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 2d02487..c28157d 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/main/resources/logback.xml b/src/main/resources/logback.xml new file mode 100644 index 0000000..30a5133 --- /dev/null +++ b/src/main/resources/logback.xml @@ -0,0 +1,21 @@ + + + + /srv/www/schultz-tomcat/tomcat/logs/test-cdd.log + + + /srv/www/schultz-tomcat/tomcat/logs/test-cdd.log.%d{yyyy-MM-dd}.gz + + + UTF-8 + %d %-4relative [%thread] %-5level %logger{35} - %msg%n + + + + + + + + + diff --git a/src/test/java/org/cbioportal/cdd/ClinicalDataDictionaryTest.java b/src/test/java/org/cbioportal/cdd/ClinicalDataDictionaryTest.java index e3f16be..f9e9a08 100644 --- a/src/test/java/org/cbioportal/cdd/ClinicalDataDictionaryTest.java +++ b/src/test/java/org/cbioportal/cdd/ClinicalDataDictionaryTest.java @@ -54,7 +54,7 @@ public class ClinicalDataDictionaryTest { private TestRestTemplate restTemplate; @Autowired - private KnowledgeSystemsClinicalAttributeMetadataRepository clinicalAttributesRepository; + private KnowledgeSystemsClinicalAttributeMetadataRepository mockClinicalAttributesRepository; @Autowired private ClinicalAttributeMetadataCache clinicalAttributesCache; @@ -63,7 +63,7 @@ public class ClinicalDataDictionaryTest { // make sure repository is working version before each test public void resetToWorkingRepository() { ClinicalDataDictionaryTestConfig config = new ClinicalDataDictionaryTestConfig(); - config.resetWorkingClinicalAttributesRepository(clinicalAttributesRepository); + config.resetWorkingClinicalAttributesRepository(mockClinicalAttributesRepository); ResponseEntity response = restTemplate.getForEntity("/api/refreshCache", String.class); } @@ -169,7 +169,7 @@ public void validateCacheTest() throws Exception { public void failedCacheRefreshTest() throws Exception { // resetting cache with a broken repository should throw a FailedCacheRefreshException ClinicalDataDictionaryTestConfig config = new ClinicalDataDictionaryTestConfig(); - config.resetNotWorkingClinicalAttributesRepository(clinicalAttributesRepository); + config.resetNotWorkingClinicalAttributesRepository(mockClinicalAttributesRepository); clinicalAttributesCache.resetCache(); } @@ -232,24 +232,24 @@ public void forceResetCacheTest() throws Exception { // test that cache is updated after GET /api/refreshCache ClinicalDataDictionaryTestConfig config = new ClinicalDataDictionaryTestConfig(); // change repository to version with 2 attributes/1 override - config.resetUpdatedClinicalAttributesRepository(clinicalAttributesRepository); + config.resetUpdatedClinicalAttributesRepository(mockClinicalAttributesRepository); ResponseEntity response = restTemplate.getForEntity("/api/refreshCache", String.class); assertThat(response.getBody(), equalTo("{\"response\":\"Success!\"}")); assertThat(response.getStatusCode(), equalTo(HttpStatus.OK)); - assertThat(clinicalAttributesRepository.getClinicalAttributeMetadata().size(), equalTo(2)); - assertThat(clinicalAttributesRepository.getClinicalAttributeMetadataOverrides(), hasKey("updated_override_study")); - assertThat(clinicalAttributesRepository.getClinicalAttributeMetadataOverrides().size(), equalTo(1)); + assertThat(mockClinicalAttributesRepository.getClinicalAttributeMetadata().size(), equalTo(2)); + assertThat(mockClinicalAttributesRepository.getClinicalAttributeMetadataOverrides(), hasKey("updated_override_study")); + assertThat(mockClinicalAttributesRepository.getClinicalAttributeMetadataOverrides().size(), equalTo(1)); // change repository to non-working version - config.resetNotWorkingClinicalAttributesRepository(clinicalAttributesRepository); + config.resetNotWorkingClinicalAttributesRepository(mockClinicalAttributesRepository); response = restTemplate.getForEntity("/api/refreshCache", String.class); assertThat(response.getBody(), containsString("org.cbioportal.cdd.service.exception.FailedCacheRefreshException")); assertThat(response.getStatusCode(), equalTo(HttpStatus.SERVICE_UNAVAILABLE)); // change repository to version with 5 attributes/2 overrides - config.resetWorkingClinicalAttributesRepository(clinicalAttributesRepository); + config.resetWorkingClinicalAttributesRepository(mockClinicalAttributesRepository); restTemplate.getForEntity("/api/refreshCache", String.class); - assertThat(clinicalAttributesRepository.getClinicalAttributeMetadata().size(), equalTo(5)); - assertThat(clinicalAttributesRepository.getClinicalAttributeMetadataOverrides().size(), equalTo(2)); - assertThat(clinicalAttributesRepository.getClinicalAttributeMetadataOverrides(), not(hasKey("updated_override_study"))); + assertThat(mockClinicalAttributesRepository.getClinicalAttributeMetadata().size(), equalTo(5)); + assertThat(mockClinicalAttributesRepository.getClinicalAttributeMetadataOverrides().size(), equalTo(2)); + assertThat(mockClinicalAttributesRepository.getClinicalAttributeMetadataOverrides(), not(hasKey("updated_override_study"))); } @Test diff --git a/src/test/java/org/cbioportal/cdd/ClinicalDataDictionaryTestConfig.java b/src/test/java/org/cbioportal/cdd/ClinicalDataDictionaryTestConfig.java index 9f7934d..131175d 100644 --- a/src/test/java/org/cbioportal/cdd/ClinicalDataDictionaryTestConfig.java +++ b/src/test/java/org/cbioportal/cdd/ClinicalDataDictionaryTestConfig.java @@ -26,27 +26,27 @@ public class ClinicalDataDictionaryTestConfig { @Bean - public KnowledgeSystemsClinicalAttributeMetadataRepository clinicalAttributesRepository() { - KnowledgeSystemsClinicalAttributeMetadataRepository clinicalAttributesRepository = Mockito.mock(KnowledgeSystemsClinicalAttributeMetadataRepository.class); - return clinicalAttributesRepository; + public KnowledgeSystemsClinicalAttributeMetadataRepository mockClinicalAttributesRepository() { + KnowledgeSystemsClinicalAttributeMetadataRepository mockClinicalAttributesRepository = Mockito.mock(KnowledgeSystemsClinicalAttributeMetadataRepository.class); + return mockClinicalAttributesRepository; } - public void resetWorkingClinicalAttributesRepository(KnowledgeSystemsClinicalAttributeMetadataRepository clinicalAttributesRepository) { - Mockito.reset(clinicalAttributesRepository); - Mockito.when(clinicalAttributesRepository.getClinicalAttributeMetadata()).thenReturn(makeMockAttributeList()); - Mockito.when(clinicalAttributesRepository.getClinicalAttributeMetadataOverrides()).thenReturn(makeMockOverridesMap()); + public void resetWorkingClinicalAttributesRepository(KnowledgeSystemsClinicalAttributeMetadataRepository mockClinicalAttributesRepository) { + Mockito.reset(mockClinicalAttributesRepository); + Mockito.when(mockClinicalAttributesRepository.getClinicalAttributeMetadata()).thenReturn(makeMockAttributeList()); + Mockito.when(mockClinicalAttributesRepository.getClinicalAttributeMetadataOverrides()).thenReturn(makeMockOverridesMap()); } - public void resetUpdatedClinicalAttributesRepository(KnowledgeSystemsClinicalAttributeMetadataRepository clinicalAttributesRepository) { - Mockito.reset(clinicalAttributesRepository); - Mockito.when(clinicalAttributesRepository.getClinicalAttributeMetadata()).thenReturn(makeUpdatedMockAttributeList()); - Mockito.when(clinicalAttributesRepository.getClinicalAttributeMetadataOverrides()).thenReturn(makeUpdatedMockOverridesMap()); + public void resetUpdatedClinicalAttributesRepository(KnowledgeSystemsClinicalAttributeMetadataRepository mockClinicalAttributesRepository) { + Mockito.reset(mockClinicalAttributesRepository); + Mockito.when(mockClinicalAttributesRepository.getClinicalAttributeMetadata()).thenReturn(makeUpdatedMockAttributeList()); + Mockito.when(mockClinicalAttributesRepository.getClinicalAttributeMetadataOverrides()).thenReturn(makeUpdatedMockOverridesMap()); } - public void resetNotWorkingClinicalAttributesRepository(KnowledgeSystemsClinicalAttributeMetadataRepository clinicalAttributesRepository) { - Mockito.reset(clinicalAttributesRepository); - Mockito.when(clinicalAttributesRepository.getClinicalAttributeMetadata()).thenThrow(new RuntimeException("faking a problem getting the clinical attribute data")); - Mockito.when(clinicalAttributesRepository.getClinicalAttributeMetadataOverrides()).thenThrow(new RuntimeException("faking a problem getting the clinical attribute data")); + public void resetNotWorkingClinicalAttributesRepository(KnowledgeSystemsClinicalAttributeMetadataRepository mockClinicalAttributesRepository) { + Mockito.reset(mockClinicalAttributesRepository); + Mockito.when(mockClinicalAttributesRepository.getClinicalAttributeMetadata()).thenThrow(new RuntimeException("faking a problem getting the clinical attribute data")); + Mockito.when(mockClinicalAttributesRepository.getClinicalAttributeMetadataOverrides()).thenThrow(new RuntimeException("faking a problem getting the clinical attribute data")); } private ArrayList makeMockAttributeList() { diff --git a/src/test/resources/test.application.properties b/src/test/resources/test.application.properties new file mode 100644 index 0000000..9143ef2 --- /dev/null +++ b/src/test/resources/test.application.properties @@ -0,0 +1,7 @@ +# ehcache unit test properties +ehcache.dev.persistence.path=/data/wanga5/unittesting +ehcache.dev.enable.statistics=false +ehcache.dev.clinicalAttributeMetadataEHCache.maxBytesLocalDisk=1000 +ehcache.dev.clinicalAttributeMetadataEHCache.maxBytesLocalDiskUnits=kB +ehcache.dev.clinicalAttributeMetadataOverridesEHCache.maxBytesLocalDisk=1000 +ehcache.dev.clinicalAttributeMetadataOverridesEHCache.maxBytesLocalDiskUnits=kB