From 1b6a128137e5d7a6ff75566869232fc054afabef Mon Sep 17 00:00:00 2001 From: RncLsn Date: Fri, 15 May 2015 17:32:22 +0100 Subject: Testing and fixing. Executed successfully on UOBM{1,2,3,4,5,6,7,8}. --- .../ac/ox/cs/pagoda/global_tests/ClauseTester.java | 158 +++++++++++++++++ .../ox/cs/pagoda/global_tests/CostEvaluation.java | 115 ++++++++++++ .../ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java | 193 +++++++++++++++++++++ .../cs/pagoda/global_tests/JAIR_Scalability.java | 91 ++++++++++ .../ox/cs/pagoda/global_tests/LightEvaluation.java | 67 +++++++ .../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 ++++++ .../ac/ox/cs/pagoda/test_units/ClauseTester.java | 164 ----------------- .../ac/ox/cs/pagoda/test_units/CostEvaluation.java | 115 ------------ .../uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java | 193 --------------------- .../ox/cs/pagoda/test_units/JAIR_Scalability.java | 91 ---------- .../ox/cs/pagoda/test_units/LightEvaluation.java | 67 ------- .../ac/ox/cs/pagoda/test_units/PagodaDBPedia.java | 30 ---- test/uk/ac/ox/cs/pagoda/test_units/PagodaELU.java | 20 --- test/uk/ac/ox/cs/pagoda/test_units/PagodaFLY.java | 25 --- test/uk/ac/ox/cs/pagoda/test_units/PagodaLUBM.java | 24 --- test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD.java | 46 ----- .../ox/cs/pagoda/test_units/PagodaNPD_bench.java | 30 ---- test/uk/ac/ox/cs/pagoda/test_units/PagodaRLU.java | 20 --- test/uk/ac/ox/cs/pagoda/test_units/PagodaUOBM.java | 24 --- .../pagoda/test_units/TestGlobalCorrectness.java | 52 ------ test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java | 10 +- 29 files changed, 930 insertions(+), 906 deletions(-) create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/ClauseTester.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaDBPedia.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaELU.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaFLY.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaLUBM.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD_bench.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaRLU.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/PagodaUOBM.java create mode 100644 test/uk/ac/ox/cs/pagoda/global_tests/TestGlobalCorrectness.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/ClauseTester.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/CostEvaluation.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/JAIR_Scalability.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/LightEvaluation.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/PagodaDBPedia.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/PagodaELU.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/PagodaFLY.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/PagodaLUBM.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD_bench.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/PagodaRLU.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/PagodaUOBM.java delete mode 100644 test/uk/ac/ox/cs/pagoda/test_units/TestGlobalCorrectness.java (limited to 'test/uk') diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/ClauseTester.java b/test/uk/ac/ox/cs/pagoda/global_tests/ClauseTester.java new file mode 100644 index 0000000..abd0741 --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/ClauseTester.java @@ -0,0 +1,158 @@ +package uk.ac.ox.cs.pagoda.global_tests; + +import org.semanticweb.HermiT.model.*; +import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.testng.Assert; +import org.testng.annotations.Test; +import uk.ac.ox.cs.pagoda.approx.Clause; +import uk.ac.ox.cs.pagoda.approx.Clausifier; + +public class ClauseTester { + + @Test + public void test_simple() { + Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"); + AtomicConcept A = AtomicConcept.create("A"); + AtomicRole r = AtomicRole.create("r"); + Atom[] bodyAtoms = new Atom[] { + Atom.create(A, x), + Atom.create(r, x, y1), + Atom.create(r, x, y2) + }; + + Atom[] headAtoms = new Atom[] { + Atom.create(Equality.INSTANCE, y1, y2) + }; + + OWLOntologyManager m = OWLManager.createOWLOntologyManager(); + OWLOntology emptyOntology = null; + try { + emptyOntology = m.createOntology(); + } catch (Exception e) { + e.printStackTrace(); + Assert.fail("failed to create a new ontology"); + } + Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); + System.out.println(c.toString()); + } + + @Test + public void test_more() { + Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"), y3 = Variable.create("y3"); + AtomicConcept A = AtomicConcept.create("A"); + AtomicRole r = AtomicRole.create("r"); + Atom[] bodyAtoms = new Atom[] { + Atom.create(A, x), + Atom.create(r, x, y1), + Atom.create(r, x, y2), + Atom.create(r, x, y3), + }; + + Atom[] headAtoms = new Atom[] { + Atom.create(Equality.INSTANCE, y1, y2), + Atom.create(Equality.INSTANCE, y1, y3), + Atom.create(Equality.INSTANCE, y2, y3) + }; + + OWLOntologyManager m = OWLManager.createOWLOntologyManager(); + OWLOntology emptyOntology = null; + try { + emptyOntology = m.createOntology(); + } catch (Exception e) { + e.printStackTrace(); + Assert.fail("failed to create a new ontology"); + } + Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); + System.out.println(c.toString()); + } + + @Test + public void test_inverse() { + Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"); + AtomicConcept A = AtomicConcept.create("A"); + AtomicRole r = AtomicRole.create("r"); + Atom[] bodyAtoms = new Atom[] { + Atom.create(A, x), + Atom.create(r, y1, x), + Atom.create(r, y2, x) + }; + + Atom[] headAtoms = new Atom[] { + Atom.create(Equality.INSTANCE, y1, y2) + }; + + OWLOntologyManager m = OWLManager.createOWLOntologyManager(); + OWLOntology emptyOntology = null; + try { + emptyOntology = m.createOntology(); + } catch (Exception e) { + e.printStackTrace(); + Assert.fail("failed to create a new ontology"); + } + Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); + System.out.println(c.toString()); + } + + @Test + public void test_fillter() { + Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"); + AtomicConcept A = AtomicConcept.create("A"); + AtomicConcept B = AtomicConcept.create("B"); + AtomicRole r = AtomicRole.create("r"); + Atom[] bodyAtoms = new Atom[] { + Atom.create(A, x), + Atom.create(r, y1, x), + Atom.create(r, y2, x), + Atom.create(B, y1), + Atom.create(B, y2) + }; + + Atom[] headAtoms = new Atom[] { + Atom.create(Equality.INSTANCE, y1, y2) + }; + + OWLOntologyManager m = OWLManager.createOWLOntologyManager(); + OWLOntology emptyOntology = null; + try { + emptyOntology = m.createOntology(); + } catch (Exception e) { + e.printStackTrace(); + Assert.fail("failed to create a new ontology"); + } + Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); + System.out.println(c.toString()); + } + + @Test + public void test_negFillter() { + Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"); + AtomicConcept A = AtomicConcept.create("A"); + AtomicConcept B = AtomicConcept.create("B"); + AtomicRole r = AtomicRole.create("r"); + Atom[] bodyAtoms = new Atom[] { + Atom.create(A, x), + Atom.create(r, y1, x), + Atom.create(r, y2, x) + }; + + Atom[] headAtoms = new Atom[] { + Atom.create(Equality.INSTANCE, y1, y2), + Atom.create(B, y1), + Atom.create(B, y2) + }; + + OWLOntologyManager m = OWLManager.createOWLOntologyManager(); + OWLOntology emptyOntology = null; + try { + emptyOntology = m.createOntology(); + } catch (Exception e) { + e.printStackTrace(); + Assert.fail("failed to create a new ontology"); + } + Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); + System.out.println(c.toString()); + } + +} diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java b/test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java new file mode 100644 index 0000000..01e8203 --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java @@ -0,0 +1,115 @@ +package uk.ac.ox.cs.pagoda.global_tests; + +import org.semanticweb.owlapi.model.OWLOntology; +import org.testng.annotations.Test; +import uk.ac.ox.cs.pagoda.owl.OWLHelper; +import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner; +import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner.Type; +import uk.ac.ox.cs.pagoda.tester.PagodaTester; +import uk.ac.ox.cs.pagoda.util.TestUtil; +import uk.ac.ox.cs.pagoda.util.Timer; +import uk.ac.ox.cs.pagoda.util.Utility; + +public class CostEvaluation { + + @Test + public void lubm100() { + int number = 1; + 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_all_pagoda.sparql") + ); +// AllTests.copy("output/log4j.log", "results-backup/jair/lubm" + number + ".out"); + } + + public void lubm1000() { + int number = 1000; + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"), + TestUtil.combinePaths(ontoDir, "lubm/data/lubm" + number + ".ttl"), + TestUtil.combinePaths(ontoDir, "lubm/queries/test_all_pagoda.sparql") + }; + OWLOntology ontology = OWLHelper.loadOntology(args[0]); + QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true); + Timer t = new Timer(); + reasoner.loadOntology(ontology); + reasoner.importData(args[1]); + if (!reasoner.preprocess()) + return ; + Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds."); + + reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2])); +// AllTests.copy("output/log4j.log", "results-backup/jair/lubm" + number + ".out"); + } + + @Test + public void uobm5() { + int number = 1; + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), + TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"), + TestUtil.combinePaths(ontoDir, "uobm/queries/standard_all_pagoda.sparql") + }; + PagodaTester.main(args); +// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out"); + } + + public void uobm100() { + int number = 200; + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), + TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"), + TestUtil.combinePaths(ontoDir, "uobm/queries/standard_group3_all.sparql") + }; + PagodaTester.main(args); +// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out"); + } + + public void uobm500() { + int number = 500; + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), + TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"), + TestUtil.combinePaths(ontoDir, "uobm/queries/standard_all_pagoda.sparql") + }; + + OWLOntology ontology = OWLHelper.loadOntology(args[0]); + QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true); + Timer t = new Timer(); + reasoner.loadOntology(ontology); + reasoner.importData(args[1]); + if (!reasoner.preprocess()) + return ; + Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds."); + + reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2])); +// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out"); + } + + + public static void main(String... args) { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + args = new String[] { + 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") + }; + + OWLOntology ontology = OWLHelper.loadOntology(args[0]); + QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true); + Timer t = new Timer(); + reasoner.loadOntology(ontology); + reasoner.importData(args[1]); + if (!reasoner.preprocess()) + return ; + Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds."); + + reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2])); + } +} diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java new file mode 100644 index 0000000..0d77fdb --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java @@ -0,0 +1,193 @@ +package uk.ac.ox.cs.pagoda.global_tests; + +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; + +public class JAIR_PAGOdA { + + @Test + public void lubm1() throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"), + TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"), + TestUtil.combinePaths(ontoDir, "lubm/queries/test.sparql") + }; + PagodaTester.main(args); + TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda"); + } + + @Test + public void lubm1_conj() throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"), + TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"), + TestUtil.combinePaths(ontoDir, "lubm/queries/test_pellet.sparql") + }; + PagodaTester.main(args); + TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_conj"); + } + + @Test + public void lubm1_rolledUp() throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + PagodaTester.main( + "/home/yzhou/backup/20141212/univ-bench-queries.owl", + TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"), + TestUtil.combinePaths(ontoDir, "lubm/queries/atomic_lubm.sparql") + ); + TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_rolledUp"); + } + + @Test + public void uobm1() throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), + TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"), + TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql") + }; + PagodaTester.main(args); + TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda"); + } + + @Test + public void uobm1_conj() throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), + TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"), + TestUtil.combinePaths(ontoDir, "uobm/queries/standard_pellet.sparql") + }; + PagodaTester.main(args); + TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_conj"); + } + + @Test + public void uobm1_rolledUp() { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl", + TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"), + TestUtil.combinePaths(ontoDir, "uobm/queries/atomic_uobm.sparql") + }; + PagodaTester.main(args); +// TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_rolledUp"); + } + + @Test + public void fly() { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"), + null, + TestUtil.combinePaths(ontoDir, "fly/queries/fly_pellet.sparql") + }; + PagodaTester.main(args); +// TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda"); + } + + @Test + public void fly_conj() throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"), + null, + TestUtil.combinePaths(ontoDir, "fly/queries/fly_pellet.sparql") + }; + PagodaTester.main(args); + TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_conj"); + } + + + public void fly_rolledUp() { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + PagodaTester.main( +// TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", + TestUtil.combinePaths(ontoDir, "fly/fly-all-in-one_rolledUp.owl"), + null, + TestUtil.combinePaths(ontoDir, "fly/queries/fly_atomic.sparql") + ); +// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_rolledUp"); + } + + public void dbpedia() { + 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/queries/atomic_ground.sparql"), + "dbpedia.ans" + ); + +// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/dbpedia/pagoda"); + } + + public void npd() { + 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_ground.sparql") + , "npd.ans" + ); + +// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/npd/pagoda"); + } + + public void reactome() throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + PagodaTester.main( + TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"), + TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl"), +// null, +// TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/atomic_ground.sparql") + TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/example.sparql") + , "pagoda_reactome.ans" + ); + TestUtil.copyFile("log4j.log", "output/jair/pagoda_reactome.example"); + +// TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_10p"); + } + + public void chembl() throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + PagodaTester.main( + TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"), + TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/graph sampling/sample_1.nt"), +// TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql") + TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/example.sparql") + , "pagoda_chembl.ans" + ); + TestUtil.copyFile("log4j.log", "output/jair/pagoda_chembl.example"); +// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_1p"); + } + + public void uniprot() throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + PagodaTester.main( + TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat-processed.owl"), + TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/graph sampling/sample_1.nt"), +// null, +// TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql") + TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/example.sparql") + , "pagoda_uniprot.ans" + ); + TestUtil.copyFile("log4j.log", "output/jair/pagoda_uniprot.example"); +// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_1p"); + } + + + public static void main(String... args) { + try { + new JAIR_PAGOdA().lubm1(); + } catch (IOException e) { + e.printStackTrace(); + } + } + +} diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java new file mode 100644 index 0000000..cdf55bd --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java @@ -0,0 +1,91 @@ +package uk.ac.ox.cs.pagoda.global_tests; + +import org.testng.annotations.Test; +import uk.ac.ox.cs.pagoda.tester.PagodaTester; +import uk.ac.ox.cs.pagoda.util.Properties; +import uk.ac.ox.cs.pagoda.util.TestUtil; + +import java.io.IOException; + +public class JAIR_Scalability { + + private static final String date = "_0123"; + + @Test + public void reactome() throws IOException { + testReactome(10, false); + } + + @Test + public void chembl() throws IOException { + testChEMBL(1, false); + } + + @Test + public void uniprot() throws IOException { + testUniProt(1, false); + } + + public void testReactome(int percentage, boolean save) throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"), + TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/simplifed_sample_" + percentage + ".ttl"), + TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/test.sparql") + , "reactome.ans" + }; + if (percentage == 10) + args[1] = args[1].replace("simplifed", "reactome"); + + PagodaTester.main(args); + if (save) + TestUtil.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_" + percentage + "p" + date); + } + + public void testChEMBL(int percentage, boolean save) throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"), + TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/sample_" + percentage + ".nt"), +// TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql") + TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/test.sparql") + , "chembl.ans" + }; + if (percentage == 1 || percentage == 10 || percentage == 50) + args[1] = args[1].replace("chembl", "chembl/graph sampling"); + else + if (percentage == 100) + args[1] = "/home/yzhou/RDFData/ChEMBL/facts/ChEMBL.ttl"; + + PagodaTester.main(args); + if (save) + TestUtil.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_" + percentage + "p" + date); + } + + public void testUniProt(int percentage, boolean save) throws IOException { + String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); + String[] args = new String[] { + TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat-processed.owl"), + TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/sample_" + percentage + ".nt"), +// TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql") + TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/test.sparql") + , "uniprot.ans" + }; + + if (percentage == 1 || percentage == 10 || percentage == 50) + args[1] = args[1].replace("uniprot", "uniprot/graph sampling"); + else + if (percentage == 100) + args[1] = "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/data/uniprot_cleaned.nt"; + + PagodaTester.main(args); + if (save) + TestUtil.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_" + percentage + "p" + date); + } + + public static void main(String... args) throws IOException { + 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 new file mode 100644 index 0000000..3ee268e --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java @@ -0,0 +1,67 @@ +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 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"); + } + + @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 new file mode 100644 index 0000000..2b9cdbd --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaDBPedia.java @@ -0,0 +1,30 @@ +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 new file mode 100644 index 0000000..da059f9 --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaELU.java @@ -0,0 +1,20 @@ +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 new file mode 100644 index 0000000..d558e0f --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaFLY.java @@ -0,0 +1,25 @@ +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 new file mode 100644 index 0000000..2014ec1 --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaLUBM.java @@ -0,0 +1,24 @@ +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 new file mode 100644 index 0000000..17d1e82 --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD.java @@ -0,0 +1,46 @@ +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 new file mode 100644 index 0000000..c908cb4 --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD_bench.java @@ -0,0 +1,30 @@ +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 new file mode 100644 index 0000000..88e0835 --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaRLU.java @@ -0,0 +1,20 @@ +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 new file mode 100644 index 0000000..065fb29 --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaUOBM.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.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 new file mode 100644 index 0000000..dff2366 --- /dev/null +++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestGlobalCorrectness.java @@ -0,0 +1,53 @@ +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/test_units/ClauseTester.java b/test/uk/ac/ox/cs/pagoda/test_units/ClauseTester.java deleted file mode 100644 index a0f16d4..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/ClauseTester.java +++ /dev/null @@ -1,164 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -import org.semanticweb.HermiT.model.Atom; -import org.semanticweb.HermiT.model.AtomicConcept; -import org.semanticweb.HermiT.model.AtomicRole; -import org.semanticweb.HermiT.model.DLClause; -import org.semanticweb.HermiT.model.Equality; -import org.semanticweb.HermiT.model.Variable; -import org.semanticweb.owlapi.apibinding.OWLManager; -import org.semanticweb.owlapi.model.OWLOntology; -import org.semanticweb.owlapi.model.OWLOntologyManager; - -import org.testng.Assert; -import org.testng.annotations.Test; -import uk.ac.ox.cs.pagoda.approx.Clause; -import uk.ac.ox.cs.pagoda.approx.Clausifier; - -public class ClauseTester { - - @Test - public void test_simple() { - Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"); - AtomicConcept A = AtomicConcept.create("A"); - AtomicRole r = AtomicRole.create("r"); - Atom[] bodyAtoms = new Atom[] { - Atom.create(A, x), - Atom.create(r, x, y1), - Atom.create(r, x, y2) - }; - - Atom[] headAtoms = new Atom[] { - Atom.create(Equality.INSTANCE, y1, y2) - }; - - OWLOntologyManager m = OWLManager.createOWLOntologyManager(); - OWLOntology emptyOntology = null; - try { - emptyOntology = m.createOntology(); - } catch (Exception e) { - e.printStackTrace(); - Assert.fail("failed to create a new ontology"); - } - Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); - System.out.println(c.toString()); - } - - @Test - public void test_more() { - Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"), y3 = Variable.create("y3"); - AtomicConcept A = AtomicConcept.create("A"); - AtomicRole r = AtomicRole.create("r"); - Atom[] bodyAtoms = new Atom[] { - Atom.create(A, x), - Atom.create(r, x, y1), - Atom.create(r, x, y2), - Atom.create(r, x, y3), - }; - - Atom[] headAtoms = new Atom[] { - Atom.create(Equality.INSTANCE, y1, y2), - Atom.create(Equality.INSTANCE, y1, y3), - Atom.create(Equality.INSTANCE, y2, y3) - }; - - OWLOntologyManager m = OWLManager.createOWLOntologyManager(); - OWLOntology emptyOntology = null; - try { - emptyOntology = m.createOntology(); - } catch (Exception e) { - e.printStackTrace(); - Assert.fail("failed to create a new ontology"); - } - Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); - System.out.println(c.toString()); - } - - @Test - public void test_inverse() { - Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"); - AtomicConcept A = AtomicConcept.create("A"); - AtomicRole r = AtomicRole.create("r"); - Atom[] bodyAtoms = new Atom[] { - Atom.create(A, x), - Atom.create(r, y1, x), - Atom.create(r, y2, x) - }; - - Atom[] headAtoms = new Atom[] { - Atom.create(Equality.INSTANCE, y1, y2) - }; - - OWLOntologyManager m = OWLManager.createOWLOntologyManager(); - OWLOntology emptyOntology = null; - try { - emptyOntology = m.createOntology(); - } catch (Exception e) { - e.printStackTrace(); - Assert.fail("failed to create a new ontology"); - } - Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); - System.out.println(c.toString()); - } - - @Test - public void test_fillter() { - Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"); - AtomicConcept A = AtomicConcept.create("A"); - AtomicConcept B = AtomicConcept.create("B"); - AtomicRole r = AtomicRole.create("r"); - Atom[] bodyAtoms = new Atom[] { - Atom.create(A, x), - Atom.create(r, y1, x), - Atom.create(r, y2, x), - Atom.create(B, y1), - Atom.create(B, y2) - }; - - Atom[] headAtoms = new Atom[] { - Atom.create(Equality.INSTANCE, y1, y2) - }; - - OWLOntologyManager m = OWLManager.createOWLOntologyManager(); - OWLOntology emptyOntology = null; - try { - emptyOntology = m.createOntology(); - } catch (Exception e) { - e.printStackTrace(); - Assert.fail("failed to create a new ontology"); - } - Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); - System.out.println(c.toString()); - } - - @Test - public void test_negFillter() { - Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"); - AtomicConcept A = AtomicConcept.create("A"); - AtomicConcept B = AtomicConcept.create("B"); - AtomicRole r = AtomicRole.create("r"); - Atom[] bodyAtoms = new Atom[] { - Atom.create(A, x), - Atom.create(r, y1, x), - Atom.create(r, y2, x) - }; - - Atom[] headAtoms = new Atom[] { - Atom.create(Equality.INSTANCE, y1, y2), - Atom.create(B, y1), - Atom.create(B, y2) - }; - - OWLOntologyManager m = OWLManager.createOWLOntologyManager(); - OWLOntology emptyOntology = null; - try { - emptyOntology = m.createOntology(); - } catch (Exception e) { - e.printStackTrace(); - Assert.fail("failed to create a new ontology"); - } - Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms)); - System.out.println(c.toString()); - } - -} diff --git a/test/uk/ac/ox/cs/pagoda/test_units/CostEvaluation.java b/test/uk/ac/ox/cs/pagoda/test_units/CostEvaluation.java deleted file mode 100644 index 968cf01..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/CostEvaluation.java +++ /dev/null @@ -1,115 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -import org.semanticweb.owlapi.model.OWLOntology; -import org.testng.annotations.Test; -import uk.ac.ox.cs.pagoda.owl.OWLHelper; -import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner; -import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner.Type; -import uk.ac.ox.cs.pagoda.tester.PagodaTester; -import uk.ac.ox.cs.pagoda.util.TestUtil; -import uk.ac.ox.cs.pagoda.util.Timer; -import uk.ac.ox.cs.pagoda.util.Utility; - -public class CostEvaluation { - - @Test - public void lubm100() { - int number = 1; - 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_all_pagoda.sparql") - ); -// AllTests.copy("output/log4j.log", "results-backup/jair/lubm" + number + ".out"); - } - - public void lubm1000() { - int number = 1000; - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"), - TestUtil.combinePaths(ontoDir, "lubm/data/lubm" + number + ".ttl"), - TestUtil.combinePaths(ontoDir, "lubm/queries/test_all_pagoda.sparql") - }; - OWLOntology ontology = OWLHelper.loadOntology(args[0]); - QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true); - Timer t = new Timer(); - reasoner.loadOntology(ontology); - reasoner.importData(args[1]); - if (!reasoner.preprocess()) - return ; - Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds."); - - reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2])); -// AllTests.copy("output/log4j.log", "results-backup/jair/lubm" + number + ".out"); - } - - @Test - public void uobm5() { - int number = 1; - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), - TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"), - TestUtil.combinePaths(ontoDir, "uobm/queries/standard_all_pagoda.sparql") - }; - PagodaTester.main(args); -// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out"); - } - - public void uobm100() { - int number = 200; - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), - TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"), - TestUtil.combinePaths(ontoDir, "uobm/queries/standard_group3_all.sparql") - }; - PagodaTester.main(args); -// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out"); - } - - public void uobm500() { - int number = 500; - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), - TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"), - TestUtil.combinePaths(ontoDir, "uobm/queries/standard_all_pagoda.sparql") - }; - - OWLOntology ontology = OWLHelper.loadOntology(args[0]); - QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true); - Timer t = new Timer(); - reasoner.loadOntology(ontology); - reasoner.importData(args[1]); - if (!reasoner.preprocess()) - return ; - Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds."); - - reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2])); -// AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out"); - } - - - public static void main(String... args) { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - args = new String[] { - 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") - }; - - OWLOntology ontology = OWLHelper.loadOntology(args[0]); - QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true); - Timer t = new Timer(); - reasoner.loadOntology(ontology); - reasoner.importData(args[1]); - if (!reasoner.preprocess()) - return ; - Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds."); - - reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2])); - } -} diff --git a/test/uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java deleted file mode 100644 index 10ac974..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java +++ /dev/null @@ -1,193 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -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; - -public class JAIR_PAGOdA { - - @Test - public void lubm1() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"), - TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"), - TestUtil.combinePaths(ontoDir, "lubm/queries/test.sparql") - }; - PagodaTester.main(args); - TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda"); - } - - @Test - public void lubm1_conj() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"), - TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"), - TestUtil.combinePaths(ontoDir, "lubm/queries/test_pellet.sparql") - }; - PagodaTester.main(args); - TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_conj"); - } - - @Test - public void lubm1_rolledUp() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - "/home/yzhou/backup/20141212/univ-bench-queries.owl", - TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"), - TestUtil.combinePaths(ontoDir, "lubm/queries/atomic_lubm.sparql") - ); - TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_rolledUp"); - } - - @Test - public void uobm1() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), - TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"), - TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql") - }; - PagodaTester.main(args); - TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda"); - } - - @Test - public void uobm1_conj() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"), - TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"), - TestUtil.combinePaths(ontoDir, "uobm/queries/standard_pellet.sparql") - }; - PagodaTester.main(args); - TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_conj"); - } - - @Test - public void uobm1_rolledUp() { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl", - TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"), - TestUtil.combinePaths(ontoDir, "uobm/queries/atomic_uobm.sparql") - }; - PagodaTester.main(args); -// TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_rolledUp"); - } - - @Test - public void fly() { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"), - null, - TestUtil.combinePaths(ontoDir, "fly/queries/fly_pellet.sparql") - }; - PagodaTester.main(args); -// TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda"); - } - - @Test - public void fly_conj() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"), - null, - TestUtil.combinePaths(ontoDir, "fly/queries/fly_pellet.sparql") - }; - PagodaTester.main(args); - TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_conj"); - } - - - public void fly_rolledUp() { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( -// TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", - TestUtil.combinePaths(ontoDir, "fly/fly-all-in-one_rolledUp.owl"), - null, - TestUtil.combinePaths(ontoDir, "fly/queries/fly_atomic.sparql") - ); -// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_rolledUp"); - } - - public void dbpedia() { - 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/queries/atomic_ground.sparql"), - "dbpedia.ans" - ); - -// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/dbpedia/pagoda"); - } - - public void npd() { - 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_ground.sparql") - , "npd.ans" - ); - -// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/npd/pagoda"); - } - - public void reactome() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"), - TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl"), -// null, -// TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/atomic_ground.sparql") - TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/example.sparql") - , "pagoda_reactome.ans" - ); - TestUtil.copyFile("log4j.log", "output/jair/pagoda_reactome.example"); - -// TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_10p"); - } - - public void chembl() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"), - TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/graph sampling/sample_1.nt"), -// TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql") - TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/example.sparql") - , "pagoda_chembl.ans" - ); - TestUtil.copyFile("log4j.log", "output/jair/pagoda_chembl.example"); -// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_1p"); - } - - public void uniprot() throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - PagodaTester.main( - TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat-processed.owl"), - TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/graph sampling/sample_1.nt"), -// null, -// TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql") - TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/example.sparql") - , "pagoda_uniprot.ans" - ); - TestUtil.copyFile("log4j.log", "output/jair/pagoda_uniprot.example"); -// TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_1p"); - } - - - public static void main(String... args) { - try { - new JAIR_PAGOdA().lubm1(); - } catch (IOException e) { - e.printStackTrace(); - } - } - -} diff --git a/test/uk/ac/ox/cs/pagoda/test_units/JAIR_Scalability.java b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_Scalability.java deleted file mode 100644 index 2cf8446..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/JAIR_Scalability.java +++ /dev/null @@ -1,91 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -import org.testng.annotations.Test; -import uk.ac.ox.cs.pagoda.tester.PagodaTester; -import uk.ac.ox.cs.pagoda.util.Properties; -import uk.ac.ox.cs.pagoda.util.TestUtil; - -import java.io.IOException; - -public class JAIR_Scalability { - - private static final String date = "_0123"; - - @Test - public void reactome() throws IOException { - testReactome(10, false); - } - - @Test - public void chembl() throws IOException { - testChEMBL(1, false); - } - - @Test - public void uniprot() throws IOException { - testUniProt(1, false); - } - - public void testReactome(int percentage, boolean save) throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"), - TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/simplifed_sample_" + percentage + ".ttl"), - TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/test.sparql") - , "reactome.ans" - }; - if (percentage == 10) - args[1] = args[1].replace("simplifed", "reactome"); - - PagodaTester.main(args); - if (save) - TestUtil.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_" + percentage + "p" + date); - } - - public void testChEMBL(int percentage, boolean save) throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"), - TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/sample_" + percentage + ".nt"), -// TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql") - TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/test.sparql") - , "chembl.ans" - }; - if (percentage == 1 || percentage == 10 || percentage == 50) - args[1] = args[1].replace("chembl", "chembl/graph sampling"); - else - if (percentage == 100) - args[1] = "/home/yzhou/RDFData/ChEMBL/facts/ChEMBL.ttl"; - - PagodaTester.main(args); - if (save) - TestUtil.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_" + percentage + "p" + date); - } - - public void testUniProt(int percentage, boolean save) throws IOException { - String ontoDir = TestUtil.getConfig().getProperty("ontoDir"); - String[] args = new String[] { - TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat-processed.owl"), - TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/sample_" + percentage + ".nt"), -// TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql") - TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/test.sparql") - , "uniprot.ans" - }; - - if (percentage == 1 || percentage == 10 || percentage == 50) - args[1] = args[1].replace("uniprot", "uniprot/graph sampling"); - else - if (percentage == 100) - args[1] = "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/data/uniprot_cleaned.nt"; - - PagodaTester.main(args); - if (save) - TestUtil.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_" + percentage + "p" + date); - } - - public static void main(String... args) throws IOException { - Properties.ShellModeDefault = true; - new JAIR_Scalability().testUniProt(50, false); - } - -} diff --git a/test/uk/ac/ox/cs/pagoda/test_units/LightEvaluation.java b/test/uk/ac/ox/cs/pagoda/test_units/LightEvaluation.java deleted file mode 100644 index 932c178..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/LightEvaluation.java +++ /dev/null @@ -1,67 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -import org.junit.Test; -import uk.ac.ox.cs.pagoda.tester.PagodaTester; -import uk.ac.ox.cs.pagoda.util.TestUtil; - -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"); - } - - @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/test_units/PagodaDBPedia.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaDBPedia.java deleted file mode 100644 index 1673179..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/PagodaDBPedia.java +++ /dev/null @@ -1,30 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -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/test_units/PagodaELU.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaELU.java deleted file mode 100644 index 70d531d..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/PagodaELU.java +++ /dev/null @@ -1,20 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -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/test_units/PagodaFLY.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaFLY.java deleted file mode 100644 index bad533f..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/PagodaFLY.java +++ /dev/null @@ -1,25 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -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/test_units/PagodaLUBM.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaLUBM.java deleted file mode 100644 index 1aded5b..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/PagodaLUBM.java +++ /dev/null @@ -1,24 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -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/test_units/PagodaNPD.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD.java deleted file mode 100644 index 5f89162..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD.java +++ /dev/null @@ -1,46 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -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/test_units/PagodaNPD_bench.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD_bench.java deleted file mode 100644 index 1aca36a..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD_bench.java +++ /dev/null @@ -1,30 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -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/test_units/PagodaRLU.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaRLU.java deleted file mode 100644 index c365196..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/PagodaRLU.java +++ /dev/null @@ -1,20 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -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/test_units/PagodaUOBM.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaUOBM.java deleted file mode 100644 index ee9cf13..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/PagodaUOBM.java +++ /dev/null @@ -1,24 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -import org.testng.annotations.Test; -import uk.ac.ox.cs.pagoda.util.TestUtil; - -import java.io.IOException; -import java.nio.file.Paths; - -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); - } - -} diff --git a/test/uk/ac/ox/cs/pagoda/test_units/TestGlobalCorrectness.java b/test/uk/ac/ox/cs/pagoda/test_units/TestGlobalCorrectness.java deleted file mode 100644 index ffaf8fc..0000000 --- a/test/uk/ac/ox/cs/pagoda/test_units/TestGlobalCorrectness.java +++ /dev/null @@ -1,52 +0,0 @@ -package uk.ac.ox.cs.pagoda.test_units; - -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()); - 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/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java index 5e49f79..b97d85e 100644 --- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java +++ b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java @@ -94,11 +94,11 @@ public class PagodaTester { 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, "/home/alessandro/Desktop/uobm1.ans"}; -// args = new String[] {fly, "null", fly_query.replace(".sparql", "_pellet.sparql") }; +// 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, null, fly_query}; + 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}; @@ -119,7 +119,7 @@ public class PagodaTester { // args[2] = args[2].replace(".sparql", "_pellet.sparql"); } - Properties properties = new Properties("config/uobm.conf"); + Properties properties = new Properties("config/uobm.properties"); int index = 0; if (args.length > index) properties.setOntologyPath(args[index++]); @@ -157,7 +157,7 @@ public class PagodaTester { if (pagoda != null) pagoda.dispose(); } - Utility.closeCurrentOut(); +// Utility.closeCurrentOut(); if (properties.getShellMode()) System.exit(0); } -- cgit v1.2.3