Merge pull request cBioPortal#6 from sheridancbio/mskvocab

Create mock MskVocabularyRepository
sheridancbio · Sep 23, 2020 · c6964b2 · c6964b2
2 parents 1eb2d10 + 68373a4
commit c6964b2
Show file tree

Hide file tree

Showing 2 changed files with 18 additions and 1 deletion.
diff --git a/.../cbioportal/cdd/repository/topbraid/ClinicalAttributeMetadataRepositoryConfiguration.java b/.../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
@@ -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<MskVocabulary>());
+        return mockMskVocabularyRepository;
+    }
+
     public void resetWorkingClinicalAttributesRepository(KnowledgeSystemsClinicalAttributeMetadataRepository mockClinicalAttributesRepository) {
         Mockito.reset(mockClinicalAttributesRepository);
         Mockito.when(mockClinicalAttributesRepository.getClinicalAttributeMetadata()).thenReturn(makeMockAttributeList());