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-rw-r--r--test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java48
-rw-r--r--test/uk/ac/ox/cs/hermit/JAIR_HermiT.java87
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/CheckAnswers.java35
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java (renamed from test/uk/ac/ox/cs/pagoda/junit/CostEvaluation.java)48
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java191
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java91
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java18
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java33
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java51
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java37
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java38
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java51
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/AllTests.java48
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java39
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java14
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/JAIR_PAGOdA.java173
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java86
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/LightEvaluation.java59
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/PagodaDBPedia.java27
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/PagodaELU.java18
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/PagodaFLY.java24
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/PagodaLUBM.java38
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/PagodaNPD.java42
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/PagodaNPD_bench.java27
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/PagodaRLU.java18
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/PagodaUOBM.java48
-rw-r--r--test/uk/ac/ox/cs/pagoda/ore/PagodaOWLReasoner.java470
-rw-r--r--test/uk/ac/ox/cs/pagoda/ore/PagodaReasonerFactory.java39
-rw-r--r--test/uk/ac/ox/cs/pagoda/rules/approximators/TestSkolemTermsManager.java14
-rw-r--r--test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java284
-rw-r--r--test/uk/ac/ox/cs/pagoda/tester/Statistics.java1
-rw-r--r--test/uk/ac/ox/cs/pagoda/util/TestUtil.java74
32 files changed, 883 insertions, 1388 deletions
diff --git a/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java b/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
index f6246f8..008fcb2 100644
--- a/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
+++ b/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
@@ -1,43 +1,21 @@
1package uk.ac.ox.cs.hermit; 1package uk.ac.ox.cs.hermit;
2 2
3import java.io.File;
4import java.io.FileNotFoundException;
5import java.io.FileOutputStream;
6import java.io.IOException;
7import java.io.PrintStream;
8import java.util.HashSet;
9import java.util.Set;
10import java.util.concurrent.Callable;
11import java.util.concurrent.ExecutionException;
12import java.util.concurrent.ExecutorService;
13import java.util.concurrent.Executors;
14import java.util.concurrent.Future;
15import java.util.concurrent.TimeUnit;
16import java.util.concurrent.TimeoutException;
17
18import org.semanticweb.HermiT.Reasoner; 3import org.semanticweb.HermiT.Reasoner;
19import org.semanticweb.HermiT.model.Atom; 4import org.semanticweb.HermiT.model.Atom;
20import org.semanticweb.HermiT.model.AtomicRole; 5import org.semanticweb.HermiT.model.AtomicRole;
21import org.semanticweb.owlapi.model.IRI; 6import org.semanticweb.owlapi.model.*;
22import org.semanticweb.owlapi.model.OWLAxiom;
23import org.semanticweb.owlapi.model.OWLClassExpression;
24import org.semanticweb.owlapi.model.OWLDataFactory;
25import org.semanticweb.owlapi.model.OWLDatatype;
26import org.semanticweb.owlapi.model.OWLIndividual;
27import org.semanticweb.owlapi.model.OWLNamedIndividual;
28import org.semanticweb.owlapi.model.OWLObjectProperty;
29import org.semanticweb.owlapi.model.OWLOntology;
30import org.semanticweb.owlapi.model.OWLOntologyCreationException;
31import org.semanticweb.owlapi.model.OWLOntologyManager;
32import org.semanticweb.owlapi.model.OWLOntologyStorageException;
33import org.semanticweb.owlapi.reasoner.Node; 7import org.semanticweb.owlapi.reasoner.Node;
34
35import uk.ac.ox.cs.pagoda.owl.OWLHelper; 8import uk.ac.ox.cs.pagoda.owl.OWLHelper;
36import uk.ac.ox.cs.pagoda.owl.QueryRoller; 9import uk.ac.ox.cs.pagoda.owl.QueryRoller;
37import uk.ac.ox.cs.pagoda.query.QueryManager; 10import uk.ac.ox.cs.pagoda.query.QueryManager;
38import uk.ac.ox.cs.pagoda.query.QueryRecord; 11import uk.ac.ox.cs.pagoda.query.QueryRecord;
39import uk.ac.ox.cs.pagoda.util.Timer; 12import uk.ac.ox.cs.pagoda.util.Timer;
40 13
14import java.io.*;
15import java.util.HashSet;
16import java.util.Set;
17import java.util.concurrent.*;
18
41public class HermitQueryReasoner { 19public class HermitQueryReasoner {
42 20
43 public static void main(String... args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException { 21 public static void main(String... args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException {
@@ -48,11 +26,13 @@ public class HermitQueryReasoner {
48// args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/npd/npd-all-minus-datatype.owl", "/media/krr-nas-share/Yujiao/ontologies/npd/data/npd-data-dump-minus-datatype-new.ttl", "/users/yzhou/ontologies/npd/queries/atomic.sparql"}; 26// args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/npd/npd-all-minus-datatype.owl", "/media/krr-nas-share/Yujiao/ontologies/npd/data/npd-data-dump-minus-datatype-new.ttl", "/users/yzhou/ontologies/npd/queries/atomic.sparql"};
49// args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/npd/npd-all.owl", "/media/krr-nas-share/Yujiao/ontologies/npd/data/npd-data-dump-processed.ttl", "/users/yzhou/ontologies/npd/queries/atomic.sparql"}; 27// args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/npd/npd-all.owl", "/media/krr-nas-share/Yujiao/ontologies/npd/data/npd-data-dump-processed.ttl", "/users/yzhou/ontologies/npd/queries/atomic.sparql"};
50// args = new String[] {PagodaTester.dbpedia_tbox, PagodaTester.dbpedia_abox, PagodaTester.dbpedia_query}; 28// args = new String[] {PagodaTester.dbpedia_tbox, PagodaTester.dbpedia_abox, PagodaTester.dbpedia_query};
51// args = new String[] {"/users/yzhou/ontologies/test/unsatisfiable.owl", null, "/users/yzhou/ontologies/test/unsatisfiable_queries.sparql"}; 29// args = new String[] {"/users/yzhou/ontologies/answersCorrectness/unsatisfiable.owl", null, "/users/yzhou/ontologies/answersCorrectness/unsatisfiable_queries.sparql"};
52 30
53// args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/cco-processed-noDPR-noDPD.ttl", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/graph sampling/sample_100.nt", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/queries/atomic_one_filtered.sparql", "../test-share/results/chembl/hermit_1p"}; 31// args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/cco-processed-noDPR-noDPD.ttl", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/graph sampling/sample_100.nt", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/queries/atomic_one_filtered.sparql", "../answersCorrectness-share/results/chembl/hermit_1p"};
54 args = new String[] {"/users/yzhou/temp/uniprot_debug/core-processed-noDis.owl", "/users/yzhou/temp/uniprot_debug/sample_1_removed.nt", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/queries/atomic_one.sparql", "../test-share/results/uniprot/hermit_1p"}; } 32 args =
55// args = new String[] {"imported.owl", "", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/queries/atomic_one.sparql", "../test-share/results/uniprot/hermit_1p"}; } 33 new String[]{"/users/yzhou/temp/uniprot_debug/core-processed-noDis.owl", "/users/yzhou/temp/uniprot_debug/sample_1_removed.nt", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/queries/atomic_one.sparql", "../answersCorrectness-share/results/uniprot/hermit_1p"};
34 }
35// args = new String[] {"imported.owl", "", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/queries/atomic_one.sparql", "../answersCorrectness-share/results/uniprot/hermit_1p"}; }
56 36
57 37
58 PrintStream ps = args.length < 4 ? null : new PrintStream(new File(args[3])); 38 PrintStream ps = args.length < 4 ? null : new PrintStream(new File(args[3]));
@@ -60,8 +40,8 @@ public class HermitQueryReasoner {
60 if (args[i] == null || args[i].equalsIgnoreCase("null")) args[i] = ""; 40 if (args[i] == null || args[i].equalsIgnoreCase("null")) args[i] = "";
61 System.out.println("Argument " + i + ": " + args[i]); 41 System.out.println("Argument " + i + ": " + args[i]);
62 } 42 }
63 43
64// PrintStream ps = null; // new PrintStream(new File("../test-share/results/reactome/ ")); 44// PrintStream ps = null; // new PrintStream(new File("../answersCorrectness-share/results/reactome/ "));
65 if (ps != null) System.setOut(ps); 45 if (ps != null) System.setOut(ps);
66 46
67 Timer t = new Timer(); 47 Timer t = new Timer();
diff --git a/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java b/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java
index 2fc478d..72e7af8 100644
--- a/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java
+++ b/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java
@@ -1,119 +1,128 @@
1package uk.ac.ox.cs.hermit; 1package uk.ac.ox.cs.hermit;
2 2
3import org.junit.Test; 3import org.junit.Test;
4 4import uk.ac.ox.cs.pagoda.util.TestUtil;
5import uk.ac.ox.cs.pagoda.tester.PagodaTester;
6 5
7public class JAIR_HermiT { 6public class JAIR_HermiT {
8 7
9 @Test 8 @Test
10 public void lubm1() throws Exception { 9 public void lubm1() throws Exception {
10 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
11 String[] args = new String[] { 11 String[] args = new String[] {
12 PagodaTester.onto_dir + "lubm/univ-bench.owl", 12 TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
13 PagodaTester.onto_dir + "lubm/data/lubm1_owl", 13 TestUtil.combinePaths(ontoDir, "lubm/data/lubm1_owl"),
14 PagodaTester.onto_dir + "lubm/queries/test.sparql" 14 TestUtil.combinePaths(ontoDir, "lubm/queries/answersCorrectness.sparql")
15// , "/home/yzhou/java-workspace/test-share/results_new/lubm1/hermit" 15// , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/lubm1/hermit"
16 }; 16 };
17 HermitQueryReasoner.main(args); 17 HermitQueryReasoner.main(args);
18 } 18 }
19 19
20 @Test 20 @Test
21 public void lubm1_rolledUp() throws Exception { 21 public void lubm1_rolledUp() throws Exception {
22 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
22 String[] args = new String[] { 23 String[] args = new String[] {
23 "/home/yzhou/backup/20141212/univ-bench-queries.owl", 24 "/home/yzhou/backup/20141212/univ-bench-queries.owl",
24 PagodaTester.onto_dir + "lubm/data/lubm1_owl", 25 TestUtil.combinePaths(ontoDir, "lubm/data/lubm1_owl"),
25 PagodaTester.onto_dir + "lubm/queries/atomic_lubm.sparql" 26 TestUtil.combinePaths(ontoDir, "lubm/queries/atomic_lubm.sparql")
26// , "/home/yzhou/java-workspace/test-share/results_new/lubm1/hermit_rolledUp" 27// , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/lubm1/hermit_rolledUp"
27 }; 28 };
28 HermitQueryReasoner.main(args); 29 HermitQueryReasoner.main(args);
29 } 30 }
30 31
31 @Test 32 @Test
32 public void uobm1() throws Exception { 33 public void uobm1() throws Exception {
34 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
33 String[] args = new String[] { 35 String[] args = new String[] {
34 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl", 36 TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
35 PagodaTester.onto_dir + "uobm/data/uobm1_owl_withDeclaration", 37 TestUtil.combinePaths(ontoDir, "uobm/data/uobm1_owl_withDeclaration"),
36 PagodaTester.onto_dir + "uobm/queries/standard.sparql" 38 TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql")
37// , "hermit_uobm1.out" 39// , "hermit_uobm1.out"
38// , "/home/yzhou/java-workspace/test-share/results_new/uobm1/hermit" 40// , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uobm1/hermit"
39 }; 41 };
40 HermitQueryReasoner.main(args); 42 HermitQueryReasoner.main(args);
41 } 43 }
42 44
43 @Test 45 @Test
44 public void uobm1_rolledUp() throws Exception { 46 public void uobm1_rolledUp() throws Exception {
47 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
45 String[] args = new String[] { 48 String[] args = new String[] {
46 "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl", 49 "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl",
47 PagodaTester.onto_dir + "uobm/data/uobm1_owl_withDeclaration", 50 TestUtil.combinePaths(ontoDir, "uobm/data/uobm1_owl_withDeclaration"),
48 PagodaTester.onto_dir + "uobm/queries/atomic_uobm.sparql" 51 TestUtil.combinePaths(ontoDir, "uobm/queries/atomic_uobm.sparql")
49 , "hermit_uobm1_rolledUp.out" 52 , "hermit_uobm1_rolledUp.out"
50// , "/home/yzhou/java-workspace/test-share/results_new/uobm1/hermit_rolledUp" 53// , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uobm1/hermit_rolledUp"
51 }; 54 };
52 HermitQueryReasoner.main(args); 55 HermitQueryReasoner.main(args);
53 } 56 }
54 57
55 @Test 58 @Test
56 public void fly_rolledUp() throws Exception { 59 public void fly_rolledUp() throws Exception {
60 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
57 HermitQueryReasoner.main( 61 HermitQueryReasoner.main(
58 PagodaTester.onto_dir + "fly/fly-all-in-one_rolledUp.owl", 62 TestUtil.combinePaths(ontoDir, "fly/fly-all-in-one_rolledUp.owl"),
59// PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", 63// TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
60 null, 64 null,
61 PagodaTester.onto_dir + "fly/queries/fly_atomic.sparql" 65 TestUtil.combinePaths(ontoDir, "fly/queries/fly_atomic.sparql")
62 , "hermit_fly.out" 66 , "hermit_fly.out"
63 ); 67 );
64 } 68 }
65 69
66 @Test 70 @Test
67 public void npd() throws Exception { 71 public void npd() throws Exception {
72 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
68 HermitQueryReasoner.main( 73 HermitQueryReasoner.main(
69 PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl", 74 TestUtil.combinePaths(ontoDir, "npd/npd-all-minus-datatype.owl"),
70 PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl", 75 TestUtil.combinePaths(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl"),
71 PagodaTester.onto_dir + "npd/queries/atomic_ground.sparql" 76 TestUtil.combinePaths(ontoDir, "npd/queries/atomic_ground.sparql")
72 , "hermit_npd.out" 77 , "hermit_npd.out"
73// , "/home/yzhou/java-workspace/test-share/results_new/npd/hermit" 78// , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/npd/hermit"
74 ); 79 );
75 } 80 }
76 81
77 @Test 82 @Test
78 public void dbpedia() throws Exception { 83 public void dbpedia() throws Exception {
84 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
79 HermitQueryReasoner.main( 85 HermitQueryReasoner.main(
80 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl", 86 TestUtil.combinePaths(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"),
81 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl", 87 TestUtil.combinePaths(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"),
82 PagodaTester.onto_dir + "dbpedia/queries/atomic_ground.sparql" 88 TestUtil.combinePaths(ontoDir, "dbpedia/queries/atomic_ground.sparql")
83 , "/home/yzhou/java-workspace/test-share/results_new/dbpedia/hermit" 89 , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/dbpedia/hermit"
84 ); 90 );
85 } 91 }
86 92
87 @Test 93 @Test
88 public void reactome() throws Exception { 94 public void reactome() throws Exception {
95 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
89 HermitQueryReasoner.main( 96 HermitQueryReasoner.main(
90 PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl", 97 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"),
91 PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl", 98 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl"),
92 PagodaTester.onto_dir + "bio2rdf/reactome/queries/atomic_ground.sparql" 99 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/atomic_ground.sparql")
93 , "/home/yzhou/java-workspace/test-share/results_new/reactome/hermit_10p" 100 , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/reactome/hermit_10p"
94 ); 101 );
95 } 102 }
96 103
97 @Test 104 @Test
98 public void chembl() throws Exception { 105 public void chembl() throws Exception {
106 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
99 HermitQueryReasoner.main( 107 HermitQueryReasoner.main(
100 PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl", 108 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"),
101// null, 109// null,
102 PagodaTester.onto_dir + "bio2rdf/chembl/graph sampling/sample_1.nt", 110 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/graph sampling/sample_1.nt"),
103 PagodaTester.onto_dir + "bio2rdf/chembl/queries/atomic_ground.sparql" 111 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql")
104 , "hermit_chembl.out" 112 , "hermit_chembl.out"
105// , "/home/yzhou/java-workspace/test-share/results_new/chembl/hermit_1p" 113// , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/chembl/hermit_1p"
106 ); 114 );
107 } 115 }
108 116
109 @Test 117 @Test
110 public void uniprot() throws Exception { 118 public void uniprot() throws Exception {
119 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
111 HermitQueryReasoner.main( 120 HermitQueryReasoner.main(
112 PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat.owl", 121 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat.owl"),
113 PagodaTester.onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt", 122 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/graph sampling/sample_1.nt"),
114 PagodaTester.onto_dir + "bio2rdf/uniprot/queries/atomic_ground.sparql" 123 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql")
115 , "hermit_uniprot.out" 124 , "hermit_uniprot.out"
116// , "/home/yzhou/java-workspace/test-share/results_new/uniprot/hermit_1p" 125// , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uniprot/hermit_1p"
117 ); 126 );
118 } 127 }
119 128
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/CheckAnswers.java b/test/uk/ac/ox/cs/pagoda/global_tests/CheckAnswers.java
new file mode 100644
index 0000000..14050ce
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/CheckAnswers.java
@@ -0,0 +1,35 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import com.google.gson.Gson;
4import com.google.gson.reflect.TypeToken;
5import org.testng.Assert;
6import uk.ac.ox.cs.pagoda.query.QueryRecord;
7
8import java.io.BufferedReader;
9import java.io.IOException;
10import java.lang.reflect.Type;
11import java.nio.file.Files;
12import java.nio.file.Path;
13import java.util.Set;
14
15/**
16 * It provides auxiliary methods for checking answers.
17 * */
18public class CheckAnswers {
19
20 private CheckAnswers() {
21 }
22
23 public static void assertSameAnswers(Path computedAnswersFile, Path givenAnswersFile) throws IOException {
24 BufferedReader computedReader = Files.newBufferedReader(computedAnswersFile);
25 BufferedReader givenReader = Files.newBufferedReader(givenAnswersFile);
26
27 Gson gson = QueryRecord.GsonCreator.getInstance();
28
29 Type cqType = new TypeToken<Set<QueryRecord>>() {}.getType();
30 Set<QueryRecord> computedAnswers = gson.fromJson(computedReader, cqType);
31 Set<QueryRecord> givenAnswers = gson.fromJson(givenReader, cqType);
32
33 Assert.assertEquals(computedAnswers, givenAnswers);
34 }
35}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/CostEvaluation.java b/test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java
index 87b01ed..01e8203 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/CostEvaluation.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java
@@ -1,12 +1,12 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.global_tests;
2 2
3import org.junit.Test;
4import org.semanticweb.owlapi.model.OWLOntology; 3import org.semanticweb.owlapi.model.OWLOntology;
5 4import org.testng.annotations.Test;
6import uk.ac.ox.cs.pagoda.owl.OWLHelper; 5import uk.ac.ox.cs.pagoda.owl.OWLHelper;
7import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner; 6import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
8import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner.Type; 7import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner.Type;
9import uk.ac.ox.cs.pagoda.tester.PagodaTester; 8import uk.ac.ox.cs.pagoda.tester.PagodaTester;
9import uk.ac.ox.cs.pagoda.util.TestUtil;
10import uk.ac.ox.cs.pagoda.util.Timer; 10import uk.ac.ox.cs.pagoda.util.Timer;
11import uk.ac.ox.cs.pagoda.util.Utility; 11import uk.ac.ox.cs.pagoda.util.Utility;
12 12
@@ -15,20 +15,22 @@ public class CostEvaluation {
15 @Test 15 @Test
16 public void lubm100() { 16 public void lubm100() {
17 int number = 1; 17 int number = 1;
18 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
18 PagodaTester.main( 19 PagodaTester.main(
19 PagodaTester.onto_dir + "lubm/univ-bench.owl", 20 TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
20 PagodaTester.onto_dir + "lubm/data/lubm" + number + ".ttl", 21 TestUtil.combinePaths(ontoDir, "lubm/data/lubm" + number + ".ttl"),
21 PagodaTester.onto_dir + "lubm/queries/test_all_pagoda.sparql" 22 TestUtil.combinePaths(ontoDir, "lubm/queries/test_all_pagoda.sparql")
22 ); 23 );
23// AllTests.copy("output/log4j.log", "results-backup/jair/lubm" + number + ".out"); 24// AllTests.copy("output/log4j.log", "results-backup/jair/lubm" + number + ".out");
24 } 25 }
25 26
26 public void lubm1000() { 27 public void lubm1000() {
27 int number = 1000; 28 int number = 1000;
29 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
28 String[] args = new String[] { 30 String[] args = new String[] {
29 PagodaTester.onto_dir + "lubm/univ-bench.owl", 31 TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
30 PagodaTester.onto_dir + "lubm/data/lubm" + number + ".ttl", 32 TestUtil.combinePaths(ontoDir, "lubm/data/lubm" + number + ".ttl"),
31 PagodaTester.onto_dir + "lubm/queries/test_all_pagoda.sparql" 33 TestUtil.combinePaths(ontoDir, "lubm/queries/test_all_pagoda.sparql")
32 }; 34 };
33 OWLOntology ontology = OWLHelper.loadOntology(args[0]); 35 OWLOntology ontology = OWLHelper.loadOntology(args[0]);
34 QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true); 36 QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true);
@@ -46,10 +48,11 @@ public class CostEvaluation {
46 @Test 48 @Test
47 public void uobm5() { 49 public void uobm5() {
48 int number = 1; 50 int number = 1;
51 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
49 String[] args = new String[] { 52 String[] args = new String[] {
50 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl", 53 TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
51 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl", 54 TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
52 PagodaTester.onto_dir + "uobm/queries/standard_all_pagoda.sparql" 55 TestUtil.combinePaths(ontoDir, "uobm/queries/standard_all_pagoda.sparql")
53 }; 56 };
54 PagodaTester.main(args); 57 PagodaTester.main(args);
55// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out"); 58// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out");
@@ -57,10 +60,11 @@ public class CostEvaluation {
57 60
58 public void uobm100() { 61 public void uobm100() {
59 int number = 200; 62 int number = 200;
63 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
60 String[] args = new String[] { 64 String[] args = new String[] {
61 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl", 65 TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
62 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl", 66 TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
63 PagodaTester.onto_dir + "uobm/queries/standard_group3_all.sparql" 67 TestUtil.combinePaths(ontoDir, "uobm/queries/standard_group3_all.sparql")
64 }; 68 };
65 PagodaTester.main(args); 69 PagodaTester.main(args);
66// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out"); 70// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out");
@@ -68,10 +72,11 @@ public class CostEvaluation {
68 72
69 public void uobm500() { 73 public void uobm500() {
70 int number = 500; 74 int number = 500;
75 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
71 String[] args = new String[] { 76 String[] args = new String[] {
72 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl", 77 TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
73 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl", 78 TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
74 PagodaTester.onto_dir + "uobm/queries/standard_all_pagoda.sparql" 79 TestUtil.combinePaths(ontoDir, "uobm/queries/standard_all_pagoda.sparql")
75 }; 80 };
76 81
77 OWLOntology ontology = OWLHelper.loadOntology(args[0]); 82 OWLOntology ontology = OWLHelper.loadOntology(args[0]);
@@ -89,10 +94,11 @@ public class CostEvaluation {
89 94
90 95
91 public static void main(String... args) { 96 public static void main(String... args) {
97 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
92 args = new String[] { 98 args = new String[] {
93 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl", 99 TestUtil.combinePaths(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"),
94 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl", 100 TestUtil.combinePaths(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"),
95 PagodaTester.onto_dir + "dbpedia/queries/atomic_ground.sparql" 101 TestUtil.combinePaths(ontoDir, "dbpedia/queries/atomic_ground.sparql")
96 }; 102 };
97 103
98 OWLOntology ontology = OWLHelper.loadOntology(args[0]); 104 OWLOntology ontology = OWLHelper.loadOntology(args[0]);
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java
new file mode 100644
index 0000000..18f6cf9
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java
@@ -0,0 +1,191 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
5import uk.ac.ox.cs.pagoda.util.TestUtil;
6
7import java.io.IOException;
8
9public class JAIR_PAGOdA {
10
11 public static void main(String... args) {
12 try {
13 new JAIR_PAGOdA().lubm1();
14 } catch(IOException e) {
15 e.printStackTrace();
16 }
17 }
18
19 @Test
20 public void lubm1() throws IOException {
21 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
22 String[] args = new String[] {
23 TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
24 TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"),
25 TestUtil.combinePaths(ontoDir, "lubm/queries/answersCorrectness.sparql")
26 };
27 PagodaTester.main(args);
28 TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/lubm1/pagoda");
29 }
30
31 @Test
32 public void lubm1_conj() throws IOException {
33 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
34 String[] args = new String[] {
35 TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
36 TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"),
37 TestUtil.combinePaths(ontoDir, "lubm/queries/test_pellet.sparql")
38 };
39 PagodaTester.main(args);
40 TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/lubm1/pagoda_conj");
41 }
42
43 @Test
44 public void lubm1_rolledUp() throws IOException {
45 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
46 PagodaTester.main(
47 "/home/yzhou/backup/20141212/univ-bench-queries.owl",
48 TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"),
49 TestUtil.combinePaths(ontoDir, "lubm/queries/atomic_lubm.sparql")
50 );
51 TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/lubm1/pagoda_rolledUp");
52 }
53
54 @Test
55 public void uobm1() throws IOException {
56 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
57 String[] args = new String[] {
58 TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
59 TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"),
60 TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql")
61 };
62 PagodaTester.main(args);
63 TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uobm1/pagoda");
64 }
65
66 @Test
67 public void uobm1_conj() throws IOException {
68 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
69 String[] args = new String[] {
70 TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
71 TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"),
72 TestUtil.combinePaths(ontoDir, "uobm/queries/standard_pellet.sparql")
73 };
74 PagodaTester.main(args);
75 TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uobm1/pagoda_conj");
76 }
77
78 @Test
79 public void uobm1_rolledUp() {
80 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
81 String[] args = new String[] {
82 "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl",
83 TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"),
84 TestUtil.combinePaths(ontoDir, "uobm/queries/atomic_uobm.sparql")
85 };
86 PagodaTester.main(args);
87// TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uobm1/pagoda_rolledUp");
88 }
89
90 @Test
91 public void fly() {
92 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
93 String[] args = new String[] {
94 TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"),
95 null,
96 TestUtil.combinePaths(ontoDir, "fly/queries/fly_pellet.sparql")
97 };
98 PagodaTester.main(args);
99// TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/fly/pagoda");
100 }
101
102 @Test
103 public void fly_conj() throws IOException {
104 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
105 String[] args = new String[] {
106 TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"),
107 null,
108 TestUtil.combinePaths(ontoDir, "fly/queries/fly_pellet.sparql")
109 };
110 PagodaTester.main(args);
111 TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/fly/pagoda_conj");
112 }
113
114 public void fly_rolledUp() {
115 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
116 PagodaTester.main(
117// TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
118 TestUtil.combinePaths(ontoDir, "fly/fly-all-in-one_rolledUp.owl"),
119 null,
120 TestUtil.combinePaths(ontoDir, "fly/queries/fly_atomic.sparql")
121 );
122// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/fly/pagoda_rolledUp");
123 }
124
125 public void dbpedia() {
126 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
127 PagodaTester.main(
128 TestUtil.combinePaths(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"),
129 TestUtil.combinePaths(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"),
130 TestUtil.combinePaths(ontoDir, "dbpedia/queries/atomic_ground.sparql"),
131 "dbpedia.ans"
132 );
133
134// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/dbpedia/pagoda");
135 }
136
137 public void npd() {
138 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
139 PagodaTester.main(
140 TestUtil.combinePaths(ontoDir, "npd/npd-all-minus-datatype.owl"),
141 TestUtil.combinePaths(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl"),
142 TestUtil.combinePaths(ontoDir, "npd/queries/atomic_ground.sparql")
143 , "npd.ans"
144 );
145
146// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/npd/pagoda");
147 }
148
149 public void reactome() throws IOException {
150 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
151 PagodaTester.main(
152 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"),
153 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl"),
154// null,
155// TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/atomic_ground.sparql")
156 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/example.sparql")
157 , "pagoda_reactome.ans"
158 );
159 TestUtil.copyFile("log4j.log", "output/jair/pagoda_reactome.example");
160
161// TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/reactome/pagoda_10p");
162 }
163
164 public void chembl() throws IOException {
165 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
166 PagodaTester.main(
167 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"),
168 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/graph sampling/sample_1.nt"),
169// TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql")
170 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/example.sparql")
171 , "pagoda_chembl.ans"
172 );
173 TestUtil.copyFile("log4j.log", "output/jair/pagoda_chembl.example");
174// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/chembl/pagoda_1p");
175 }
176
177 public void uniprot() throws IOException {
178 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
179 PagodaTester.main(
180 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat-processed.owl"),
181 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/graph sampling/sample_1.nt"),
182// null,
183// TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql")
184 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/example.sparql")
185 , "pagoda_uniprot.ans"
186 );
187 TestUtil.copyFile("log4j.log", "output/jair/pagoda_uniprot.example");
188// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uniprot/pagoda_1p");
189 }
190
191}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java
new file mode 100644
index 0000000..01f3568
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java
@@ -0,0 +1,91 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
5import uk.ac.ox.cs.pagoda.util.PagodaProperties;
6import uk.ac.ox.cs.pagoda.util.TestUtil;
7
8import java.io.IOException;
9
10public class JAIR_Scalability {
11
12 private static final String date = "_0123";
13
14 public static void main(String... args) throws IOException {
15 PagodaProperties.shellModeDefault = true;
16 new JAIR_Scalability().testUniProt(50, false);
17 }
18
19 @Test
20 public void reactome() throws IOException {
21 testReactome(10, false);
22 }
23
24 @Test
25 public void chembl() throws IOException {
26 testChEMBL(1, false);
27 }
28
29 @Test
30 public void uniprot() throws IOException {
31 testUniProt(1, false);
32 }
33
34 public void testReactome(int percentage, boolean save) throws IOException {
35 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
36 String[] args = new String[] {
37 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"),
38 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/simplifed_sample_" + percentage + ".ttl"),
39 TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/answersCorrectness.sparql")
40 , "reactome.ans"
41 };
42 if (percentage == 10)
43 args[1] = args[1].replace("simplifed", "reactome");
44
45 PagodaTester.main(args);
46 if (save)
47 TestUtil.copyFile("log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/reactome/pagoda_" + percentage + "p" + date);
48 }
49
50 public void testChEMBL(int percentage, boolean save) throws IOException {
51 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
52 String[] args = new String[] {
53 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"),
54 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/sample_" + percentage + ".nt"),
55// TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql")
56 TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/answersCorrectness.sparql")
57 , "chembl.ans"
58 };
59 if (percentage == 1 || percentage == 10 || percentage == 50)
60 args[1] = args[1].replace("chembl", "chembl/graph sampling");
61 else
62 if (percentage == 100)
63 args[1] = "/home/yzhou/RDFData/ChEMBL/facts/ChEMBL.ttl";
64
65 PagodaTester.main(args);
66 if (save)
67 TestUtil.copyFile("log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/chembl/pagoda_" + percentage + "p" + date);
68 }
69
70 public void testUniProt(int percentage, boolean save) throws IOException {
71 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
72 String[] args = new String[] {
73 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat-processed.owl"),
74 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/sample_" + percentage + ".nt"),
75// TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql")
76 TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/answersCorrectness.sparql")
77 , "uniprot.ans"
78 };
79
80 if (percentage == 1 || percentage == 10 || percentage == 50)
81 args[1] = args[1].replace("uniprot", "uniprot/graph sampling");
82 else
83 if (percentage == 100)
84 args[1] = "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/data/uniprot_cleaned.nt";
85
86 PagodaTester.main(args);
87 if (save)
88 TestUtil.copyFile("log4j.log", "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uniprot/pagoda_" + percentage + "p" + date);
89 }
90
91}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java b/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java
new file mode 100644
index 0000000..3551b9b
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java
@@ -0,0 +1,18 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4
5import java.io.IOException;
6
7@Deprecated
8public class LightEvaluation {
9
10 @Test
11 public void evaluation() throws IOException {
12 new TestPagodaUOBM().answersCorrectness(1);
13 new TestPagodaLUBM().answersCorrectness(100);
14// new TestPagodaFLY().answersCorrectness();
15 new TestPagodaDBPedia().answersCorrectness();
16 new TestPagodaNPD().testNPDwithoutDataType();
17 }
18}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java
new file mode 100644
index 0000000..3642147
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java
@@ -0,0 +1,33 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.Pagoda;
5import uk.ac.ox.cs.pagoda.util.TestUtil;
6
7import java.io.IOException;
8import java.nio.file.Paths;
9
10public class TestPagodaDBPedia {
11
12 public static final String ANSWER_PATH = "~/TestPagodaDEBPedia.json";
13
14 @Test
15 public void just_execute() throws IOException {
16 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
17 Pagoda pagoda = Pagoda.builder()
18 .ontology(Paths.get(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"))
19 .data(Paths.get(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"))
20 .query(Paths.get(ontoDir, "dbpedia/atomic.sparql"))
21 .answer(ANSWER_PATH)
22 .classify(true)
23 .hermit(true)
24 .build();
25 pagoda.run();
26 }
27
28 @Test
29 public void answersCorrectness() {
30 // TODO implement
31 }
32
33}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
new file mode 100644
index 0000000..d8d2b76
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
@@ -0,0 +1,51 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.Pagoda;
5import uk.ac.ox.cs.pagoda.util.TestUtil;
6
7import java.io.File;
8import java.io.IOException;
9import java.nio.file.Path;
10import java.nio.file.Paths;
11
12public class TestPagodaFLY {
13
14 @Test(groups = {"light"})
15 public void answersCorrectness_withGJFC() throws IOException {
16 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
17 Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
18 new File(answers.toString()).deleteOnExit();
19 Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-fly-with-GJ-FC-individuals.json");
20
21 Pagoda pagoda = Pagoda.builder()
22 .ontology(TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"))
23 .query(TestUtil.combinePaths(ontoDir, "fly/queries/fly.sparql"))
24 .answer(answers)
25 .classify(false)
26 .hermit(true)
27 .build();
28
29 pagoda.run();
30 CheckAnswers.assertSameAnswers(answers, givenAnswers);
31 }
32
33 @Test(groups = {"light"})
34 public void answersCorrectness_rolledUp() throws IOException {
35 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
36 Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
37 new File(answers.toString()).deleteOnExit();
38 Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-fly-rolledup.json");
39
40 Pagoda pagoda = Pagoda.builder()
41 .ontology(TestUtil.combinePaths(ontoDir, "fly/fly_rolledUp.owl"))
42 .query(TestUtil.combinePaths(ontoDir, "fly/queries/fly_rolledUp.sparql"))
43 .answer(answers)
44 .classify(false)
45 .hermit(true)
46 .build();
47
48 pagoda.run();
49 CheckAnswers.assertSameAnswers(answers, givenAnswers);
50 }
51}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
new file mode 100644
index 0000000..d261d84
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
@@ -0,0 +1,37 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.Pagoda;
5import uk.ac.ox.cs.pagoda.util.TestUtil;
6
7import java.io.File;
8import java.io.IOException;
9import java.nio.file.Path;
10import java.nio.file.Paths;
11
12public class TestPagodaLUBM {
13
14 public void answersCorrectness(int number) throws IOException {
15 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
16 Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
17 new File(answers.toString()).deleteOnExit();
18 Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-lubm" + number + ".json");
19
20 Pagoda pagoda = Pagoda.builder()
21 .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl"))
22 .data(Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl"))
23 .query(Paths.get(ontoDir, "lubm/queries/test.sparql"))
24 .answer(answers)
25 .classify(true)
26 .hermit(true)
27 .build();
28
29 pagoda.run();
30 CheckAnswers.assertSameAnswers(answers, givenAnswers);
31 }
32
33 @Test(groups = {"light"})
34 public void answersCorrectness_1() throws IOException {
35 answersCorrectness(1);
36 }
37}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java
new file mode 100644
index 0000000..939ee6e
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java
@@ -0,0 +1,38 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.Test;
4import uk.ac.ox.cs.pagoda.Pagoda;
5import uk.ac.ox.cs.pagoda.util.TestUtil;
6
7import java.io.IOException;
8import java.nio.file.Paths;
9
10public class TestPagodaNPD {
11
12 public static final String ANSWER_PATH = "~/PagodaNPDWithoutDatatype.json";
13
14 @Test
15 public void justExecuteNPDWithoutDataType() {
16 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
17 Pagoda pagoda = Pagoda.builder()
18 .ontology(Paths.get(ontoDir, "npd/npd-all-minus-datatype.owl"))
19 .data(Paths.get(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl"))
20 .query(Paths.get(ontoDir, "npd/queries/atomic.sparql"))
21 .answer(ANSWER_PATH)
22 .classify(true)
23 .hermit(true)
24 .build();
25 pagoda.run();
26 }
27
28 @Test
29 public void testNPDwithoutDataType() throws IOException {
30 // TODO implement
31 }
32
33 @Test
34 public void testNPD() throws IOException {
35 // TODO implement
36 }
37
38}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
new file mode 100644
index 0000000..558ac1f
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
@@ -0,0 +1,51 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.testng.annotations.DataProvider;
4import org.testng.annotations.Test;
5import uk.ac.ox.cs.pagoda.Pagoda;
6import uk.ac.ox.cs.pagoda.util.TestUtil;
7
8import java.io.File;
9import java.io.IOException;
10import java.nio.file.Path;
11import java.nio.file.Paths;
12
13public class TestPagodaUOBM {
14
15 private static final int N_1 = 1;
16 private static final int N_2 = 4;
17
18 @DataProvider(name = "UOBMNumbers")
19 private static Object[][] UOBMNumbers() {
20 Integer[][] integers = new Integer[N_2 - N_1 + 1][1];
21 for(int i = 0; i < N_2 - N_1 + 1; i++)
22 integers[i][0] = N_1 + i;
23 return integers;
24 }
25
26 @Test(groups = {"light"})
27 public void answersCorrectness_1() throws IOException {
28 answersCorrectness(1);
29 }
30
31 @Test(groups = {"heavy"}, dataProvider = "UOBMNumbers")
32 public void answersCorrectness(int number) throws IOException {
33 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
34 Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
35 new File(answers.toString()).deleteOnExit();
36 Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-uobm" + number + ".json");
37
38 Pagoda pagoda = Pagoda.builder()
39 .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
40 .data(Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl"))
41 .query(Paths.get(ontoDir, "uobm/queries/test.sparql"))
42 .answer(answers)
43 .classify(true)
44 .hermit(true)
45 .build();
46
47 pagoda.run();
48 CheckAnswers.assertSameAnswers(answers, givenAnswers);
49 }
50
51}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/AllTests.java b/test/uk/ac/ox/cs/pagoda/junit/AllTests.java
deleted file mode 100644
index fb38787..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/AllTests.java
+++ /dev/null
@@ -1,48 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import java.io.BufferedWriter;
4import java.io.FileInputStream;
5import java.io.FileNotFoundException;
6import java.io.FileOutputStream;
7import java.io.IOException;
8import java.io.InputStream;
9import java.io.OutputStream;
10import java.io.OutputStreamWriter;
11
12import org.junit.runner.RunWith;
13import org.junit.runners.Suite;
14import org.junit.runners.Suite.SuiteClasses;
15
16@RunWith(Suite.class)
17@SuiteClasses({ PagodaUOBM.class
18 })
19public class AllTests {
20
21 public static void copy(String source, String dest) {
22 InputStream is = null;
23 OutputStream os = null;
24 try {
25 is = new FileInputStream(source);
26 os = new FileOutputStream(dest);
27 byte[] buffer = new byte[1024];
28 int length;
29 while ((length = is.read(buffer)) > 0) {
30 os.write(buffer, 0, length);
31 }
32 is.close();
33 os.close();
34
35 BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(source)));
36 writer.write("");
37 writer.close();
38 } catch (FileNotFoundException e) {
39 e.printStackTrace();
40 } catch (IOException e) {
41 e.printStackTrace();
42 }
43
44// File src = new File(source);
45// src.delete();
46 }
47
48}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java b/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
index ff98b3c..ad4b2de 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
+++ b/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
@@ -1,48 +1,41 @@
1package uk.ac.ox.cs.pagoda.junit; 1package uk.ac.ox.cs.pagoda.junit;
2 2
3import static org.junit.Assert.*;
4
5import org.junit.Test; 3import org.junit.Test;
6import org.semanticweb.HermiT.model.Atom; 4import org.semanticweb.HermiT.model.*;
7import org.semanticweb.HermiT.model.AtomicConcept;
8import org.semanticweb.HermiT.model.AtomicRole;
9import org.semanticweb.HermiT.model.DLClause;
10import org.semanticweb.HermiT.model.Equality;
11import org.semanticweb.HermiT.model.Individual;
12import org.semanticweb.HermiT.model.Variable;
13import org.semanticweb.owlapi.apibinding.OWLManager; 5import org.semanticweb.owlapi.apibinding.OWLManager;
14import org.semanticweb.owlapi.model.OWLOntology; 6import org.semanticweb.owlapi.model.OWLOntology;
15import org.semanticweb.owlapi.model.OWLOntologyManager; 7import org.semanticweb.owlapi.model.OWLOntologyManager;
16
17import uk.ac.ox.cs.pagoda.approx.Clause; 8import uk.ac.ox.cs.pagoda.approx.Clause;
18import uk.ac.ox.cs.pagoda.approx.Clausifier; 9import uk.ac.ox.cs.pagoda.approx.Clausifier;
19 10
11import static org.junit.Assert.fail;
12
20public class ClauseTester { 13public class ClauseTester {
21 14
22 public void test_clause(Atom[] headAtoms, Atom[] bodyAtoms) { 15 public void test_clause(Atom[] headAtoms, Atom[] bodyAtoms) {
23 OWLOntologyManager m = OWLManager.createOWLOntologyManager(); 16 OWLOntologyManager m = OWLManager.createOWLOntologyManager();
24 OWLOntology emptyOntology = null; 17 OWLOntology emptyOntology = null;
25 try { 18 try {
26 emptyOntology = m.createOntology(); 19 emptyOntology = m.createOntology();
27 } catch (Exception e) { 20 } catch(Exception e) {
28 e.printStackTrace(); 21 e.printStackTrace();
29 fail("failed to create a new ontology"); 22 fail("failed to create a new ontology");
30 } 23 }
31 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); 24 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
32 System.out.println(c.toString()); 25 System.out.println(c.toString());
33 } 26 }
34 27
35 @Test 28 @Test
36 public void test_nominal() { 29 public void test_nominal() {
37 Variable x = Variable.create("X"); 30 Variable x = Variable.create("X");
38 AtomicRole r = AtomicRole.create("r"); 31 AtomicRole r = AtomicRole.create("r");
39 Individual o = Individual.create("o"); 32 Individual o = Individual.create("o");
40 Atom[] bodyAtoms = new Atom[] { Atom.create(r, x, o) }; 33 Atom[] bodyAtoms = new Atom[]{Atom.create(r, x, o)};
41 AtomicConcept A = AtomicConcept.create("A"); 34 AtomicConcept A = AtomicConcept.create("A");
42 Atom[] headAtoms = new Atom[] { Atom.create(A, x) }; 35 Atom[] headAtoms = new Atom[]{Atom.create(A, x)};
43 test_clause(headAtoms, bodyAtoms); 36 test_clause(headAtoms, bodyAtoms);
44 } 37 }
45 38
46 @Test 39 @Test
47 public void test_simple() { 40 public void test_simple() {
48 Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"); 41 Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2");
diff --git a/test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java b/test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java
deleted file mode 100644
index 3406ed2..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java
+++ /dev/null
@@ -1,14 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import org.junit.runner.RunWith;
4import org.junit.runners.Suite;
5import org.junit.runners.Suite.SuiteClasses;
6
7@RunWith(Suite.class)
8@SuiteClasses({ LightEvaluation.class,
9 CostEvaluation.class
10 })
11
12public class FullEvaluation {
13
14}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/JAIR_PAGOdA.java b/test/uk/ac/ox/cs/pagoda/junit/JAIR_PAGOdA.java
deleted file mode 100644
index 2a148cc..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/JAIR_PAGOdA.java
+++ /dev/null
@@ -1,173 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import org.junit.Test;
4
5import uk.ac.ox.cs.pagoda.tester.PagodaTester;
6
7public class JAIR_PAGOdA {
8
9 public void lubm1() {
10 String[] args = new String[] {
11 PagodaTester.onto_dir + "lubm/univ-bench.owl",
12 PagodaTester.onto_dir + "lubm/data/lubm1.ttl",
13 PagodaTester.onto_dir + "lubm/queries/test.sparql"
14 };
15 PagodaTester.main(args);
16 AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda");
17 }
18
19
20 public void lubm1_conj() {
21 String[] args = new String[] {
22 PagodaTester.onto_dir + "lubm/univ-bench.owl",
23 PagodaTester.onto_dir + "lubm/data/lubm1.ttl",
24 PagodaTester.onto_dir + "lubm/queries/test_pellet.sparql"
25 };
26 PagodaTester.main(args);
27 AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_conj");
28 }
29
30
31 public void lubm1_rolledUp() {
32 String[] args = new String[] {
33 "/home/yzhou/backup/20141212/univ-bench-queries.owl",
34 PagodaTester.onto_dir + "lubm/data/lubm1.ttl",
35 PagodaTester.onto_dir + "lubm/queries/atomic_lubm.sparql"
36 };
37 PagodaTester.main(args);
38 AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_rolledUp");
39 }
40
41
42 public void uobm1() {
43 String[] args = new String[] {
44 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
45 PagodaTester.onto_dir + "uobm/data/uobm1.ttl",
46 PagodaTester.onto_dir + "uobm/queries/standard.sparql"
47 };
48 PagodaTester.main(args);
49 AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda");
50 }
51
52
53 public void uobm1_conj() {
54 String[] args = new String[] {
55 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
56 PagodaTester.onto_dir + "uobm/data/uobm1.ttl",
57 PagodaTester.onto_dir + "uobm/queries/standard_pellet.sparql"
58 };
59 PagodaTester.main(args);
60 AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_conj");
61 }
62
63
64 public void uobm1_rolledUp() {
65 String[] args = new String[] {
66 "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl",
67 PagodaTester.onto_dir + "uobm/data/uobm1.ttl",
68 PagodaTester.onto_dir + "uobm/queries/atomic_uobm.sparql"
69 };
70 PagodaTester.main(args);
71// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_rolledUp");
72 }
73
74
75 public void fly() {
76 String[] args = new String[] {
77 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
78 null,
79 PagodaTester.onto_dir + "fly/queries/fly_pellet.sparql"
80 };
81 PagodaTester.main(args);
82// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda");
83 }
84
85 @Test
86 public void fly_conj() {
87 String[] args = new String[] {
88 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
89 null,
90 PagodaTester.onto_dir + "fly/queries/fly_pellet.sparql"
91 };
92 PagodaTester.main(args);
93 AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_conj");
94 }
95
96
97 public void fly_rolledUp() {
98 PagodaTester.main(new String[] {
99// PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
100 PagodaTester.onto_dir + "fly/fly-all-in-one_rolledUp.owl",
101 null,
102 PagodaTester.onto_dir + "fly/queries/fly_atomic.sparql"
103 });
104// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_rolledUp");
105 }
106
107 public void dbpedia() {
108 PagodaTester.main(
109 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl",
110 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl",
111 PagodaTester.onto_dir + "dbpedia/queries/atomic_ground.sparql"
112 , "dbpedia.ans"
113 );
114
115// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/dbpedia/pagoda");
116 }
117
118 public void npd() {
119 PagodaTester.main(
120 PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl",
121 PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl",
122 PagodaTester.onto_dir + "npd/queries/atomic_ground.sparql"
123 , "npd.ans"
124 );
125
126// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/npd/pagoda");
127 }
128
129 public void reactome() {
130 PagodaTester.main(
131 PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl",
132 PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl",
133// null,
134// PagodaTester.onto_dir + "bio2rdf/reactome/queries/atomic_ground.sparql"
135 PagodaTester.onto_dir + "bio2rdf/reactome/queries/example.sparql"
136 , "pagoda_reactome.ans"
137 );
138 AllTests.copy("log4j.log", "output/jair/pagoda_reactome.example");
139
140// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_10p");
141 }
142
143 public void chembl() {
144 PagodaTester.main(
145 PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl",
146 PagodaTester.onto_dir + "bio2rdf/chembl/graph sampling/sample_1.nt",
147// PagodaTester.onto_dir + "bio2rdf/chembl/queries/atomic_ground.sparql"
148 PagodaTester.onto_dir + "bio2rdf/chembl/queries/example.sparql"
149 , "pagoda_chembl.ans"
150 );
151 AllTests.copy("log4j.log", "output/jair/pagoda_chembl.example");
152// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_1p");
153 }
154
155 public void uniprot() {
156 PagodaTester.main(
157 PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat-processed.owl",
158 PagodaTester.onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt",
159// null,
160// PagodaTester.onto_dir + "bio2rdf/uniprot/queries/atomic_ground.sparql"
161 PagodaTester.onto_dir + "bio2rdf/uniprot/queries/example.sparql"
162 , "pagoda_uniprot.ans"
163 );
164 AllTests.copy("log4j.log", "output/jair/pagoda_uniprot.example");
165// AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_1p");
166 }
167
168
169 public static void main(String... args) {
170 new JAIR_PAGOdA().fly();
171 }
172
173}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java b/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java
deleted file mode 100644
index 5e2b1d7..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java
+++ /dev/null
@@ -1,86 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import org.junit.Test;
4
5import uk.ac.ox.cs.pagoda.tester.PagodaTester;
6import uk.ac.ox.cs.pagoda.util.Properties;
7
8public class JAIR_Scalability {
9
10 private static final String date = "_0123";
11
12 @Test
13 public void reactome() {
14 testReactome(10, false);
15 }
16
17 @Test
18 public void chembl() {
19 testChEMBL(1, false);
20 }
21
22 @Test
23 public void uniprot() {
24 testUniProt(1, false);
25 }
26
27 public void testReactome(int percentage, boolean save) {
28 String[] args = new String[] {
29 PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl",
30 PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/simplifed_sample_" + percentage + ".ttl",
31 PagodaTester.onto_dir + "bio2rdf/reactome/queries/test.sparql"
32 , "reactome.ans"
33 };
34 if (percentage == 10)
35 args[1] = args[1].replace("simplifed", "reactome");
36
37 PagodaTester.main(args);
38 if (save)
39 AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_" + percentage + "p" + date);
40 }
41
42 public void testChEMBL(int percentage, boolean save) {
43 String[] args = new String[] {
44 PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl",
45 PagodaTester.onto_dir + "bio2rdf/chembl/sample_" + percentage + ".nt",
46// PagodaTester.onto_dir + "bio2rdf/chembl/queries/atomic_ground.sparql"
47 PagodaTester.onto_dir + "bio2rdf/chembl/queries/test.sparql"
48 , "chembl.ans"
49 };
50 if (percentage == 1 || percentage == 10 || percentage == 50)
51 args[1] = args[1].replace("chembl", "chembl/graph sampling");
52 else
53 if (percentage == 100)
54 args[1] = "/home/yzhou/RDFData/ChEMBL/facts/ChEMBL.ttl";
55
56 PagodaTester.main(args);
57 if (save)
58 AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_" + percentage + "p" + date);
59 }
60
61 public void testUniProt(int percentage, boolean save) {
62 String[] args = new String[] {
63 PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat-processed.owl",
64 PagodaTester.onto_dir + "bio2rdf/uniprot/sample_" + percentage + ".nt",
65// PagodaTester.onto_dir + "bio2rdf/uniprot/queries/atomic_ground.sparql"
66 PagodaTester.onto_dir + "bio2rdf/uniprot/queries/test.sparql"
67 , "uniprot.ans"
68 };
69
70 if (percentage == 1 || percentage == 10 || percentage == 50)
71 args[1] = args[1].replace("uniprot", "uniprot/graph sampling");
72 else
73 if (percentage == 100)
74 args[1] = "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/data/uniprot_cleaned.nt";
75
76 PagodaTester.main(args);
77 if (save)
78 AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_" + percentage + "p" + date);
79 }
80
81 public static void main(String... args) {
82 Properties.ShellModeDefault = true;
83 new JAIR_Scalability().testUniProt(50, false);
84 }
85
86}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/LightEvaluation.java b/test/uk/ac/ox/cs/pagoda/junit/LightEvaluation.java
deleted file mode 100644
index 1ddca15..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/LightEvaluation.java
+++ /dev/null
@@ -1,59 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import org.junit.Test;
4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
5
6public class LightEvaluation {
7
8 @Test
9 public void uobm1() {
10 int number = 1;
11 PagodaTester.main(
12 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
13 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
14 PagodaTester.onto_dir + "uobm/queries/standard.sparql"
15 );
16 AllTests.copy("log4j.log", "output/jair/uobm1.out");
17 }
18
19 @Test
20 public void lubm100() {
21 int number = 100;
22 PagodaTester.main(
23 PagodaTester.onto_dir + "lubm/univ-bench.owl",
24 PagodaTester.onto_dir + "lubm/data/lubm" + number + ".ttl",
25 PagodaTester.onto_dir + "lubm/queries/test.sparql"
26 );
27 AllTests.copy("log4j.log", "results-backup/current/lubm100.out");
28 }
29
30 @Test
31 public void fly() {
32 PagodaTester.main(
33 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
34 PagodaTester.onto_dir + "fly/queries/fly.sparql"
35 );
36 AllTests.copy("log4j.log", "results-backup/current/fly.out");
37 }
38
39 @Test
40 public void dbpedia() {
41 PagodaTester.main(
42 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl",
43 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl",
44 PagodaTester.onto_dir + "dbpedia/atomic.sparql"
45 );
46 AllTests.copy("log4j.log", "results-backup/current/dbpedia.out");
47 }
48
49 @Test
50 public void npdWithoutDataType() {
51 PagodaTester.main(
52 PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl",
53 PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl",
54 PagodaTester.onto_dir + "npd/queries/atomic.sparql"
55 );
56 AllTests.copy("log4j.log", "results-backup/current/npd_minus.out");
57 }
58
59}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaDBPedia.java b/test/uk/ac/ox/cs/pagoda/junit/PagodaDBPedia.java
deleted file mode 100644
index 37ffb44..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaDBPedia.java
+++ /dev/null
@@ -1,27 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import static org.junit.Assert.fail;
4
5import org.junit.Test;
6
7import uk.ac.ox.cs.pagoda.tester.PagodaTester;
8import uk.ac.ox.cs.pagoda.tester.Statistics;
9
10public class PagodaDBPedia {
11
12 @Test
13 public void test() {
14 PagodaTester.main(
15 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl",
16 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl",
17 PagodaTester.onto_dir + "dbpedia/atomic.sparql"
18 );
19
20 Statistics stat = new Statistics("output/log4j.log");
21 String diff = stat.diff("results-backup/benchmark/dbpedia.out");
22 AllTests.copy("output/log4j.log", "results-backup/current/dbpedia.out");
23 if (!diff.isEmpty())
24 fail(diff);
25 }
26
27}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaELU.java b/test/uk/ac/ox/cs/pagoda/junit/PagodaELU.java
deleted file mode 100644
index d999a6e..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaELU.java
+++ /dev/null
@@ -1,18 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import org.junit.Test;
4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
5
6public class PagodaELU {
7
8 @Test void test() {
9 int number = 1;
10 PagodaTester.main(
11 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
12 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
13 PagodaTester.onto_dir + "uobm/queries/standard.sparql"
14 );
15 }
16
17
18}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaFLY.java b/test/uk/ac/ox/cs/pagoda/junit/PagodaFLY.java
deleted file mode 100644
index 4631837..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaFLY.java
+++ /dev/null
@@ -1,24 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import org.junit.Test;
4
5import uk.ac.ox.cs.pagoda.tester.PagodaTester;
6
7public class PagodaFLY {
8
9 @Test
10 public void test() {
11 PagodaTester.main(
12 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
13 PagodaTester.onto_dir + "fly/queries/fly_pellet.sparql"
14 );
15
16// Statistics stat = new Statistics("output/log4j.log");
17// String diff = stat.diff("results-backup/benchmark/fly.out");
18// AllTests.copy("output/log4j.log", "results-backup/current/fly.out");
19// if (!diff.isEmpty())
20// fail(diff);
21 }
22
23
24}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaLUBM.java b/test/uk/ac/ox/cs/pagoda/junit/PagodaLUBM.java
deleted file mode 100644
index f8fef0e..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaLUBM.java
+++ /dev/null
@@ -1,38 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import static org.junit.Assert.*;
4
5import org.junit.Test;
6
7import uk.ac.ox.cs.pagoda.tester.PagodaTester;
8import uk.ac.ox.cs.pagoda.tester.Statistics;
9
10public class PagodaLUBM {
11
12 public void test_all(int number) {
13 PagodaTester.main(
14 PagodaTester.onto_dir + "lubm/univ-bench.owl",
15 PagodaTester.onto_dir + "lubm/data/lubm" + number + ".ttl",
16 PagodaTester.onto_dir + "lubm/queries/test_all_pagoda.sparql"
17 );
18
19 AllTests.copy("log4j.log", "output/jair/lubm" + number + ".out");
20 }
21
22 @Test
23 public void test1() { test_all(1); }
24
25 public void test() {
26 int number = 100;
27 test_all(number);
28 }
29
30 public void check(int number) {
31 Statistics stat = new Statistics("output/log4j.log");
32 String diff = stat.diff("results-backup/benchmark/lubm" + number + ".out");
33 AllTests.copy("output/log4j.log", "results-backup/current/lubm" + number + ".out");
34 if (!diff.isEmpty())
35 fail(diff);
36 }
37
38}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD.java b/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD.java
deleted file mode 100644
index 96edbb4..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD.java
+++ /dev/null
@@ -1,42 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import static org.junit.Assert.fail;
4
5import org.junit.Test;
6
7import uk.ac.ox.cs.pagoda.tester.PagodaTester;
8import uk.ac.ox.cs.pagoda.tester.Statistics;
9
10public class PagodaNPD {
11
12 @Test
13 public void testNPDwithoutDataType() {
14 PagodaTester.main(
15 PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl",
16 PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl",
17 PagodaTester.onto_dir + "npd/queries/atomic.sparql"
18 );
19
20 Statistics stat = new Statistics("output/log4j.log");
21 String diff = stat.diff("results-backup/benchmark/npd_minus.out");
22 AllTests.copy("output/log4j.log", "results-backup/current/npd_minus.out");
23 if (!diff.isEmpty())
24 fail(diff);
25 }
26
27 @Test
28 public void testNPD() {
29 PagodaTester.main(
30 PagodaTester.onto_dir + "npd/npd-all.owl",
31 PagodaTester.onto_dir + "npd/data/npd-data-dump-processed.ttl",
32 PagodaTester.onto_dir + "npd/queries/atomic.sparql"
33 );
34
35 Statistics stat = new Statistics("output/log4j.log");
36 String diff = stat.diff("results-backup/benchmark/npd.out");
37 AllTests.copy("output/log4j.log", "results-backup/current/npd.out");
38 if (!diff.isEmpty())
39 fail(diff);
40 }
41
42}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD_bench.java b/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD_bench.java
deleted file mode 100644
index df1a57d..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD_bench.java
+++ /dev/null
@@ -1,27 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import static org.junit.Assert.fail;
4
5import org.junit.Test;
6
7import uk.ac.ox.cs.pagoda.tester.PagodaTester;
8import uk.ac.ox.cs.pagoda.tester.Statistics;
9
10public class PagodaNPD_bench {
11
12 @Test
13 public void test() {
14 PagodaTester.main(
15 PagodaTester.onto_dir + "npd-benchmark/npd-v2-ql_a.owl",
16 PagodaTester.onto_dir + "npd-benchmark/npd-v2-ql_a.ttl",
17 PagodaTester.onto_dir + "npd-benchmark/queries/all.sparql"
18 );
19
20 Statistics stat = new Statistics("output/log4j.log");
21 String diff = stat.diff("results-backup/benchmark/npd-bench.out");
22 AllTests.copy("output/log4j.log", "results-backup/current/npd-bench.out");
23 if (!diff.isEmpty())
24 fail(diff);
25 }
26
27}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaRLU.java b/test/uk/ac/ox/cs/pagoda/junit/PagodaRLU.java
deleted file mode 100644
index 5d93302..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaRLU.java
+++ /dev/null
@@ -1,18 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import org.junit.Test;
4import uk.ac.ox.cs.pagoda.tester.PagodaTester;
5
6public class PagodaRLU {
7
8 @Test
9 public void testRL() {
10 int number = 1;
11 PagodaTester.main(
12 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
13 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
14 PagodaTester.onto_dir + "uobm/queries/standard.sparql"
15 );
16 }
17
18}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaUOBM.java b/test/uk/ac/ox/cs/pagoda/junit/PagodaUOBM.java
deleted file mode 100644
index 5b56c6d..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaUOBM.java
+++ /dev/null
@@ -1,48 +0,0 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import org.junit.Test;
4
5import uk.ac.ox.cs.pagoda.tester.PagodaTester;
6import uk.ac.ox.cs.pagoda.tester.Statistics;
7
8public class PagodaUOBM {
9
10 public void test_all(int number ) {
11 PagodaTester.main(
12 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
13 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
14 PagodaTester.onto_dir + "uobm/queries/standard_all_pagoda.sparql"
15// PagodaTester.onto_dir + "uobm/queries/standard_group3_all_less.sparql;" +
16// PagodaTester.onto_dir + "uobm/queries/G3.sparql;" +
17// PagodaTester.onto_dir + "uobm/queries/last.sparql"
18 );
19
20 AllTests.copy("log4j.log", "output/jair/newuobm/uobm" + number + ".out");
21 }
22
23 public void test_upToSum(int number) {
24 PagodaTester.main(
25 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
26 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
27 PagodaTester.onto_dir + "uobm/queries/standard_group3_all.sparql"
28 );
29
30// AllTests.copy("log4j.log", "output/jair/uobm" + number + ".out");
31 }
32
33 @Test
34 public void test1() { test_all(1); }
35
36 public void test500() { test_upToSum(500); }
37
38 public static void main(String... args) {
39 new PagodaUOBM().test_all(1);
40 }
41
42 public void check() {
43 Statistics stat = new Statistics("results-backup/current/uobm1.out");
44 String diff = stat.diff("results-backup/benchmark/uobm1.out");
45 System.out.println(diff);
46 }
47
48}
diff --git a/test/uk/ac/ox/cs/pagoda/ore/PagodaOWLReasoner.java b/test/uk/ac/ox/cs/pagoda/ore/PagodaOWLReasoner.java
deleted file mode 100644
index a07323d..0000000
--- a/test/uk/ac/ox/cs/pagoda/ore/PagodaOWLReasoner.java
+++ /dev/null
@@ -1,470 +0,0 @@
1package uk.ac.ox.cs.pagoda.ore;
2
3import java.util.HashMap;
4import java.util.HashSet;
5import java.util.List;
6import java.util.Map;
7import java.util.Set;
8
9import org.semanticweb.owlapi.model.AxiomType;
10import org.semanticweb.owlapi.model.IRI;
11import org.semanticweb.owlapi.model.OWLAxiom;
12import org.semanticweb.owlapi.model.OWLClass;
13import org.semanticweb.owlapi.model.OWLClassExpression;
14import org.semanticweb.owlapi.model.OWLDataFactory;
15import org.semanticweb.owlapi.model.OWLDataProperty;
16import org.semanticweb.owlapi.model.OWLDataPropertyExpression;
17import org.semanticweb.owlapi.model.OWLLiteral;
18import org.semanticweb.owlapi.model.OWLNamedIndividual;
19import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
20import org.semanticweb.owlapi.model.OWLOntology;
21import org.semanticweb.owlapi.model.OWLOntologyChange;
22import org.semanticweb.owlapi.reasoner.AxiomNotInProfileException;
23import org.semanticweb.owlapi.reasoner.BufferingMode;
24import org.semanticweb.owlapi.reasoner.ClassExpressionNotInProfileException;
25import org.semanticweb.owlapi.reasoner.FreshEntitiesException;
26import org.semanticweb.owlapi.reasoner.FreshEntityPolicy;
27import org.semanticweb.owlapi.reasoner.InconsistentOntologyException;
28import org.semanticweb.owlapi.reasoner.IndividualNodeSetPolicy;
29import org.semanticweb.owlapi.reasoner.InferenceType;
30import org.semanticweb.owlapi.reasoner.Node;
31import org.semanticweb.owlapi.reasoner.NodeSet;
32import org.semanticweb.owlapi.reasoner.OWLReasoner;
33import org.semanticweb.owlapi.reasoner.ReasonerInterruptedException;
34import org.semanticweb.owlapi.reasoner.TimeOutException;
35import org.semanticweb.owlapi.reasoner.UnsupportedEntailmentTypeException;
36import org.semanticweb.owlapi.reasoner.impl.OWLClassNodeSet;
37import org.semanticweb.owlapi.util.Version;
38
39import uk.ac.ox.cs.JRDFox.model.GroundTerm;
40import uk.ac.ox.cs.JRDFox.model.Individual;
41import uk.ac.ox.cs.pagoda.query.AnswerTuples;
42import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
43import uk.ac.ox.cs.pagoda.util.Utility;
44
45public class PagodaOWLReasoner implements OWLReasoner {
46
47 QueryReasoner reasoner;
48 OWLOntology ontology;
49 OWLDataFactory factory;
50 boolean sat;
51
52 public PagodaOWLReasoner(OWLOntology ontology) {
53 this.ontology = ontology;
54 factory = ontology.getOWLOntologyManager().getOWLDataFactory();
55 reasoner = QueryReasoner.getInstance(ontology);
56 reasoner.setToClassify(false);
57 reasoner.loadOntology(ontology);
58 sat = reasoner.preprocess();
59 thing = new OWLClassNodeSet(factory.getOWLThing());
60 }
61
62 @Override
63 public String getReasonerName() {
64 return "PAGOdA";
65 }
66
67 @Override
68 public Version getReasonerVersion() {
69 return null;
70 }
71
72 @Override
73 public BufferingMode getBufferingMode() {
74 // TODO Auto-generated method stub
75 return null;
76 }
77
78 @Override
79 public void flush() {
80 // TODO Auto-generated method stub
81
82 }
83
84 @Override
85 public List<OWLOntologyChange> getPendingChanges() {
86 // TODO Auto-generated method stub
87 return null;
88 }
89
90 @Override
91 public Set<OWLAxiom> getPendingAxiomAdditions() {
92 // TODO Auto-generated method stub
93 return null;
94 }
95
96 @Override
97 public Set<OWLAxiom> getPendingAxiomRemovals() {
98 // TODO Auto-generated method stub
99 return null;
100 }
101
102 @Override
103 public OWLOntology getRootOntology() {
104 return ontology;
105 }
106
107 @Override
108 public void interrupt() {
109 // TODO Auto-generated method stub
110
111 }
112
113 @Override
114 public void precomputeInferences(InferenceType... inferenceTypes) throws ReasonerInterruptedException, TimeOutException, InconsistentOntologyException {
115 if (!sat) {
116 throw new InconsistentOntologyException();
117 }
118 if (inferenceTypes.length == 1 && inferenceTypes[0].equals(InferenceType.CLASS_ASSERTIONS) && types.isEmpty()) {
119 Set<OWLClass> queriedClasses = new HashSet<OWLClass>();
120 for (OWLOntology onto: ontology.getImportsClosure())
121 for (OWLClass cls: onto.getClassesInSignature(true)) {
122// if (cls.toStringID().equals("http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#Meritage"));
123// else continue;
124 if (!cls.equals(factory.getOWLThing()) && !queriedClasses.contains(cls)) {
125 queriedClasses.add(cls);
126 AnswerTuples tuples = null;
127 try {
128 tuples = reasoner.evaluate(String.format("select distinct ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <%s> .}", cls.toStringID()));
129 int cnt = 0;
130 for (GroundTerm t; tuples.isValid(); tuples.moveNext()) {
131 t = tuples.getTuple().getGroundTerm(0);
132 if (t instanceof Individual) {
133 addType(((Individual) t).getIRI(), cls);
134 ++cnt;
135 }
136 }
137 Utility.logInfo("The number of answers: " + cnt);
138 } finally {
139 if (tuples != null) tuples.dispose();
140 }
141 }
142 }
143 }
144 }
145
146 private void addType(String iri, OWLClass cls) {
147 OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(iri));
148 OWLClassNodeSet set;
149 if (types.containsKey(ind)) {
150 set = types.get(ind);
151 }
152 else {
153 set = new OWLClassNodeSet(factory.getOWLThing());
154 types.put(ind, set);
155 }
156 set.addEntity(cls);
157 }
158
159 @Override
160 public boolean isPrecomputed(InferenceType inferenceType) {
161 // TODO Auto-generated method stub
162 return false;
163 }
164
165 @Override
166 public Set<InferenceType> getPrecomputableInferenceTypes() {
167 return java.util.Collections.singleton(InferenceType.CLASS_ASSERTIONS);
168 }
169
170 @Override
171 public boolean isConsistent() throws ReasonerInterruptedException, TimeOutException {
172 return sat;
173 }
174
175 @Override
176 public boolean isSatisfiable(OWLClassExpression classExpression) throws ReasonerInterruptedException, TimeOutException, ClassExpressionNotInProfileException, FreshEntitiesException, InconsistentOntologyException {
177 // TODO Auto-generated method stub
178 return false;
179 }
180
181 @Override
182 public Node<OWLClass> getUnsatisfiableClasses() throws ReasonerInterruptedException, TimeOutException, InconsistentOntologyException {
183 // TODO Auto-generated method stub
184 return null;
185 }
186
187 @Override
188 public boolean isEntailed(OWLAxiom axiom)
189 throws ReasonerInterruptedException,
190 UnsupportedEntailmentTypeException, TimeOutException,
191 AxiomNotInProfileException, FreshEntitiesException,
192 InconsistentOntologyException {
193 // TODO Auto-generated method stub
194 return false;
195 }
196
197 @Override
198 public boolean isEntailed(Set<? extends OWLAxiom> axioms)
199 throws ReasonerInterruptedException,
200 UnsupportedEntailmentTypeException, TimeOutException,
201 AxiomNotInProfileException, FreshEntitiesException,
202 InconsistentOntologyException {
203 // TODO Auto-generated method stub
204 return false;
205 }
206
207 @Override
208 public boolean isEntailmentCheckingSupported(AxiomType<?> axiomType) {
209 // TODO Auto-generated method stub
210 return false;
211 }
212
213 @Override
214 public Node<OWLClass> getTopClassNode() {
215 // TODO Auto-generated method stub
216 return null;
217 }
218
219 @Override
220 public Node<OWLClass> getBottomClassNode() {
221 // TODO Auto-generated method stub
222 return null;
223 }
224
225 @Override
226 public NodeSet<OWLClass> getSubClasses(OWLClassExpression ce, boolean direct)
227 throws ReasonerInterruptedException, TimeOutException,
228 FreshEntitiesException, InconsistentOntologyException,
229 ClassExpressionNotInProfileException {
230 // TODO Auto-generated method stub
231 return null;
232 }
233
234 @Override
235 public NodeSet<OWLClass> getSuperClasses(OWLClassExpression ce,
236 boolean direct) throws InconsistentOntologyException,
237 ClassExpressionNotInProfileException, FreshEntitiesException,
238 ReasonerInterruptedException, TimeOutException {
239 // TODO Auto-generated method stub
240 return null;
241 }
242
243 @Override
244 public Node<OWLClass> getEquivalentClasses(OWLClassExpression ce)
245 throws InconsistentOntologyException,
246 ClassExpressionNotInProfileException, FreshEntitiesException,
247 ReasonerInterruptedException, TimeOutException {
248 // TODO Auto-generated method stub
249 return null;
250 }
251
252 @Override
253 public NodeSet<OWLClass> getDisjointClasses(OWLClassExpression ce)
254 throws ReasonerInterruptedException, TimeOutException,
255 FreshEntitiesException, InconsistentOntologyException {
256 // TODO Auto-generated method stub
257 return null;
258 }
259
260 @Override
261 public Node<OWLObjectPropertyExpression> getTopObjectPropertyNode() {
262 // TODO Auto-generated method stub
263 return null;
264 }
265
266 @Override
267 public Node<OWLObjectPropertyExpression> getBottomObjectPropertyNode() {
268 // TODO Auto-generated method stub
269 return null;
270 }
271
272 @Override
273 public NodeSet<OWLObjectPropertyExpression> getSubObjectProperties(
274 OWLObjectPropertyExpression pe, boolean direct)
275 throws InconsistentOntologyException, FreshEntitiesException,
276 ReasonerInterruptedException, TimeOutException {
277 // TODO Auto-generated method stub
278 return null;
279 }
280
281 @Override
282 public NodeSet<OWLObjectPropertyExpression> getSuperObjectProperties(
283 OWLObjectPropertyExpression pe, boolean direct)
284 throws InconsistentOntologyException, FreshEntitiesException,
285 ReasonerInterruptedException, TimeOutException {
286 // TODO Auto-generated method stub
287 return null;
288 }
289
290 @Override
291 public Node<OWLObjectPropertyExpression> getEquivalentObjectProperties(
292 OWLObjectPropertyExpression pe)
293 throws InconsistentOntologyException, FreshEntitiesException,
294 ReasonerInterruptedException, TimeOutException {
295 // TODO Auto-generated method stub
296 return null;
297 }
298
299 @Override
300 public NodeSet<OWLObjectPropertyExpression> getDisjointObjectProperties(
301 OWLObjectPropertyExpression pe)
302 throws InconsistentOntologyException, FreshEntitiesException,
303 ReasonerInterruptedException, TimeOutException {
304 // TODO Auto-generated method stub
305 return null;
306 }
307
308 @Override
309 public Node<OWLObjectPropertyExpression> getInverseObjectProperties(
310 OWLObjectPropertyExpression pe)
311 throws InconsistentOntologyException, FreshEntitiesException,
312 ReasonerInterruptedException, TimeOutException {
313 // TODO Auto-generated method stub
314 return null;
315 }
316
317 @Override
318 public NodeSet<OWLClass> getObjectPropertyDomains(
319 OWLObjectPropertyExpression pe, boolean direct)
320 throws InconsistentOntologyException, FreshEntitiesException,
321 ReasonerInterruptedException, TimeOutException {
322 // TODO Auto-generated method stub
323 return null;
324 }
325
326 @Override
327 public NodeSet<OWLClass> getObjectPropertyRanges(
328 OWLObjectPropertyExpression pe, boolean direct)
329 throws InconsistentOntologyException, FreshEntitiesException,
330 ReasonerInterruptedException, TimeOutException {
331 // TODO Auto-generated method stub
332 return null;
333 }
334
335 @Override
336 public Node<OWLDataProperty> getTopDataPropertyNode() {
337 // TODO Auto-generated method stub
338 return null;
339 }
340
341 @Override
342 public Node<OWLDataProperty> getBottomDataPropertyNode() {
343 // TODO Auto-generated method stub
344 return null;
345 }
346
347 @Override
348 public NodeSet<OWLDataProperty> getSubDataProperties(OWLDataProperty pe,
349 boolean direct) throws InconsistentOntologyException,
350 FreshEntitiesException, ReasonerInterruptedException,
351 TimeOutException {
352 // TODO Auto-generated method stub
353 return null;
354 }
355
356 @Override
357 public NodeSet<OWLDataProperty> getSuperDataProperties(OWLDataProperty pe,
358 boolean direct) throws InconsistentOntologyException,
359 FreshEntitiesException, ReasonerInterruptedException,
360 TimeOutException {
361 // TODO Auto-generated method stub
362 return null;
363 }
364
365 @Override
366 public Node<OWLDataProperty> getEquivalentDataProperties(OWLDataProperty pe)
367 throws InconsistentOntologyException, FreshEntitiesException,
368 ReasonerInterruptedException, TimeOutException {
369 // TODO Auto-generated method stub
370 return null;
371 }
372
373 @Override
374 public NodeSet<OWLDataProperty> getDisjointDataProperties(
375 OWLDataPropertyExpression pe) throws InconsistentOntologyException,
376 FreshEntitiesException, ReasonerInterruptedException,
377 TimeOutException {
378 // TODO Auto-generated method stub
379 return null;
380 }
381
382 @Override
383 public NodeSet<OWLClass> getDataPropertyDomains(OWLDataProperty pe,
384 boolean direct) throws InconsistentOntologyException,
385 FreshEntitiesException, ReasonerInterruptedException,
386 TimeOutException {
387 // TODO Auto-generated method stub
388 return null;
389 }
390
391 private Map<OWLNamedIndividual, OWLClassNodeSet> types = new HashMap<OWLNamedIndividual, OWLClassNodeSet>();
392 private OWLClassNodeSet thing;
393
394 @Override
395 public NodeSet<OWLClass> getTypes(OWLNamedIndividual ind, boolean direct) throws InconsistentOntologyException, FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
396 if (!sat) {
397 throw new InconsistentOntologyException();
398 }
399 if (types.containsKey(ind)) return types.get(ind);
400 return thing;
401 }
402
403 @Override
404 public NodeSet<OWLNamedIndividual> getInstances(OWLClassExpression ce,
405 boolean direct) throws InconsistentOntologyException,
406 ClassExpressionNotInProfileException, FreshEntitiesException,
407 ReasonerInterruptedException, TimeOutException {
408 // TODO Auto-generated method stub
409 return null;
410 }
411
412 @Override
413 public NodeSet<OWLNamedIndividual> getObjectPropertyValues(
414 OWLNamedIndividual ind, OWLObjectPropertyExpression pe)
415 throws InconsistentOntologyException, FreshEntitiesException,
416 ReasonerInterruptedException, TimeOutException {
417 // TODO Auto-generated method stub
418 return null;
419 }
420
421 @Override
422 public Set<OWLLiteral> getDataPropertyValues(OWLNamedIndividual ind,
423 OWLDataProperty pe) throws InconsistentOntologyException,
424 FreshEntitiesException, ReasonerInterruptedException,
425 TimeOutException {
426 // TODO Auto-generated method stub
427 return null;
428 }
429
430 @Override
431 public Node<OWLNamedIndividual> getSameIndividuals(OWLNamedIndividual ind)
432 throws InconsistentOntologyException, FreshEntitiesException,
433 ReasonerInterruptedException, TimeOutException {
434 // TODO Auto-generated method stub
435 return null;
436 }
437
438 @Override
439 public NodeSet<OWLNamedIndividual> getDifferentIndividuals(
440 OWLNamedIndividual ind) throws InconsistentOntologyException,
441 FreshEntitiesException, ReasonerInterruptedException,
442 TimeOutException {
443 // TODO Auto-generated method stub
444 return null;
445 }
446
447 @Override
448 public long getTimeOut() {
449 // TODO Auto-generated method stub
450 return 0;
451 }
452
453 @Override
454 public FreshEntityPolicy getFreshEntityPolicy() {
455 // TODO Auto-generated method stub
456 return null;
457 }
458
459 @Override
460 public IndividualNodeSetPolicy getIndividualNodeSetPolicy() {
461 // TODO Auto-generated method stub
462 return null;
463 }
464
465 @Override
466 public void dispose() {
467 reasoner.dispose();
468 }
469
470}
diff --git a/test/uk/ac/ox/cs/pagoda/ore/PagodaReasonerFactory.java b/test/uk/ac/ox/cs/pagoda/ore/PagodaReasonerFactory.java
deleted file mode 100644
index 8ecdf1d..0000000
--- a/test/uk/ac/ox/cs/pagoda/ore/PagodaReasonerFactory.java
+++ /dev/null
@@ -1,39 +0,0 @@
1package uk.ac.ox.cs.pagoda.ore;
2
3import org.semanticweb.owlapi.model.OWLOntology;
4import org.semanticweb.owlapi.reasoner.IllegalConfigurationException;
5import org.semanticweb.owlapi.reasoner.OWLReasoner;
6import org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration;
7import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
8
9public class PagodaReasonerFactory implements OWLReasonerFactory {
10
11 @Override
12 public String getReasonerName() {
13 return "PAGOdA";
14 }
15
16 @Override
17 public OWLReasoner createNonBufferingReasoner(OWLOntology ontology) {
18 // TODO Auto-generated method stub
19 return null;
20 }
21
22 @Override
23 public OWLReasoner createReasoner(OWLOntology ontology) {
24 return new PagodaOWLReasoner(ontology);
25 }
26
27 @Override
28 public OWLReasoner createNonBufferingReasoner(OWLOntology ontology, OWLReasonerConfiguration config) throws IllegalConfigurationException {
29 // TODO Auto-generated method stub
30 return null;
31 }
32
33 @Override
34 public OWLReasoner createReasoner(OWLOntology ontology, OWLReasonerConfiguration config) throws IllegalConfigurationException {
35 // TODO Auto-generated method stub
36 return null;
37 }
38
39}
diff --git a/test/uk/ac/ox/cs/pagoda/rules/approximators/TestSkolemTermsManager.java b/test/uk/ac/ox/cs/pagoda/rules/approximators/TestSkolemTermsManager.java
new file mode 100644
index 0000000..6bd8f05
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/rules/approximators/TestSkolemTermsManager.java
@@ -0,0 +1,14 @@
1package uk.ac.ox.cs.pagoda.rules.approximators;
2
3import org.testng.annotations.Test;
4
5/**
6 * Tests for the class <tt>SkolemTermsManager</tt>
7 */
8public class TestSkolemTermsManager {
9
10 @Test
11 public void test() {
12 // TODO some test
13 }
14}
diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
index 05a7d70..d741d3b 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
+++ b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
@@ -1,23 +1,24 @@
1package uk.ac.ox.cs.pagoda.tester; 1package uk.ac.ox.cs.pagoda.tester;
2 2
3import java.io.File;
4import java.io.FileNotFoundException;
5import java.io.IOException;
6import java.util.Scanner;
7
8import uk.ac.ox.cs.pagoda.query.AnswerTuple; 3import uk.ac.ox.cs.pagoda.query.AnswerTuple;
9import uk.ac.ox.cs.pagoda.query.AnswerTuples; 4import uk.ac.ox.cs.pagoda.query.AnswerTuples;
10import uk.ac.ox.cs.pagoda.reasoner.*; 5import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
11import uk.ac.ox.cs.pagoda.util.Properties; 6import uk.ac.ox.cs.pagoda.util.PagodaProperties;
12import uk.ac.ox.cs.pagoda.util.Timer; 7import uk.ac.ox.cs.pagoda.util.Timer;
13import uk.ac.ox.cs.pagoda.util.Utility; 8import uk.ac.ox.cs.pagoda.util.Utility;
14 9
10import java.io.File;
11import java.io.FileNotFoundException;
12import java.io.IOException;
13import java.util.Scanner;
14
15@Deprecated
15public class PagodaTester { 16public class PagodaTester {
16 17
17// public static final String onto_dir = "/media/RDFData/yzhou/"; 18 // public static final String onto_dir = "/media/RDFData/yzhou/";
18// public static final String onto_dir = "/users/yzhou/ontologies/"; 19// public static final String onto_dir = "/users/yzhou/ontologies/";
19// public static final String onto_dir = "/home/scratch/yzhou/ontologies/"; 20// public static final String onto_dir = "/home/scratch/yzhou/ontologies/";
20 public static final String onto_dir = "/home/yzhou/krr-nas-share/Yujiao/ontologies/"; 21 public static final String onto_dir = "/home/alessandro/Big_files/Ontologies/";
21 22
22 public static final String fly = onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"; 23 public static final String fly = onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl";
23 public static final String fly_query = onto_dir + "fly/queries/fly.sparql"; 24 public static final String fly_query = onto_dir + "fly/queries/fly.sparql";
@@ -37,7 +38,7 @@ public class PagodaTester {
37 public static final int uobm_number = 1; 38 public static final int uobm_number = 1;
38 public static final String uobm_tbox = onto_dir + "uobm/univ-bench-dl.owl"; 39 public static final String uobm_tbox = onto_dir + "uobm/univ-bench-dl.owl";
39 public static final String uobm_abox = onto_dir + "uobm/data/uobm" + uobm_number + ".ttl"; 40 public static final String uobm_abox = onto_dir + "uobm/data/uobm" + uobm_number + ".ttl";
40 public static final String uobm_query = onto_dir + "uobm/queries/standard.sparql"; 41 public static final String uobm_query = onto_dir + "uobm/queries/test.sparql";
41 public static final String uobm_query_temp = onto_dir + "uobm/queries/temp.sparql"; 42 public static final String uobm_query_temp = onto_dir + "uobm/queries/temp.sparql";
42 public static final String uobm_query2 = onto_dir + "uobm/queries/standard_q2.sparql"; 43 public static final String uobm_query2 = onto_dir + "uobm/queries/standard_q2.sparql";
43 public static final String uobm_query9 = onto_dir + "uobm/queries/standard_q9.sparql"; 44 public static final String uobm_query9 = onto_dir + "uobm/queries/standard_q9.sparql";
@@ -46,138 +47,149 @@ public class PagodaTester {
46 public static final String uobm_query14 = onto_dir + "uobm/queries/standard_q14.sparql"; 47 public static final String uobm_query14 = onto_dir + "uobm/queries/standard_q14.sparql";
47 public static final String uobm_query15 = onto_dir + "uobm/queries/standard_q15.sparql"; 48 public static final String uobm_query15 = onto_dir + "uobm/queries/standard_q15.sparql";
48 public static final String uobm_query_multi = onto_dir + "uobm/queries/standard_multi.sparql"; 49 public static final String uobm_query_multi = onto_dir + "uobm/queries/standard_multi.sparql";
49 public static final String uobm_generated_query1 = onto_dir + "uobm/queries/generated_q1.sparql"; 50 public static final String uobm_generated_query1 = onto_dir + "uobm/queries/generated_q1.sparql";
50 public static final String uobm_query_group3 = onto_dir + "uobm/queries/standard_group3.sparql"; 51 public static final String uobm_query_group3 = onto_dir + "uobm/queries/standard_group3.sparql";
51 52
52 public static final String npd_tbox = onto_dir + "npd/npd-all-minus-datatype.owl"; 53 public static final String npd_tbox = onto_dir + "npd/npd-all-minus-datatype.owl";
53 // "npd/npd-all.owl"; 54 // "npd/npd-all.owl";
54 // "npd-all-minus-datatype.owl"; 55 // "npd-all-minus-datatype.owl";
55 public static final String npd_abox = onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl"; 56 public static final String npd_abox = onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl";
56 // "npd/data/npd-data-dump-processed.ttl"; 57 // "npd/data/npd-data-dump-processed.ttl";
57 // "npd-data-dump-minus-datatype-old.ttl"; 58 // "npd-data-dump-minus-datatype-old.ttl";
58 public static final String npd_query = onto_dir + "npd/queries/atomic.sparql"; 59 public static final String npd_query = onto_dir + "npd/queries/atomic.sparql";
59 60
60 public static final String npd_bench_tbox = onto_dir + "npd-benchmark/npd-v2-ql_a.owl"; // npd-all-minus-datatype.owl"; 61 public static final String npd_bench_tbox = onto_dir + "npd-benchmark/npd-v2-ql_a.owl";
61 public static final String npd_bench_abox = onto_dir + "npd-benchmark/npd-v2-ql_a.ttl"; // npd-data-dump-minus-datatype-old.ttl"; 62 // npd-all-minus-datatype.owl";
63 public static final String npd_bench_abox = onto_dir + "npd-benchmark/npd-v2-ql_a.ttl";
64 // npd-data-dump-minus-datatype-old.ttl";
62 public static final String npd_bench_query = onto_dir + "npd-benchmark/queries/all.sparql"; 65 public static final String npd_bench_query = onto_dir + "npd-benchmark/queries/all.sparql";
63 66
64 public static final String dbpedia_tbox = onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"; 67 public static final String dbpedia_tbox = onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl";
65 public static final String dbpedia_abox = onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl"; 68 public static final String dbpedia_abox = onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl";
66 public static final String dbpedia_query = onto_dir + "dbpedia/queries/atomic_ground.sparql"; 69 public static final String dbpedia_query = onto_dir + "dbpedia/queries/atomic_ground.sparql";
67 public static final String dbpedia_query274 = onto_dir + "dbpedia/atomic_q274.sparql"; 70 public static final String dbpedia_query274 = onto_dir + "dbpedia/atomic_q274.sparql";
68 71
69 public static final String dbpedia_latest_tbox = onto_dir + "dbpedia/dbpedia_2014.owl"; 72 public static final String dbpedia_latest_tbox = onto_dir + "dbpedia/dbpedia_2014.owl";
70 public static final String travel_tbox = onto_dir + "dbpedia/travel.owl"; 73 public static final String travel_tbox = onto_dir + "dbpedia/travel.owl";
71 public static final String dbpedia_tbox_simple = onto_dir + "dbpedia/dbpedia_simple.owl"; 74 public static final String dbpedia_tbox_simple = onto_dir + "dbpedia/dbpedia_simple.owl";
72 75
73 public static final String bioModels_tbox = onto_dir + "biomodels/biomodels-21.owl"; 76 public static final String bioModels_tbox = onto_dir + "biomodels/biomodels-21.owl";
74 public static final String bioModels_abox = onto_dir + "biomodels/data_processed_1.ttl"; 77 public static final String bioModels_abox = onto_dir + "biomodels/data_processed_1.ttl";
75 public static final String bioModels_queries = onto_dir + "biomodels/queries/queries.sparql"; 78 public static final String bioModels_queries = onto_dir + "biomodels/queries/queries.sparql";
76 79
77 public static final String chembl_tbox = onto_dir + "bio2rdf/chembl/cco-processed-noDPR-noDPD.ttl"; 80 public static final String chembl_tbox = onto_dir + "bio2rdf/chembl/cco-processed-noDPR-noDPD.ttl";
78 public static final String chembl_abox = onto_dir + "bio2rdf/chembl/graph sampling old/sample_100.nt"; 81 public static final String chembl_abox = onto_dir + "bio2rdf/chembl/graph sampling old/sample_100.nt";
79 public static final String chembl_queries = onto_dir + "bio2rdf/chembl/queries/problematic.sparql"; //"bio2rdf/chembl/queries/atomic_one_filtered.sparql"; // 82 public static final String chembl_queries = onto_dir + "bio2rdf/chembl/queries/problematic.sparql";
80 83 //"bio2rdf/chembl/queries/atomic_one_filtered.sparql"; //
81 public static final String reactome_tbox = onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl"; 84
82 public static final String reactome_abox = onto_dir + "bio2rdf/reactome/graph sampling old/sample.ttl"; //data/data.ttl"; //graph sampling old/reactome_sample_10.ttl"; // 85 public static final String reactome_tbox = onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl";
83 public static final String reactome_queries = onto_dir +"bio2rdf/reactome/queries/atomic.sparql"; 86 public static final String reactome_abox = onto_dir + "bio2rdf/reactome/graph sampling old/sample.ttl";
84 87 //data/data.ttl"; //graph sampling old/reactome_sample_10.ttl"; //
85 public static final String uniprot_tbox = onto_dir + "bio2rdf/uniprot/core-processed.owl"; 88 public static final String reactome_queries = onto_dir + "bio2rdf/reactome/queries/atomic.sparql";
86 public static final String uniprot_abox = onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt"; 89
87 public static final String uniprot_queries = onto_dir + "bio2rdf/uniprot/queries/atomic_one.sparql"; 90 public static final String uniprot_tbox = onto_dir + "bio2rdf/uniprot/core-processed.owl";
88 91 public static final String uniprot_abox = onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt";
89 public static final String atlas_tbox = onto_dir + "bio2rdf/atlas/gxaterms.owl"; 92 public static final String uniprot_queries = onto_dir + "bio2rdf/uniprot/queries/atomic_one.sparql";
90 public static final String atlas_abox = onto_dir + "bio2rdf/atlas/graph sampling/sample_1.nt"; 93
91 public static final String atlas_queries = onto_dir + "bio2rdf/atlas/queries/atomic_one.sparql"; 94 public static final String atlas_tbox = onto_dir + "bio2rdf/atlas/gxaterms.owl";
92 95 public static final String atlas_abox = onto_dir + "bio2rdf/atlas/graph sampling/sample_1.nt";
96 public static final String atlas_queries = onto_dir + "bio2rdf/atlas/queries/atomic_one.sparql";
97 QueryReasoner pagoda;
98
99 // private void printPredicatesWithGap() {
100// for (String p: ((MyQueryReasoner) pagoda).getPredicatesWithGap()) {
101// System.out.println(p);
102// }
103// }
104 Timer timer = new Timer();
105
106 public PagodaTester(QueryReasoner reasoner) {
107 pagoda = reasoner;
108 }
109
93 public static void main(String... args) { 110 public static void main(String... args) {
94 if (args.length == 0) { 111 if(args.length == 0) {
95// args = new String[] {test_tbox, test_abox, test_query}; 112// args = new String[] {test_tbox, test_abox, test_query};
96// args = new String[] {lubm_tbox, lubm_abox, lubm_query.replace(".sparql", "_all_pagoda.sparql")}; 113// args = new String[] {lubm_tbox, lubm_abox, lubm_query};
97// args = new String[] {uobm_tbox, uobm_abox, uobm_query.replace(".sparql", "_all_pagoda.sparql")}; 114// args = new String[] {uobm_tbox, uobm_abox, uobm_query};
98// args = new String[] {fly, "null", fly_query.replace(".sparql", "_pellet.sparql") }; 115// args = new String[] {fly, "null", fly_query};
99// args = new String[] {dbpedia_tbox, dbpedia_abox, dbpedia_query}; 116// args = new String[] {dbpedia_tbox, dbpedia_abox, dbpedia_query};
100// args = new String[] {travel_tbox, null, dbpedia_query274}; 117// args = new String[] {travel_tbox, null, dbpedia_query274};
101// args = new String[] {fly, null, fly_query}; 118 args = new String[]{fly, fly_query};
102// args = new String[] {npd_tbox, npd_abox, npd_query}; 119// args = new String[] {npd_tbox, npd_abox, npd_query};
103// args = new String[] {npd_bench_tbox, npd_bench_abox, npd_bench_query}; 120// args = new String[] {npd_bench_tbox, npd_bench_abox, npd_bench_query};
104// args = new String[] {"../SemFacet/WebContent/WEB-INF/data/dbpedia.owl", "../SemFacet/WebContent/WEB-INF/data/dbpediaA.nt", null}; 121// args = new String[] {"../SemFacet/WebContent/WEB-INF/data/dbpedia.owl", "../SemFacet/WebContent/WEB-INF/data/dbpediaA.nt", null};
105// args = new String[] {"../core/WebContent/WEB-INF/data/fly.owl", "../core/WebContent/WEB-INF/data/fly-data.nt", null}; 122// args = new String[] {"../core/WebContent/WEB-INF/data/fly.owl", "../core/WebContent/WEB-INF/data/fly-data.nt", null};
106// args = new String[] {"data/lubm/univ-bench.owl", "data/lubm/lubm1.ttl", "data/lubm/lubm.sparql", "lubm.ans"}; 123// args = new String[] {"data/lubm/univ-bench.owl", "data/lubm/lubm1.ttl", "data/lubm/lubm.sparql", "lubm.ans"};
107// args = new String[] {"data/uobm/univ-bench-dl.owl", "data/uobm/uobm1.ttl", "data/uobm/uobm.sparql", "uobm.ans"}; 124// args = new String[] {"data/uobm/univ-bench-dl.owl", "data/uobm/uobm1.ttl", "data/uobm/uobm.sparql", "uobm.ans"};
108// args = new String[] {"data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", "data/fly/fly.sparql", "fly.ans"}; 125// args = new String[] {"data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", "data/fly/fly.sparql", "fly.ans"};
109// args = new String[] {bioModels_tbox, bioModels_abox, bioModels_queries}; 126// args = new String[] {bioModels_tbox, bioModels_abox, bioModels_queries};
110// args = new String[] {chembl_tbox, chembl_abox, chembl_queries}; 127// args = new String[] {chembl_tbox, chembl_abox, chembl_queries};
111// args = new String[] {reactome_tbox, reactome_abox, reactome_queries}; 128// args = new String[] {reactome_tbox, reactome_abox, reactome_queries};
112// args = new String[] {reactome_tbox, "/users/yzhou/temp/reactome_debug.ttl", onto_dir +"bio2rdf/reactome/queries/atomic_one_q65.sparql"}; 129// args = new String[] {reactome_tbox, "/users/yzhou/temp/reactome_debug.ttl", onto_dir +"bio2rdf/reactome/queries/atomic_one_q65.sparql"};
113// args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), "/users/yzhou/temp/uniprot_debug/sample_1_string.nt", uniprot_queries}; 130// args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), "/users/yzhou/temp/uniprot_debug/sample_1_string.nt", uniprot_queries};
114// args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), uniprot_abox, uniprot_queries}; 131// args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), uniprot_abox, uniprot_queries};
115// args = new String[] {atlas_tbox, atlas_abox, atlas_queries}; 132// args = new String[] {atlas_tbox, atlas_abox, atlas_queries};
116// args = new String[] {onto_dir + "test/unsatisfiable.owl", null, onto_dir + "test/unsatisfiable_queries.sparql"}; 133// args = new String[] {onto_dir + "test/unsatisfiable.owl", null, onto_dir + "test/unsatisfiable_queries.sparql"};
117// args = new String[] {onto_dir + "test/jair-example.owl", null, onto_dir + "test/jair-example_query.sparql"}; 134// args = new String[] {onto_dir + "test/jair-example.owl", null, onto_dir + "test/jair-example_query.sparql"};
118// args[2] = args[2].replace(".sparql", "_all_pagoda.sparql"); 135// args[2] = args[2].replace(".sparql", "_all_pagoda.sparql");
119// args[2] = args[2].replace(".sparql", "_pellet.sparql"); 136// args[2] = args[2].replace(".sparql", "_pellet.sparql");
120 } 137 }
121 138
122 Properties properties = new Properties("config/uobm.conf"); 139 PagodaProperties properties = new PagodaProperties("config/uobm.properties");
123 140
124 int index = 0; 141 int index = 0;
125 if (args.length > index) properties.setOntologyPath(args[index++]); 142 if(args.length > index) properties.setOntologyPath(args[index++]);
126 if (args.length > index && (args[index].endsWith(".ttl") || args[index].endsWith(".nt"))) properties.setDataPath(args[index++]); 143 if(args.length > index && (args[index].endsWith(".ttl") || args[index].endsWith(".nt")))
127 if (args.length > index && args[index].endsWith(".sparql")) properties.setQueryPath(args[index++]); 144 properties.setDataPath(args[index++]);
128 if (args.length > index && !args[index].startsWith("-")) properties.setAnswerPath(args[index++]); 145 if(args.length > index && args[index].endsWith(".sparql")) properties.setQueryPath(args[index++]);
129 if (args.length > index) properties.setToClassify(Boolean.parseBoolean(args[index++].substring(1))); 146 if(args.length > index && !args[index].startsWith("-")) properties.setAnswerPath(args[index++]);
130 if (args.length > index) properties.setToCallHermiT(Boolean.parseBoolean(args[index++].substring(1))); 147 if(args.length > index) properties.setToClassify(Boolean.parseBoolean(args[index++].substring(1)));
131 148 if(args.length > index) properties.setToCallHermiT(Boolean.parseBoolean(args[index++].substring(1)));
132 System.out.println("Ontology file: " + properties.getOntologyPath()); 149
133 System.out.println("Data files: " + properties.getDataPath()); 150 Utility.logInfo("Ontology file: " + properties.getOntologyPath());
134 System.out.println("Query files: " + properties.getQueryPath()); 151 Utility.logInfo("Data files: " + properties.getDataPath());
135 System.out.println("Answer file: " + properties.getAnswerPath()); 152 Utility.logInfo("Query files: " + properties.getQueryPath());
136 153 Utility.logInfo("Answer file: " + properties.getAnswerPath());
137 QueryReasoner pagoda = null; 154
138 155 QueryReasoner pagoda = null;
156
139 try { 157 try {
140 Timer t = new Timer(); 158 Timer t = new Timer();
141 pagoda = QueryReasoner.getInstance(properties); 159 pagoda = QueryReasoner.getInstance(properties);
142 if (pagoda == null) return; 160 if (pagoda == null) return;
143 161
144 Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds."); 162 Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
145 163
146 if (properties.getQueryPath() != null) 164 if (properties.getQueryPath() != null)
147 for (String queryFile: properties.getQueryPath().split(";")) 165 for (String queryFile: properties.getQueryPath().split(";"))
148 pagoda.evaluate(pagoda.getQueryManager().collectQueryRecords(queryFile), properties.getAnswerPath()); 166 pagoda.evaluate(pagoda.getQueryManager().collectQueryRecords(queryFile));
149 167
150 if (properties.getShellMode()) 168 if(properties.getShellMode())
151 try { 169 try {
152 evaluateConsoleQuery(pagoda); 170 evaluateConsoleQuery(pagoda);
153 } catch (IOException e) { 171 } catch(IOException e) {
154 e.printStackTrace(); 172 e.printStackTrace();
155 } 173 }
156 } finally { 174 } finally {
157 if (pagoda != null) pagoda.dispose(); 175 if (pagoda != null) pagoda.dispose();
158 } 176 }
159 177
160 Utility.closeCurrentOut(); 178// Utility.closeCurrentOut();
161 179
162 if (properties.getShellMode()) System.exit(0); 180 if(properties.getShellMode()) System.exit(0);
163 } 181 }
164
165// private void printPredicatesWithGap() {
166// for (String p: ((MyQueryReasoner) pagoda).getPredicatesWithGap()) {
167// System.out.println(p);
168// }
169// }
170 182
171 private static void evaluateConsoleQuery(QueryReasoner pagoda) throws IOException { 183 private static void evaluateConsoleQuery(QueryReasoner pagoda) throws IOException {
172 int ending = (int) '$', symbol; 184 int ending = (int) '$', symbol;
173 while (true) { 185 while(true) {
174 Utility.logInfo("Input your query ending with $"); 186 Utility.logInfo("Input your query ending with $");
175 StringBuilder queryBuilder = new StringBuilder(); 187 StringBuilder queryBuilder = new StringBuilder();
176 while ((symbol = System.in.read()) != ending) { 188 while((symbol = System.in.read()) != ending) {
177 queryBuilder.append((char) symbol); 189 queryBuilder.append((char) symbol);
178 } 190 }
179 System.in.read(); 191 System.in.read();
180 if (queryBuilder.length() == 0) return ; 192 if(queryBuilder.length() == 0) return;
181 pagoda.evaluate_shell(queryBuilder.toString()); 193 pagoda.evaluate_shell(queryBuilder.toString());
182 } 194 }
183 } 195 }
@@ -185,14 +197,14 @@ public class PagodaTester {
185 void testReactomeQueries() { 197 void testReactomeQueries() {
186 evaluate("select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level3.owl#DnaReference> . }"); 198 evaluate("select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level3.owl#DnaReference> . }");
187 evaluate("select ?y ?z where { <http://identifiers.org/ensembl/ENSG00000157557> ?y ?z . }"); 199 evaluate("select ?y ?z where { <http://identifiers.org/ensembl/ENSG00000157557> ?y ?z . }");
188 evaluate("select ?y where { <http://identifiers.org/ensembl/ENSG00000157557> <http://www.biopax.org/release/biopax-level3.owl#name> ?y . }", true); 200 evaluate("select ?y where { <http://identifiers.org/ensembl/ENSG00000157557> <http://www.biopax.org/release/biopax-level3.owl#name> ?y . }", true);
189 201
190 } 202 }
191 203
192 void testSemFacetQueries() { 204 void testSemFacetQueries() {
193// try { 205// try {
194// BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream("query.line"))); 206// BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream("query.line")));
195// for (String line; (line = reader.readLine()) != null && !line.isEmpty(); ) 207// for (String line; (line = reader.readLine()) != null && !line.isEmpty(); )
196// evaluate(line, true); 208// evaluate(line, true);
197// reader.close(); 209// reader.close();
198// } catch (FileNotFoundException e) { 210// } catch (FileNotFoundException e) {
@@ -203,36 +215,36 @@ public class PagodaTester {
203 evaluate("select ?x ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z }", true); 215 evaluate("select ?x ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z }", true);
204 evaluate("select distinct ?y where { ?x ?y ?z }", true); 216 evaluate("select distinct ?y where { ?x ?y ?z }", true);
205 evaluate("select distinct ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z }", true); 217 evaluate("select distinct ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z }", true);
206 evaluate("select ?y ?z where { <http://www.reactome.org/biopax/46/49633#Protein3885> ?y ?z .}", true); 218 evaluate("select ?y ?z where { <http://www.reactome.org/biopax/46/49633#Protein3885> ?y ?z .}", true);
207 } 219 }
208 220
209 void testISGQueries() { 221 void testISGQueries() {
210 evaluate("select ?z where {<http://cs.ox.ac.uk/Evgeny_Kharlamov> <http://cs.ox.ac.uk/lat> ?z .}", false); 222 evaluate("select ?z where {<http://cs.ox.ac.uk/Evgeny_Kharlamov> <http://cs.ox.ac.uk/lat> ?z .}", false);
211 evaluate("select ?x where {?x <http://cs.ox.ac.uk/type> <http://cs.ox.ac.uk/person> .}", false); 223 evaluate("select ?x where {?x <http://cs.ox.ac.uk/type> <http://cs.ox.ac.uk/person> .}", false);
212 } 224 }
213 225
214 void testSomeTravelQueries() { 226 void testSomeTravelQueries() {
215 evaluate("select ?y ?z where {<http://www.owl-ontologies.com/travel.owl#BlueMountains> ?y ?z. }", true); 227 evaluate("select ?y ?z where {<http://www.owl-ontologies.com/travel.owl#BlueMountains> ?y ?z. }", true);
216 evaluate("select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/travel.owl#RetireeDestination>. }"); 228 evaluate("select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/travel.owl#RetireeDestination>. }");
217 evaluate("select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/travel.owl#BackpackersDestination>. }"); 229 evaluate("select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/travel.owl#BackpackersDestination>. }");
218 } 230 }
219 231
220 void testSomeFlyQueries() { 232 void testSomeFlyQueries() {
221 evaluate("select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00005106> . }", false); 233 evaluate("select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00005106> . }", false);
222 234
223 evaluate("select DISTINCT ?z where { ?x <http://purl.obolibrary.org/obo/FBbt#develops_from> ?any . ?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z . ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00067123> . } ", true); 235 evaluate("select DISTINCT ?z where { ?x <http://purl.obolibrary.org/obo/FBbt#develops_from> ?any . ?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z . ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00067123> . } ", true);
224 236
225 evaluate("Select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> " 237 evaluate("Select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
226 + "<http://purl.obolibrary.org/obo/FBbt_00067123>. ?x " 238 + "<http://purl.obolibrary.org/obo/FBbt_00067123>. ?x "
227 + "<http://purl.obolibrary.org/obo/RO_0002131> ?any . ?any " 239 + "<http://purl.obolibrary.org/obo/RO_0002131> ?any . ?any "
228 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> " 240 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
229 + "<http://purl.obolibrary.org/obo/FBbt_00005140> . }", true); 241 + "<http://purl.obolibrary.org/obo/FBbt_00005140> . }", true);
230 242
231 evaluate("Select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> " 243 evaluate("Select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
232 + "<http://purl.obolibrary.org/obo/FBbt_00067363> . ?x " 244 + "<http://purl.obolibrary.org/obo/FBbt_00067363> . ?x "
233 + "<http://purl.obolibrary.org/obo/RO_0002131> ?any . ?any " 245 + "<http://purl.obolibrary.org/obo/RO_0002131> ?any . ?any "
234 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> " 246 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
235 + "<http://purl.obolibrary.org/obo/FBbt_00005140> . }", true); 247 + "<http://purl.obolibrary.org/obo/FBbt_00005140> . }", true);
236 248
237// evaluate("Select ?x where { " 249// evaluate("Select ?x where { "
238// + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00003660>. " 250// + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00003660>. "
@@ -240,18 +252,18 @@ public class PagodaTester {
240// + "?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00001446> . }", true); 252// + "?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00001446> . }", true);
241 253
242 evaluate("select DISTINCT ?z where { ?x <http://purl.obolibrary.org/obo/RO_0002110> ?any . " 254 evaluate("select DISTINCT ?z where { ?x <http://purl.obolibrary.org/obo/RO_0002110> ?any . "
243 + "?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z . " 255 + "?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z . "
244 + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007016> . } ", true); 256 + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007016> . } ", true);
245 257
246 evaluate("Select * where {" 258 evaluate("Select * where {"
247 + "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100607> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007364>. " 259 + "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100607> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007364>. "
248 + "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100607> <http://www.w3.org/2002/07/owl#sameAs> ?z }", true); 260 + "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100607> <http://www.w3.org/2002/07/owl#sameAs> ?z }", true);
249 261
250 evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://www.w3.org/2002/07/owl#sameAs> ?z}", true); 262 evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://www.w3.org/2002/07/owl#sameAs> ?z}", true);
251 evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://purl.obolibrary.org/obo/BFO_0000051> ?z}", true); 263 evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://purl.obolibrary.org/obo/BFO_0000051> ?z}", true);
252 264
253 evaluate("select DISTINCT ?y where { ?x ?y ?z . " 265 evaluate("select DISTINCT ?y where { ?x ?y ?z . "
254 + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007364> }", true); 266 + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007364> }", true);
255 267
256 evaluateQueriesFromFile("/users/yzhou/Downloads/logs(1).log"); 268 evaluateQueriesFromFile("/users/yzhou/Downloads/logs(1).log");
257 evaluateQueriesFromFile("/users/yzhou/Downloads/logs.log"); 269 evaluateQueriesFromFile("/users/yzhou/Downloads/logs.log");
@@ -268,46 +280,38 @@ public class PagodaTester {
268 try { 280 try {
269 scanner = new Scanner(new File(fileName)); 281 scanner = new Scanner(new File(fileName));
270 String line; 282 String line;
271 while (scanner.hasNextLine()) { 283 while(scanner.hasNextLine()) {
272 line = scanner.nextLine(); 284 line = scanner.nextLine();
273 if (line.startsWith("select")) 285 if(line.startsWith("select"))
274 evaluate(line, true); 286 evaluate(line, true);
275 } 287 }
276 } catch (FileNotFoundException e) { 288 } catch(FileNotFoundException e) {
277 e.printStackTrace(); 289 e.printStackTrace();
278 } finally { 290 } finally {
279 if (scanner != null) 291 if(scanner != null)
280 scanner.close(); 292 scanner.close();
281 } 293 }
282 } 294 }
283 295
284 QueryReasoner pagoda;
285
286 public PagodaTester(QueryReasoner reasoner) {
287 pagoda = reasoner;
288 }
289
290 Timer timer = new Timer();
291
292 private void evaluate(String query) { 296 private void evaluate(String query) {
293 evaluate(query, false); 297 evaluate(query, false);
294 } 298 }
295 299
296 private void evaluate(String query, boolean tag) { 300 private void evaluate(String query, boolean tag) {
297 timer.reset(); 301 timer.reset();
298 AnswerTuples tuples = pagoda.evaluate(query, tag); 302 AnswerTuples tuples = pagoda.evaluate(query, tag);
299 int arity = tuples.getArity(); 303 int arity = tuples.getArity();
300 int count = 0; 304 int count = 0;
301 for (AnswerTuple tuple; tuples.isValid(); tuples.moveNext()) { 305 for(AnswerTuple tuple; tuples.isValid(); tuples.moveNext()) {
302 tuple = tuples.getTuple(); 306 tuple = tuples.getTuple();
303 for (int i = 0; i < arity; ++i) 307 for(int i = 0; i < arity; ++i)
304 tuple.getGroundTerm(i).toString(); 308 tuple.getGroundTerm(i).toString();
305// System.out.print(tuple.getGroundTerm(i).toString() + "\t"); 309// System.out.print(tuple.getGroundTerm(i).toString() + "\t");
306// System.out.println(); 310// System.out.println();
307 ++count; 311 ++count;
308 } 312 }
309 tuples.dispose(); 313 tuples.dispose();
310 Utility.logInfo("The number of answers for this SemFacet query: " + count); 314 Utility.logInfo("The number of answers for this SemFacet query: " + count);
311 Utility.logInfo("Total time for this SemFacet query: " + timer.duration()); 315 Utility.logInfo("Total time for this SemFacet query: " + timer.duration());
312 } 316 }
313 317
diff --git a/test/uk/ac/ox/cs/pagoda/tester/Statistics.java b/test/uk/ac/ox/cs/pagoda/tester/Statistics.java
index 71f1726..13d7f90 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/Statistics.java
+++ b/test/uk/ac/ox/cs/pagoda/tester/Statistics.java
@@ -6,6 +6,7 @@ import java.util.Iterator;
6import java.util.LinkedList; 6import java.util.LinkedList;
7import java.util.Scanner; 7import java.util.Scanner;
8 8
9@Deprecated
9public class Statistics { 10public class Statistics {
10 11
11 double satCheckTime; 12 double satCheckTime;
diff --git a/test/uk/ac/ox/cs/pagoda/util/TestUtil.java b/test/uk/ac/ox/cs/pagoda/util/TestUtil.java
new file mode 100644
index 0000000..c3909d5
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/util/TestUtil.java
@@ -0,0 +1,74 @@
1package uk.ac.ox.cs.pagoda.util;
2
3import org.apache.log4j.Appender;
4import org.apache.log4j.FileAppender;
5import org.apache.log4j.Logger;
6
7import java.io.File;
8import java.io.IOException;
9import java.io.InputStream;
10import java.net.URL;
11import java.nio.file.Files;
12import java.nio.file.Path;
13import java.nio.file.Paths;
14import java.util.Enumeration;
15import java.util.Properties;
16
17import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
18
19/**
20 * A collection of utility methods for testing.
21 */
22public class TestUtil {
23
24 public static final String CONFIG_FILE = "test.properties";
25
26 private static boolean isConfigLoaded = false;
27 private static Properties config;
28
29 public static Properties getConfig() {
30 if(!isConfigLoaded) {
31 try(InputStream in = TestUtil.class.getClassLoader().getResourceAsStream(CONFIG_FILE)) {
32 config = new java.util.Properties();
33 config.load(in);
34 in.close();
35 isConfigLoaded = true;
36 } catch (IOException e) {
37 e.printStackTrace();
38 }
39 }
40 return config;
41 }
42
43 public static String combinePaths(String path1, String path2) {
44 File file1 = new File(path1);
45 File file2 = new File(file1, path2);
46 return file2.getPath();
47 }
48
49 public static void copyFile(String src, String dst) throws IOException {
50 Files.copy(Paths.get(src), Paths.get(dst), REPLACE_EXISTING);
51 }
52
53 /**
54 * Get the log file, which is assumed unique.
55 * */
56 public static String getLogFileName() {
57 Enumeration e = Logger.getRootLogger().getAllAppenders();
58 while (e.hasMoreElements()){
59 Appender app = (Appender)e.nextElement();
60 if (app instanceof FileAppender){
61 return ((FileAppender)app).getFile();
62 }
63 }
64 return null;
65 }
66
67 public static Path getAnswersFilePath(String name) {
68 URL givenAnswersURL = TestUtil.class.getClassLoader()
69 .getResource(name);
70 if(givenAnswersURL == null) throw new RuntimeException("Missing answers file:" + name);
71 return Paths.get(givenAnswersURL.getPath());
72 }
73
74}
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-06 07:50:16 +0000