 52 for (Thread thread: threads) thread.start();
58 53
59 for (Thread thread: threads) { 54 for (Thread thread: threads) {
60 try { 55 try {
61 thread.join(); 56 thread.join();
62 } catch (InterruptedException e) { 57 } catch (InterruptedException e) {
63 e.printStackTrace(); 58 e.printStackTrace();
64 } 59 }
65 } 60 }
66 61
67 Utility.logDebug("HermiT was called " + counter.get() + " times."); 62 Utility.logDebug("HermiT was called " + counter.get() + " times.");
68 63
69 int count = 0; 64 int count = 0;
70 for (Clique c: dGraph.getTopologicalOrder()) { 65 for (Clique c: dGraph.getTopologicalOrder()) {
71 if (validated.contains(c)) 66 if (validated.contains(c))
72 count += c.getNodeTuples().size() + 1; 67 count += c.getNodeTuples().size();
73 } 68 }
74 return count; 69 return count;
75 } 70 }
76 71
77 private void setMarkCascadely(Clique clique, Set<Clique> marked, Map<Clique, Collection<Clique>> edges) { 72 private void setMarkCascadely(Clique clique, Set<Clique> marked, Map<Clique, Collection<Clique>> edges) {
78 marked.add(clique); 73 marked.add(clique);
79 if (edges.containsKey(clique)) 74 if (edges.containsKey(clique))
80 for (Clique c: edges.get(clique)) 75 for (Clique c: edges.get(clique))
81 if (!marked.contains(c)) 76 if(!marked.contains(c))
82 setMarkCascadely(c, marked, edges); 77 setMarkCascadely(c, marked, edges);
83 } 78 }
84
85 AtomicInteger counter = new AtomicInteger();
86 79
87 class SubThread implements Runnable { 80 class SubThread implements Runnable {
88 81
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndPlan.java b/src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndPlan.java
index 19d567a..3294c31 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndPlan.java
+++ b/src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndPlan.java
@@ -17,37 +17,39 @@ public class OpenEndPlan implements CheckPlan {
17 public static final int TIME_OUT_MIN = 1; 17 public static final int TIME_OUT_MIN = 1;
18 18
19 Checker checker; 19 Checker checker;
20 DependencyGraph dGraph; 20 DependencyGraph dGraph;
21 QueryRecord m_record; 21 QueryRecord m_record;
22 22 int m_answerArity;
23 Set<Clique> validated = new HashSet<Clique>();
24 Set<Clique> falsified = new HashSet<Clique>();
25 Set<AnswerTuple> passedAnswers = new HashSet<AnswerTuple>();
23 public OpenEndPlan(Checker checker, DependencyGraph dGraph, QueryRecord record) { 26 public OpenEndPlan(Checker checker, DependencyGraph dGraph, QueryRecord record) {
24 this.checker = checker; 27 this.checker = checker;
25 this.dGraph = dGraph; 28 this.dGraph = dGraph;
26 m_record = record; 29 m_record = record;
30 m_answerArity = record.getAnswerVariables().length;
27 } 31 }
28 32
29 @Override 33 @Override
30 public int check() { 34 public int check() {
31 Deque<Clique> topo = new LinkedList<Clique>(dGraph.getTopologicalOrder()); 35 LinkedList<Clique> topo = new LinkedList<Clique>(dGraph.getTopologicalOrder());
32 Utility.logInfo("Entrances: " + dGraph.getEntrances().size() + " Exists: " + dGraph.getExits().size()); 36 Utility.logInfo("Entrances: " + dGraph.getEntrances().size() + " Exists: " + dGraph.getExits().size());
33 Set<Clique> validated = new HashSet<Clique>();
34 Set<Clique> falsified = new HashSet<Clique>();
35 37
36 boolean flag = true; 38 boolean flag = true;
37 Clique clique; 39 Clique clique;
38 Timer t = new Timer(); 40 Timer t = new Timer();
39
40 41
41 AnswerTuple answerTuple; 42 AnswerTuple answerTuple;
42 while (!topo.isEmpty()) { 43 while (!topo.isEmpty()) {
43 if (flag) { 44 if (flag) {
44 clique = topo.removeFirst(); 45 clique = topo.removeFirst();
46 if(redundant(clique)) continue;
45 if (validated.contains(clique)) continue; 47 if (validated.contains(clique)) continue;
46 if (falsified.contains(clique)) { flag = false; continue; } 48 if (falsified.contains(clique)) { flag = false; continue; }
47 Utility.logDebug("start checking front ... " + (answerTuple = clique.getRepresentative().getAnswerTuple())); 49 Utility.logDebug("start checking front ... " + (answerTuple = clique.getRepresentative().getAnswerTuple()));
48 if (checker.check(answerTuple)) { 50 if (checker.check(answerTuple)) {
49 Utility.logDebug(answerTuple.toString() + " is verified."); 51 Utility.logDebug(answerTuple.toString() + " is verified.");
50 setMarkCascadely(clique, validated, dGraph.getOutGoingEdges()); 52 setMarkCascadelyValidated(clique);
51 } 53 }
52 else { 54 else {
53 falsified.add(clique); 55 falsified.add(clique);
@@ -58,12 +60,12 @@ public class OpenEndPlan implements CheckPlan {
58 clique = topo.removeLast(); 60 clique = topo.removeLast();
59 if (falsified.contains(clique)) continue; 61 if (falsified.contains(clique)) continue;
60 if (validated.contains(clique)) { flag = true; continue; } 62 if (validated.contains(clique)) { flag = true; continue; }
61 Utility.logDebug("start checking back ... " + (answerTuple = clique.getRepresentative().getAnswerTuple())); 63 Utility.logDebug("start checking back ... " + (answerTuple = clique.getRepresentative().getAnswerTuple()));
62 if (!checker.check(answerTuple)) 64 if(!checker.check(answerTuple))
63 setMarkCascadely(clique, falsified, dGraph.getInComingEdges()); 65 setMarkCascadelyFasified(clique);
64 else { 66 else {
65 Utility.logDebug(answerTuple.toString() + " is verified."); 67 Utility.logDebug(answerTuple.toString() + " is verified.");
66 validated.add(clique); 68 addProjections(clique);
67 flag = true; 69 flag = true;
68 } 70 }
69 } 71 }
@@ -76,9 +78,8 @@ public class OpenEndPlan implements CheckPlan {
76 Collection<AnswerTuple> validAnswers = new LinkedList<AnswerTuple>(); 78 Collection<AnswerTuple> validAnswers = new LinkedList<AnswerTuple>();
77 for (Clique c: dGraph.getTopologicalOrder()) 79 for (Clique c: dGraph.getTopologicalOrder())
78 if (validated.contains(c)) { 80 if (validated.contains(c)) {
79 count += c.getNodeTuples().size() + 1; 81 count += c.getNodeTuples().size();
80 validAnswers.add(c.getRepresentative().getAnswerTuple()); 82// validAnswers.add(c.getRepresentative().getAnswerTuple());
81
82 for (NodeTuple nodeTuple: c.getNodeTuples()) { 83 for (NodeTuple nodeTuple: c.getNodeTuples()) {
83 ans = nodeTuple.getAnswerTuple(); 84 ans = nodeTuple.getAnswerTuple();
84 validAnswers.add(ans); 85 validAnswers.add(ans);
@@ -91,12 +92,35 @@ public class OpenEndPlan implements CheckPlan {
91 return count; 92 return count;
92 } 93 }
93 94
94 private void setMarkCascadely(Clique clique, Set<Clique> marked, Map<Clique, Collection<Clique>> edges) { 95 private boolean redundant(Clique clique) {
95 marked.add(clique); 96 for(NodeTuple nodeTuple : clique.getNodeTuples())
97 if(!passedAnswers.contains(AnswerTuple.getInstance(nodeTuple.getAnswerTuple(), m_answerArity)))
98 return false;
99 return true;
100 }
101
102 private void addProjections(Clique clique) {
103 for(NodeTuple nodeTuple : clique.getNodeTuples())
104 passedAnswers.add(AnswerTuple.getInstance(nodeTuple.getAnswerTuple(), m_answerArity));
105 }
106
107 private void setMarkCascadelyValidated(Clique clique) {
108 validated.add(clique);
109 addProjections(clique);
110 Map<Clique, Collection<Clique>> edges = dGraph.getOutGoingEdges();
96 if (edges.containsKey(clique)) 111 if (edges.containsKey(clique))
97 for (Clique c: edges.get(clique)) 112 for (Clique c: edges.get(clique))
98 if (!marked.contains(c)) 113 if(!validated.contains(c))
99 setMarkCascadely(c, marked, edges); 114 setMarkCascadelyValidated(c);
115 }
116
117 private void setMarkCascadelyFasified(Clique clique) {
118 falsified.add(clique);
119 Map<Clique, Collection<Clique>> edges = dGraph.getInComingEdges();
120 if(edges.containsKey(clique))
121 for(Clique c : edges.get(clique))
122 if(!falsified.contains(c))
123 setMarkCascadelyFasified(c);
100 } 124 }
101 125
102} 126}
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/plan/PlainPlan.java b/src/uk/ac/ox/cs/pagoda/endomorph/plan/PlainPlan.java
index d6067d0..5e1a700 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/plan/PlainPlan.java
+++ b/src/uk/ac/ox/cs/pagoda/endomorph/plan/PlainPlan.java
@@ -1,12 +1,12 @@
1package uk.ac.ox.cs.pagoda.endomorph.plan; 1package uk.ac.ox.cs.pagoda.endomorph.plan;
2 2
3import java.util.Set;
4
5import uk.ac.ox.cs.pagoda.endomorph.Clique; 3import uk.ac.ox.cs.pagoda.endomorph.Clique;
6import uk.ac.ox.cs.pagoda.reasoner.full.Checker; 4import uk.ac.ox.cs.pagoda.reasoner.full.Checker;
7import uk.ac.ox.cs.pagoda.summary.NodeTuple; 5import uk.ac.ox.cs.pagoda.summary.NodeTuple;
8import uk.ac.ox.cs.pagoda.util.Utility; 6import uk.ac.ox.cs.pagoda.util.Utility;
9 7
8import java.util.Set;
9
10public class PlainPlan implements CheckPlan { 10public class PlainPlan implements CheckPlan {
11 11
12 Checker checker; 12 Checker checker;
@@ -22,7 +22,7 @@ public class PlainPlan implements CheckPlan {
22 int count = 0; 22 int count = 0;
23 for (Clique clique: toCheck) 23 for (Clique clique: toCheck)
24 if (checker.check(clique.getRepresentative().getAnswerTuple())) { 24 if (checker.check(clique.getRepresentative().getAnswerTuple())) {
25 count += clique.getNodeTuples().size() + 1; 25 count += clique.getNodeTuples().size();
26 for (NodeTuple nodeTuple: clique.getNodeTuples()) 26 for (NodeTuple nodeTuple: clique.getNodeTuples())
27 Utility.logDebug(nodeTuple.getAnswerTuple().toString()); 27 Utility.logDebug(nodeTuple.getAnswerTuple().toString());
28 } 28 }
diff --git a/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java b/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java
index 1c0eb48..02db18d 100644
--- a/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java
+++ b/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java
@@ -1,103 +1,106 @@
1package uk.ac.ox.cs.pagoda.query; 1package uk.ac.ox.cs.pagoda.query;
2 2
3import java.util.HashMap; 3import uk.ac.ox.cs.JRDFox.JRDFStoreException;
4import java.util.LinkedList; 4import uk.ac.ox.cs.JRDFox.store.DataStore;
5import java.util.Map; 5import uk.ac.ox.cs.JRDFox.store.TupleIterator;
6
7import uk.ac.ox.cs.pagoda.MyPrefixes; 6import uk.ac.ox.cs.pagoda.MyPrefixes;
8//import uk.ac.ox.cs.pagoda.multistage.AnswerTupleID;
9import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine; 7import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
10import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxTripleManager; 8import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxTripleManager;
9import uk.ac.ox.cs.pagoda.util.Namespace;
11import uk.ac.ox.cs.pagoda.util.Timer; 10import uk.ac.ox.cs.pagoda.util.Timer;
12import uk.ac.ox.cs.pagoda.util.Utility; 11import uk.ac.ox.cs.pagoda.util.Utility;
13import uk.ac.ox.cs.JRDFox.JRDFStoreException; 12
14import uk.ac.ox.cs.JRDFox.store.DataStore; 13import java.util.HashMap;
15import uk.ac.ox.cs.JRDFox.store.TupleIterator; 14import java.util.LinkedList;
15import java.util.Map;
16
17//import uk.ac.ox.cs.pagoda.multistage.AnswerTupleID;
16 18
17//public class GapByStore4ID extends GapTupleIterator<AnswerTupleID> { 19//public class GapByStore4ID extends GapTupleIterator<AnswerTupleID> {
18public class GapByStore4ID extends GapTupleIterator<int[]> { 20public class GapByStore4ID extends GapTupleIterator<int[]> {
19 21
20 private MyPrefixes prefixes = MyPrefixes.PAGOdAPrefixes; 22 protected MyPrefixes prefixes = MyPrefixes.PAGOdAPrefixes;
21 private TupleIterator iterator = null; 23 protected TupleIterator iterator = null;
22 24
23// AnswerTupleID tuple; 25// AnswerTupleID tuple;
24 int[] tuple; 26protected int[] tuple;
25 private BasicQueryEngine m_engine; 27 protected BasicQueryEngine m_engine;
26 private DataStore m_store; 28 protected DataStore m_store;
27 private RDFoxTripleManager tripleManager; 29 protected RDFoxTripleManager tripleManager;
30 protected long multi;
31 Map<Integer, Integer> original2gap = new HashMap<Integer, Integer>();
32 LinkedList<String> predicatesWithGap = new LinkedList<String>();
28 33
29 public GapByStore4ID(BasicQueryEngine engine) { 34 public GapByStore4ID(BasicQueryEngine engine) {
30 m_engine = engine; 35 m_engine = engine;
31 m_store = engine.getDataStore(); 36 m_store = engine.getDataStore();
32 tripleManager = new RDFoxTripleManager(m_store, false); 37 tripleManager = new RDFoxTripleManager(m_store, false);
33 } 38 }
34 39
35 long multi;
36
37 @Override 40 @Override
38 public void compile(String program) throws JRDFStoreException { 41 public void compile(String program) throws JRDFStoreException {
39 clear(); 42 clear();
40 43
41 boolean incrementally = true; 44 boolean incrementally = true;
42 Timer t = new Timer(); 45 Timer t = new Timer();
43 long oldTripleCount = m_store.getTriplesCount(); 46 long oldTripleCount = m_store.getTriplesCount();
44 47
45 if (program != null) { 48 if (program != null) {
46// m_store.addRules(new String[] {program}); 49// m_store.addRules(new String[] {program});
47 m_store.importRules(program); 50 m_store.importRules(program);
48 incrementally = false; 51 incrementally = false;
49 } 52 }
50 53
51 m_store.applyReasoning(incrementally); 54 m_store.applyReasoning(incrementally);
52 55
53 long tripleCount = m_store.getTriplesCount(); 56 long tripleCount = m_store.getTriplesCount();
54 57
55 Utility.logDebug("current store after materialising upper related rules: " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)", 58 Utility.logDebug("current store after materialising upper related rules: " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)",
56 "current store finished the materialisation of upper related rules in " + t.duration() + " seconds."); 59 "current store finished the materialisation of upper related rules in " + t.duration() + " seconds.");
57 60
58 m_engine.setExpandEquality(false); 61 m_engine.setExpandEquality(false);
59 iterator = m_engine.internal_evaluateAgainstIDBs("select ?x ?y ?z where { ?x ?y ?z . }"); 62 iterator = m_engine.internal_evaluateAgainstIDBs("select ?x ?y ?z where { ?x ?y ?z . }");
60 m_engine.setExpandEquality(true); 63 m_engine.setExpandEquality(true);
61 64
62 multi = iterator.open(); 65 multi = iterator.open();
63 Utility.logDebug("gap query evaluted ..."); 66 Utility.logDebug("gap query evaluted ...");
64 } 67 }
65 68
66 @Override 69 @Override
67 public boolean hasNext() { 70 public boolean hasNext() {
68 if (iterator == null) return false; 71 if(iterator == null) return false;
69 try { 72 try {
70// tuple = new AnswerTupleID(3); 73// tuple = new AnswerTupleID(3);
71 tuple = new int[3]; 74 tuple = new int[3];
72 Integer predicate; 75 Integer predicate;
73 for (; multi != 0; multi = iterator.getNext()) { 76 for (; multi != 0; multi = iterator.getNext()) {
74 for (int i = 0; i < 3; ++i) 77 for (int i = 0; i < 3; ++i)
75// tuple.setTerm(i, (int) iterator.getResourceID(i)); 78// tuple.setTerm(i, (int) iterator.getResourceID(i));
76 tuple[i] = (int) iterator.getResourceID(i); 79 tuple[i] = iterator.getResourceID(i);
77 80
78 if (isRDF_TYPE()) { 81 if (isRDF_TYPE()) {
79// predicate = getGapPredicateID(tuple.getTerm(2)); 82// predicate = getGapPredicateID(tuple.getTerm(2));
80 predicate = getGapPredicateID(tuple[2]); 83 predicate = getGapPredicateID(tuple[2]);
81 if (predicate == null) continue; 84 if(predicate == null) continue;
82// tuple.setTerm(2, predicate); 85// tuple.setTerm(2, predicate);
83 tuple[2] = predicate; 86 tuple[2] = predicate;
84 } 87 }
85 else { 88 else {
86// predicate = getGapPredicateID(tuple.getTerm(1)); 89// predicate = getGapPredicateID(tuple.getTerm(1));
87 predicate = getGapPredicateID(tuple[1]); 90 predicate = getGapPredicateID(tuple[1]);
88 if (predicate == null) continue; 91 if(predicate == null) continue;
89// tuple.setTerm(1, predicate); 92// tuple.setTerm(1, predicate);
90 tuple[1] = predicate; 93 tuple[1] = predicate;
91 } 94 }
92 return true; 95 return true;
93 } 96 }
94 } catch (JRDFStoreException e) { 97 } catch (JRDFStoreException e) {
95 e.printStackTrace(); 98 e.printStackTrace();
96 return false; 99 return false;
97 } 100 }
98 return false; 101 return false;
99 } 102 }
100 103
101 @Override 104 @Override
102// public AnswerTupleID next() { 105// public AnswerTupleID next() {
103 public int[] next() { 106 public int[] next() {
@@ -105,19 +108,16 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
105 multi = iterator.getNext(); 108 multi = iterator.getNext();
106 } catch (JRDFStoreException e) { 109 } catch (JRDFStoreException e) {
107 e.printStackTrace(); 110 e.printStackTrace();
108 } 111 }
109 112
110 return tuple; 113 return tuple;
111 } 114 }
112 115
113 Map<Integer, Integer> original2gap = new HashMap<Integer, Integer>();
114 LinkedList<String> predicatesWithGap = new LinkedList<String>();
115
116 public LinkedList<String> getPredicatesWithGap() { 116 public LinkedList<String> getPredicatesWithGap() {
117 return predicatesWithGap; 117 return predicatesWithGap;
118 } 118 }
119 119
120 private Integer getGapPredicateID(int originalID) { 120 protected Integer getGapPredicateID(int originalID) {
121 Integer gapID; 121 Integer gapID;
122 if ((gapID = original2gap.get(originalID)) != null) 122 if ((gapID = original2gap.get(originalID)) != null)
123 return gapID; 123 return gapID;
@@ -136,11 +136,14 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
136 return gapID; 136 return gapID;
137 } 137 }
138 138
139 private boolean isAuxPredicate(String originalPredicate) { 139 protected boolean isAuxPredicate(String originalPredicate) {
140 return originalPredicate.contains("_AUX"); 140 if(originalPredicate.equals(Namespace.EQUALITY_QUOTED)) return false;
141 return originalPredicate.contains("_AUX") ||
142 originalPredicate.startsWith("<" + Namespace.OWL_NS) ||
143 originalPredicate.startsWith("<" + Namespace.PAGODA_ORIGINAL);
141 } 144 }
142 145
143 private boolean isRDF_TYPE() { 146 protected boolean isRDF_TYPE() {
144// return tripleManager.isRdfTypeID(tuple.getTerm(1)); 147// return tripleManager.isRdfTypeID(tuple.getTerm(1));
145 return tripleManager.isRdfTypeID(tuple[1]); 148 return tripleManager.isRdfTypeID(tuple[1]);
146 } 149 }
@@ -150,8 +153,6 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
150 Utility.logError("Unsupported operation!"); 153 Utility.logError("Unsupported operation!");
151 } 154 }
152 155
153 private boolean valid = false;
154
155 @Override 156 @Override
156 public void save(String file) { 157 public void save(String file) {
157 Utility.logError("Unsupported Operation..."); 158 Utility.logError("Unsupported Operation...");
@@ -168,7 +169,6 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
168 ++tupleCounter; 169 ++tupleCounter;
169 tripleManager.addTripleByID(tuple); 170 tripleManager.addTripleByID(tuple);
170 } 171 }
171 valid = true;
172 172
173 long tripleCounter = m_store.getTriplesCount(); 173 long tripleCounter = m_store.getTriplesCount();
174 Utility.logDebug("There are " + tupleCounter + " tuples in the gap between lower and upper bound materialisation.", 174 Utility.logDebug("There are " + tupleCounter + " tuples in the gap between lower and upper bound materialisation.",
@@ -183,8 +183,6 @@ public class GapByStore4ID extends GapTupleIterator<int[]> {
183 } 183 }
184 } 184 }
185 185
186 public boolean isValid() {return valid; }
187
188 @Override 186 @Override
189 public void addTo(DataStore store) throws JRDFStoreException { 187 public void addTo(DataStore store) throws JRDFStoreException {
190 Utility.logError("Unsupported Operation..."); 188 Utility.logError("Unsupported Operation...");
diff --git a/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID2.java b/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID2.java
new file mode 100644
index 0000000..19efc58
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID2.java
@@ -0,0 +1,141 @@
1package uk.ac.ox.cs.pagoda.query;
2
3import uk.ac.ox.cs.JRDFox.JRDFStoreException;
4import uk.ac.ox.cs.JRDFox.store.TupleIterator;
5import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
6import uk.ac.ox.cs.pagoda.util.UFS;
7
8import java.util.*;
9
10public class GapByStore4ID2 extends GapByStore4ID {
11
12 private BasicQueryEngine m_baseEngine;
13 private UFS<String> m_equality = null, m_baseEquality = null;
14 private LinkedList<String> toAddedIndividuals = null;
15 private TupleIterator iter_individual = null;
16 private int currentID = -1;
17
18 public GapByStore4ID2(BasicQueryEngine engine, BasicQueryEngine baseEngine) {
19 super(engine);
20 m_baseEngine = baseEngine;
21 }
22
23 @Override
24 public boolean hasNext() {
25 if(getNewGapTuple(iterator, -1)) return true;
26 if(iterator != null) {
27 iterator.dispose();
28 iterator = null;
29 }
30 return getNextGapFactAboutEquality();
31 }
32
33 private boolean getNewGapTuple(TupleIterator it, int firstElement) {
34 if(it == null) return false;
35 int firstIndex = 0;
36 tuple = new int[3];
37 if(firstElement > 0) {
38 tuple[0] = firstElement;
39 firstIndex = 1;
40 }
41 Integer predicate;
42 try {
43 for(; multi != 0; multi = it.getNext()) {
44 for(int i = firstIndex; i < 3; ++i)
45 tuple[i] = it.getResourceID(i - firstIndex);
46
47 if(isRDF_TYPE()) {
48 predicate = getGapPredicateID(tuple[2]);
49 if(predicate == null) continue;
50 tuple[2] = predicate;
51 } else {
52 predicate = getGapPredicateID(tuple[1]);
53 if(predicate == null) continue;
54 tuple[1] = predicate;
55 }
56 return true;
57 }
58 } catch(JRDFStoreException e) {
59 e.printStackTrace();
60 return false;
61 }
62 return false;
63 }
64
65 private boolean getNextGapFactAboutEquality() {
66 if(toAddedIndividuals == null) {
67 m_equality = m_engine.getEqualityGroups(false);
68 m_baseEquality = m_baseEngine.getEqualityGroups(false);
69 toAddedIndividuals = new LinkedList<String>();
70 Map<String, Integer> rep2cnt = new HashMap<String, Integer>();
71 Map<String, Integer> rep2cnt_base = new HashMap<String, Integer>();
72 count(m_engine, m_equality, rep2cnt);
73 count(m_baseEngine, m_baseEquality, rep2cnt_base);
74 Set<String> visitedrep = new HashSet<String>();
75 for(String individual : m_equality.keySet()) {
76 String rep = m_equality.find(individual);
77 if(visitedrep.contains(rep)) continue;
78 visitedrep.add(rep);
79 String rep_base = m_baseEquality.find(individual);
80 if(!rep2cnt.get(rep).equals(rep2cnt_base.get(rep_base))) {
81 toAddedIndividuals.add(rep);
82 }
83 }
84
85 }
86 while(true) {
87 if(getNewGapTuple(iter_individual, currentID)) return true;
88 if(iter_individual != null) {
89 iter_individual.dispose();
90 iter_individual = null;
91 }
92 if(toAddedIndividuals.isEmpty()) {
93 currentID = -1;
94 return false;
95 }
96 String individual = toAddedIndividuals.remove();
97 currentID = tripleManager.getResourceID(individual);
98 try {
99 iter_individual =
100 m_engine.internal_evaluateNotExpanded(String.format("select distinct ?y ?z where { <%s> ?y ?z }", individual));
101 multi = iter_individual.open();
102 } catch(JRDFStoreException e) {
103 e.printStackTrace();
104 }
105 }
106 }
107
108 private void count(BasicQueryEngine engine, UFS<String> equality, Map<String, Integer> map) {
109 for(String ind : equality.keySet()) {
110 Integer exist = map.get(ind);
111 if(exist == null)
112 map.put(equality.find(ind), 1);
113 else
114 map.put(equality.find(ind), ++exist);
115 }
116 }
117
118 @Override
119 public int[] next() {
120 try {
121 if(iterator != null)
122 multi = iterator.getNext();
123 else if(iter_individual != null)
124 multi = iter_individual.getNext();
125 else
126 multi = 0;
127 } catch(JRDFStoreException e) {
128 e.printStackTrace();
129 }
130 return tuple;
131 }
132
133 public void clear() {
134 super.clear();
135 if(iter_individual != null) {
136 iter_individual.dispose();
137 iter_individual = null;
138 }
139 }
140
141}
diff --git a/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java b/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java
index a1c1b0e..eaa629b 100644
--- a/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java
+++ b/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java
@@ -1,36 +1,29 @@
1package uk.ac.ox.cs.pagoda.query; 1package uk.ac.ox.cs.pagoda.query;
2 2
3import java.io.BufferedWriter; 3import org.semanticweb.HermiT.model.*;
4import java.io.FileOutputStream; 4import uk.ac.ox.cs.JRDFox.JRDFStoreException;
5import java.io.IOException; 5import uk.ac.ox.cs.JRDFox.Prefixes;
6import java.io.OutputStreamWriter; 6import uk.ac.ox.cs.JRDFox.store.DataStore;
7import java.util.Collection; 7import uk.ac.ox.cs.JRDFox.store.Parameters;
8 8import uk.ac.ox.cs.JRDFox.store.TupleIterator;
9import org.semanticweb.HermiT.model.Atom;
10import org.semanticweb.HermiT.model.AtomicConcept;
11import org.semanticweb.HermiT.model.AtomicRole;
12import org.semanticweb.HermiT.model.DLClause;
13import org.semanticweb.HermiT.model.Individual;
14
15import uk.ac.ox.cs.pagoda.MyPrefixes; 9import uk.ac.ox.cs.pagoda.MyPrefixes;
16import uk.ac.ox.cs.pagoda.owl.OWLHelper; 10import uk.ac.ox.cs.pagoda.owl.OWLHelper;
17import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine; 11import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
18import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxTripleManager; 12import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxTripleManager;
19import uk.ac.ox.cs.pagoda.util.Namespace; 13import uk.ac.ox.cs.pagoda.util.Namespace;
20import uk.ac.ox.cs.pagoda.util.Utility; 14import uk.ac.ox.cs.pagoda.util.Utility;
21import uk.ac.ox.cs.JRDFox.JRDFStoreException; 15
22import uk.ac.ox.cs.JRDFox.Prefixes; 16import java.io.BufferedWriter;
23import uk.ac.ox.cs.JRDFox.store.DataStore; 17import java.io.FileOutputStream;
24import uk.ac.ox.cs.JRDFox.store.Parameters; 18import java.io.IOException;
25import uk.ac.ox.cs.JRDFox.store.TupleIterator; 19import java.io.OutputStreamWriter;
20import java.util.Collection;
26 21
27public class GapByTriple extends GapTupleIterator<String> { 22public class GapByTriple extends GapTupleIterator<String> {
28 23
29 private static final String RDF_TYPE = Namespace.RDF_NS + "type";
30 private static final String BRIEF_RDF_TYPE = "rdf:type";
31
32 static final String allTripleQuery = "SELECT ?X ?Y ?Z WHERE { ?X ?Y ?Z }"; 24 static final String allTripleQuery = "SELECT ?X ?Y ?Z WHERE { ?X ?Y ?Z }";
33 25 private static final String RDF_TYPE = Namespace.RDF_NS + "type";
26 private static final String BRIEF_RDF_TYPE = "rdf:type";
34 DataStore lowerStore, upperStore; 27 DataStore lowerStore, upperStore;
35 long multi; 28 long multi;
36 TupleIterator iterator; 29 TupleIterator iterator;
@@ -164,11 +157,6 @@ public class GapByTriple extends GapTupleIterator<String> {
164 } 157 }
165 158
166 @Override 159 @Override
167 public boolean isValid() {
168 return true;
169 }
170
171 @Override
172 public void clear() { 160 public void clear() {
173 iterator.dispose(); 161 iterator.dispose();
174 } 162 }
diff --git a/src/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java b/src/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java
index 58303bb..2983b2e 100644
--- a/src/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java
+++ b/src/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java
@@ -1,10 +1,10 @@
1package uk.ac.ox.cs.pagoda.query; 1package uk.ac.ox.cs.pagoda.query;
2 2
3import java.util.Iterator;
4
5import uk.ac.ox.cs.JRDFox.JRDFStoreException; 3import uk.ac.ox.cs.JRDFox.JRDFStoreException;
6import uk.ac.ox.cs.JRDFox.store.DataStore; 4import uk.ac.ox.cs.JRDFox.store.DataStore;
7 5
6import java.util.Iterator;
7
8public abstract class GapTupleIterator<T> implements Iterator<T> { 8public abstract class GapTupleIterator<T> implements Iterator<T> {
9 9
10 public static final String gapPredicateSuffix = "_AUXg"; 10 public static final String gapPredicateSuffix = "_AUXg";
@@ -17,8 +17,6 @@ public abstract class GapTupleIterator<T> implements Iterator<T> {
17 17
18 public void compile(String programText) throws JRDFStoreException {} 18 public void compile(String programText) throws JRDFStoreException {}
19 19
20 public abstract boolean isValid();
21
22 public abstract void save(String file); 20 public abstract void save(String file);
23 21
24 public abstract void addBackTo() throws JRDFStoreException; 22 public abstract void addBackTo() throws JRDFStoreException;
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index b5b9534..618fb70 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -7,6 +7,7 @@ import uk.ac.ox.cs.pagoda.owl.EqualitiesEliminator;
7import uk.ac.ox.cs.pagoda.owl.OWLHelper; 7import uk.ac.ox.cs.pagoda.owl.OWLHelper;
8import uk.ac.ox.cs.pagoda.query.AnswerTuples; 8import uk.ac.ox.cs.pagoda.query.AnswerTuples;
9import uk.ac.ox.cs.pagoda.query.GapByStore4ID; 9import uk.ac.ox.cs.pagoda.query.GapByStore4ID;
10import uk.ac.ox.cs.pagoda.query.GapByStore4ID2;
10import uk.ac.ox.cs.pagoda.query.QueryRecord; 11import uk.ac.ox.cs.pagoda.query.QueryRecord;
11import uk.ac.ox.cs.pagoda.query.QueryRecord.Step; 12import uk.ac.ox.cs.pagoda.query.QueryRecord.Step;
12import uk.ac.ox.cs.pagoda.reasoner.full.Checker; 13import uk.ac.ox.cs.pagoda.reasoner.full.Checker;
@@ -164,7 +165,9 @@ class MyQueryReasoner extends QueryReasoner {
164 trackingStore.importRDFData(name, datafile); 165 trackingStore.importRDFData(name, datafile);
165 trackingStore.materialise("saturate named individuals", originalMarkProgram); 166 trackingStore.materialise("saturate named individuals", originalMarkProgram);
166 167
167 GapByStore4ID gap = new GapByStore4ID(trackingStore); 168// materialiseFullUpper();
169// GapByStore4ID gap = new GapByStore4ID(trackingStore);
170 GapByStore4ID gap = new GapByStore4ID2(trackingStore, rlLowerStore);
168 trackingStore.materialiseFoldedly(program, gap); 171 trackingStore.materialiseFoldedly(program, gap);
169 predicatesWithGap = gap.getPredicatesWithGap(); 172 predicatesWithGap = gap.getPredicatesWithGap();
170 gap.clear(); 173 gap.clear();
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 5d2e411..9aa6235 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
@@ -19,16 +19,18 @@ import java.util.*;
19 19
20public class BasicQueryEngine extends RDFoxQueryEngine { 20public class BasicQueryEngine extends RDFoxQueryEngine {
21 21
22 protected DataStore store; 22 protected DataStore store;
23 protected Parameters parameters = new Parameters(); 23 protected Parameters parameters = new Parameters();
24 Set<DLClause> materialisedRules = new HashSet<DLClause>();
25 private UFS<String> equalityGroups = null;
24 26
25 public BasicQueryEngine(String name) { 27 public BasicQueryEngine(String name) {
26 super(name); 28 super(name);
27 store = RDFoxQueryEngine.createDataStore(); 29 store = RDFoxQueryEngine.createDataStore();
28 parameters.m_allAnswersInRoot = true; 30 parameters.m_allAnswersInRoot = true;
29 parameters.m_useBushy = true; 31 parameters.m_useBushy = true;
30 } 32 }
31 33
32 public void materialiseFoldedly(DatalogProgram dProgram, GapByStore4ID gap) { 34 public void materialiseFoldedly(DatalogProgram dProgram, GapByStore4ID gap) {
33 if (gap != null) { 35 if (gap != null) {
34 materialise("lower program", dProgram.getLower().toString()); 36 materialise("lower program", dProgram.getLower().toString());
@@ -40,10 +42,9 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
40 } catch (JRDFStoreException e) { 42 } catch (JRDFStoreException e) {
41 e.printStackTrace(); 43 e.printStackTrace();
42 } finally { 44 } finally {
43 gap.clear(); 45 gap.clear();
44 } 46 }
45 } 47 } else
46 else
47 materialise("upper program", dProgram.getUpper().toString()); 48 materialise("upper program", dProgram.getUpper().toString());
48 } 49 }
49 50
@@ -58,24 +59,23 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
58 } catch (JRDFStoreException e) { 59 } catch (JRDFStoreException e) {
59 e.printStackTrace(); 60 e.printStackTrace();
60 } finally { 61 } finally {
61 gap.clear(); 62 gap.clear();
62 } 63 }
63 } 64 } else
64 else
65 materialise("upper program", dProgram.getUpper().toString()); 65 materialise("upper program", dProgram.getUpper().toString());
66
67 return 1;
68 }
69 66
67 return 1;
68 }
69
70 public int materialiseSkolemly(DatalogProgram dProgram, GapByStore4ID gap) { 70 public int materialiseSkolemly(DatalogProgram dProgram, GapByStore4ID gap) {
71 throw new UnsupportedOperationException(); 71 throw new UnsupportedOperationException();
72 } 72 }
73 73
74 @Override 74 @Override
75 public AnswerTuples evaluate(String queryText) { 75 public AnswerTuples evaluate(String queryText) {
76 return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0]); 76 return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0]);
77 } 77 }
78 78
79 @Override 79 @Override
80 public AnswerTuples evaluate(String queryText, String[] answerVars) { 80 public AnswerTuples evaluate(String queryText, String[] answerVars) {
81 TupleIterator tupleIterator; 81 TupleIterator tupleIterator;
@@ -83,9 +83,9 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
83 tupleIterator = store.compileQuery(queryText.replace("_:", "?"), prefixes, parameters); 83 tupleIterator = store.compileQuery(queryText.replace("_:", "?"), prefixes, parameters);
84 } catch (JRDFStoreException e) { 84 } catch (JRDFStoreException e) {
85 e.printStackTrace(); 85 e.printStackTrace();
86 return null; 86 return null;
87 } 87 }
88 return new RDFoxAnswerTuples(answerVars, tupleIterator); 88 return new RDFoxAnswerTuples(answerVars, tupleIterator);
89 } 89 }
90 90
91 @Override 91 @Override
@@ -95,17 +95,18 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
95 95
96 @Override 96 @Override
97 public void dispose() { 97 public void dispose() {
98 store.dispose(); 98 store.dispose();
99 } 99 }
100 100
101 protected void outputClassAssertions(String filename) { 101 protected void outputClassAssertions(String filename) {
102 TupleIterator allTuples = null; 102 TupleIterator allTuples = null;
103 boolean redirect = false; 103 boolean redirect = false;
104 try { 104 try {
105 allTuples = getDataStore().compileQuery("SELECT ?X ?Z WHERE { ?X <" + Namespace.RDF_TYPE + "> ?Z }", prefixes, parameters); 105 allTuples = getDataStore().compileQuery("SELECT ?X ?Z WHERE { ?X <" + Namespace.RDF_TYPE + "> ?Z }", prefixes, parameters);
106 redirect = Utility.redirectCurrentOut(filename); 106 redirect = Utility.redirectCurrentOut(filename);
107 for (long multi = allTuples.open(); multi != 0; multi = allTuples.getNext()) 107 for(long multi = allTuples.open(); multi != 0; multi = allTuples.getNext())
108 System.out.println(RDFoxTripleManager.getQuotedTerm(allTuples.getResource(0)) + " " + RDFoxTripleManager.getQuotedTerm(allTuples.getResource(1))); 108 System.out.println(RDFoxTripleManager.getQuotedTerm(allTuples.getResource(0)) + " " + RDFoxTripleManager
109 .getQuotedTerm(allTuples.getResource(1)));
109 } catch (JRDFStoreException e) { 110 } catch (JRDFStoreException e) {
110 e.printStackTrace(); 111 e.printStackTrace();
111 } finally { 112 } finally {
@@ -123,137 +124,134 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
123 public void outputInstance4BinaryPredicate(String iri) { 124 public void outputInstance4BinaryPredicate(String iri) {
124 outputAnswers("select ?x ?y where { ?x <" + iri + "> ?y . }"); 125 outputAnswers("select ?x ?y where { ?x <" + iri + "> ?y . }");
125 } 126 }
126 127
127 public void outputInstanceNumbers(String filename) { 128 public void outputInstanceNumbers(String filename) {
128 TupleIterator predicateTuples = null; 129 TupleIterator predicateTuples = null;
129 TupleIterator instanceTuples; 130 TupleIterator instanceTuples;
130 Set<String> number = new HashSet<String>(); 131 Set<String> number = new HashSet<String>();
131 String predicate; 132 String predicate;
132 try { 133 try {
133 predicateTuples = getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X <" + Namespace.RDF_TYPE + "> ?Y }", prefixes, parameters); 134 predicateTuples = getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X <" + Namespace.RDF_TYPE + "> ?Y }", prefixes, parameters);
134 for (long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) { 135 for (long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) {
135 predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0)); 136 predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0));
136 instanceTuples = null; 137 instanceTuples = null;
137 try { 138 try {
138 instanceTuples = getDataStore().compileQuery("SELECT ?X WHERE { ?X <" + Namespace.RDF_TYPE + "> " + predicate + " }", prefixes, parameters); 139 instanceTuples = getDataStore().compileQuery("SELECT ?X WHERE { ?X <" + Namespace.RDF_TYPE + "> " + predicate + " }", prefixes, parameters);
139 long totalCount = 0; 140 long totalCount = 0;
140 for (long multi1 = instanceTuples.open(); multi1 != 0; multi1 = instanceTuples.getNext()) { 141 for (long multi1 = instanceTuples.open(); multi1 != 0; multi1 = instanceTuples.getNext()) {
141 totalCount += instanceTuples.getMultiplicity(); 142 totalCount += instanceTuples.getMultiplicity();
142 } 143 }
143 number.add(predicate + " * " + totalCount); 144 number.add(predicate + " * " + totalCount);
144 } finally { 145 } finally {
145 if (instanceTuples != null) instanceTuples.dispose(); 146 if(instanceTuples != null) instanceTuples.dispose();
146 } 147 }
147 } 148 }
148 } catch (JRDFStoreException e) { 149 } catch (JRDFStoreException e) {
149 e.printStackTrace(); 150 e.printStackTrace();
150 } finally { 151 } finally {
151 if (predicateTuples != null) predicateTuples.dispose(); 152 if (predicateTuples != null) predicateTuples.dispose();
152 predicateTuples = null; 153 predicateTuples = null;
153 } 154 }
154 155
155 try { 156 try {
156 predicateTuples = getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X ?Y ?Z }", prefixes, parameters); 157 predicateTuples = getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X ?Y ?Z }", prefixes, parameters);
157 for (long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) { 158 for (long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) {
158 predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0)); 159 predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0));
159 instanceTuples = null; 160 instanceTuples = null;
160 try { 161 try {
161 instanceTuples = getDataStore().compileQuery("SELECT ?X ?Z WHERE { ?X " + predicate + " ?Z }", prefixes, parameters); 162 instanceTuples = getDataStore().compileQuery("SELECT ?X ?Z WHERE { ?X " + predicate + " ?Z }", prefixes, parameters);
162 long totalCount = 0; 163 long totalCount = 0;
163 for (long multi1 = instanceTuples.open(); multi1 != 0; multi1 = instanceTuples.getNext()) 164 for (long multi1 = instanceTuples.open(); multi1 != 0; multi1 = instanceTuples.getNext())
164 totalCount += instanceTuples.getMultiplicity(); 165 totalCount += instanceTuples.getMultiplicity();
165 number.add(predicate + " * " + totalCount); 166 number.add(predicate + " * " + totalCount);
166 } finally { 167 } finally {
167 if (instanceTuples != null) instanceTuples.dispose(); 168 if(instanceTuples != null) instanceTuples.dispose();
168 } 169 }
169 } 170 }
170 171
171 } catch (JRDFStoreException e) { 172 } catch (JRDFStoreException e) {
172 e.printStackTrace(); 173 e.printStackTrace();
173 } finally { 174 } finally {
174 if (predicateTuples != null) predicateTuples.dispose(); 175 if (predicateTuples != null) predicateTuples.dispose();
175 predicateTuples = null; 176 predicateTuples = null;
176 } 177 }
177 178
178 Utility.redirectCurrentOut(filename); 179 Utility.redirectCurrentOut(filename);
179 String[] ordered = number.toArray(new String[0]); 180 String[] ordered = number.toArray(new String[0]);
180 Arrays.sort(ordered, new DLPredicateComparator()); 181 Arrays.sort(ordered, new DLPredicateComparator());
181 for (String line: ordered) System.out.println(line); 182 for(String line : ordered) System.out.println(line);
182 Utility.closeCurrentOut(); 183 Utility.closeCurrentOut();
183 184
184 } 185 }
185 186
186 public TupleIterator internal_evaluateAgainstIDBs(String queryText) throws JRDFStoreException { 187 public TupleIterator internal_evaluateAgainstIDBs(String queryText) throws JRDFStoreException {
187 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters, TripleStatus.TUPLE_STATUS_IDB.union(TripleStatus.TUPLE_STATUS_EDB), TripleStatus.TUPLE_STATUS_IDB); 188 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters, TripleStatus.TUPLE_STATUS_IDB.union(TripleStatus.TUPLE_STATUS_EDB), TripleStatus.TUPLE_STATUS_IDB);
188// iter.open(); 189// iter.open();
189 return iter; 190 return iter;
190 } 191 }
191 192
192 public TupleIterator internal_evaluate(String queryText) throws JRDFStoreException { 193 public TupleIterator internal_evaluate(String queryText) throws JRDFStoreException {
193 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters); 194 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters);
194// iter.open(); 195// iter.open();
195 return iter; 196 return iter;
196 } 197 }
197 198
198 public void setExpandEquality(boolean flag) { 199 public void setExpandEquality(boolean flag) {
199 parameters.m_expandEquality = flag; 200 parameters.m_expandEquality = flag;
200 } 201 }
201 202
202 public TupleIterator internal_evaluateNotExpanded(String queryText) throws JRDFStoreException { 203 public TupleIterator internal_evaluateNotExpanded(String queryText) throws JRDFStoreException {
203 parameters.m_expandEquality = false; 204 parameters.m_expandEquality = false;
204 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters); 205 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters);
205// iter.open(); 206// iter.open();
206 parameters.m_expandEquality = true; 207 parameters.m_expandEquality = true;
207 return iter; 208 return iter;
208 } 209 }
209
210 210
211 public TupleIterator internal_evaluate(String queryText, boolean incrementally) throws JRDFStoreException { 211 public TupleIterator internal_evaluate(String queryText, boolean incrementally) throws JRDFStoreException {
212 return incrementally ? internal_evaluateAgainstIDBs(queryText) : internal_evaluate(queryText); 212 return incrementally ? internal_evaluateAgainstIDBs(queryText) : internal_evaluate(queryText);
213 } 213 }
214 214
215 Set<DLClause> materialisedRules = new HashSet<DLClause>();
216
217 public String getUnusedRules(Collection<DLClause> clauses, boolean toUpdate) { 215 public String getUnusedRules(Collection<DLClause> clauses, boolean toUpdate) {
218 DLClause clause; 216 DLClause clause;
219 for (Iterator<DLClause> iter = clauses.iterator(); iter.hasNext(); ) { 217 for (Iterator<DLClause> iter = clauses.iterator(); iter.hasNext(); ) {
220 if (materialisedRules.contains(clause = iter.next())) 218 if (materialisedRules.contains(clause = iter.next()))
221 iter.remove(); 219 iter.remove();
222 else if (toUpdate) materialisedRules.add(clause); 220 else if(toUpdate) materialisedRules.add(clause);
223 } 221 }
224 222
225 if (clauses.isEmpty()) return null; 223 if (clauses.isEmpty()) return null;
226 224
227 return Program.toString(clauses); 225 return Program.toString(clauses);
228 } 226 }
229 227
230 public void outputMaterialisedRules() { 228 public void outputMaterialisedRules() {
231 System.out.println(DLClauseHelper.toString(materialisedRules)); 229 System.out.println(DLClauseHelper.toString(materialisedRules));
232 } 230 }
233 231
234 public void outputAnswers(String query) { 232 public void outputAnswers(String query) {
235 TupleIterator iter = null; 233 TupleIterator iter = null;
236 try { 234 try {
237 iter = internal_evaluate(query); 235 iter = internal_evaluate(query);
238 System.out.println(query); 236 System.out.println(query);
239 int arity = iter.getArity(); 237 int arity = iter.getArity();
240 for (long multi = iter.open(); multi != 0; multi = iter.getNext()) { 238 for (long multi = iter.open(); multi != 0; multi = iter.getNext()) {
241 for (int i = 0; i < arity; ++i) 239 for (int i = 0; i < arity; ++i)
242 System.out.print(RDFoxTripleManager.getQuotedTerm(iter.getResource(i)) + "\t"); 240 System.out.print(RDFoxTripleManager.getQuotedTerm(iter.getResource(i)) + "\t");
243 System.out.println(); 241 System.out.println();
244 } 242 }
245 } catch (JRDFStoreException e) { 243 } catch (JRDFStoreException e) {
246 e.printStackTrace(); 244 e.printStackTrace();
247 } finally { 245 } finally {
248 if (iter != null) iter.dispose(); 246 if(iter != null) iter.dispose();
249 } 247 }
250 } 248 }
251 249
252 public void outputInstance4UnaryPredicate(String iri) { 250 public void outputInstance4UnaryPredicate(String iri) {
253 outputAnswers("select ?x where { ?x " 251 outputAnswers("select ?x where { ?x "
254 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <" 252 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <"
255 + iri 253 + iri
256 + "> .}"); 254 + "> .}");
257 } 255 }
258 256
259 public void outputSubjects(String p, String o) { 257 public void outputSubjects(String p, String o) {
@@ -265,13 +263,13 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
265 } 263 }
266 264
267 public void outputIDBFacts() { 265 public void outputIDBFacts() {
268 TupleIterator iter = null; 266 TupleIterator iter = null;
269 try { 267 try {
270 iter = internal_evaluateAgainstIDBs("select distict ?x ?y ?z where { ?x ?y ?z }"); 268 iter = internal_evaluateAgainstIDBs("select distict ?x ?y ?z where { ?x ?y ?z }");
271 for (long multi = iter.open(); multi != 0; multi = iter.getNext()) { 269 for (long multi = iter.open(); multi != 0; multi = iter.getNext()) {
272 for (int i = 0; i < 3; ++i) 270 for (int i = 0; i < 3; ++i)
273 System.out.print(RDFoxTripleManager.getQuotedTerm(iter.getResource(i)) + "\t"); 271 System.out.print(RDFoxTripleManager.getQuotedTerm(iter.getResource(i)) + "\t");
274 System.out.println(); 272 System.out.println();
275 } 273 }
276 } catch (JRDFStoreException e) { 274 } catch (JRDFStoreException e) {
277 // TODO Auto-generated catch block 275 // TODO Auto-generated catch block
@@ -279,7 +277,7 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
279 } finally { 277 } finally {
280 if (iter != null) iter.dispose(); 278 if (iter != null) iter.dispose();
281 } 279 }
282 280
283 } 281 }
284 282
285 public void outputType4Individual(String iri) { 283 public void outputType4Individual(String iri) {
@@ -287,25 +285,23 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
287 } 285 }
288 286
289 public int getSameAsNumber() { 287 public int getSameAsNumber() {
290 TupleIterator iter = null; 288 TupleIterator iter = null;
291 int counter = 0; 289 int counter = 0;
292 try { 290 try {
293 iter = internal_evaluate("select ?x ?y where {?x " + Namespace.EQUALITY_QUOTED + " ?y . }"); 291 iter = internal_evaluate("select ?x ?y where {?x " + Namespace.EQUALITY_QUOTED + " ?y . }");
294 for (long multi = iter.open(); multi != 0; multi = iter.getNext()) 292 for(long multi = iter.open(); multi != 0; multi = iter.getNext())
295 if (iter.getResourceID(0) != iter.getResourceID(1)) 293 if (iter.getResourceID(0) != iter.getResourceID(1))
296 ++counter; 294 ++counter;
297 } catch (JRDFStoreException e) { 295 } catch (JRDFStoreException e) {
298 e.printStackTrace(); 296 e.printStackTrace();
299 } finally { 297 } finally {
300 if (iter != null) iter.dispose(); 298 if (iter != null) iter.dispose();
301 } 299 }
302 return counter; 300 return counter;
303 } 301 }
304 302
305 private UFS<String> equalityGroups = null; 303 public UFS<String> getEqualityGroups(boolean reuse) {
306 304 if(reuse && equalityGroups != null) return equalityGroups;
307 public UFS<String> getEqualityGroups() {
308 if (equalityGroups != null) return equalityGroups;
309 305
310 equalityGroups = new UFS<String>(); 306 equalityGroups = new UFS<String>();
311 307
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java b/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java
index ee55be7..d2d041f 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java
+++ b/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java
@@ -42,7 +42,7 @@ public class QueryTracker {
42 m_record = queryRecord; 42 m_record = queryRecord;
43 43
44 m_manager = m_encoder.getOntology().getOWLOntologyManager(); 44 m_manager = m_encoder.getOntology().getOWLOntologyManager();
45 equalityGroups = m_dataStore.getEqualityGroups(); 45 equalityGroups = m_dataStore.getEqualityGroups(true);
46 46
47 } 47 }
48 48
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
index 67d07a8..c3694ad 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
+++ b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
@@ -1,25 +1,21 @@
1package uk.ac.ox.cs.pagoda.tracking; 1package uk.ac.ox.cs.pagoda.tracking;
2 2
3import java.util.Collection; 3import org.semanticweb.HermiT.model.*;
4import java.util.LinkedList; 4import org.semanticweb.owlapi.model.IRI;
5
6import org.semanticweb.HermiT.model.AnnotatedEquality;
7import org.semanticweb.HermiT.model.Atom;
8import org.semanticweb.HermiT.model.AtomicConcept;
9import org.semanticweb.HermiT.model.AtomicRole;
10import org.semanticweb.HermiT.model.DLClause;
11import org.semanticweb.HermiT.model.Equality;
12import org.semanticweb.HermiT.model.Variable;
13import org.semanticweb.owlapi.model.OWLClass; 5import org.semanticweb.owlapi.model.OWLClass;
14import org.semanticweb.owlapi.model.OWLObjectProperty; 6import org.semanticweb.owlapi.model.OWLObjectProperty;
15import org.semanticweb.owlapi.model.OWLOntology; 7import org.semanticweb.owlapi.model.OWLOntology;
16
17import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper; 8import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
18import uk.ac.ox.cs.pagoda.query.*; 9import uk.ac.ox.cs.pagoda.query.GapTupleIterator;
19import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine; 10import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
20import uk.ac.ox.cs.pagoda.rules.UpperDatalogProgram; 11import uk.ac.ox.cs.pagoda.rules.UpperDatalogProgram;
21import uk.ac.ox.cs.pagoda.util.Namespace; 12import uk.ac.ox.cs.pagoda.util.Namespace;
22 13
14import java.util.Collection;
15import java.util.HashSet;
16import java.util.LinkedList;
17import java.util.Set;
18
23public class TrackingRuleEncoderWithGap extends TrackingRuleEncoder { 19public class TrackingRuleEncoderWithGap extends TrackingRuleEncoder {
24 20
25 public TrackingRuleEncoderWithGap(UpperDatalogProgram program, BasicQueryEngine store) { 21 public TrackingRuleEncoderWithGap(UpperDatalogProgram program, BasicQueryEngine store) {
@@ -34,8 +30,9 @@ public class TrackingRuleEncoderWithGap extends TrackingRuleEncoder {
34 Variable X = Variable.create("X"); 30 Variable X = Variable.create("X");
35 AtomicRole trackingSameAs = AtomicRole.create(Namespace.EQUALITY + "_tn"); 31 AtomicRole trackingSameAs = AtomicRole.create(Namespace.EQUALITY + "_tn");
36 OWLOntology onto = program.getOntology(); 32 OWLOntology onto = program.getOntology();
37 Atom[] headAtom = new Atom[] {Atom.create(trackingSameAs, X, X)}, bodyAtom; 33 Atom[] headAtom = new Atom[]{Atom.create(trackingSameAs, X, X)}, bodyAtom;
38 for (OWLClass cls: onto.getClassesInSignature(true)) { 34 for(OWLOntology o : onto.getImportsClosure())
35 for(OWLClass cls : o.getClassesInSignature()) {
39 String clsIRI = cls.getIRI().toString(); 36 String clsIRI = cls.getIRI().toString();
40 unaryPredicates.add(clsIRI); 37 unaryPredicates.add(clsIRI);
41 bodyAtom = new Atom[] { 38 bodyAtom = new Atom[] {
@@ -43,9 +40,16 @@ public class TrackingRuleEncoderWithGap extends TrackingRuleEncoder {
43 Atom.create(AtomicConcept.create(GapTupleIterator.getGapPredicate(clsIRI)), X)}; 40 Atom.create(AtomicConcept.create(GapTupleIterator.getGapPredicate(clsIRI)), X)};
44 equalityRelatedClauses.add(DLClause.create(headAtom, bodyAtom)); 41 equalityRelatedClauses.add(DLClause.create(headAtom, bodyAtom));
45 } 42 }
46 43
47 Variable Y = Variable.create("Y"); 44 Variable Y = Variable.create("Y");
48 for (OWLObjectProperty prop: onto.getObjectPropertiesInSignature(true)) { 45 Set<OWLObjectProperty> setOfProperties = new HashSet<OWLObjectProperty>();
46 for(OWLOntology o : onto.getImportsClosure())
47 for(OWLObjectProperty prop : o.getObjectPropertiesInSignature())
48 setOfProperties.add(prop);
49 setOfProperties.add(onto.getOWLOntologyManager()
50 .getOWLDataFactory()
51 .getOWLObjectProperty(IRI.create(Namespace.INEQUALITY)));
52 for(OWLObjectProperty prop : setOfProperties) {
49 String propIRI = prop.getIRI().toString(); 53 String propIRI = prop.getIRI().toString();
50 binaryPredicates.add(propIRI); 54 binaryPredicates.add(propIRI);
51 AtomicRole trackingRole = AtomicRole.create(propIRI + "_tn"); 55 AtomicRole trackingRole = AtomicRole.create(propIRI + "_tn");
diff --git a/src/uk/ac/ox/cs/pagoda/util/Utility.java b/src/uk/ac/ox/cs/pagoda/util/Utility.java
index 7b23e0d..e98cc81 100644
--- a/src/uk/ac/ox/cs/pagoda/util/Utility.java
+++ b/src/uk/ac/ox/cs/pagoda/util/Utility.java
@@ -12,25 +12,30 @@ import java.util.*;
12 12
13public class Utility { 13public class Utility {
14 14
15 private static Logger LOGS;
16 static {
17 LOGS = Logger.getLogger("PAGOdA");
18 LOGS.setLevel(Level.INFO);
19 }
20
21 public static final String JAVA_FILE_SEPARATOR = "/"; 15 public static final String JAVA_FILE_SEPARATOR = "/";
22 public static final String FILE_SEPARATOR = System.getProperty("file.separator"); 16 public static final String FILE_SEPARATOR = System.getProperty("file.separator");
23 public static final String LINE_SEPARATOR = System.getProperty("line.separator"); 17 public static final String LINE_SEPARATOR = System.getProperty("line.separator");
24 18 public static final int TEST = -1;
25 private static final String TEMP_DIR_PATH= "pagoda_tmp";
26 private static String tempDir;
27
28 public static final int TEST = -1;
29 public static final int FLY = 0; 19 public static final int FLY = 0;
30 public static final int UOBM = 1; 20 public static final int UOBM = 1;
31 public static final int LUBM = 2; 21 public static final int LUBM = 2;
32 public static final int AEO = 3; 22 public static final int AEO = 3;
33 public static final int WINE = 4; 23 public static final int WINE = 4;
24 private static final String TEMP_DIR_PATH = "pagoda_tmp";
25 static Stack<PrintStream> outs = new Stack<PrintStream>();
26 private static Logger LOGS;
27 private static String tempDir;
28 private static int asciiX = (int) 'X';
29 private static StringBuilder logMessage = new StringBuilder();
30
31 static {
32 LOGS = Logger.getLogger("PAGOdA");
33 LOGS.setLevel(Level.DEBUG);
34 }
35
36 static {
37 outs.push(System.out);
38 }
34 39
35 public static String getGlobalTempDirAbsolutePath() { 40 public static String getGlobalTempDirAbsolutePath() {
36 if(tempDir == null) { 41 if(tempDir == null) {
@@ -38,7 +43,7 @@ public class Utility {
38 Path path = Files.createTempDirectory(TEMP_DIR_PATH); 43 Path path = Files.createTempDirectory(TEMP_DIR_PATH);
39 tempDir = path.toString(); 44 tempDir = path.toString();
40 new File(tempDir).deleteOnExit(); 45 new File(tempDir).deleteOnExit();
41 } catch (IOException e) { 46 } catch(IOException e) {
42 e.printStackTrace(); 47 e.printStackTrace();
43 System.exit(1); 48 System.exit(1);
44 } 49 }
@@ -46,46 +51,39 @@ public class Utility {
46 return tempDir; 51 return tempDir;
47 } 52 }
48 53
49 public static Set<Atom> toSet(Atom[] data) 54 public static Set<Atom> toSet(Atom[] data) {
50 {
51 HashSet<Atom> ret = new HashSet<Atom>(); 55 HashSet<Atom> ret = new HashSet<Atom>();
52 for (Atom element: data) 56 for(Atom element : data)
53 ret.add(element); 57 ret.add(element);
54 return ret; 58 return ret;
55 } 59 }
56 60
57 static Stack<PrintStream> outs = new Stack<PrintStream>();
58
59 static {
60 outs.push(System.out);
61 }
62
63 public static boolean redirectSystemOut() 61 public static boolean redirectSystemOut()
64 { 62 {
65 String stamp = new SimpleDateFormat( "HH:mm:ss").format(new Date()); 63 String stamp = new SimpleDateFormat( "HH:mm:ss").format(new Date());
66 return redirectCurrentOut("./console" + stamp + ".txt"); 64 return redirectCurrentOut("./console" + stamp + ".txt");
67 } 65 }
68 66
69 public static boolean redirectCurrentOut(String fileName) 67 public static boolean redirectCurrentOut(String fileName)
70 { 68 {
71 File file = new File(fileName); 69 File file = new File(fileName);
72 PrintStream out; 70 PrintStream out;
73 try { 71 try {
74 out = new PrintStream(new FileOutputStream(file)); 72 out = new PrintStream(new FileOutputStream(file));
75 } catch (FileNotFoundException e) { 73 } catch (FileNotFoundException e) {
76 e.printStackTrace(); 74 e.printStackTrace();
77 return false; 75 return false;
78 } 76 }
79 outs.push(out); 77 outs.push(out);
80 System.setOut(out); 78 System.setOut(out);
81 return true; 79 return true;
82 } 80 }
83 81
84 public static void closeCurrentOut() { 82 public static void closeCurrentOut() {
85 if (!outs.isEmpty()) 83 if (!outs.isEmpty())
86 outs.pop().close(); 84 outs.pop().close();
87 85
88 if (!outs.isEmpty()) 86 if(!outs.isEmpty())
89 System.setOut(outs.peek()); 87 System.setOut(outs.peek());
90 } 88 }
91 89
@@ -103,7 +101,7 @@ public class Utility {
103 while ((line = reader.readLine()) != null && !line.startsWith("}")) 101 while ((line = reader.readLine()) != null && !line.startsWith("}"))
104 if (first) { 102 if (first) {
105 first = false; 103 first = false;
106 query = expression(line.trim()); 104 query = expression(line.trim());
107 } 105 }
108 else query += ", " + expression(line.trim()); 106 else query += ", " + expression(line.trim());
109 writer.write(query); 107 writer.write(query);
@@ -122,8 +120,6 @@ public class Utility {
122 else return parts[1] + "(?" + variableIndex(parts[0]) + ",?" + variableIndex(parts[2]) + ")"; 120 else return parts[1] + "(?" + variableIndex(parts[0]) + ",?" + variableIndex(parts[2]) + ")";
123 } 121 }
124 122
125 private static int asciiX = (int)'X';
126
127 private static int variableIndex(String exp) { 123 private static int variableIndex(String exp) {
128 char var = exp.charAt(1); 124 char var = exp.charAt(1);
129 return (int)var - asciiX; 125 return (int)var - asciiX;
@@ -135,12 +131,12 @@ public class Utility {
135 return null; 131 return null;
136 return line.trim(); 132 return line.trim();
137 } 133 }
138 134
139 public static String getTextfromFile(String fileName) throws FileNotFoundException { 135 public static String getTextfromFile(String fileName) throws FileNotFoundException {
140 Scanner scanner = new Scanner(new File(fileName)); 136 Scanner scanner = new Scanner(new File(fileName));
141 String program = scanner.useDelimiter("\\Z").next(); 137 String program = scanner.useDelimiter("\\Z").next();
142 scanner.close(); 138 scanner.close();
143 return program; 139 return program;
144 } 140 }
145 141
146 public static String[] getPattern(BufferedReader answerReader) throws IOException { 142 public static String[] getPattern(BufferedReader answerReader) throws IOException {
@@ -152,59 +148,57 @@ public class Utility {
152 148
153 public static void removeRecursively(File file) { 149 public static void removeRecursively(File file) {
154 if (!file.exists()) return; 150 if (!file.exists()) return;
155 151
156 if (file.isDirectory()) 152 if (file.isDirectory())
157 for (File tFile: file.listFiles()) 153 for (File tFile: file.listFiles())
158 removeRecursively(tFile); 154 removeRecursively(tFile);
159 file.delete(); 155 file.delete();
160 } 156 }
161 157
162 public static void removeRecursively(String fileName) { 158 public static void removeRecursively(String fileName) {
163 removeRecursively(new File(fileName)); 159 removeRecursively(new File(fileName));
164 } 160 }
165 161
166 public static Collection<String> getQueryTexts(String fileName) throws IOException { 162 public static Collection<String> getQueryTexts(String fileName) throws IOException {
167 BufferedReader queryReader = new BufferedReader(new InputStreamReader(new FileInputStream(fileName))); 163 BufferedReader queryReader = new BufferedReader(new InputStreamReader(new FileInputStream(fileName)));
168 String line; 164 String line;
169 Collection<String> queryTexts = new LinkedList<String>(); 165 Collection<String> queryTexts = new LinkedList<String>();
170 while (true) { 166 while (true) {
171 while ((line = queryReader.readLine()) != null && ((line = line.trim()).isEmpty() || line.startsWith("#"))); 167 while((line = queryReader.readLine()) != null && ((line = line.trim()).isEmpty() || line.startsWith("#"))) ;
172 if (line == null) { 168 if (line == null) {
173 queryReader.close(); 169 queryReader.close();
174 return queryTexts; 170 return queryTexts;
175 } 171 }
176 172
177 StringBuffer query = new StringBuffer(); 173 StringBuffer query = new StringBuffer();
178 if (!line.startsWith("^[")) 174 if (!line.startsWith("^["))
179 query.append(line).append(LINE_SEPARATOR); 175 query.append(line).append(LINE_SEPARATOR);
180 176
181 while ((line = queryReader.readLine()) != null && !line.trim().endsWith("}")) 177 while((line = queryReader.readLine()) != null && !line.trim().endsWith("}"))
182 query.append(line).append(LINE_SEPARATOR); 178 query.append(line).append(LINE_SEPARATOR);
183 query.append(line); 179 query.append(line);
184 queryTexts.add(query.toString()); 180 queryTexts.add(query.toString());
185 } 181 }
186 } 182 }
187 183
188 /** 184 /**
189 * 185 *
190 * @param answerReader 186 * @param answerReader
191 * @return all lines before the next empty line 187 * @return all lines before the next empty line
192 * @throws IOException 188 * @throws IOException
193 */ 189 */
194 public static Collection<String> getLines(BufferedReader answerReader) throws IOException { 190 public static Collection<String> getLines(BufferedReader answerReader) throws IOException {
195 Collection<String> answerTuples = new LinkedList<String>(); 191 Collection<String> answerTuples = new LinkedList<String>();
196 String line; 192 String line;
197 while ((line = answerReader.readLine()) != null) { 193 while ((line = answerReader.readLine()) != null) {
198 line = line.trim(); 194 line = line.trim();
199 if (line.isEmpty()) 195 if (line.isEmpty())
200 break; 196 break;
201 answerTuples.add(line); 197 answerTuples.add(line);
202 } 198 }
203 return answerTuples; 199 return answerTuples;
204 } 200 }
205 201
206 private static StringBuilder logMessage = new StringBuilder();
207
208 private static String getLogMessage(Object[] messages) { 202 private static String getLogMessage(Object[] messages) {
209 if (messages.length == 1) return messages[0].toString(); 203 if (messages.length == 1) return messages[0].toString();
210 else { 204 else {
@@ -242,20 +236,6 @@ public class Utility {
242 if (LOGS != null) 236 if (LOGS != null)
243 LOGS.error(getLogMessage(messages)); 237 LOGS.error(getLogMessage(messages));
244 } 238 }
245
246// public static void initialise() {
247// File tmp = new File(TempDirectory);
248// if (!tmp.exists()) tmp.mkdirs();
249// }
250//
251// public static void cleanup() {
252// File tmp = new File(TempDirectory);
253// if (tmp.exists()) {
254// for (File file: tmp.listFiles())
255// file.delete();
256// tmp.delete();
257// }
258// }
259 239
260 public static String toFileIRI(String path) { 240 public static String toFileIRI(String path) {
261 String iri; 241 String iri;
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-05 15:24:14 +0000