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-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java269
-rw-r--r--test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java14
2 files changed, 283 insertions, 0 deletions
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java b/test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java
new file mode 100644
index 0000000..2fc682b
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java
@@ -0,0 +1,269 @@
1package uk.ac.ox.cs.pagoda.global_tests;
2
3import org.semanticweb.owlapi.apibinding.OWLManager;
4import org.semanticweb.owlapi.model.*;
5import org.testng.Assert;
6import org.testng.annotations.Test;
7import uk.ac.ox.cs.pagoda.query.AnswerTuple;
8import uk.ac.ox.cs.pagoda.query.AnswerTuples;
9import uk.ac.ox.cs.pagoda.query.QueryRecord;
10import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
11import uk.ac.ox.cs.pagoda.util.TestUtil;
12
13import java.io.IOException;
14import java.nio.file.Files;
15import java.nio.file.Paths;
16
17public class SkolemisationTests {
18
19 public static final String NS = "http://example.org/test#%s";
20
21 private IRI getEntityIRI(String name) {
22 return IRI.create(String.format(NS, name));
23 }
24
25// @Test
26 public void commonSuccessorTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
27
28 /*
29 * Build test ontology
30 * */
31
32 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
33 OWLDataFactory factory = manager.getOWLDataFactory();
34 OWLOntology ontology = manager.createOntology();
35
36 OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
37 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
38 OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
39 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
40 OWLClass classC = factory.getOWLClass(getEntityIRI("C"));
41 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classC));
42 OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
43 OWLNamedIndividual d = factory.getOWLNamedIndividual(getEntityIRI("d"));
44 OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
45 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
46
47 // Class assertions
48 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, c)); // A(c)
49 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, d)); // A(d)
50
51 // Minimum cardinality axiom
52 manager.addAxiom(ontology,
53 factory.getOWLSubClassOfAxiom(classA,
54 factory.getOWLObjectUnionOf(
55 factory.getOWLObjectSomeValuesFrom(roleR, classB),
56 factory.getOWLObjectSomeValuesFrom(roleR, classC))));
57
58 /*
59 * Save the ontology
60 * */
61
62// manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
63
64 /*
65 * Test one query
66 * */
67
68 QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
69 pagoda.loadOntology(ontology);
70 if(pagoda.preprocess()) {
71 String queryStr = "select distinct ?x ?y " +
72 " where { "
73 + " ?x <" + roleR.toStringID() + "> _:z . "
74 + " ?y <" + roleR.toStringID() + "> _:z " +
75 " }";
76 QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
77 pagoda.evaluate(queryRecord);
78 AnswerTuples answers = queryRecord.getAnswers();
79 System.out.println("Difficulty: " + queryRecord.getDifficulty());
80 int count = 0;
81 for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
82 ans = answers.getTuple();
83 TestUtil.logInfo(ans);
84 count++;
85 }
86 Assert.assertEquals(count, 2);
87 }
88 pagoda.dispose();
89 }
90
91// @Test
92 public void yTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
93
94 /*
95 * Build test ontology
96 * */
97
98 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
99 OWLDataFactory factory = manager.getOWLDataFactory();
100 OWLOntology ontology = manager.createOntology();
101
102 OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
103 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
104 OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
105 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
106 OWLClass classC = factory.getOWLClass(getEntityIRI("C"));
107 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classC));
108 OWLClass classD = factory.getOWLClass(getEntityIRI("D"));
109 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classD));
110 OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
111 OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
112 OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
113 OWLNamedIndividual d = factory.getOWLNamedIndividual(getEntityIRI("d"));
114 OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
115 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
116 OWLObjectProperty roleS = factory.getOWLObjectProperty(IRI.create(String.format(NS, "S")));
117 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleS));
118 OWLObjectProperty roleP = factory.getOWLObjectProperty(IRI.create(String.format(NS, "P")));
119 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleP));
120
121 // Class assertions
122 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classD, a)); // D(a)
123 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classD, b)); // D(b)
124 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleS, c, a)); // S(c,a)
125 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleP, d, b)); // P(d,b)
126
127 // Axioms
128 // subsetOf(D someValuesFrom(R owl:Thing))
129 manager.addAxiom(ontology,
130 factory.getOWLSubClassOfAxiom(classD,
131 factory.getOWLObjectSomeValuesFrom(roleR,
132 factory.getOWLThing())));
133 // subsetOf(someValuesFrom(inverseOf(S) owl:Thing) allValuesFrom(R A))
134 manager.addAxiom(ontology,
135 factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleS.getInverseProperty(),
136 factory.getOWLThing()),
137 factory.getOWLObjectAllValuesFrom(roleR, classA)));
138 // subsetOf(someValuesFrom(inverseOf(P) owl:Thing) B)
139 manager.addAxiom(ontology,
140 factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleP.getInverseProperty(),
141 factory.getOWLThing()),
142 classB));
143 // subsetOf(someValuesFrom(R A) C)
144 manager.addAxiom(ontology,
145 factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleR, classA), classC));
146
147 /*
148 * Save the ontology
149 * */
150
151 manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
152
153 /*
154 * Test one query
155 * */
156
157 QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
158 pagoda.loadOntology(ontology);
159 if(pagoda.preprocess()) {
160 String queryStr = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
161 "select distinct ?x" +
162 " where { "
163// + " ?x rdf:type " + classB + " ."
164// + " ?x " + roleR + " "+ "_:y . "
165 + " ?x rdf:type " + classC +
166 " }";
167 QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
168 System.out.println(queryRecord);
169 pagoda.evaluate(queryRecord);
170 AnswerTuples answers = queryRecord.getAnswers();
171 System.out.println("Difficulty: " + queryRecord.getDifficulty());
172 int count = 0;
173 for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
174 ans = answers.getTuple();
175 TestUtil.logInfo(ans);
176 count++;
177 }
178// Assert.assertEquals(count, 1);
179 }
180 pagoda.dispose();
181 }
182
183 @Test
184 public void rTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
185
186 /*
187 * Build test ontology
188 * */
189
190 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
191 OWLDataFactory factory = manager.getOWLDataFactory();
192 OWLOntology ontology = manager.createOntology();
193
194 OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
195 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
196 OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
197 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
198// OWLClass classC = factory.getOWLClass(getEntityIRI("C"));
199// manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classC));
200// OWLClass classD = factory.getOWLClass(getEntityIRI("D"));
201// manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classD));
202 OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
203 OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
204 OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
205// OWLNamedIndividual d = factory.getOWLNamedIndividual(getEntityIRI("d"));
206 OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
207 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
208// OWLObjectProperty roleF = factory.getOWLObjectProperty(IRI.create(String.format(NS, "F")));
209// manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleF));
210 OWLObjectProperty roleP = factory.getOWLObjectProperty(IRI.create(String.format(NS, "P")));
211 manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleP));
212// OWLObjectProperty roleL = factory.getOWLObjectProperty(IRI.create(String.format(NS, "L")));
213// manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleL));
214
215 // Class assertions
216 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, a)); // A(a)
217 manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, b)); // A(b)
218 manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleP, c, a)); // P(c,a)
219
220 // Axioms
221 // subsetOf(A someValuesFrom(R owl:Thing))
222 manager.addAxiom(ontology,
223 factory.getOWLSubClassOfAxiom(classA,
224 factory.getOWLObjectSomeValuesFrom(roleR,
225 factory.getOWLThing())));
226
227 // inverseFunctional(R)
228 manager.addAxiom(ontology,
229 factory.getOWLInverseFunctionalObjectPropertyAxiom(roleR));
230
231 // subsetOf(someValuesFrom(inverseOf(P) owl:thing) B)
232 manager.addAxiom(ontology,
233 factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleP.getInverseProperty(),
234 factory.getOWLThing()),
235 classB));
236 /*
237 * Save the ontology
238 * */
239
240 manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
241
242 /*
243 * Test one query
244 * */
245
246 QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
247 pagoda.loadOntology(ontology);
248 if(pagoda.preprocess()) {
249 String queryStr = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
250 "select distinct ?x" +
251 " where { "
252 + " ?x rdf:type " + classB +
253 " }";
254 QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
255 System.out.println(queryRecord);
256 pagoda.evaluate(queryRecord);
257 AnswerTuples answers = queryRecord.getAnswers();
258 System.out.println("Difficulty: " + queryRecord.getDifficulty());
259 int count = 0;
260 for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
261 ans = answers.getTuple();
262 TestUtil.logInfo(ans);
263 count++;
264 }
265// Assert.assertEquals(count, 1);
266 }
267 pagoda.dispose();
268 }
269}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
index 5c05b94..30f3d93 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
@@ -23,4 +23,18 @@ public class TestPagodaReactome {
23 .run(); 23 .run();
24 } 24 }
25 25
26 @Test(groups = {"sygenia"})
27 public void justExecute_sygenia() throws IOException {
28 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
29
30 Pagoda.builder()
31 .ontology(Paths.get(ontoDir, "reactome/biopax-level3-processed.owl"))
32 .data(Paths.get(ontoDir, "reactome/data/sample_10.ttl"))
33 .query(Paths.get(ontoDir, "reactome/reactome_sygenia_queries.sparql"))
34 .classify(true)
35 .hermit(true)
36 .build()
37 .run();
38 }
39
26} 40}
generated by cgit v1.2.3 (git 2.25.1) at 2025-11-05 12:45:35 +0000