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-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/AllTests.java50
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java165
-rw-r--r--test/uk/ac/ox/cs/pagoda/junit/CostEvaluation.java109
-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.java85
-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
15 files changed, 897 insertions, 0 deletions
diff --git a/test/uk/ac/ox/cs/pagoda/junit/AllTests.java b/test/uk/ac/ox/cs/pagoda/junit/AllTests.java
new file mode 100644
index 0000000..6884081
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/AllTests.java
@@ -0,0 +1,50 @@
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
16import uk.ac.ox.cs.data.WriteIntoTurtle;
17
18@RunWith(Suite.class)
19@SuiteClasses({ WriteIntoTurtle.class, PagodaUOBM.class
20 })
21public class AllTests {
22
23 public static void copy(String source, String dest) {
24 InputStream is = null;
25 OutputStream os = null;
26 try {
27 is = new FileInputStream(source);
28 os = new FileOutputStream(dest);
29 byte[] buffer = new byte[1024];
30 int length;
31 while ((length = is.read(buffer)) > 0) {
32 os.write(buffer, 0, length);
33 }
34 is.close();
35 os.close();
36
37 BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(source)));
38 writer.write("");
39 writer.close();
40 } catch (FileNotFoundException e) {
41 e.printStackTrace();
42 } catch (IOException e) {
43 e.printStackTrace();
44 }
45
46// File src = new File(source);
47// src.delete();
48 }
49
50}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java b/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
new file mode 100644
index 0000000..d23f186
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
@@ -0,0 +1,165 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import static org.junit.Assert.*;
4
5import org.junit.Test;
6import org.semanticweb.HermiT.model.Atom;
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.Variable;
12import org.semanticweb.owlapi.apibinding.OWLManager;
13import org.semanticweb.owlapi.model.OWLOntology;
14import org.semanticweb.owlapi.model.OWLOntologyManager;
15
16import uk.ac.ox.cs.pagoda.approx.Clause;
17import uk.ac.ox.cs.pagoda.approx.Clausifier;
18
19public class ClauseTester {
20
21 @Test
22 public void test_simple() {
23 Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2");
24 AtomicConcept A = AtomicConcept.create("A");
25 AtomicRole r = AtomicRole.create("r");
26 Atom[] bodyAtoms = new Atom[] {
27 Atom.create(A, x),
28 Atom.create(r, x, y1),
29 Atom.create(r, x, y2)
30 };
31
32 Atom[] headAtoms = new Atom[] {
33 Atom.create(Equality.INSTANCE, y1, y2)
34 };
35
36 OWLOntologyManager m = OWLManager.createOWLOntologyManager();
37 OWLOntology emptyOntology = null;
38 try {
39 emptyOntology = m.createOntology();
40 } catch (Exception e) {
41 e.printStackTrace();
42 fail("failed to create a new ontology");
43 }
44 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
45 System.out.println(c.toString());
46 }
47
48 @Test
49 public void test_more() {
50 Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"), y3 = Variable.create("y3");
51 AtomicConcept A = AtomicConcept.create("A");
52 AtomicRole r = AtomicRole.create("r");
53 Atom[] bodyAtoms = new Atom[] {
54 Atom.create(A, x),
55 Atom.create(r, x, y1),
56 Atom.create(r, x, y2),
57 Atom.create(r, x, y3),
58 };
59
60 Atom[] headAtoms = new Atom[] {
61 Atom.create(Equality.INSTANCE, y1, y2),
62 Atom.create(Equality.INSTANCE, y1, y3),
63 Atom.create(Equality.INSTANCE, y2, y3)
64 };
65
66 OWLOntologyManager m = OWLManager.createOWLOntologyManager();
67 OWLOntology emptyOntology = null;
68 try {
69 emptyOntology = m.createOntology();
70 } catch (Exception e) {
71 e.printStackTrace();
72 fail("failed to create a new ontology");
73 }
74 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
75 System.out.println(c.toString());
76 }
77
78 @Test
79 public void test_inverse() {
80 Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2");
81 AtomicConcept A = AtomicConcept.create("A");
82 AtomicRole r = AtomicRole.create("r");
83 Atom[] bodyAtoms = new Atom[] {
84 Atom.create(A, x),
85 Atom.create(r, y1, x),
86 Atom.create(r, y2, x)
87 };
88
89 Atom[] headAtoms = new Atom[] {
90 Atom.create(Equality.INSTANCE, y1, y2)
91 };
92
93 OWLOntologyManager m = OWLManager.createOWLOntologyManager();
94 OWLOntology emptyOntology = null;
95 try {
96 emptyOntology = m.createOntology();
97 } catch (Exception e) {
98 e.printStackTrace();
99 fail("failed to create a new ontology");
100 }
101 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
102 System.out.println(c.toString());
103 }
104
105 @Test
106 public void test_fillter() {
107 Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2");
108 AtomicConcept A = AtomicConcept.create("A");
109 AtomicConcept B = AtomicConcept.create("B");
110 AtomicRole r = AtomicRole.create("r");
111 Atom[] bodyAtoms = new Atom[] {
112 Atom.create(A, x),
113 Atom.create(r, y1, x),
114 Atom.create(r, y2, x),
115 Atom.create(B, y1),
116 Atom.create(B, y2)
117 };
118
119 Atom[] headAtoms = new Atom[] {
120 Atom.create(Equality.INSTANCE, y1, y2)
121 };
122
123 OWLOntologyManager m = OWLManager.createOWLOntologyManager();
124 OWLOntology emptyOntology = null;
125 try {
126 emptyOntology = m.createOntology();
127 } catch (Exception e) {
128 e.printStackTrace();
129 fail("failed to create a new ontology");
130 }
131 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
132 System.out.println(c.toString());
133 }
134
135 @Test
136 public void test_negFillter() {
137 Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2");
138 AtomicConcept A = AtomicConcept.create("A");
139 AtomicConcept B = AtomicConcept.create("B");
140 AtomicRole r = AtomicRole.create("r");
141 Atom[] bodyAtoms = new Atom[] {
142 Atom.create(A, x),
143 Atom.create(r, y1, x),
144 Atom.create(r, y2, x)
145 };
146
147 Atom[] headAtoms = new Atom[] {
148 Atom.create(Equality.INSTANCE, y1, y2),
149 Atom.create(B, y1),
150 Atom.create(B, y2)
151 };
152
153 OWLOntologyManager m = OWLManager.createOWLOntologyManager();
154 OWLOntology emptyOntology = null;
155 try {
156 emptyOntology = m.createOntology();
157 } catch (Exception e) {
158 e.printStackTrace();
159 fail("failed to create a new ontology");
160 }
161 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
162 System.out.println(c.toString());
163 }
164
165}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/CostEvaluation.java b/test/uk/ac/ox/cs/pagoda/junit/CostEvaluation.java
new file mode 100644
index 0000000..87b01ed
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/CostEvaluation.java
@@ -0,0 +1,109 @@
1package uk.ac.ox.cs.pagoda.junit;
2
3import org.junit.Test;
4import org.semanticweb.owlapi.model.OWLOntology;
5
6import uk.ac.ox.cs.pagoda.owl.OWLHelper;
7import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
8import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner.Type;
9import uk.ac.ox.cs.pagoda.tester.PagodaTester;
10import uk.ac.ox.cs.pagoda.util.Timer;
11import uk.ac.ox.cs.pagoda.util.Utility;
12
13public class CostEvaluation {
14
15 @Test
16 public void lubm100() {
17 int number = 1;
18 PagodaTester.main(
19 PagodaTester.onto_dir + "lubm/univ-bench.owl",
20 PagodaTester.onto_dir + "lubm/data/lubm" + number + ".ttl",
21 PagodaTester.onto_dir + "lubm/queries/test_all_pagoda.sparql"
22 );
23// AllTests.copy("output/log4j.log", "results-backup/jair/lubm" + number + ".out");
24 }
25
26 public void lubm1000() {
27 int number = 1000;
28 String[] args = new String[] {
29 PagodaTester.onto_dir + "lubm/univ-bench.owl",
30 PagodaTester.onto_dir + "lubm/data/lubm" + number + ".ttl",
31 PagodaTester.onto_dir + "lubm/queries/test_all_pagoda.sparql"
32 };
33 OWLOntology ontology = OWLHelper.loadOntology(args[0]);
34 QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true);
35 Timer t = new Timer();
36 reasoner.loadOntology(ontology);
37 reasoner.importData(args[1]);
38 if (!reasoner.preprocess())
39 return ;
40 Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
41
42 reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2]));
43// AllTests.copy("output/log4j.log", "results-backup/jair/lubm" + number + ".out");
44 }
45
46 @Test
47 public void uobm5() {
48 int number = 1;
49 String[] args = new String[] {
50 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
51 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
52 PagodaTester.onto_dir + "uobm/queries/standard_all_pagoda.sparql"
53 };
54 PagodaTester.main(args);
55// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out");
56 }
57
58 public void uobm100() {
59 int number = 200;
60 String[] args = new String[] {
61 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
62 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
63 PagodaTester.onto_dir + "uobm/queries/standard_group3_all.sparql"
64 };
65 PagodaTester.main(args);
66// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out");
67 }
68
69 public void uobm500() {
70 int number = 500;
71 String[] args = new String[] {
72 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
73 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
74 PagodaTester.onto_dir + "uobm/queries/standard_all_pagoda.sparql"
75 };
76
77 OWLOntology ontology = OWLHelper.loadOntology(args[0]);
78 QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true);
79 Timer t = new Timer();
80 reasoner.loadOntology(ontology);
81 reasoner.importData(args[1]);
82 if (!reasoner.preprocess())
83 return ;
84 Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
85
86 reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2]));
87// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out");
88 }
89
90
91 public static void main(String... args) {
92 args = new String[] {
93 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl",
94 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl",
95 PagodaTester.onto_dir + "dbpedia/queries/atomic_ground.sparql"
96 };
97
98 OWLOntology ontology = OWLHelper.loadOntology(args[0]);
99 QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true);
100 Timer t = new Timer();
101 reasoner.loadOntology(ontology);
102 reasoner.importData(args[1]);
103 if (!reasoner.preprocess())
104 return ;
105 Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
106
107 reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2]));
108 }
109}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java b/test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java
new file mode 100644
index 0000000..3406ed2
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java
@@ -0,0 +1,14 @@
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
new file mode 100644
index 0000000..2a148cc
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/JAIR_PAGOdA.java
@@ -0,0 +1,173 @@
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
new file mode 100644
index 0000000..5bd3134
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java
@@ -0,0 +1,85 @@
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_Scalability {
8
9 private static final String date = "_0123";
10
11 @Test
12 public void reactome() {
13 testReactome(10, false);
14 }
15
16 @Test
17 public void chembl() {
18 testChEMBL(1, false);
19 }
20
21 @Test
22 public void uniprot() {
23 testUniProt(1, false);
24 }
25
26 public void testReactome(int percentage, boolean save) {
27 String[] args = new String[] {
28 PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl",
29 PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/simplifed_sample_" + percentage + ".ttl",
30 PagodaTester.onto_dir + "bio2rdf/reactome/queries/test.sparql"
31 , "reactome.ans"
32 };
33 if (percentage == 10)
34 args[1] = args[1].replace("simplifed", "reactome");
35
36 PagodaTester.main(args);
37 if (save)
38 AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_" + percentage + "p" + date);
39 }
40
41 public void testChEMBL(int percentage, boolean save) {
42 String[] args = new String[] {
43 PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl",
44 PagodaTester.onto_dir + "bio2rdf/chembl/sample_" + percentage + ".nt",
45// PagodaTester.onto_dir + "bio2rdf/chembl/queries/atomic_ground.sparql"
46 PagodaTester.onto_dir + "bio2rdf/chembl/queries/test.sparql"
47 , "chembl.ans"
48 };
49 if (percentage == 1 || percentage == 10 || percentage == 50)
50 args[1] = args[1].replace("chembl", "chembl/graph sampling");
51 else
52 if (percentage == 100)
53 args[1] = "/home/yzhou/RDFData/ChEMBL/facts/ChEMBL.ttl";
54
55 PagodaTester.main(args);
56 if (save)
57 AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_" + percentage + "p" + date);
58 }
59
60 public void testUniProt(int percentage, boolean save) {
61 String[] args = new String[] {
62 PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat-processed.owl",
63 PagodaTester.onto_dir + "bio2rdf/uniprot/sample_" + percentage + ".nt",
64// PagodaTester.onto_dir + "bio2rdf/uniprot/queries/atomic_ground.sparql"
65 PagodaTester.onto_dir + "bio2rdf/uniprot/queries/test.sparql"
66 , "uniprot.ans"
67 };
68
69 if (percentage == 1 || percentage == 10 || percentage == 50)
70 args[1] = args[1].replace("uniprot", "uniprot/graph sampling");
71 else
72 if (percentage == 100)
73 args[1] = "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/data/uniprot_cleaned.nt";
74
75 PagodaTester.main(args);
76 if (save)
77 AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_" + percentage + "p" + date);
78 }
79
80 public static void main(String... args) {
81 PagodaTester.ShellMode = true;
82 new JAIR_Scalability().testUniProt(50, false);
83 }
84
85}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/LightEvaluation.java b/test/uk/ac/ox/cs/pagoda/junit/LightEvaluation.java
new file mode 100644
index 0000000..1ddca15
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/LightEvaluation.java
@@ -0,0 +1,59 @@
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
new file mode 100644
index 0000000..37ffb44
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/PagodaDBPedia.java
@@ -0,0 +1,27 @@
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
new file mode 100644
index 0000000..d999a6e
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/PagodaELU.java
@@ -0,0 +1,18 @@
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
new file mode 100644
index 0000000..4631837
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/PagodaFLY.java
@@ -0,0 +1,24 @@
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
new file mode 100644
index 0000000..f8fef0e
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/PagodaLUBM.java
@@ -0,0 +1,38 @@
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
new file mode 100644
index 0000000..96edbb4
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD.java
@@ -0,0 +1,42 @@
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
new file mode 100644
index 0000000..df1a57d
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD_bench.java
@@ -0,0 +1,27 @@
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
new file mode 100644
index 0000000..5d93302
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/PagodaRLU.java
@@ -0,0 +1,18 @@
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
new file mode 100644
index 0000000..5b56c6d
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/junit/PagodaUOBM.java
@@ -0,0 +1,48 @@
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}
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-06 22:39:09 +0000