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Ensure that inference works across ontologies
Add a test case where a term from TGEMO has a parent defined in EFO.
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...a-core/src/test/java/ubic/gemma/core/ontology/GemmaAndExperimentalFactorOntologyTest.java
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| package ubic.gemma.core.ontology; | ||
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| import org.junit.Test; | ||
| import org.junit.experimental.categories.Category; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.beans.factory.annotation.Qualifier; | ||
| import org.springframework.cache.CacheManager; | ||
| import org.springframework.cache.concurrent.ConcurrentMapCacheManager; | ||
| import org.springframework.context.annotation.Bean; | ||
| import org.springframework.context.annotation.Configuration; | ||
| import org.springframework.core.task.AsyncTaskExecutor; | ||
| import org.springframework.core.task.SimpleAsyncTaskExecutor; | ||
| import org.springframework.core.task.TaskExecutor; | ||
| import org.springframework.test.context.ContextConfiguration; | ||
| import org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests; | ||
| import ubic.basecode.ontology.model.OntologyTerm; | ||
| import ubic.basecode.ontology.providers.ExperimentalFactorOntologyService; | ||
| import ubic.basecode.ontology.providers.ObiService; | ||
| import ubic.gemma.core.genome.gene.service.GeneService; | ||
| import ubic.gemma.core.ontology.providers.GemmaOntologyService; | ||
| import ubic.gemma.core.ontology.providers.GeneOntologyService; | ||
| import ubic.gemma.core.search.SearchService; | ||
| import ubic.gemma.core.util.test.TestPropertyPlaceholderConfigurer; | ||
| import ubic.gemma.core.util.test.category.SlowTest; | ||
| import ubic.gemma.persistence.service.common.description.CharacteristicService; | ||
| import ubic.gemma.persistence.util.TestComponent; | ||
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| import java.util.Collections; | ||
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| import static org.assertj.core.api.Assertions.assertThat; | ||
| import static org.junit.Assert.assertNotNull; | ||
| import static org.mockito.Mockito.mock; | ||
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| /** | ||
| * This test covers cases where inference is done across two distinct {@link ubic.basecode.ontology.providers.OntologyService}. | ||
| * @author poirigui | ||
| */ | ||
| @Category(SlowTest.class) | ||
| @ContextConfiguration | ||
| public class GemmaAndExperimentalFactorOntologyTest extends AbstractJUnit4SpringContextTests { | ||
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| @Configuration | ||
| @TestComponent | ||
| static class GemmaOntologyAndEfoTestContextConfiguration { | ||
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| @Bean | ||
| public static TestPropertyPlaceholderConfigurer testPropertyPlaceholderConfigurer() { | ||
| return new TestPropertyPlaceholderConfigurer( "load.ontologies=false" ); | ||
| } | ||
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| @Bean | ||
| public ExperimentalFactorOntologyService experimentalFactorOntologyService() { | ||
| ExperimentalFactorOntologyService ontology = new ExperimentalFactorOntologyService(); | ||
| ontology.setSearchEnabled( false ); | ||
| ontology.initialize( true, false ); | ||
| return ontology; | ||
| } | ||
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| @Bean | ||
| public GemmaOntologyService gemmaOntologyService() { | ||
| GemmaOntologyService ontology = new GemmaOntologyService(); | ||
| ontology.setProcessImports( false ); // FIXME: remove this once https://github.com/PavlidisLab/TGEMO/pull/20 is merged in TGEMO | ||
| ontology.initialize( true, false ); | ||
| return ontology; | ||
| } | ||
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| @Bean | ||
| public OntologyService ontologyService() { | ||
| return new OntologyServiceImpl(); | ||
| } | ||
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| @Bean | ||
| public CharacteristicService characteristicService() { | ||
| return mock(); | ||
| } | ||
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| @Bean | ||
| public SearchService searchService() { | ||
| return mock(); | ||
| } | ||
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| @Bean | ||
| public GeneOntologyService geneOntologyService() { | ||
| return mock(); | ||
| } | ||
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| @Bean | ||
| public GeneService geneService() { | ||
| return mock(); | ||
| } | ||
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| @Bean | ||
| public AsyncTaskExecutor taskExecutor() { | ||
| return new SimpleAsyncTaskExecutor(); | ||
| } | ||
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| @Bean | ||
| public ObiService obiService() { | ||
| return mock(); | ||
| } | ||
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| @Bean | ||
| @Qualifier("ontologyTaskExecutor") | ||
| public TaskExecutor ontologyTaskExecutor() { | ||
| return mock(); | ||
| } | ||
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| @Bean | ||
| public CacheManager cacheManager() { | ||
| return new ConcurrentMapCacheManager(); | ||
| } | ||
| } | ||
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| @Autowired | ||
| private ExperimentalFactorOntologyService experimentalFactorOntologyService; | ||
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| @Autowired | ||
| private GemmaOntologyService gemmaOntologyService; | ||
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| @Autowired | ||
| private OntologyService ontologyService; | ||
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| @Test | ||
| @Category(SlowTest.class) | ||
| public void testInferenceInGemma() { | ||
| OntologyTerm overexpression = ontologyService.getTerm( "http://gemma.msl.ubc.ca/ont/TGEMO_00004" ); | ||
| assertNotNull( overexpression ); | ||
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| assertThat( gemmaOntologyService.getParents( Collections.singleton( overexpression ), false, false ) ) | ||
| .extracting( OntologyTerm::getUri ) | ||
| .containsExactly( "http://www.ebi.ac.uk/efo/EFO_0000510" ); | ||
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| OntologyTerm geneticModification = experimentalFactorOntologyService.getTerm( "http://www.ebi.ac.uk/efo/EFO_0000510" ); | ||
| assertNotNull( geneticModification ); | ||
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| assertThat( experimentalFactorOntologyService.getParents( Collections.singleton( geneticModification ), false, false ) ) | ||
| .extracting( OntologyTerm::getUri ) | ||
| .containsExactly( "http://www.ebi.ac.uk/efo/EFO_0000001", | ||
| "http://purl.obolibrary.org/obo/BFO_0000015", | ||
| "http://www.ebi.ac.uk/efo/EFO_0004542", | ||
| "http://www.ebi.ac.uk/efo/EFO_0002694" ); | ||
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| // ensure that parents are combined when using the OS | ||
| assertThat( ontologyService.getParents( Collections.singleton( overexpression ), false, false ) ) | ||
| .extracting( OntologyTerm::getUri ) | ||
| .containsExactlyInAnyOrder( | ||
| "http://www.ebi.ac.uk/efo/EFO_0000001", | ||
| "http://purl.obolibrary.org/obo/BFO_0000015", | ||
| "http://www.ebi.ac.uk/efo/EFO_0004542", | ||
| "http://www.ebi.ac.uk/efo/EFO_0002694", | ||
| "http://www.ebi.ac.uk/efo/EFO_0000510" ); | ||
| } | ||
| } |