From c7dbc7c61c7094ea4ec49bd630023f23b92fd9d1 Mon Sep 17 00:00:00 2001 From: RncLsn Date: Mon, 18 May 2015 18:27:32 +0100 Subject: Configured Maven and improved executable class and tests. --- test/AllTests.xml | 18 - test/FullEvaluation.xml | 18 - test/resources/AllTests.xml | 18 + test/resources/FullEvaluation.xml | 18 + test/resources/test.properties | 1 + test/uk/ac/ox/cs/hermit/JAIR_HermiT.java | 69 +-- .../global_tests/CheckAnswersOverDataset.java | 48 +++ .../cs/pagoda/global_tests/JAIR_Scalability.java | 2 +- .../ox/cs/pagoda/global_tests/LightEvaluation.java | 64 +-- .../ox/cs/pagoda/global_tests/PagodaDBPedia.java | 30 -- .../uk/ac/ox/cs/pagoda/global_tests/PagodaELU.java | 20 - .../uk/ac/ox/cs/pagoda/global_tests/PagodaFLY.java | 25 -- .../ac/ox/cs/pagoda/global_tests/PagodaLUBM.java | 24 -- .../uk/ac/ox/cs/pagoda/global_tests/PagodaNPD.java | 46 -- .../ox/cs/pagoda/global_tests/PagodaNPD_bench.java | 30 -- .../uk/ac/ox/cs/pagoda/global_tests/PagodaRLU.java | 20 - .../ac/ox/cs/pagoda/global_tests/PagodaUOBM.java | 53 --- .../pagoda/global_tests/TestGlobalCorrectness.java | 53 --- .../cs/pagoda/global_tests/TestPagodaDBPedia.java | 33 ++ .../ox/cs/pagoda/global_tests/TestPagodaFLY.java | 28 ++ .../ox/cs/pagoda/global_tests/TestPagodaLUBM.java | 45 ++ .../ox/cs/pagoda/global_tests/TestPagodaNPD.java | 38 ++ .../ox/cs/pagoda/global_tests/TestPagodaUOBM.java | 53 +++ test/uk/ac/ox/cs/pagoda/ore/PagodaOWLReasoner.java | 470 --------------------- .../ac/ox/cs/pagoda/ore/PagodaReasonerFactory.java | 39 -- test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java | 276 +----------- test/uk/ac/ox/cs/pagoda/util/TestUtil.java | 7 +- 27 files changed, 337 insertions(+), 1209 deletions(-) delete mode 100644 test/AllTests.xml delete mode 100644 test/FullEvaluation.xml create mode 100644 test/resources/AllTests.xml create mode 100644 test/resources/FullEvaluation.xml create mode 100644 test/resources/test.properties create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/CheckAnswersOverDataset.java delete mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaDBPedia.java delete mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaELU.java delete mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaFLY.java delete mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaLUBM.java delete mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD.java delete mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD_bench.java delete mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaRLU.java delete mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaUOBM.java delete mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/TestGlobalCorrectness.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java delete mode 100644 test/uk/ac/ox/cs/pagoda/ore/PagodaOWLReasoner.java delete mode 100644 test/uk/ac/ox/cs/pagoda/ore/PagodaReasonerFactory.java (limited to 'test') diff --git a/test/AllTests.xml b/test/AllTests.xml deleted file mode 100644 index c2567a8..0000000 --- a/test/AllTests.xml +++ /dev/null @@ -1,18 +0,0 @@ - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/test/FullEvaluation.xml b/test/FullEvaluation.xml deleted file mode 100644 index c4a3ebe..0000000 --- a/test/FullEvaluation.xml +++ /dev/null @@ -1,18 +0,0 @@ - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/test/resources/AllTests.xml b/test/resources/AllTests.xml new file mode 100644 index 0000000..bc3e5cc --- /dev/null +++ b/test/resources/AllTests.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/test/resources/FullEvaluation.xml b/test/resources/FullEvaluation.xml new file mode 100644 index 0000000..c4a3ebe --- /dev/null +++ b/test/resources/FullEvaluation.xml @@ -0,0 +1,18 @@ + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/test/resources/test.properties b/test/resources/test.properties new file mode 100644 index 0000000..c4a25d0 --- /dev/null +++ b/test/resources/test.properties @@ -0,0 +1 @@ +ontoDir=/home/alessandro/Big_files/Ontologies/ \ No newline at end of file diff --git a/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java b/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java index 2fc478d..a3264ba 100644 --- a/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java +++ b/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java @@ -1,17 +1,17 @@ package uk.ac.ox.cs.hermit; import org.junit.Test; - -import uk.ac.ox.cs.pagoda.tester.PagodaTester; +import uk.ac.ox.cs.pagoda.util.TestUtil; public class JAIR_HermiT { @Test public void lubm1() throws Exception { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); String[] args = new String[] { - PagodaTester.onto_dir + "lubm/univ-bench.owl", - PagodaTester.onto_dir + "lubm/data/lubm1_owl", - PagodaTester.onto_dir + "lubm/queries/test.sparql" + TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"), + TestUtil.combinePaths(ontoDir, "lubm/data/lubm1_owl"), + TestUtil.combinePaths(ontoDir, "lubm/queries/test.sparql") // , "/home/yzhou/java-workspace/test-share/results_new/lubm1/hermit" }; HermitQueryReasoner.main(args); @@ -19,10 +19,11 @@ public class JAIR_HermiT { @Test public void lubm1_rolledUp() throws Exception { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); String[] args = new String[] { "/home/yzhou/backup/20141212/univ-bench-queries.owl", - PagodaTester.onto_dir + "lubm/data/lubm1_owl", - PagodaTester.onto_dir + "lubm/queries/atomic_lubm.sparql" + TestUtil.combinePaths(ontoDir, "lubm/data/lubm1_owl"), + TestUtil.combinePaths(ontoDir, "lubm/queries/atomic_lubm.sparql") // , "/home/yzhou/java-workspace/test-share/results_new/lubm1/hermit_rolledUp" }; HermitQueryReasoner.main(args); @@ -30,10 +31,11 @@ public class JAIR_HermiT { @Test public void uobm1() throws Exception { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); String[] args = new String[] { - PagodaTester.onto_dir + "uobm/univ-bench-dl.owl", - PagodaTester.onto_dir + "uobm/data/uobm1_owl_withDeclaration", - PagodaTester.onto_dir + "uobm/queries/standard.sparql" + TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), + TestUtil.combinePaths(ontoDir, "uobm/data/uobm1_owl_withDeclaration"), + TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql") // , "hermit_uobm1.out" // , "/home/yzhou/java-workspace/test-share/results_new/uobm1/hermit" }; @@ -42,10 +44,11 @@ public class JAIR_HermiT { @Test public void uobm1_rolledUp() throws Exception { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); String[] args = new String[] { "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl", - PagodaTester.onto_dir + "uobm/data/uobm1_owl_withDeclaration", - PagodaTester.onto_dir + "uobm/queries/atomic_uobm.sparql" + TestUtil.combinePaths(ontoDir, "uobm/data/uobm1_owl_withDeclaration"), + TestUtil.combinePaths(ontoDir, "uobm/queries/atomic_uobm.sparql") , "hermit_uobm1_rolledUp.out" // , "/home/yzhou/java-workspace/test-share/results_new/uobm1/hermit_rolledUp" }; @@ -54,21 +57,23 @@ public class JAIR_HermiT { @Test public void fly_rolledUp() throws Exception { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); HermitQueryReasoner.main( - PagodaTester.onto_dir + "fly/fly-all-in-one_rolledUp.owl", -// PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", + TestUtil.combinePaths(ontoDir, "fly/fly-all-in-one_rolledUp.owl"), +// TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", null, - PagodaTester.onto_dir + "fly/queries/fly_atomic.sparql" + TestUtil.combinePaths(ontoDir, "fly/queries/fly_atomic.sparql") , "hermit_fly.out" ); } @Test public void npd() throws Exception { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); HermitQueryReasoner.main( - PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl", - PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl", - PagodaTester.onto_dir + "npd/queries/atomic_ground.sparql" + TestUtil.combinePaths(ontoDir, "npd/npd-all-minus-datatype.owl"), + TestUtil.combinePaths(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl"), + TestUtil.combinePaths(ontoDir, "npd/queries/atomic_ground.sparql") , "hermit_npd.out" // , "/home/yzhou/java-workspace/test-share/results_new/npd/hermit" ); @@ -76,31 +81,34 @@ public class JAIR_HermiT { @Test public void dbpedia() throws Exception { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); HermitQueryReasoner.main( - PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl", - PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl", - PagodaTester.onto_dir + "dbpedia/queries/atomic_ground.sparql" + TestUtil.combinePaths(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"), + TestUtil.combinePaths(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"), + TestUtil.combinePaths(ontoDir, "dbpedia/queries/atomic_ground.sparql") , "/home/yzhou/java-workspace/test-share/results_new/dbpedia/hermit" ); } @Test public void reactome() throws Exception { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); HermitQueryReasoner.main( - PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl", - PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl", - PagodaTester.onto_dir + "bio2rdf/reactome/queries/atomic_ground.sparql" + TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"), + TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl"), + TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/atomic_ground.sparql") , "/home/yzhou/java-workspace/test-share/results_new/reactome/hermit_10p" ); } @Test public void chembl() throws Exception { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); HermitQueryReasoner.main( - PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl", + TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"), // null, - PagodaTester.onto_dir + "bio2rdf/chembl/graph sampling/sample_1.nt", - PagodaTester.onto_dir + "bio2rdf/chembl/queries/atomic_ground.sparql" + TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/graph sampling/sample_1.nt"), + TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql") , "hermit_chembl.out" // , "/home/yzhou/java-workspace/test-share/results_new/chembl/hermit_1p" ); @@ -108,10 +116,11 @@ public class JAIR_HermiT { @Test public void uniprot() throws Exception { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); HermitQueryReasoner.main( - PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat.owl", - PagodaTester.onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt", - PagodaTester.onto_dir + "bio2rdf/uniprot/queries/atomic_ground.sparql" + TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat.owl"), + TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/graph sampling/sample_1.nt"), + TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql") , "hermit_uniprot.out" // , "/home/yzhou/java-workspace/test-share/results_new/uniprot/hermit_1p" ); diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/CheckAnswersOverDataset.java b/test/uk/ac/ox/cs/pagoda/global_tests/CheckAnswersOverDataset.java new file mode 100644 index 0000000..424afa2 --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/CheckAnswersOverDataset.java @@ -0,0 +1,48 @@ +package uk.ac.ox.cs.pagoda.global_tests; + +import com.google.gson.Gson; +import com.google.gson.reflect.TypeToken; +import org.testng.Assert; +import uk.ac.ox.cs.pagoda.Pagoda; +import uk.ac.ox.cs.pagoda.query.QueryRecord; + +import java.io.BufferedReader; +import java.io.File; +import java.io.IOException; +import java.lang.reflect.Type; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.Set; + +/** + * Given an instance of Pagoda, it checks the returned answers. + * */ +public class CheckAnswersOverDataset { + + public static void check(Pagoda pagoda, Path givenAnswers) { + try { +// Utility.setLogLevel(Level.DEBUG); // uncomment for outputting partial results + Path computedAnswers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath()); + new File(computedAnswers.toString()).deleteOnExit(); + + pagoda.run(); + assertSameContent(computedAnswers, givenAnswers); + } catch (IOException e) { + e.printStackTrace(); + } + } + + private static void assertSameContent(Path computedAnswersFile, Path givenAnswersFile) throws IOException { + BufferedReader computedReader = Files.newBufferedReader(computedAnswersFile); + BufferedReader givenReader = Files.newBufferedReader(givenAnswersFile); + + Gson gson = QueryRecord.GsonCreator.getInstance(); + + Type cqType = new TypeToken>() {}.getType(); + Set computedAnswers = gson.fromJson(computedReader, cqType); + Set givenAnswers = gson.fromJson(givenReader, cqType); + + Assert.assertEquals(computedAnswers, givenAnswers); + } +} 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 index cdf55bd..687ffee 100644 --- a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java +++ b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java @@ -84,7 +84,7 @@ public class JAIR_Scalability { } public static void main(String... args) throws IOException { - Properties.ShellModeDefault = true; + Properties.shellModeDefault = true; new JAIR_Scalability().testUniProt(50, false); } diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java b/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java index 3ee268e..b073a26 100644 --- a/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java +++ b/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java @@ -1,67 +1,17 @@ package uk.ac.ox.cs.pagoda.global_tests; -import org.junit.Test; -import uk.ac.ox.cs.pagoda.tester.PagodaTester; -import uk.ac.ox.cs.pagoda.util.TestUtil; +import org.testng.annotations.Test; import java.io.IOException; public class LightEvaluation { @Test - public void uobm1() throws IOException { - int number = 1; - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), - TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"), - TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql") - ); - TestUtil.copyFile("log4j.log", "output/jair/uobm1.out"); + public void evaluation() throws IOException { + new TestPagodaUOBM().test(1); + new TestPagodaLUBM().test(100); + new TestPagodaFLY().test(); + new TestPagodaDBPedia().test(); + new TestPagodaNPD().testNPDwithoutDataType(); } - - @Test - public void lubm100() throws IOException { - int number = 100; - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"), - TestUtil.combinePaths(ontoDir, "lubm/data/lubm" + number + ".ttl"), - TestUtil.combinePaths(ontoDir, "lubm/queries/test.sparql") - ); - TestUtil.copyFile("log4j.log", "results-backup/current/lubm100.out"); - } - - @Test - public void fly() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"), - TestUtil.combinePaths(ontoDir, "fly/queries/fly.sparql") - ); - TestUtil.copyFile("log4j.log", "results-backup/current/fly.out"); - } - - @Test - public void dbpedia() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"), - TestUtil.combinePaths(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"), - TestUtil.combinePaths(ontoDir, "dbpedia/atomic.sparql") - ); - TestUtil.copyFile("log4j.log", "results-backup/current/dbpedia.out"); - } - - @Test - public void npdWithoutDataType() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "npd/npd-all-minus-datatype.owl"), - TestUtil.combinePaths(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl"), - TestUtil.combinePaths(ontoDir, "npd/queries/atomic.sparql") - ); - TestUtil.copyFile("log4j.log", "results-backup/current/npd_minus.out"); - } - } diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaDBPedia.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaDBPedia.java deleted file mode 100644 index 2b9cdbd..0000000 --- a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaDBPedia.java +++ /dev/null @@ -1,30 +0,0 @@ -package uk.ac.ox.cs.pagoda.global_tests; - -import org.junit.Test; -import uk.ac.ox.cs.pagoda.tester.PagodaTester; -import uk.ac.ox.cs.pagoda.tester.Statistics; -import uk.ac.ox.cs.pagoda.util.TestUtil; - -import java.io.IOException; - -import static org.junit.Assert.fail; - -public class PagodaDBPedia { - - @Test - public void test() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"), - TestUtil.combinePaths(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"), - TestUtil.combinePaths(ontoDir, "dbpedia/atomic.sparql") - ); - - Statistics stat = new Statistics("output/log4j.log"); - String diff = stat.diff("results-backup/benchmark/dbpedia.out"); - TestUtil.copyFile("output/log4j.log", "results-backup/current/dbpedia.out"); - if (!diff.isEmpty()) - fail(diff); - } - -} diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaELU.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaELU.java deleted file mode 100644 index da059f9..0000000 --- a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaELU.java +++ /dev/null @@ -1,20 +0,0 @@ -package uk.ac.ox.cs.pagoda.global_tests; - -import org.junit.Test; -import uk.ac.ox.cs.pagoda.tester.PagodaTester; -import uk.ac.ox.cs.pagoda.util.TestUtil; - -public class PagodaELU { - - @Test void test() { - int number = 1; - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), - TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"), - TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql") - ); - } - - -} diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaFLY.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaFLY.java deleted file mode 100644 index d558e0f..0000000 --- a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaFLY.java +++ /dev/null @@ -1,25 +0,0 @@ -package uk.ac.ox.cs.pagoda.global_tests; - -import org.junit.Test; -import uk.ac.ox.cs.pagoda.tester.PagodaTester; -import uk.ac.ox.cs.pagoda.util.TestUtil; - -public class PagodaFLY { - - @Test - public void test() { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"), - TestUtil.combinePaths(ontoDir, "fly/queries/fly_pellet.sparql") - ); - -// Statistics stat = new Statistics("output/log4j.log"); -// String diff = stat.diff("results-backup/benchmark/fly.out"); -// AllTests.copy("output/log4j.log", "results-backup/current/fly.out"); -// if (!diff.isEmpty()) -// fail(diff); - } - - -} diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaLUBM.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaLUBM.java deleted file mode 100644 index 2014ec1..0000000 --- a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaLUBM.java +++ /dev/null @@ -1,24 +0,0 @@ -package uk.ac.ox.cs.pagoda.global_tests; - -import org.testng.annotations.Test; -import uk.ac.ox.cs.pagoda.util.TestUtil; - -import java.io.IOException; -import java.nio.file.Paths; - -public class PagodaLUBM { - - private void testN(int number ) throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - TestGlobalCorrectness.test(Paths.get(ontoDir, "lubm/univ-bench.owl"), - Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl"), - Paths.get(ontoDir, "lubm/queries/test.sparql"), - Paths.get(ontoDir, "lubm/lubm" + number + ".json")); - } - - @Test - public void test1() throws IOException { - testN(1); - } - -} diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD.java deleted file mode 100644 index 17d1e82..0000000 --- a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD.java +++ /dev/null @@ -1,46 +0,0 @@ -package uk.ac.ox.cs.pagoda.global_tests; - -import org.junit.Test; -import uk.ac.ox.cs.pagoda.tester.PagodaTester; -import uk.ac.ox.cs.pagoda.tester.Statistics; -import uk.ac.ox.cs.pagoda.util.TestUtil; - -import java.io.IOException; - -import static org.junit.Assert.fail; - -public class PagodaNPD { - - @Test - public void testNPDwithoutDataType() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "npd/npd-all-minus-datatype.owl"), - TestUtil.combinePaths(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl"), - TestUtil.combinePaths(ontoDir, "npd/queries/atomic.sparql") - ); - - Statistics stat = new Statistics("output/log4j.log"); - String diff = stat.diff("results-backup/benchmark/npd_minus.out"); - TestUtil.copyFile("output/log4j.log", "results-backup/current/npd_minus.out"); - if (!diff.isEmpty()) - fail(diff); - } - - @Test - public void testNPD() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "npd/npd-all.owl"), - TestUtil.combinePaths(ontoDir, "npd/data/npd-data-dump-processed.ttl"), - TestUtil.combinePaths(ontoDir, "npd/queries/atomic.sparql") - ); - - Statistics stat = new Statistics("output/log4j.log"); - String diff = stat.diff("results-backup/benchmark/npd.out"); - TestUtil.copyFile("output/log4j.log", "results-backup/current/npd.out"); - if (!diff.isEmpty()) - fail(diff); - } - -} diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD_bench.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD_bench.java deleted file mode 100644 index c908cb4..0000000 --- a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD_bench.java +++ /dev/null @@ -1,30 +0,0 @@ -package uk.ac.ox.cs.pagoda.global_tests; - -import org.junit.Test; -import uk.ac.ox.cs.pagoda.tester.PagodaTester; -import uk.ac.ox.cs.pagoda.tester.Statistics; -import uk.ac.ox.cs.pagoda.util.TestUtil; - -import java.io.IOException; - -import static org.junit.Assert.fail; - -public class PagodaNPD_bench { - - @Test - public void test() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "npd-benchmark/npd-v2-ql_a.owl"), - TestUtil.combinePaths(ontoDir, "npd-benchmark/npd-v2-ql_a.ttl"), - TestUtil.combinePaths(ontoDir, "npd-benchmark/queries/all.sparql") - ); - - Statistics stat = new Statistics("output/log4j.log"); - String diff = stat.diff("results-backup/benchmark/npd-bench.out"); - TestUtil.copyFile("output/log4j.log", "results-backup/current/npd-bench.out"); - if (!diff.isEmpty()) - fail(diff); - } - -} diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaRLU.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaRLU.java deleted file mode 100644 index 88e0835..0000000 --- a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaRLU.java +++ /dev/null @@ -1,20 +0,0 @@ -package uk.ac.ox.cs.pagoda.global_tests; - -import org.junit.Test; -import uk.ac.ox.cs.pagoda.tester.PagodaTester; -import uk.ac.ox.cs.pagoda.util.TestUtil; - -public class PagodaRLU { - - @Test - public void testRL() { - int number = 1; - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), - TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"), - TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql") - ); - } - -} diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaUOBM.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaUOBM.java deleted file mode 100644 index 065fb29..0000000 --- a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaUOBM.java +++ /dev/null @@ -1,53 +0,0 @@ -package uk.ac.ox.cs.pagoda.global_tests; - -import org.testng.annotations.DataProvider; -import org.testng.annotations.Test; -import uk.ac.ox.cs.pagoda.tester.PagodaTester; -import uk.ac.ox.cs.pagoda.util.TestUtil; - -import java.io.IOException; -import java.nio.file.Paths; - -import static uk.ac.ox.cs.pagoda.util.TestUtil.combinePaths; - -public class PagodaUOBM { - - private void testN(int number ) throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - TestGlobalCorrectness.test(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"), - Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl"), - Paths.get(ontoDir, "uobm/queries/test.sparql"), - Paths.get(ontoDir, "uobm/uobm" + number + ".json")); - } - - @Test - public void test1() throws IOException { - testN(1); - } - - private static final int N_1 = 8; - private static final int N_2 = 10; - - - @DataProvider(name = "uobmNumbers") - public static Object[][] uobmNumbers() { - Integer[][] integers = new Integer[N_2 - N_1 + 1][1]; - for (int i = 0; i < N_2 - N_1 + 1; i++) - integers[i][0]= N_1 + i; - return integers; - } - -// @Test -// public void justExecute3() { -// justExecute(1); -// } - - @Test(dataProvider = "uobmNumbers") - public void justExecute(int number) { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main(combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), - combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"), - combinePaths(ontoDir, "uobm/queries/test.sparql")); - } - -} diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestGlobalCorrectness.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestGlobalCorrectness.java deleted file mode 100644 index dff2366..0000000 --- a/test/uk/ac/ox/cs/pagoda/global_tests/TestGlobalCorrectness.java +++ /dev/null @@ -1,53 +0,0 @@ -package uk.ac.ox.cs.pagoda.global_tests; - -import com.google.gson.Gson; -import com.google.gson.reflect.TypeToken; -import org.apache.log4j.Level; -import org.testng.Assert; -import uk.ac.ox.cs.pagoda.query.QueryRecord; -import uk.ac.ox.cs.pagoda.tester.PagodaTester; -import uk.ac.ox.cs.pagoda.util.Utility; - -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.lang.reflect.Type; -import java.nio.file.Files; -import java.nio.file.Path; -import java.nio.file.Paths; -import java.util.Set; - -/** - * This is a unit test for TestNG. - *

- * It tests the correctness on the final output. - * */ -public class TestGlobalCorrectness { - - public static void test(Path ontology, Path data, Path queries, Path givenAnswers) { - try { - Utility.setLogLevel(Level.DEBUG); - Path computedAnswers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath()); - new File(computedAnswers.toString()).deleteOnExit(); - PagodaTester.main(ontology.toString(), data.toString(), queries.toString(), computedAnswers.toString()); - assertSameContent(computedAnswers, givenAnswers); - } catch (IOException e) { - e.printStackTrace(); - } - } - - private static void assertSameContent(Path computedAnswersFile, Path givenAnswersFile) throws IOException { - BufferedReader computedReader = Files.newBufferedReader(computedAnswersFile); - BufferedReader givenReader = Files.newBufferedReader(givenAnswersFile); - - Gson gson = QueryRecord.GsonCreator.getInstance(); - - Type cqType = new TypeToken>() {}.getType(); - Set computedAnswers = gson.fromJson(computedReader, cqType); - Set givenAnswers = gson.fromJson(givenReader, cqType); - - Assert.assertEquals(computedAnswers, givenAnswers); - } - - -} 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..04c9f3b --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java @@ -0,0 +1,33 @@ +package uk.ac.ox.cs.pagoda.global_tests; + +import org.testng.annotations.Test; +import uk.ac.ox.cs.pagoda.Pagoda; +import uk.ac.ox.cs.pagoda.util.TestUtil; + +import java.io.IOException; +import java.nio.file.Paths; + +public class TestPagodaDBPedia { + + public static final String ANSWER_PATH = "~/TestPagodaDEBPedia.json"; + + @Test + public void just_execute() throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + Pagoda pagoda = Pagoda.builder() + .ontology(Paths.get(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl")) + .data(Paths.get(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl")) + .query(Paths.get(ontoDir, "dbpedia/atomic.sparql")) + .answer(ANSWER_PATH) + .classify(true) + .hermit(true) + .build(); + pagoda.run(); + } + + @Test + public void test() { + // TODO implement + } + +} 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..623034e --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java @@ -0,0 +1,28 @@ +package uk.ac.ox.cs.pagoda.global_tests; + +import org.testng.annotations.Test; +import uk.ac.ox.cs.pagoda.Pagoda; +import uk.ac.ox.cs.pagoda.util.TestUtil; + +public class TestPagodaFLY { + + public static final String ANSWER_PATH = "~/TestPagodaFLY.json"; + + @Test + public void just_execute() { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + Pagoda pagoda = Pagoda.builder() + .ontology(TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl")) + .query(TestUtil.combinePaths(ontoDir, "fly/queries/fly.sparql")) +// .answer(ANSWER_PATH) + .classify(true) + .hermit(true) + .build(); + pagoda.run(); + } + + @Test + public void test() { + // TODO implement + } +} 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..bb58681 --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java @@ -0,0 +1,45 @@ +package uk.ac.ox.cs.pagoda.global_tests; + +import org.testng.annotations.Test; +import uk.ac.ox.cs.pagoda.Pagoda; +import uk.ac.ox.cs.pagoda.util.TestUtil; + +import java.io.IOException; +import java.nio.file.Paths; + +public class TestPagodaLUBM { + + public void test(int number) throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + Pagoda pagoda = Pagoda.builder() + .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl")) + .data(Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl")) + .query(Paths.get(ontoDir, "lubm/queries/test.sparql")) + .classify(true) + .hermit(true) + .build(); + CheckAnswersOverDataset.check(pagoda, Paths.get(ontoDir, "lubm/lubm" + number + ".json")); + } + + @Test + public void test_1() throws IOException { + test(1); + } + + public void justExecute_100() { + int number = 100; + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + Pagoda pagoda = Pagoda.builder() + .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl")) + .data(Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl")) + .query(Paths.get(ontoDir, "lubm/queries/test.sparql")) + .classify(true) + .hermit(true) + .build(); + pagoda.run(); + } + + public static void main(String... args) { + new TestPagodaLUBM().justExecute_100(); + } +} 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 @@ +package uk.ac.ox.cs.pagoda.global_tests; + +import org.testng.annotations.Test; +import uk.ac.ox.cs.pagoda.Pagoda; +import uk.ac.ox.cs.pagoda.util.TestUtil; + +import java.io.IOException; +import java.nio.file.Paths; + +public class TestPagodaNPD { + + public static final String ANSWER_PATH = "~/PagodaNPDWithoutDatatype.json"; + + @Test + public void justExecuteNPDWithoutDataType() { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + Pagoda pagoda = Pagoda.builder() + .ontology(Paths.get(ontoDir, "npd/npd-all-minus-datatype.owl")) + .data(Paths.get(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl")) + .query(Paths.get(ontoDir, "npd/queries/atomic.sparql")) + .answer(ANSWER_PATH) + .classify(true) + .hermit(true) + .build(); + pagoda.run(); + } + + @Test + public void testNPDwithoutDataType() throws IOException { + // TODO implement + } + + @Test + public void testNPD() throws IOException { + // TODO implement + } + +} 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..61235d3 --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java @@ -0,0 +1,53 @@ +package uk.ac.ox.cs.pagoda.global_tests; + +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; +import uk.ac.ox.cs.pagoda.Pagoda; +import uk.ac.ox.cs.pagoda.tester.PagodaTester; +import uk.ac.ox.cs.pagoda.util.TestUtil; + +import java.io.IOException; +import java.nio.file.Paths; + +import static uk.ac.ox.cs.pagoda.util.TestUtil.combinePaths; + +public class TestPagodaUOBM { + + public void test(int number) throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + Pagoda pagoda = Pagoda.builder() + .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl")) + .data(Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl")) + .query(Paths.get(ontoDir, "uobm/queries/test.sparql")) + .classify(true) + .hermit(true) + .build(); + CheckAnswersOverDataset.check(pagoda, + Paths.get(ontoDir, "uobm/uobm" + number + ".json")); + } + + @Test + public void test_1() throws IOException { + test(1); + } + + private static final int N_1 = 1; + private static final int N_2 = 10; + + @DataProvider(name = "uobmNumbers") + public static Object[][] uobmNumbers() { + Integer[][] integers = new Integer[N_2 - N_1 + 1][1]; + for (int i = 0; i < N_2 - N_1 + 1; i++) + integers[i][0]= N_1 + i; + return integers; + } + + @Test(dataProvider = "uobmNumbers") + public void justExecute(int number) { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + PagodaTester.main(combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), + combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"), + combinePaths(ontoDir, "uobm/queries/test.sparql")); + } + +} 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 @@ -package uk.ac.ox.cs.pagoda.ore; - -import java.util.HashMap; -import java.util.HashSet; -import java.util.List; -import java.util.Map; -import java.util.Set; - -import org.semanticweb.owlapi.model.AxiomType; -import org.semanticweb.owlapi.model.IRI; -import org.semanticweb.owlapi.model.OWLAxiom; -import org.semanticweb.owlapi.model.OWLClass; -import org.semanticweb.owlapi.model.OWLClassExpression; -import org.semanticweb.owlapi.model.OWLDataFactory; -import org.semanticweb.owlapi.model.OWLDataProperty; -import org.semanticweb.owlapi.model.OWLDataPropertyExpression; -import org.semanticweb.owlapi.model.OWLLiteral; -import org.semanticweb.owlapi.model.OWLNamedIndividual; -import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; -import org.semanticweb.owlapi.model.OWLOntology; -import org.semanticweb.owlapi.model.OWLOntologyChange; -import org.semanticweb.owlapi.reasoner.AxiomNotInProfileException; -import org.semanticweb.owlapi.reasoner.BufferingMode; -import org.semanticweb.owlapi.reasoner.ClassExpressionNotInProfileException; -import org.semanticweb.owlapi.reasoner.FreshEntitiesException; -import org.semanticweb.owlapi.reasoner.FreshEntityPolicy; -import org.semanticweb.owlapi.reasoner.InconsistentOntologyException; -import org.semanticweb.owlapi.reasoner.IndividualNodeSetPolicy; -import org.semanticweb.owlapi.reasoner.InferenceType; -import org.semanticweb.owlapi.reasoner.Node; -import org.semanticweb.owlapi.reasoner.NodeSet; -import org.semanticweb.owlapi.reasoner.OWLReasoner; -import org.semanticweb.owlapi.reasoner.ReasonerInterruptedException; -import org.semanticweb.owlapi.reasoner.TimeOutException; -import org.semanticweb.owlapi.reasoner.UnsupportedEntailmentTypeException; -import org.semanticweb.owlapi.reasoner.impl.OWLClassNodeSet; -import org.semanticweb.owlapi.util.Version; - -import uk.ac.ox.cs.JRDFox.model.GroundTerm; -import uk.ac.ox.cs.JRDFox.model.Individual; -import uk.ac.ox.cs.pagoda.query.AnswerTuples; -import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner; -import uk.ac.ox.cs.pagoda.util.Utility; - -public class PagodaOWLReasoner implements OWLReasoner { - - QueryReasoner reasoner; - OWLOntology ontology; - OWLDataFactory factory; - boolean sat; - - public PagodaOWLReasoner(OWLOntology ontology) { - this.ontology = ontology; - factory = ontology.getOWLOntologyManager().getOWLDataFactory(); - reasoner = QueryReasoner.getInstance(ontology); - reasoner.setToClassify(false); - reasoner.loadOntology(ontology); - sat = reasoner.preprocess(); - thing = new OWLClassNodeSet(factory.getOWLThing()); - } - - @Override - public String getReasonerName() { - return "PAGOdA"; - } - - @Override - public Version getReasonerVersion() { - return null; - } - - @Override - public BufferingMode getBufferingMode() { - // TODO Auto-generated method stub - return null; - } - - @Override - public void flush() { - // TODO Auto-generated method stub - - } - - @Override - public List getPendingChanges() { - // TODO Auto-generated method stub - return null; - } - - @Override - public Set getPendingAxiomAdditions() { - // TODO Auto-generated method stub - return null; - } - - @Override - public Set getPendingAxiomRemovals() { - // TODO Auto-generated method stub - return null; - } - - @Override - public OWLOntology getRootOntology() { - return ontology; - } - - @Override - public void interrupt() { - // TODO Auto-generated method stub - - } - - @Override - public void precomputeInferences(InferenceType... inferenceTypes) throws ReasonerInterruptedException, TimeOutException, InconsistentOntologyException { - if (!sat) { - throw new InconsistentOntologyException(); - } - if (inferenceTypes.length == 1 && inferenceTypes[0].equals(InferenceType.CLASS_ASSERTIONS) && types.isEmpty()) { - Set queriedClasses = new HashSet(); - for (OWLOntology onto: ontology.getImportsClosure()) - for (OWLClass cls: onto.getClassesInSignature(true)) { -// if (cls.toStringID().equals("http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#Meritage")); -// else continue; - if (!cls.equals(factory.getOWLThing()) && !queriedClasses.contains(cls)) { - queriedClasses.add(cls); - AnswerTuples tuples = null; - try { - tuples = reasoner.evaluate(String.format("select distinct ?x where { ?x <%s> .}", cls.toStringID())); - int cnt = 0; - for (GroundTerm t; tuples.isValid(); tuples.moveNext()) { - t = tuples.getTuple().getGroundTerm(0); - if (t instanceof Individual) { - addType(((Individual) t).getIRI(), cls); - ++cnt; - } - } - Utility.logInfo("The number of answers: " + cnt); - } finally { - if (tuples != null) tuples.dispose(); - } - } - } - } - } - - private void addType(String iri, OWLClass cls) { - OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(iri)); - OWLClassNodeSet set; - if (types.containsKey(ind)) { - set = types.get(ind); - } - else { - set = new OWLClassNodeSet(factory.getOWLThing()); - types.put(ind, set); - } - set.addEntity(cls); - } - - @Override - public boolean isPrecomputed(InferenceType inferenceType) { - // TODO Auto-generated method stub - return false; - } - - @Override - public Set getPrecomputableInferenceTypes() { - return java.util.Collections.singleton(InferenceType.CLASS_ASSERTIONS); - } - - @Override - public boolean isConsistent() throws ReasonerInterruptedException, TimeOutException { - return sat; - } - - @Override - public boolean isSatisfiable(OWLClassExpression classExpression) throws ReasonerInterruptedException, TimeOutException, ClassExpressionNotInProfileException, FreshEntitiesException, InconsistentOntologyException { - // TODO Auto-generated method stub - return false; - } - - @Override - public Node getUnsatisfiableClasses() throws ReasonerInterruptedException, TimeOutException, InconsistentOntologyException { - // TODO Auto-generated method stub - return null; - } - - @Override - public boolean isEntailed(OWLAxiom axiom) - throws ReasonerInterruptedException, - UnsupportedEntailmentTypeException, TimeOutException, - AxiomNotInProfileException, FreshEntitiesException, - InconsistentOntologyException { - // TODO Auto-generated method stub - return false; - } - - @Override - public boolean isEntailed(Set axioms) - throws ReasonerInterruptedException, - UnsupportedEntailmentTypeException, TimeOutException, - AxiomNotInProfileException, FreshEntitiesException, - InconsistentOntologyException { - // TODO Auto-generated method stub - return false; - } - - @Override - public boolean isEntailmentCheckingSupported(AxiomType axiomType) { - // TODO Auto-generated method stub - return false; - } - - @Override - public Node getTopClassNode() { - // TODO Auto-generated method stub - return null; - } - - @Override - public Node getBottomClassNode() { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getSubClasses(OWLClassExpression ce, boolean direct) - throws ReasonerInterruptedException, TimeOutException, - FreshEntitiesException, InconsistentOntologyException, - ClassExpressionNotInProfileException { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getSuperClasses(OWLClassExpression ce, - boolean direct) throws InconsistentOntologyException, - ClassExpressionNotInProfileException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public Node getEquivalentClasses(OWLClassExpression ce) - throws InconsistentOntologyException, - ClassExpressionNotInProfileException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getDisjointClasses(OWLClassExpression ce) - throws ReasonerInterruptedException, TimeOutException, - FreshEntitiesException, InconsistentOntologyException { - // TODO Auto-generated method stub - return null; - } - - @Override - public Node getTopObjectPropertyNode() { - // TODO Auto-generated method stub - return null; - } - - @Override - public Node getBottomObjectPropertyNode() { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getSubObjectProperties( - OWLObjectPropertyExpression pe, boolean direct) - throws InconsistentOntologyException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getSuperObjectProperties( - OWLObjectPropertyExpression pe, boolean direct) - throws InconsistentOntologyException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public Node getEquivalentObjectProperties( - OWLObjectPropertyExpression pe) - throws InconsistentOntologyException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getDisjointObjectProperties( - OWLObjectPropertyExpression pe) - throws InconsistentOntologyException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public Node getInverseObjectProperties( - OWLObjectPropertyExpression pe) - throws InconsistentOntologyException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getObjectPropertyDomains( - OWLObjectPropertyExpression pe, boolean direct) - throws InconsistentOntologyException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getObjectPropertyRanges( - OWLObjectPropertyExpression pe, boolean direct) - throws InconsistentOntologyException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public Node getTopDataPropertyNode() { - // TODO Auto-generated method stub - return null; - } - - @Override - public Node getBottomDataPropertyNode() { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getSubDataProperties(OWLDataProperty pe, - boolean direct) throws InconsistentOntologyException, - FreshEntitiesException, ReasonerInterruptedException, - TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getSuperDataProperties(OWLDataProperty pe, - boolean direct) throws InconsistentOntologyException, - FreshEntitiesException, ReasonerInterruptedException, - TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public Node getEquivalentDataProperties(OWLDataProperty pe) - throws InconsistentOntologyException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getDisjointDataProperties( - OWLDataPropertyExpression pe) throws InconsistentOntologyException, - FreshEntitiesException, ReasonerInterruptedException, - TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getDataPropertyDomains(OWLDataProperty pe, - boolean direct) throws InconsistentOntologyException, - FreshEntitiesException, ReasonerInterruptedException, - TimeOutException { - // TODO Auto-generated method stub - return null; - } - - private Map types = new HashMap(); - private OWLClassNodeSet thing; - - @Override - public NodeSet getTypes(OWLNamedIndividual ind, boolean direct) throws InconsistentOntologyException, FreshEntitiesException, ReasonerInterruptedException, TimeOutException { - if (!sat) { - throw new InconsistentOntologyException(); - } - if (types.containsKey(ind)) return types.get(ind); - return thing; - } - - @Override - public NodeSet getInstances(OWLClassExpression ce, - boolean direct) throws InconsistentOntologyException, - ClassExpressionNotInProfileException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getObjectPropertyValues( - OWLNamedIndividual ind, OWLObjectPropertyExpression pe) - throws InconsistentOntologyException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public Set getDataPropertyValues(OWLNamedIndividual ind, - OWLDataProperty pe) throws InconsistentOntologyException, - FreshEntitiesException, ReasonerInterruptedException, - TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public Node getSameIndividuals(OWLNamedIndividual ind) - throws InconsistentOntologyException, FreshEntitiesException, - ReasonerInterruptedException, TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public NodeSet getDifferentIndividuals( - OWLNamedIndividual ind) throws InconsistentOntologyException, - FreshEntitiesException, ReasonerInterruptedException, - TimeOutException { - // TODO Auto-generated method stub - return null; - } - - @Override - public long getTimeOut() { - // TODO Auto-generated method stub - return 0; - } - - @Override - public FreshEntityPolicy getFreshEntityPolicy() { - // TODO Auto-generated method stub - return null; - } - - @Override - public IndividualNodeSetPolicy getIndividualNodeSetPolicy() { - // TODO Auto-generated method stub - return null; - } - - @Override - public void dispose() { - reasoner.dispose(); - } - -} 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 @@ -package uk.ac.ox.cs.pagoda.ore; - -import org.semanticweb.owlapi.model.OWLOntology; -import org.semanticweb.owlapi.reasoner.IllegalConfigurationException; -import org.semanticweb.owlapi.reasoner.OWLReasoner; -import org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration; -import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; - -public class PagodaReasonerFactory implements OWLReasonerFactory { - - @Override - public String getReasonerName() { - return "PAGOdA"; - } - - @Override - public OWLReasoner createNonBufferingReasoner(OWLOntology ontology) { - // TODO Auto-generated method stub - return null; - } - - @Override - public OWLReasoner createReasoner(OWLOntology ontology) { - return new PagodaOWLReasoner(ontology); - } - - @Override - public OWLReasoner createNonBufferingReasoner(OWLOntology ontology, OWLReasonerConfiguration config) throws IllegalConfigurationException { - // TODO Auto-generated method stub - return null; - } - - @Override - public OWLReasoner createReasoner(OWLOntology ontology, OWLReasonerConfiguration config) throws IllegalConfigurationException { - // TODO Auto-generated method stub - return null; - } - -} diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java index b97d85e..7d9b49c 100644 --- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java +++ b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java @@ -1,126 +1,18 @@ package uk.ac.ox.cs.pagoda.tester; -import uk.ac.ox.cs.pagoda.query.AnswerTuple; -import uk.ac.ox.cs.pagoda.query.AnswerTuples; import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner; import uk.ac.ox.cs.pagoda.util.Properties; import uk.ac.ox.cs.pagoda.util.Timer; import uk.ac.ox.cs.pagoda.util.Utility; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.IOException; -import java.util.Scanner; - +// TODO clean it, or code another one public class PagodaTester { -// public static final String onto_dir = "/media/RDFData/yzhou/"; -// public static final String onto_dir = "/users/yzhou/ontologies/"; -// public static final String onto_dir = "/home/scratch/yzhou/ontologies/"; - public static final String onto_dir = "/home/alessandro/Big_files/Ontologies/"; - - public static final String fly = onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"; - public static final String fly_query = onto_dir + "fly/queries/fly.sparql"; - - public static final String test_tbox = onto_dir + "smallExampleFromAna/dummy.owl"; - public static final String test_abox = onto_dir + "smallExampleFromAna/initialABox.ttl"; - public static final String test_query = onto_dir + "smallExampleFromAna/queries.dlog"; - - public static final int lubm_number = 1; - public static final String lubm_tbox = onto_dir + "lubm/univ-bench.owl"; - public static final String lubm_abox = onto_dir + "lubm/data/lubm" + lubm_number + ".ttl"; - public static final String lubm_abox_copy = onto_dir + "lubm/data/lubm" + lubm_number + " (copy).ttl"; - public static final String lubm_query = onto_dir + "lubm/queries/test.sparql"; - public static final String lubm_query6 = onto_dir + "lubm/queries/test_q6.sparql"; - public static final String lubm_query20 = onto_dir + "lubm/queries/test_q16.sparql"; - - public static final int uobm_number = 1; - public static final String uobm_tbox = onto_dir + "uobm/univ-bench-dl.owl"; - public static final String uobm_abox = onto_dir + "uobm/data/uobm" + uobm_number + ".ttl"; - public static final String uobm_query = onto_dir + "uobm/queries/test.sparql"; - public static final String uobm_query_temp = onto_dir + "uobm/queries/temp.sparql"; - public static final String uobm_query2 = onto_dir + "uobm/queries/standard_q2.sparql"; - public static final String uobm_query9 = onto_dir + "uobm/queries/standard_q9.sparql"; - public static final String uobm_query11 = onto_dir + "uobm/queries/standard_q11.sparql"; - public static final String uobm_query12 = onto_dir + "uobm/queries/standard_q12.sparql"; - public static final String uobm_query14 = onto_dir + "uobm/queries/standard_q14.sparql"; - public static final String uobm_query15 = onto_dir + "uobm/queries/standard_q15.sparql"; - public static final String uobm_query_multi = onto_dir + "uobm/queries/standard_multi.sparql"; - public static final String uobm_generated_query1 = onto_dir + "uobm/queries/generated_q1.sparql"; - public static final String uobm_query_group3 = onto_dir + "uobm/queries/standard_group3.sparql"; - - public static final String npd_tbox = onto_dir + "npd/npd-all-minus-datatype.owl"; - // "npd/npd-all.owl"; - // "npd-all-minus-datatype.owl"; - public static final String npd_abox = onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl"; - // "npd/data/npd-data-dump-processed.ttl"; - // "npd-data-dump-minus-datatype-old.ttl"; - public static final String npd_query = onto_dir + "npd/queries/atomic.sparql"; - - public static final String npd_bench_tbox = onto_dir + "npd-benchmark/npd-v2-ql_a.owl"; // npd-all-minus-datatype.owl"; - public static final String npd_bench_abox = onto_dir + "npd-benchmark/npd-v2-ql_a.ttl"; // npd-data-dump-minus-datatype-old.ttl"; - public static final String npd_bench_query = onto_dir + "npd-benchmark/queries/all.sparql"; - - public static final String dbpedia_tbox = onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"; - public static final String dbpedia_abox = onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl"; - public static final String dbpedia_query = onto_dir + "dbpedia/queries/atomic_ground.sparql"; - public static final String dbpedia_query274 = onto_dir + "dbpedia/atomic_q274.sparql"; - - public static final String dbpedia_latest_tbox = onto_dir + "dbpedia/dbpedia_2014.owl"; - public static final String travel_tbox = onto_dir + "dbpedia/travel.owl"; - public static final String dbpedia_tbox_simple = onto_dir + "dbpedia/dbpedia_simple.owl"; - - public static final String bioModels_tbox = onto_dir + "biomodels/biomodels-21.owl"; - public static final String bioModels_abox = onto_dir + "biomodels/data_processed_1.ttl"; - public static final String bioModels_queries = onto_dir + "biomodels/queries/queries.sparql"; - - public static final String chembl_tbox = onto_dir + "bio2rdf/chembl/cco-processed-noDPR-noDPD.ttl"; - public static final String chembl_abox = onto_dir + "bio2rdf/chembl/graph sampling old/sample_100.nt"; - public static final String chembl_queries = onto_dir + "bio2rdf/chembl/queries/problematic.sparql"; //"bio2rdf/chembl/queries/atomic_one_filtered.sparql"; // - - public static final String reactome_tbox = onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl"; - 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"; // - public static final String reactome_queries = onto_dir +"bio2rdf/reactome/queries/atomic.sparql"; - - public static final String uniprot_tbox = onto_dir + "bio2rdf/uniprot/core-processed.owl"; - public static final String uniprot_abox = onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt"; - public static final String uniprot_queries = onto_dir + "bio2rdf/uniprot/queries/atomic_one.sparql"; - - public static final String atlas_tbox = onto_dir + "bio2rdf/atlas/gxaterms.owl"; - public static final String atlas_abox = onto_dir + "bio2rdf/atlas/graph sampling/sample_1.nt"; - public static final String atlas_queries = onto_dir + "bio2rdf/atlas/queries/atomic_one.sparql"; - public static void main(String... args) { - if (args.length == 0) { -// args = new String[] {test_tbox, test_abox, test_query}; -// args = new String[] {lubm_tbox, lubm_abox, lubm_query}; -// args = new String[] {uobm_tbox, uobm_abox, uobm_query}; -// args = new String[] {fly, "null", fly_query}; -// args = new String[] {dbpedia_tbox, dbpedia_abox, dbpedia_query}; -// args = new String[] {travel_tbox, null, dbpedia_query274}; - args = new String[] {fly, fly_query}; -// args = new String[] {npd_tbox, npd_abox, npd_query}; -// args = new String[] {npd_bench_tbox, npd_bench_abox, npd_bench_query}; -// args = new String[] {"../SemFacet/WebContent/WEB-INF/data/dbpedia.owl", "../SemFacet/WebContent/WEB-INF/data/dbpediaA.nt", null}; -// args = new String[] {"../core/WebContent/WEB-INF/data/fly.owl", "../core/WebContent/WEB-INF/data/fly-data.nt", null}; -// args = new String[] {"data/lubm/univ-bench.owl", "data/lubm/lubm1.ttl", "data/lubm/lubm.sparql", "lubm.ans"}; -// args = new String[] {"data/uobm/univ-bench-dl.owl", "data/uobm/uobm1.ttl", "data/uobm/uobm.sparql", "uobm.ans"}; -// args = new String[] {"data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", "data/fly/fly.sparql", "fly.ans"}; -// args = new String[] {bioModels_tbox, bioModels_abox, bioModels_queries}; -// args = new String[] {chembl_tbox, chembl_abox, chembl_queries}; -// args = new String[] {reactome_tbox, reactome_abox, reactome_queries}; -// args = new String[] {reactome_tbox, "/users/yzhou/temp/reactome_debug.ttl", onto_dir +"bio2rdf/reactome/queries/atomic_one_q65.sparql"}; -// args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), "/users/yzhou/temp/uniprot_debug/sample_1_string.nt", uniprot_queries}; -// args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), uniprot_abox, uniprot_queries}; -// args = new String[] {atlas_tbox, atlas_abox, atlas_queries}; -// args = new String[] {onto_dir + "test/unsatisfiable.owl", null, onto_dir + "test/unsatisfiable_queries.sparql"}; -// args = new String[] {onto_dir + "test/jair-example.owl", null, onto_dir + "test/jair-example_query.sparql"}; -// args[2] = args[2].replace(".sparql", "_all_pagoda.sparql"); -// args[2] = args[2].replace(".sparql", "_pellet.sparql"); - } +// Properties properties = new Properties(PagodaTester.class. +// getClassLoader().getResource("uobm.properties").getPath()); + Properties properties = new Properties(); - Properties properties = new Properties("config/uobm.properties"); - int index = 0; if (args.length > index) properties.setOntologyPath(args[index++]); if (args.length > index && (args[index].endsWith(".ttl") || args[index].endsWith(".nt"))) properties.setDataPath(args[index++]); @@ -146,169 +38,9 @@ public class PagodaTester { if (properties.getQueryPath() != null) for (String queryFile: properties.getQueryPath().split(";")) pagoda.evaluate(pagoda.getQueryManager().collectQueryRecords(queryFile)); - - if (properties.getShellMode()) - try { - evaluateConsoleQuery(pagoda); - } catch (IOException e) { - e.printStackTrace(); - } } finally { if (pagoda != null) pagoda.dispose(); } - -// Utility.closeCurrentOut(); - - if (properties.getShellMode()) System.exit(0); - } - -// private void printPredicatesWithGap() { -// for (String p: ((MyQueryReasoner) pagoda).getPredicatesWithGap()) { -// System.out.println(p); -// } -// } - - private static void evaluateConsoleQuery(QueryReasoner pagoda) throws IOException { - int ending = (int) '$', symbol; - while (true) { - Utility.logInfo("Input your query ending with $"); - StringBuilder queryBuilder = new StringBuilder(); - while ((symbol = System.in.read()) != ending) { - queryBuilder.append((char) symbol); - } - System.in.read(); - if (queryBuilder.length() == 0) return ; - pagoda.evaluate_shell(queryBuilder.toString()); - } - } - - void testReactomeQueries() { - evaluate("select ?x where { ?x . }"); - evaluate("select ?y ?z where { ?y ?z . }"); - evaluate("select ?y where { ?y . }", true); - - } - - void testSemFacetQueries() { -// try { -// BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream("query.line"))); -// for (String line; (line = reader.readLine()) != null && !line.isEmpty(); ) -// evaluate(line, true); -// reader.close(); -// } catch (FileNotFoundException e) { -// e.printStackTrace(); -// } catch (IOException e) { -// e.printStackTrace(); -// } - evaluate("select ?x ?z where { ?x ?z }", true); - evaluate("select distinct ?y where { ?x ?y ?z }", true); - evaluate("select distinct ?z where { ?x ?z }", true); - evaluate("select ?y ?z where { ?y ?z .}", true); - } - - void testISGQueries() { - evaluate("select ?z where { ?z .}", false); - evaluate("select ?x where {?x .}", false); - } - - void testSomeTravelQueries() { - evaluate("select ?y ?z where { ?y ?z. }", true); - evaluate("select ?x where {?x . }"); - evaluate("select ?x where {?x . }"); - } - - void testSomeFlyQueries() { - evaluate("select ?x where { ?x . }", false); - - evaluate("select DISTINCT ?z where { ?x ?any . ?any ?z . ?x . } ", true); - - evaluate("Select ?x where { ?x " - + ". ?x " - + " ?any . ?any " - + " " - + " . }", true); - - evaluate("Select ?x where {?x " - + " . ?x " - + " ?any . ?any " - + " " - + " . }", true); - -// evaluate("Select ?x where { " -// + "?x . " -// + "?x ?any . " -// + "?any . }", true); - - evaluate("select DISTINCT ?z where { ?x ?any . " - + "?any ?z . " - + "?x . } ", true); - - evaluate("Select * where {" - + " . " - + " ?z }", true); - - evaluate("SELECT DISTINCT ?x ?z WHERE {?x ?z}", true); - evaluate("SELECT DISTINCT ?x ?z WHERE {?x ?z}", true); - - evaluate("select DISTINCT ?y where { ?x ?y ?z . " - + "?x }", true); - - evaluateQueriesFromFile("/users/yzhou/Downloads/logs(1).log"); - evaluateQueriesFromFile("/users/yzhou/Downloads/logs.log"); - - evaluate("SELECT DISTINCT ?x ?z WHERE {?x ?z}", true); - evaluate("SELECT DISTINCT ?x ?z WHERE {?x ?z}", true); - - evaluate("select ?x ?z where { ?x ?z } ", true); - evaluate("select ?x ?z where { ?x ?z } ", true); - } - - public void evaluateQueriesFromFile(String fileName) { - Scanner scanner = null; - try { - scanner = new Scanner(new File(fileName)); - String line; - while (scanner.hasNextLine()) { - line = scanner.nextLine(); - if (line.startsWith("select")) - evaluate(line, true); - } - } catch (FileNotFoundException e) { - e.printStackTrace(); - } finally { - if (scanner != null) - scanner.close(); - } - } - - QueryReasoner pagoda; - - public PagodaTester(QueryReasoner reasoner) { - pagoda = reasoner; - } - - Timer timer = new Timer(); - - private void evaluate(String query) { - evaluate(query, false); - } - - private void evaluate(String query, boolean tag) { - timer.reset(); - AnswerTuples tuples = pagoda.evaluate(query, tag); - int arity = tuples.getArity(); - int count = 0; - for (AnswerTuple tuple; tuples.isValid(); tuples.moveNext()) { - tuple = tuples.getTuple(); - for (int i = 0; i < arity; ++i) - tuple.getGroundTerm(i).toString(); -// System.out.print(tuple.getGroundTerm(i).toString() + "\t"); -// System.out.println(); - ++count; - } - tuples.dispose(); - Utility.logInfo("The number of answers for this SemFacet query: " + count); - Utility.logInfo("Total time for this SemFacet query: " + timer.duration()); } } diff --git a/test/uk/ac/ox/cs/pagoda/util/TestUtil.java b/test/uk/ac/ox/cs/pagoda/util/TestUtil.java index 06d391a..1802147 100644 --- a/test/uk/ac/ox/cs/pagoda/util/TestUtil.java +++ b/test/uk/ac/ox/cs/pagoda/util/TestUtil.java @@ -5,8 +5,8 @@ import org.apache.log4j.FileAppender; import org.apache.log4j.Logger; import java.io.File; -import java.io.FileInputStream; import java.io.IOException; +import java.io.InputStream; import java.nio.file.Files; import java.nio.file.Paths; import java.util.Enumeration; @@ -19,14 +19,15 @@ import static java.nio.file.StandardCopyOption.REPLACE_EXISTING; */ public class TestUtil { - public static final String CONFIG_FILE = "config/test.properties"; + public static final String CONFIG_FILE = "test.properties"; private static boolean isConfigLoaded = false; private static Properties config; public static Properties getConfig() { if(!isConfigLoaded) { - try (FileInputStream in = new FileInputStream(CONFIG_FILE)) { + try (InputStream in = TestUtil.class.getClassLoader() + .getResourceAsStream(CONFIG_FILE)) { config = new java.util.Properties(); config.load(in); in.close(); -- cgit v1.2.3