broken tets

sheridancbio · Sep 23, 2020 · 1eb2d10 · 1eb2d10
1 parent 95ce989
commit 1eb2d10
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Showing 5 changed files with 56 additions and 28 deletions.
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/main/resources/logback.xml b/src/main/resources/logback.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configuration scan="true">
+    <appender name="FILE" class="ch.qos.logback.core.rolling.RollingFileAppender">
+        <file>/srv/www/schultz-tomcat/tomcat/logs/test-cdd.log</file>
+        <rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
+            <!-- daily rollover. Make sure the path matches the one in the file element or else
+             the rollover logs are placed in the working directory. -->
+            <fileNamePattern>/srv/www/schultz-tomcat/tomcat/logs/test-cdd.log.%d{yyyy-MM-dd}.gz</fileNamePattern>
+        </rollingPolicy>
+        <encoder>
+            <charset>UTF-8</charset>
+            <pattern>%d %-4relative [%thread] %-5level %logger{35} - %msg%n</pattern>
+        </encoder>
+    </appender>
+    <logger name="org.cbioportal.cdd" additivity="false" level="info">
+        <appender-ref ref="FILE" />
+    </logger>
+    <root level="INFO">
+        <appender-ref ref="FILE"/>
+    </root>
+</configuration>
diff --git 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<String> 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<String> 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
@@ -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<ClinicalAttributeMetadata> makeMockAttributeList() {

diff --git a/src/test/resources/test.application.properties 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