diff --git a/src/main/java/org/cbioportal/cdd/repository/topbraid/ClinicalAttributeMetadataRepositoryConfiguration.java b/src/main/java/org/cbioportal/cdd/repository/topbraid/ClinicalAttributeMetadataRepositoryConfiguration.java index c28157d..2d02487 100644 --- a/src/main/java/org/cbioportal/cdd/repository/topbraid/ClinicalAttributeMetadataRepositoryConfiguration.java +++ b/src/main/java/org/cbioportal/cdd/repository/topbraid/ClinicalAttributeMetadataRepositoryConfiguration.java @@ -81,7 +81,7 @@ public TopBraidSessionManager mskVocabularySessionManager() { return new TopBraidSessionManager(mskVocabularySessionConfiguration()); } - // @Bean + @Bean // TODO : rename to knowledgeSystemsRepository @Qualifier("knowledgeSystemsClinicalAttributeMetadataRepository") public KnowledgeSystemsClinicalAttributeMetadataRepository knowledgeSystemsClinicalAttributeMetadataRepository() { diff --git a/src/test/java/org/cbioportal/cdd/ClinicalDataDictionaryTestConfig.java b/src/test/java/org/cbioportal/cdd/ClinicalDataDictionaryTestConfig.java index 131175d..7aca56f 100644 --- a/src/test/java/org/cbioportal/cdd/ClinicalDataDictionaryTestConfig.java +++ b/src/test/java/org/cbioportal/cdd/ClinicalDataDictionaryTestConfig.java @@ -19,18 +19,35 @@ import org.mockito.Mockito; import org.cbioportal.cdd.model.ClinicalAttributeMetadata; import org.cbioportal.cdd.repository.topbraid.KnowledgeSystemsClinicalAttributeMetadataRepository; +import org.cbioportal.cdd.repository.topbraid.MskVocabularyRepository; +import org.cbioportal.cdd.model.MskVocabulary; +import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; +import org.springframework.context.annotation.Primary; @Configuration public class ClinicalDataDictionaryTestConfig { @Bean + @Primary + @Qualifier("mockedKnowledgeSystemsClinicalAttributeMetadataRepository") public KnowledgeSystemsClinicalAttributeMetadataRepository mockClinicalAttributesRepository() { KnowledgeSystemsClinicalAttributeMetadataRepository mockClinicalAttributesRepository = Mockito.mock(KnowledgeSystemsClinicalAttributeMetadataRepository.class); return mockClinicalAttributesRepository; } + @Bean + @Primary + @Qualifier("mockedMskVocabularyRepository") + public MskVocabularyRepository mockMskVocabularyRepository() { + MskVocabularyRepository mockMskVocabularyRepository = Mockito.mock(MskVocabularyRepository.class); + Mockito.reset(mockMskVocabularyRepository); + // TODO : mock realistic behavior and write unit tests against the MskVocabularyRepository + Mockito.when(mockMskVocabularyRepository.getClinicalAttributeMetadata()).thenReturn(new ArrayList()); + return mockMskVocabularyRepository; + } + public void resetWorkingClinicalAttributesRepository(KnowledgeSystemsClinicalAttributeMetadataRepository mockClinicalAttributesRepository) { Mockito.reset(mockClinicalAttributesRepository); Mockito.when(mockClinicalAttributesRepository.getClinicalAttributeMetadata()).thenReturn(makeMockAttributeList());