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