diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
index 408d1981a4ee4343780cb17bf249a53a427d6bc3..0a66b94d754160543164841201c7f39888406014 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
@@ -2,6 +2,8 @@ package lcsb.mapviewer.annotation.cache;
import java.lang.reflect.Constructor;
import java.util.Calendar;
+import java.util.Collection;
+import java.util.LinkedList;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
@@ -143,8 +145,8 @@ public class PermanentDatabaseLevelCache extends XmlParser
if (object instanceof CachableInterface) {
cachableInterface = (CachableInterface) object;
} else {
- logger.fatal(
- "Invalid class type: " + object.getClass() + ". Class cannot be cast into " + CachableInterface.class);
+ logger.fatal("Invalid class type: " + object.getClass() + " [" + object.toString()
+ + "]. Class cannot be cast into " + CachableInterface.class);
}
applicationContext.getAutowireCapableBeanFactory().autowireBean(object);
@@ -563,16 +565,6 @@ public class PermanentDatabaseLevelCache extends XmlParser
return ((ScheduledThreadPoolExecutor) cacheRefreshService).getQueue().size();
}
- @Override
- public boolean refreshIsBusy() {
- return getRefreshPendingQueueSize() != 0 || getRefreshExecutingTasksSize() != 0;
- }
-
- @Override
- public int getRefreshExecutingTasksSize() {
- return ((ScheduledThreadPoolExecutor) cacheRefreshService).getActiveCount();
- }
-
@Override
public CacheQueryDao getCacheQueryDao() {
return cacheQueryDao;
@@ -584,9 +576,24 @@ public class PermanentDatabaseLevelCache extends XmlParser
}
@Override
- public boolean databaseCacheIsBusy() {
- return refreshIsBusy() || ((ScheduledThreadPoolExecutor) service).getActiveCount() > 0
- || ((ScheduledThreadPoolExecutor) service).getQueue().size() > 0;
+ public void waitToFinishTasks() throws InterruptedException, ExecutionException {
+ Collection<Future<?>> futures = new LinkedList<Future<?>>();
+ futures.add(cacheRefreshService.submit(new Callable<Void>() {
+ @Override
+ public Void call() throws Exception {
+ return null;
+ }
+ }));
+ futures.add(service.submit(new Callable<Void>() {
+ @Override
+ public Void call() throws Exception {
+ return null;
+ }
+ }));
+
+ for (Future<?> future:futures) {
+ future.get();
+ }
}
}
\ No newline at end of file
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheInterface.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheInterface.java
index 1d6ee14bee1f13e2210f3ccb979172d58c4c74d3..59099aedabc6cd5b4f722402eebb3762e90192b8 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheInterface.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheInterface.java
@@ -1,5 +1,7 @@
package lcsb.mapviewer.annotation.cache;
+import java.util.concurrent.ExecutionException;
+
import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
/**
@@ -20,25 +22,11 @@ public interface PermanentDatabaseLevelCacheInterface extends QueryCacheInterfac
int getRefreshPendingQueueSize();
/**
- * Returns true if refreshing of entries in database is in progress.
- *
- * @return true if refreshing of entries in database is in progress.
- */
- boolean refreshIsBusy();
-
- /**
- * Returns approximate number of refresh tasks that are currently executed.
- *
- * @return approximate number of refresh tasks that are currently executed.
- */
- int getRefreshExecutingTasksSize();
-
- /**
- * Returns true if database cache has any task in progress.
- *
- * @return true if database cache has any task in progress.
+ * Waits for all tasks in the cache to finish (refresh/get/etc).
+ * @throws ExecutionException
+ * @throws InterruptedException
*/
- boolean databaseCacheIsBusy();
+ void waitToFinishTasks() throws InterruptedException, ExecutionException;
/**
* Returns {@link CacheQueryDao} used by the cache.
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
index 73690ea7ee6c0c0fe8abaea5c850ecee265ff160..8d1e262d9a943c295c928269cd4c220d860946e4 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
@@ -283,12 +283,4 @@ public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit
throw exception;
}
- protected void waitForRefreshCacheQueueToEmpty() throws InterruptedException {
- while (cache.refreshIsBusy()) {
- logger.debug("Waiting for refresh queue to empty. " + cache.getRefreshPendingQueueSize() + " pending. "
- + cache.getRefreshExecutingTasksSize() + " tasks are executed.");
- Thread.sleep(300);
- }
- }
-
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheTest.java
index a1672a47742f10e7a6700999852b84d0f62c0dcc..1b8b5b7fefd6f3e33fd874475d9f675862ebaee6 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheTest.java
@@ -18,6 +18,7 @@ import org.junit.Test;
import org.mockito.Mockito;
import org.mockito.invocation.InvocationOnMock;
import org.mockito.stubbing.Answer;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.annotation.Rollback;
import org.w3c.dom.Node;
@@ -34,6 +35,9 @@ public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
Logger logger = Logger.getLogger(PermanentDatabaseLevelCacheTest.class);
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
+
@Before
public void setUp() throws Exception {
}
@@ -115,7 +119,6 @@ public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
@Test(timeout = 15000)
public void testRefresh() throws Exception {
try {
- waitForRefreshCacheQueueToEmpty();
CacheType invalidType = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
String query = "test query";
@@ -129,7 +132,7 @@ public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
// wasn't updated)
assertEquals(val, res);
// sleep a bit to wait for the second thread
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
// for the second time it should change
dbUtils.createSessionForCurrentThread();
res = cache.getStringByQuery(query, invalidType);
@@ -300,9 +303,8 @@ public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
cache.invalidateByQuery(query, invalidType);
- while (cache.databaseCacheIsBusy()) {
- Thread.sleep(10);
- }
+ cache.waitToFinishTasks();
+
assertEquals(1, getFatals().size());
} catch (Exception e) {
@@ -337,9 +339,8 @@ public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
cache.invalidateByQuery(query, invalidType);
- while (cache.databaseCacheIsBusy()) {
- Thread.sleep(10);
- }
+ cache.waitToFinishTasks();
+
assertEquals(1, getFatals().size());
} catch (Exception e) {
@@ -373,9 +374,7 @@ public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
cache.invalidateByQuery(query, type);
- while (cache.refreshIsBusy()) {
- Thread.sleep(10);
- }
+ permanentDatabaseLevelCache.waitToFinishTasks();
assertEquals(1, getErrors().size());
} catch (Exception e) {
@@ -409,9 +408,7 @@ public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
cache.invalidateByQuery(query, type);
- while (cache.getRefreshExecutingTasksSize() + cache.getRefreshPendingQueueSize() > 0) {
- Thread.sleep(10);
- }
+ permanentDatabaseLevelCache.waitToFinishTasks();
assertEquals(0, getErrors().size());
assertEquals(0, getFatals().size());
@@ -427,8 +424,6 @@ public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
public void testRefreshQueryWithExceptionThrown() throws Exception {
CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
try {
- waitForRefreshCacheQueueToEmpty();
-
CacheType type = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
String query = ChebiAnnotator.ID_PREFIX + "1234";
@@ -450,7 +445,7 @@ public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
cache.invalidateByQuery(query, type);
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
assertEquals(1, getErrors().size());
@@ -488,9 +483,8 @@ public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
cache.invalidateByQuery(query, type);
- while (cache.getRefreshExecutingTasksSize() + cache.getRefreshPendingQueueSize() > 0) {
- Thread.sleep(10);
- }
+ permanentDatabaseLevelCache.waitToFinishTasks();
+
// errors are not caught
assertEquals(0, getErrors().size());
assertEquals(0, getFatals().size());
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
index 0207d4f35efa15f0839f7e71bb5cbd6615c4d74b..9c8d2e8a27cd3116ec3e2974c2d366e63655ae0c 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
@@ -6,9 +6,9 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -24,7 +24,8 @@ import org.w3c.dom.Node;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.cache.XmlSerializer;
@@ -46,6 +47,9 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
@Autowired
private GeneralCacheInterface cache;
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
+
@Autowired
private ChEMBLParser chemblParser;
@@ -740,12 +744,10 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
String query = "http://google.lu/";
String newRes = "hello";
try {
- waitForRefreshCacheQueueToEmpty();
-
cache.setCachedQuery(query, chemblParser.getCacheType(), newRes);
cache.invalidateByQuery(query, chemblParser.getCacheType());
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
String res = cache.getStringByQuery(query, chemblParser.getCacheType());
@@ -765,12 +767,10 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
String query = ChEMBLParser.NAME_PREFIX + "TRIMETHOPRIM";
String newRes = "hello";
try {
- waitForRefreshCacheQueueToEmpty();
-
cache.setCachedQuery(query, chemblParser.getCacheType(), newRes);
cache.invalidateByQuery(query, chemblParser.getCacheType());
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
String res = cache.getStringByQuery(query, chemblParser.getCacheType());
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
index 2cbcc496a929a3782d763ea8a377836e909674a7..0ef26253308c893606da6664106e753b9931e215 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
@@ -24,6 +24,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.data.Chemical;
@@ -55,6 +57,9 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
@Autowired
private GeneralCacheInterface cache;
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
+
@Test
public void testCreateChemicalListFromDB() throws Exception {
try {
@@ -229,12 +234,10 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
assertNotNull(chemcials);
assertTrue(chemcials.size() > 0);
- waitForRefreshCacheQueueToEmpty();
-
cache.invalidateByQuery(chemicalParser.getIdentifier(parkinsonDiseaseId, chemcials.get(0).getChemicalId()),
chemicalParser.getCacheType());
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
idsList.clear();
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
index 68cc3d43f09b287c9c0c3f4eb4cd6e8df9022c2b..5c57c7005861f678786ea3a09028f450876fe124 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
@@ -21,6 +21,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.data.Drug;
@@ -38,6 +40,9 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
@Autowired
private DrugbankHTMLParser drugBankHTMLParser;
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
+
@Test
public void test1FindDrug() throws Exception {
try {
@@ -373,12 +378,10 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
String query = "http://google.lu/";
String newRes = "hello";
try {
- waitForRefreshCacheQueueToEmpty();
-
cache.setCachedQuery(query, drugBankHTMLParser.getCacheType(), newRes);
cache.invalidateByQuery(query, drugBankHTMLParser.getCacheType());
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
String res = cache.getStringByQuery(query, drugBankHTMLParser.getCacheType());
@@ -399,12 +402,10 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
String query = "drug:amantadine";
String newRes = "hello";
try {
- waitForRefreshCacheQueueToEmpty();
-
cache.setCachedQuery(query, drugBankHTMLParser.getCacheType(), newRes);
cache.invalidateByQuery(query, drugBankHTMLParser.getCacheType());
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
String res = cache.getStringByQuery(query, drugBankHTMLParser.getCacheType());
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
index ddc7a6b812668a3a9889bf6408bcb78527bcc89a..aacd382a99dbf0822b7bc02b8d18922915c979d0 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
@@ -6,8 +6,8 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -21,6 +21,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.data.MeSH;
@@ -35,6 +37,9 @@ public class MeSHParserTest extends AnnotationTestFunctions {
@Autowired
MeSHParser meshParser;
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
+
@Autowired
private GeneralCacheInterface cache;
@@ -173,7 +178,8 @@ public class MeSHParserTest extends AnnotationTestFunctions {
MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D004298");
MeSHParser parserUnderTest = new MeSHParser();
WebPageDownloader webPageDownloader = Mockito.mock(WebPageDownloader.class);
- when(webPageDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(webPageDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
parserUnderTest.setWebPageDownloader(webPageDownloader);
parserUnderTest.getMeSH(meshID);
@@ -203,11 +209,9 @@ public class MeSHParserTest extends AnnotationTestFunctions {
MeSH mesh = meshParser.getMeSH(meshID);
assertNotNull(mesh);
- waitForRefreshCacheQueueToEmpty();
-
cache.invalidateByQuery(meshParser.getIdentifier(meshID), meshParser.getCacheType());
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
MeSH mesh2 = meshParser.getMeSH(meshID);
assertNotNull(mesh2);
@@ -281,7 +285,8 @@ public class MeSHParserTest extends AnnotationTestFunctions {
try {
meshParser.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
meshParser.setWebPageDownloader(mockDownloader);
MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D010300");
@@ -304,7 +309,8 @@ public class MeSHParserTest extends AnnotationTestFunctions {
WebPageDownloader downloader = meshParser.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
meshParser.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, meshParser.getServiceStatus().getStatus());
} catch (Exception e) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java
index 677503288dd3e1ad8af84a9ab5e63fa63b41b17a..ac1e12c007a1b3cdcc779573c752409b8ce0e228 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java
@@ -6,7 +6,7 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import static org.mockito.Matchers.anyString;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.Mockito.when;
import java.util.ArrayList;
@@ -23,6 +23,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.data.MiRNA;
import lcsb.mapviewer.annotation.data.Target;
@@ -38,6 +40,9 @@ public class MiRNAParserTest extends AnnotationTestFunctions {
@Autowired
MiRNAParser miRNAParser;
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
+
@Before
public void setUp() throws Exception {
}
@@ -164,11 +169,9 @@ public class MiRNAParserTest extends AnnotationTestFunctions {
assertTrue(!list.isEmpty());
assertEquals(1, list.get(0).getTargets().size());
- waitForRefreshCacheQueueToEmpty();
-
cache.invalidateByQuery(MiRNAParser.MI_RNA_PREFIX + list.get(0).getName(), miRNAParser.getCacheType());
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
listIds.clear();
listIds.add(list.get(0).getName());
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
index 7b5c21f24733f0b4d21fcebda25375c8006c0b7e..72735c2f47ed788734b8ec9d382aaf22f0dfde67 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
@@ -23,6 +23,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.cache.XmlSerializer;
@@ -31,396 +32,404 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
public class PubmedParserTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(PubmedParserTest.class);
- private boolean status;
- private boolean status2;
- @Autowired
- PubmedParser pubmedParser;
-
- @Autowired
- private GeneralCacheInterface cache;
-
- @Before
- public void setUp() throws Exception {
- status = Configuration.isDbCacheOn();
- status2 = Configuration.isApplicationCacheOn();
- }
-
- @After
- public void tearDown() throws Exception {
- Configuration.setDbCacheOn(status);
- Configuration.setApplicationCacheOn(status2);
- }
-
- @Test
- public void test() {
- try {
- Configuration.setDbCacheOn(false);
- Configuration.setApplicationCacheOn(false);
- Article art = pubmedParser.getPubmedArticleById(9481670);
- assertNotNull(art);
- assertEquals(
- "Adjacent asparagines in the NR2-subunit of the NMDA receptor channel control the voltage-dependent block by extracellular Mg2+.", art.getTitle());
- assertEquals((Integer) 1998, art.getYear());
- assertEquals("The Journal of physiology", art.getJournal());
- assertTrue(art.getStringAuthors().contains("Wollmuth"));
- assertTrue(art.getStringAuthors().contains("Kuner"));
- assertTrue(art.getStringAuthors().contains("Sakmann"));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testCache() {
- try {
- Configuration.setDbCacheOn(true);
- Configuration.setApplicationCacheOn(true);
-
- Article art = pubmedParser.getPubmedArticleById(9481671);
- assertNotNull(art);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testSerialization() {
- try {
-
- Article art = new Article();
- List<String> list = new ArrayList<String>();
- list.add("aaa");
- list.add("bbb");
- art.setTitle("ttt");
- art.setAuthors(list);
- art.setJournal("jjjj");
- art.setYear(123);
-
- String serialString = pubmedParser.getArticleSerializer().objectToString(art);
-
- assertTrue(serialString.contains("aaa"));
- assertTrue(serialString.contains("bbb"));
- assertTrue(serialString.contains("ttt"));
- assertTrue(serialString.contains("jjjj"));
- assertTrue(serialString.contains("123"));
-
- Article art2 = pubmedParser.getArticleSerializer().xmlToObject(getNodeFromXmlString(serialString));
-
- assertEquals(art.getStringAuthors(), art2.getStringAuthors());
- assertEquals(art.getTitle(), art2.getTitle());
- assertEquals(art.getJournal(), art2.getJournal());
- assertEquals(art.getYear(), art2.getYear());
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occurred");
- }
- }
-
- /**
- * This case was problematic with old API used to retrieve data from pubmed
- */
- @Test
- public void testProblematicCase() {
- try {
-
- Article art = pubmedParser.getPubmedArticleById(22363258);
- assertNotNull(art);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testCitationCount() {
- try {
-
- Article art = pubmedParser.getPubmedArticleById(18400456);
- assertNotNull(art);
- assertTrue(art.getCitationCount() >= 53);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testGetSummary() throws Exception {
- try {
- String summary = pubmedParser.getSummary(18400456);
- assertNotNull(summary);
- assertFalse(summary.isEmpty());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSummary2() throws Exception {
- try {
-
- String summary = pubmedParser.getSummary(23644949);
- assertNull(summary);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSummary3() throws Exception {
- try {
- String summary = pubmedParser.getSummary("18400456");
- assertNotNull(summary);
- assertFalse(summary.isEmpty());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- // wait max 15 second
- public void testCachableInterface() throws Exception {
- String query = "pubmed: 2112";
- try {
- String newRes = "hello";
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, pubmedParser.getCacheType(), newRes);
- cache.invalidateByQuery(query, pubmedParser.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- String res = cache.getStringByQuery(query, pubmedParser.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- pubmedParser.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshWhenExternalNotAvailable() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- try {
- pubmedParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
- pubmedParser.setWebPageDownloader(mockDownloader);
-
- String query = PubmedParser.PUBMED_PREFIX + PubmedParser.SERVICE_STATUS_PUBMED_ID;
-
- pubmedParser.refreshCacheQuery(query);
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setWebPageDownloader(downloader);
- pubmedParser.setCache(cache);
- }
-
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- pubmedParser.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetHtmlFullLinkForId() throws Exception {
- try {
- String htmlString = pubmedParser.getHtmlFullLinkForId(1234);
- assertTrue(htmlString.contains("Change in the kinetics of sulphacetamide tissue distribution"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, pubmedParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
- pubmedParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, pubmedParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateDownStatus2() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
- .thenReturn("<responseWrapper><version>" + PubmedParser.SUPPORTED_VERSION + "</version></responseWrapper>");
- pubmedParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, pubmedParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangeStatus() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
- .thenReturn("<responseWrapper><version>" + PubmedParser.SUPPORTED_VERSION + "blabla</version></responseWrapper>");
- pubmedParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, pubmedParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetApiVersion() throws Exception {
- try {
- assertNotNull(pubmedParser.getApiVersion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetApiVersionWhenProblemWithExternalDb() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- pubmedParser.setCache(null);
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn("unknown response");
- pubmedParser.setWebPageDownloader(mockDownloader);
- pubmedParser.getApiVersion();
- fail("Exception expected");
- } catch (PubmedSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setCache(cache);
- pubmedParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetApiVersionWhenProblemWithExternalDb3() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- pubmedParser.setCache(null);
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn("<xml/>");
- pubmedParser.setWebPageDownloader(mockDownloader);
- assertNull(pubmedParser.getApiVersion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setCache(cache);
- pubmedParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetApiVersionWhenProblemWithExternalDb2() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- pubmedParser.setCache(null);
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
- pubmedParser.setWebPageDownloader(mockDownloader);
- pubmedParser.getApiVersion();
- fail("Exception expected");
- } catch (PubmedSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setCache(cache);
- pubmedParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetters() throws Exception {
- try {
- MiriamConnector mc = new MiriamConnector();
- XmlSerializer<Article> serializer = new XmlSerializer<>(Article.class);
- PubmedParser parser = new PubmedParser();
-
- parser.setMiriamConnector(mc);
- assertEquals(mc, parser.getMiriamConnector());
-
- parser.setArticleSerializer(serializer);
-
- assertEquals(serializer, parser.getArticleSerializer());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(PubmedParserTest.class);
+ private boolean status;
+ private boolean status2;
+ @Autowired
+ PubmedParser pubmedParser;
+
+ @Autowired
+ private GeneralCacheInterface cache;
+
+ @Autowired
+ protected PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCacheInterface;
+
+ @Before
+ public void setUp() throws Exception {
+ status = Configuration.isDbCacheOn();
+ status2 = Configuration.isApplicationCacheOn();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ Configuration.setDbCacheOn(status);
+ Configuration.setApplicationCacheOn(status2);
+ }
+
+ @Test
+ public void test() {
+ try {
+ Configuration.setDbCacheOn(false);
+ Configuration.setApplicationCacheOn(false);
+ Article art = pubmedParser.getPubmedArticleById(9481670);
+ assertNotNull(art);
+ assertEquals(
+ "Adjacent asparagines in the NR2-subunit of the NMDA receptor channel control the voltage-dependent block by extracellular Mg2+.",
+ art.getTitle());
+ assertEquals((Integer) 1998, art.getYear());
+ assertEquals("The Journal of physiology", art.getJournal());
+ assertTrue(art.getStringAuthors().contains("Wollmuth"));
+ assertTrue(art.getStringAuthors().contains("Kuner"));
+ assertTrue(art.getStringAuthors().contains("Sakmann"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testCache() {
+ try {
+ Configuration.setDbCacheOn(true);
+ Configuration.setApplicationCacheOn(true);
+
+ Article art = pubmedParser.getPubmedArticleById(9481671);
+ assertNotNull(art);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+
+ Article art = new Article();
+ List<String> list = new ArrayList<String>();
+ list.add("aaa");
+ list.add("bbb");
+ art.setTitle("ttt");
+ art.setAuthors(list);
+ art.setJournal("jjjj");
+ art.setYear(123);
+
+ String serialString = pubmedParser.getArticleSerializer().objectToString(art);
+
+ assertTrue(serialString.contains("aaa"));
+ assertTrue(serialString.contains("bbb"));
+ assertTrue(serialString.contains("ttt"));
+ assertTrue(serialString.contains("jjjj"));
+ assertTrue(serialString.contains("123"));
+
+ Article art2 = pubmedParser.getArticleSerializer().xmlToObject(getNodeFromXmlString(serialString));
+
+ assertEquals(art.getStringAuthors(), art2.getStringAuthors());
+ assertEquals(art.getTitle(), art2.getTitle());
+ assertEquals(art.getJournal(), art2.getJournal());
+ assertEquals(art.getYear(), art2.getYear());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Exception occurred");
+ }
+ }
+
+ /**
+ * This case was problematic with old API used to retrieve data from pubmed
+ */
+ @Test
+ public void testProblematicCase() {
+ try {
+
+ Article art = pubmedParser.getPubmedArticleById(22363258);
+ assertNotNull(art);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testCitationCount() {
+ try {
+
+ Article art = pubmedParser.getPubmedArticleById(18400456);
+ assertNotNull(art);
+ assertTrue(art.getCitationCount() >= 53);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testGetSummary() throws Exception {
+ try {
+ String summary = pubmedParser.getSummary(18400456);
+ assertNotNull(summary);
+ assertFalse(summary.isEmpty());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSummary2() throws Exception {
+ try {
+
+ String summary = pubmedParser.getSummary(23644949);
+ assertNull(summary);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSummary3() throws Exception {
+ try {
+ String summary = pubmedParser.getSummary("18400456");
+ assertNotNull(summary);
+ assertFalse(summary.isEmpty());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ // wait max 15 second
+ public void testCachableInterface() throws Exception {
+ String query = "pubmed: 2112";
+ try {
+ String newRes = "hello";
+ permanentDatabaseLevelCacheInterface.waitToFinishTasks();
+
+ cache.setCachedQuery(query, pubmedParser.getCacheType(), newRes);
+ cache.invalidateByQuery(query, pubmedParser.getCacheType());
+
+ permanentDatabaseLevelCacheInterface.waitToFinishTasks();
+
+ String res = cache.getStringByQuery(query, pubmedParser.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ pubmedParser.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshWhenExternalNotAvailable() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ try {
+ pubmedParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
+ pubmedParser.setWebPageDownloader(mockDownloader);
+
+ String query = PubmedParser.PUBMED_PREFIX + PubmedParser.SERVICE_STATUS_PUBMED_ID;
+
+ pubmedParser.refreshCacheQuery(query);
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setWebPageDownloader(downloader);
+ pubmedParser.setCache(cache);
+ }
+
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ pubmedParser.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetHtmlFullLinkForId() throws Exception {
+ try {
+ String htmlString = pubmedParser.getHtmlFullLinkForId(1234);
+ assertTrue(htmlString.contains("Change in the kinetics of sulphacetamide tissue distribution"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, pubmedParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
+ pubmedParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, pubmedParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus2() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenReturn("<responseWrapper><version>" + PubmedParser.SUPPORTED_VERSION + "</version></responseWrapper>");
+ pubmedParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, pubmedParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangeStatus() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn(
+ "<responseWrapper><version>" + PubmedParser.SUPPORTED_VERSION + "blabla</version></responseWrapper>");
+ pubmedParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, pubmedParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetApiVersion() throws Exception {
+ try {
+ assertNotNull(pubmedParser.getApiVersion());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetApiVersionWhenProblemWithExternalDb() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ pubmedParser.setCache(null);
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenReturn("unknown response");
+ pubmedParser.setWebPageDownloader(mockDownloader);
+ pubmedParser.getApiVersion();
+ fail("Exception expected");
+ } catch (PubmedSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setCache(cache);
+ pubmedParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetApiVersionWhenProblemWithExternalDb3() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ pubmedParser.setCache(null);
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn("<xml/>");
+ pubmedParser.setWebPageDownloader(mockDownloader);
+ assertNull(pubmedParser.getApiVersion());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setCache(cache);
+ pubmedParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetApiVersionWhenProblemWithExternalDb2() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ pubmedParser.setCache(null);
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
+ pubmedParser.setWebPageDownloader(mockDownloader);
+ pubmedParser.getApiVersion();
+ fail("Exception expected");
+ } catch (PubmedSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setCache(cache);
+ pubmedParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetters() throws Exception {
+ try {
+ MiriamConnector mc = new MiriamConnector();
+ XmlSerializer<Article> serializer = new XmlSerializer<>(Article.class);
+ PubmedParser parser = new PubmedParser();
+
+ parser.setMiriamConnector(mc);
+ assertEquals(mc, parser.getMiriamConnector());
+
+ parser.setArticleSerializer(serializer);
+
+ assertEquals(serializer, parser.getArticleSerializer());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java
index 802ee10b476223705cb6c2261b9955cc77e10fad..99f2734a3de5cd491310b7a96cf991111f9c9530 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java
@@ -20,6 +20,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
@@ -27,335 +28,336 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
public class BiocompendiumAnnotatorTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(BiocompendiumAnnotatorTest.class);
-
- MiriamData camk4 = new MiriamData(MiriamType.HGNC_SYMBOL, "CAMK4");
- MiriamData slc25a27 = new MiriamData(MiriamType.HGNC_SYMBOL, "SLC25A27");
- MiriamData nsmf = new MiriamData(MiriamType.HGNC_SYMBOL, "NSMF");
- MiriamData mir449a = new MiriamData(MiriamType.HGNC_SYMBOL, "MIR449A");
-
- @Autowired
- private GeneralCacheInterface cache;
-
- @Autowired
- private BiocompendiumAnnotator restService;
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- @Ignore("Bug 32")
- public void testGetAnnotationsForSpecies() throws Exception {
- try {
- String response = restService.getAnnotation(camk4);
- assertNotNull(response);
- assertTrue(response.contains("Symbol: CAMK4"));
-
- response = restService.getAnnotation(slc25a27);
- assertNotNull(response);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() throws Exception {
- try {
- assertNotNull(restService.getCommonName());
- assertNotNull(restService.getUrl());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForInvalidMiriam() throws Exception {
- try {
- restService.getAnnotation(new MiriamData());
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXml() throws Exception {
- BufferedReader reader;
- try {
- reader = new BufferedReader(new FileReader("testFiles/annotation/sampleResponse.xml"));
- String line = null;
- StringBuilder stringBuilder = new StringBuilder();
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- reader.close();
-
- Map<String, String> res = restService.getAnnotationsFromXml(stringBuilder.toString());
-
- assertEquals(2, res.keySet().size());
- String response = res.get("CAMK4");
- assertNotNull(response);
- assertTrue(response.contains("Symbol: CAMK4"));
-
- assertNotNull(res.get("SLC25A27"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 10000)
- @Ignore("Bug 32")
- public void testGetAnnotationsForMiceSpecies() throws Exception {
- ArrayList<String> names = new ArrayList<String>();
-
- names.add("Fmo3");
- names.add("Nqo1");
- names.add("Abcc12");
- names.add("Mgst3");
- names.add("Txnrd1");
- names.add("Cbr3");
- names.add("Hspa1b");
- names.add("Prdx1");
- names.add("Ppard");
- names.add("Tgfb2");
- names.add("Fth1");
- names.add("Prdx6");
- names.add("Nr4a1");
- names.add("Tgfb1");
- names.add("Abcc4");
- names.add("Ager");
- names.add("Gsr");
- names.add("Sod3");
- names.add("Maff");
- names.add("Eif2ak3");
- names.add("Tgfa");
- names.add("Hbegf");
- names.add("Mafg");
- names.add("Adh7");
- names.add("Slc7a11");
- names.add("Epha3");
- names.add("Blvrb");
- // problematic one
- // names.add("Me1");
- names.add("Csnk2a2");
- names.add("Gpx3");
- names.add("Mapk8");
- names.add("Gclm");
- names.add("Epha2");
- names.add("Bdnf");
- // problematic one
- // names.add("ACC2");
- names.add("Ptgr1");
- names.add("Pdgfb");
- names.add("Mapk7");
- names.add("Cbr1");
- names.add("Hsp90aa1");
- names.add("Pgd");
- names.add("Sqstm1");
- names.add("Aldh9a1");
- names.add("Txn");
- names.add("Txnrd3");
- names.add("Srxn1");
- names.add("Gpx2");
- names.add("Npas4");
- names.add("Mapk1");
- names.add("Nrg1");
- names.add("Cbr");
- names.add("Hspa1a");
- names.add("Mgst2");
- names.add("Tgfbr2");
- names.add("Ephx1");
- names.add("Dnajb1");
- names.add("Abcc2");
- names.add("Gclc");
- names.add("Abcc5");
- names.add("Ggt1");
- names.add("Ftl");
- names.add("Egr1");
- names.add("Fgf13");
- // problematic one
- // names.add("Hgf");
- // problematic one
- // names.add("UbcH7");
- names.add("Abcc3");
- names.add("Nfe2l2");
- // problematic one
- // names.add("Hsp70");
- names.add("Hsp90ab1");
-
- try {
- for (int i = 0; i < names.size(); i++) {
- String geneName = names.get(i);
- String annotation = restService.getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, geneName));
- assertNotNull("Problem with annotation of mouse gene: " + geneName, annotation);
- assertTrue("Problem with annotation of mouse gene: " + geneName, !annotation.trim().equals(""));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- @Ignore("Bug 451")
- public void testGetAnnotationsForNSMF() throws Exception {
- try {
- String response = restService.getAnnotation(nsmf);
- assertNotNull(response);
- assertFalse(response.trim().equals(""));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- @Ignore("Bug 451")
- public void testGetAnnotationsForMIR449A() throws Exception {
- try {
- String response = restService.getAnnotation(mir449a);
- assertNotNull(response);
- assertFalse(response.trim().equals(""));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testCachableInterfaceInvalidate() throws Exception {
- String query = "GLUD1";
- try {
- String newRes = "hello";
-
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, restService.getCacheType(), newRes);
- String res = cache.getStringByQuery(query, restService.getCacheType());
- assertEquals(newRes, res);
- cache.invalidateByQuery(query, restService.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- res = cache.getStringByQuery(query, restService.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testNameWithNewLine() throws Exception {
- try {
- String response = restService.getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, "some\nname"));
- assertNotNull(response);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidValue() throws Exception {
- try {
- restService.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do "));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshValueWhenProblemWithSource() throws Exception {
- try {
- BiocompendiumAnnotator annotatorUnderTest = new BiocompendiumAnnotator() {
- @Override
- Map<String, String> getAnnotationsFromXml(String xml) throws InvalidXmlSchemaException {
- throw new InvalidXmlSchemaException();
- }
- };
- annotatorUnderTest.refreshCacheQuery(camk4.getResource());
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetInvalidAnnotations() throws Exception {
- try {
- restService.getAnnotation(new MiriamData(MiriamType.WIKIPEDIA, "world"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testInvalidDataToStrubg() throws Exception {
- try {
- restService.dataToString(new MiriamData(MiriamType.WIKIPEDIA, "world"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsFromInvaldXml() throws Exception {
- try {
- Map<String, String> map = restService.getAnnotationsFromXml("");
- assertEquals(0, map.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsFromInvaldXml2() throws Exception {
- try {
- Map<String, String> map = restService.getAnnotationsFromXml(null);
- assertEquals(0, map.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(BiocompendiumAnnotatorTest.class);
+
+ MiriamData camk4 = new MiriamData(MiriamType.HGNC_SYMBOL, "CAMK4");
+ MiriamData slc25a27 = new MiriamData(MiriamType.HGNC_SYMBOL, "SLC25A27");
+ MiriamData nsmf = new MiriamData(MiriamType.HGNC_SYMBOL, "NSMF");
+ MiriamData mir449a = new MiriamData(MiriamType.HGNC_SYMBOL, "MIR449A");
+
+ @Autowired
+ private GeneralCacheInterface cache;
+
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
+
+ @Autowired
+ private BiocompendiumAnnotator restService;
+
+ @Before
+ public void setUp() {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ @Ignore("Bug 32")
+ public void testGetAnnotationsForSpecies() throws Exception {
+ try {
+ String response = restService.getAnnotation(camk4);
+ assertNotNull(response);
+ assertTrue(response.contains("Symbol: CAMK4"));
+
+ response = restService.getAnnotation(slc25a27);
+ assertNotNull(response);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() throws Exception {
+ try {
+ assertNotNull(restService.getCommonName());
+ assertNotNull(restService.getUrl());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForInvalidMiriam() throws Exception {
+ try {
+ restService.getAnnotation(new MiriamData());
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXml() throws Exception {
+ BufferedReader reader;
+ try {
+ reader = new BufferedReader(new FileReader("testFiles/annotation/sampleResponse.xml"));
+ String line = null;
+ StringBuilder stringBuilder = new StringBuilder();
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ reader.close();
+
+ Map<String, String> res = restService.getAnnotationsFromXml(stringBuilder.toString());
+
+ assertEquals(2, res.keySet().size());
+ String response = res.get("CAMK4");
+ assertNotNull(response);
+ assertTrue(response.contains("Symbol: CAMK4"));
+
+ assertNotNull(res.get("SLC25A27"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 10000)
+ @Ignore("Bug 32")
+ public void testGetAnnotationsForMiceSpecies() throws Exception {
+ ArrayList<String> names = new ArrayList<String>();
+
+ names.add("Fmo3");
+ names.add("Nqo1");
+ names.add("Abcc12");
+ names.add("Mgst3");
+ names.add("Txnrd1");
+ names.add("Cbr3");
+ names.add("Hspa1b");
+ names.add("Prdx1");
+ names.add("Ppard");
+ names.add("Tgfb2");
+ names.add("Fth1");
+ names.add("Prdx6");
+ names.add("Nr4a1");
+ names.add("Tgfb1");
+ names.add("Abcc4");
+ names.add("Ager");
+ names.add("Gsr");
+ names.add("Sod3");
+ names.add("Maff");
+ names.add("Eif2ak3");
+ names.add("Tgfa");
+ names.add("Hbegf");
+ names.add("Mafg");
+ names.add("Adh7");
+ names.add("Slc7a11");
+ names.add("Epha3");
+ names.add("Blvrb");
+ // problematic one
+ // names.add("Me1");
+ names.add("Csnk2a2");
+ names.add("Gpx3");
+ names.add("Mapk8");
+ names.add("Gclm");
+ names.add("Epha2");
+ names.add("Bdnf");
+ // problematic one
+ // names.add("ACC2");
+ names.add("Ptgr1");
+ names.add("Pdgfb");
+ names.add("Mapk7");
+ names.add("Cbr1");
+ names.add("Hsp90aa1");
+ names.add("Pgd");
+ names.add("Sqstm1");
+ names.add("Aldh9a1");
+ names.add("Txn");
+ names.add("Txnrd3");
+ names.add("Srxn1");
+ names.add("Gpx2");
+ names.add("Npas4");
+ names.add("Mapk1");
+ names.add("Nrg1");
+ names.add("Cbr");
+ names.add("Hspa1a");
+ names.add("Mgst2");
+ names.add("Tgfbr2");
+ names.add("Ephx1");
+ names.add("Dnajb1");
+ names.add("Abcc2");
+ names.add("Gclc");
+ names.add("Abcc5");
+ names.add("Ggt1");
+ names.add("Ftl");
+ names.add("Egr1");
+ names.add("Fgf13");
+ // problematic one
+ // names.add("Hgf");
+ // problematic one
+ // names.add("UbcH7");
+ names.add("Abcc3");
+ names.add("Nfe2l2");
+ // problematic one
+ // names.add("Hsp70");
+ names.add("Hsp90ab1");
+
+ try {
+ for (int i = 0; i < names.size(); i++) {
+ String geneName = names.get(i);
+ String annotation = restService.getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, geneName));
+ assertNotNull("Problem with annotation of mouse gene: " + geneName, annotation);
+ assertTrue("Problem with annotation of mouse gene: " + geneName, !annotation.trim().equals(""));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ @Ignore("Bug 451")
+ public void testGetAnnotationsForNSMF() throws Exception {
+ try {
+ String response = restService.getAnnotation(nsmf);
+ assertNotNull(response);
+ assertFalse(response.trim().equals(""));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ @Ignore("Bug 451")
+ public void testGetAnnotationsForMIR449A() throws Exception {
+ try {
+ String response = restService.getAnnotation(mir449a);
+ assertNotNull(response);
+ assertFalse(response.trim().equals(""));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testCachableInterfaceInvalidate() throws Exception {
+ String query = "GLUD1";
+ try {
+ String newRes = "hello";
+
+ cache.setCachedQuery(query, restService.getCacheType(), newRes);
+ String res = cache.getStringByQuery(query, restService.getCacheType());
+ assertEquals(newRes, res);
+ cache.invalidateByQuery(query, restService.getCacheType());
+
+ permanentDatabaseLevelCache.waitToFinishTasks();
+
+ res = cache.getStringByQuery(query, restService.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testNameWithNewLine() throws Exception {
+ try {
+ String response = restService.getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, "some\nname"));
+ assertNotNull(response);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidValue() throws Exception {
+ try {
+ restService.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do "));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshValueWhenProblemWithSource() throws Exception {
+ try {
+ BiocompendiumAnnotator annotatorUnderTest = new BiocompendiumAnnotator() {
+ @Override
+ Map<String, String> getAnnotationsFromXml(String xml) throws InvalidXmlSchemaException {
+ throw new InvalidXmlSchemaException();
+ }
+ };
+ annotatorUnderTest.refreshCacheQuery(camk4.getResource());
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetInvalidAnnotations() throws Exception {
+ try {
+ restService.getAnnotation(new MiriamData(MiriamType.WIKIPEDIA, "world"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testInvalidDataToStrubg() throws Exception {
+ try {
+ restService.dataToString(new MiriamData(MiriamType.WIKIPEDIA, "world"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsFromInvaldXml() throws Exception {
+ try {
+ Map<String, String> map = restService.getAnnotationsFromXml("");
+ assertEquals(0, map.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsFromInvaldXml2() throws Exception {
+ try {
+ Map<String, String> map = restService.getAnnotationsFromXml(null);
+ assertEquals(0, map.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
index e6918c2a94203528ef0d40c652477c130b618e3f..1f449c43e4b5e1e34b49f0b4b66b20c78a74e5be 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
@@ -6,9 +6,9 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.eq;
import static org.mockito.Mockito.when;
import java.util.List;
@@ -22,6 +22,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.data.Chebi;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
@@ -48,6 +49,9 @@ public class ChebiAnnotatorTest extends AnnotationTestFunctions {
@Autowired
private GeneralCacheInterface cache;
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
+
@Before
public void setUp() throws Exception {
}
@@ -184,12 +188,10 @@ public class ChebiAnnotatorTest extends AnnotationTestFunctions {
String query = "id: CHEBI:28423";
String newRes = "hello";
try {
- waitForRefreshCacheQueueToEmpty();
-
cache.setCachedQuery(query, backend.getCacheType(), newRes);
cache.invalidateByQuery(query, backend.getCacheType());
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
String res = cache.getStringByQuery(query, backend.getCacheType());
@@ -207,12 +209,10 @@ public class ChebiAnnotatorTest extends AnnotationTestFunctions {
String query = "name: water";
String newRes = "hello";
try {
- waitForRefreshCacheQueueToEmpty();
-
cache.setCachedQuery(query, backend.getCacheType(), newRes);
cache.invalidateByQuery(query, backend.getCacheType());
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
String res = cache.getStringByQuery(query, backend.getCacheType());
@@ -271,8 +271,8 @@ public class ChebiAnnotatorTest extends AnnotationTestFunctions {
res = backend.getOntologyChebiIdsForChebiName("h2o");
assertNotNull(res);
assertTrue(res.size() > 1);
- assertTrue(
- res.contains(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "CHEBI:24431", ChebiAnnotator.class)));
+ assertTrue(res.contains(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI,
+ "CHEBI:24431", ChebiAnnotator.class)));
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
index a8e8f29254480817122ac985c6cb7fbce68a88b4..425cc3e45c73bff9b6198ba881e5b33671896a36 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
@@ -6,8 +6,8 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -20,6 +20,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
@@ -32,315 +34,321 @@ import lcsb.mapviewer.model.map.species.Species;
public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
- @Autowired
- EnsemblAnnotator ensemblAnnotator;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetAnnotationsForEnsemblId() throws Exception {
- try {
- MiriamData nsmf = new MiriamData(MiriamType.ENSEMBL, "ENSG00000157764");
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(nsmf);
- ensemblAnnotator.annotateElement(proteinAlias);
- assertNotNull(proteinAlias.getSymbol());
- assertNotNull(proteinAlias.getFullName());
- assertTrue(proteinAlias.getMiriamData().size() > 1);
- assertTrue(proteinAlias.getSynonyms().size() > 0);
-
- boolean ensemble = false;
- boolean hgncId = false;
- boolean hgncSymbol = false;
- boolean entrez = false;
- for (MiriamData md : proteinAlias.getMiriamData()) {
- if (MiriamType.ENSEMBL.equals(md.getDataType())) {
- ensemble = true;
- } else if (MiriamType.HGNC.equals(md.getDataType())) {
- hgncId = true;
- } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- hgncSymbol = true;
- } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
- entrez = true;
- }
- }
-
- assertTrue("Ensemble symbol cannot be found", ensemble);
- assertTrue("Hgnc id cannot be found", hgncId);
- assertTrue("Hgnc symbol cannot be found", hgncSymbol);
- assertTrue("Entrez cannot be found", entrez);
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsWhenMoreThanOneId() throws Exception {
- try {
- MiriamData nsmf = new MiriamData(MiriamType.ENSEMBL, "ENSG00000157764");
- MiriamData nsmf1 = new MiriamData(MiriamType.ENSEMBL, "ENSG00000157765");
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(nsmf);
- proteinAlias.addMiriamData(nsmf1);
- ensemblAnnotator.annotateElement(proteinAlias);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsWhenNoIdFound() throws Exception {
- try {
- GenericProtein proteinAlias = new GenericProtein("id");
- ensemblAnnotator.annotateElement(proteinAlias);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForInvalid() throws Exception {
- try {
- MiriamData nsmf = new MiriamData(MiriamType.ENSEMBL, "blabla");
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(nsmf);
- ensemblAnnotator.annotateElement(proteinAlias);
-
- assertEquals("There should be warning about invalid ensembl identifier", 1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testCachableInterfaceInvalidate() throws Exception {
- String query = "http://google.pl/";
- try {
- String newRes = "hello";
-
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, ensemblAnnotator.getCacheType(), newRes);
- String res = cache.getStringByQuery(query, ensemblAnnotator.getCacheType());
- assertEquals(newRes, res);
- cache.invalidateByQuery(query, ensemblAnnotator.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- res = cache.getStringByQuery(query, ensemblAnnotator.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, ensemblAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testStatusDown() throws Exception {
- WebPageDownloader downloader = ensemblAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = ensemblAnnotator.getCache();
- try {
- // exclude first cached value
- ensemblAnnotator.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
- ensemblAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, ensemblAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- ensemblAnnotator.setWebPageDownloader(downloader);
- ensemblAnnotator.setCache(originalCache);
- }
- }
-
- @Test
- public void testStatusChanged() throws Exception {
- WebPageDownloader downloader = ensemblAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = ensemblAnnotator.getCache();
- try {
- // exclude first cached value
- ensemblAnnotator.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- String dataXml = "<opt></opt>";
- String versionXml = "<opt><data release=\"" + EnsemblAnnotator.SUPPORTED_VERSION + "\"/></opt>";
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn(dataXml).thenReturn(versionXml);
- ensemblAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, ensemblAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- ensemblAnnotator.setWebPageDownloader(downloader);
- ensemblAnnotator.setCache(originalCache);
- }
- }
-
- @Test
- public void testStatusChanged2() throws Exception {
- WebPageDownloader downloader = ensemblAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = ensemblAnnotator.getCache();
- try {
- // exclude first cached value
- ensemblAnnotator.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- String dataXml = "<opt></opt>";
- String versionXml = "<opt><data release=\"blablabla\"/></opt>";
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn(dataXml).thenReturn(versionXml);
- ensemblAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, ensemblAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- ensemblAnnotator.setWebPageDownloader(downloader);
- ensemblAnnotator.setCache(originalCache);
- }
- }
-
- @Test
- public void testEnsemblToEntrez() throws Exception {
- try {
- MiriamData ensembl = new MiriamData(MiriamType.ENSEMBL, "ENSG00000154930");
- MiriamData entrez = ensemblAnnotator.ensemblIdToEntrezId(ensembl);
- assertEquals(new MiriamData(MiriamType.ENTREZ, "84532", EnsemblAnnotator.class), entrez);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidEnsemblToEntrez() throws Exception {
- try {
- MiriamData ensembl = new MiriamData(MiriamType.WIKIPEDIA, "ENSG00000154930");
- ensemblAnnotator.ensemblIdToEntrezId(ensembl);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEnsemblToEntrez2() throws Exception {
- try {
- MiriamData ensembl = new MiriamData(MiriamType.ENSEMBL, "ENSRNOG00000050619");
- MiriamData entrez = ensemblAnnotator.ensemblIdToEntrezId(ensembl);
- assertNull(entrez);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotateWhenEntrezReturnWrongResponse() throws Exception {
- WebPageDownloader downloader = ensemblAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new WrongResponseCodeIOException(null, 0));
- ensemblAnnotator.setWebPageDownloader(mockDownloader);
- Species proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(new MiriamData(MiriamType.ENSEMBL, "1234"));
- ensemblAnnotator.annotateElement(proteinAlias);
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- ensemblAnnotator.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = ensemblAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = ensemblAnnotator.getCache();
- try {
- // exclude first cached value
- ensemblAnnotator.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
- ensemblAnnotator.setWebPageDownloader(mockDownloader);
- ensemblAnnotator.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- ensemblAnnotator.setWebPageDownloader(downloader);
- ensemblAnnotator.setCache(originalCache);
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- ensemblAnnotator.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- ensemblAnnotator.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Autowired
+ EnsemblAnnotator ensemblAnnotator;
+
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetAnnotationsForEnsemblId() throws Exception {
+ try {
+ MiriamData nsmf = new MiriamData(MiriamType.ENSEMBL, "ENSG00000157764");
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(nsmf);
+ ensemblAnnotator.annotateElement(proteinAlias);
+ assertNotNull(proteinAlias.getSymbol());
+ assertNotNull(proteinAlias.getFullName());
+ assertTrue(proteinAlias.getMiriamData().size() > 1);
+ assertTrue(proteinAlias.getSynonyms().size() > 0);
+
+ boolean ensemble = false;
+ boolean hgncId = false;
+ boolean hgncSymbol = false;
+ boolean entrez = false;
+ for (MiriamData md : proteinAlias.getMiriamData()) {
+ if (MiriamType.ENSEMBL.equals(md.getDataType())) {
+ ensemble = true;
+ } else if (MiriamType.HGNC.equals(md.getDataType())) {
+ hgncId = true;
+ } else if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ hgncSymbol = true;
+ } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ entrez = true;
+ }
+ }
+
+ assertTrue("Ensemble symbol cannot be found", ensemble);
+ assertTrue("Hgnc id cannot be found", hgncId);
+ assertTrue("Hgnc symbol cannot be found", hgncSymbol);
+ assertTrue("Entrez cannot be found", entrez);
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsWhenMoreThanOneId() throws Exception {
+ try {
+ MiriamData nsmf = new MiriamData(MiriamType.ENSEMBL, "ENSG00000157764");
+ MiriamData nsmf1 = new MiriamData(MiriamType.ENSEMBL, "ENSG00000157765");
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(nsmf);
+ proteinAlias.addMiriamData(nsmf1);
+ ensemblAnnotator.annotateElement(proteinAlias);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsWhenNoIdFound() throws Exception {
+ try {
+ GenericProtein proteinAlias = new GenericProtein("id");
+ ensemblAnnotator.annotateElement(proteinAlias);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForInvalid() throws Exception {
+ try {
+ MiriamData nsmf = new MiriamData(MiriamType.ENSEMBL, "blabla");
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(nsmf);
+ ensemblAnnotator.annotateElement(proteinAlias);
+
+ assertEquals("There should be warning about invalid ensembl identifier", 1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testCachableInterfaceInvalidate() throws Exception {
+ String query = "http://google.pl/";
+ try {
+ String newRes = "hello";
+
+ cache.setCachedQuery(query, ensemblAnnotator.getCacheType(), newRes);
+ String res = cache.getStringByQuery(query, ensemblAnnotator.getCacheType());
+ assertEquals(newRes, res);
+ cache.invalidateByQuery(query, ensemblAnnotator.getCacheType());
+
+ permanentDatabaseLevelCache.waitToFinishTasks();
+
+ res = cache.getStringByQuery(query, ensemblAnnotator.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, ensemblAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatusDown() throws Exception {
+ WebPageDownloader downloader = ensemblAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = ensemblAnnotator.getCache();
+ try {
+ // exclude first cached value
+ ensemblAnnotator.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
+ ensemblAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, ensemblAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ ensemblAnnotator.setWebPageDownloader(downloader);
+ ensemblAnnotator.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testStatusChanged() throws Exception {
+ WebPageDownloader downloader = ensemblAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = ensemblAnnotator.getCache();
+ try {
+ // exclude first cached value
+ ensemblAnnotator.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ String dataXml = "<opt></opt>";
+ String versionXml = "<opt><data release=\"" + EnsemblAnnotator.SUPPORTED_VERSION + "\"/></opt>";
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn(dataXml)
+ .thenReturn(versionXml);
+ ensemblAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, ensemblAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ ensemblAnnotator.setWebPageDownloader(downloader);
+ ensemblAnnotator.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testStatusChanged2() throws Exception {
+ WebPageDownloader downloader = ensemblAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = ensemblAnnotator.getCache();
+ try {
+ // exclude first cached value
+ ensemblAnnotator.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ String dataXml = "<opt></opt>";
+ String versionXml = "<opt><data release=\"blablabla\"/></opt>";
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn(dataXml)
+ .thenReturn(versionXml);
+ ensemblAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, ensemblAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ ensemblAnnotator.setWebPageDownloader(downloader);
+ ensemblAnnotator.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testEnsemblToEntrez() throws Exception {
+ try {
+ MiriamData ensembl = new MiriamData(MiriamType.ENSEMBL, "ENSG00000154930");
+ MiriamData entrez = ensemblAnnotator.ensemblIdToEntrezId(ensembl);
+ assertEquals(new MiriamData(MiriamType.ENTREZ, "84532", EnsemblAnnotator.class), entrez);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidEnsemblToEntrez() throws Exception {
+ try {
+ MiriamData ensembl = new MiriamData(MiriamType.WIKIPEDIA, "ENSG00000154930");
+ ensemblAnnotator.ensemblIdToEntrezId(ensembl);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEnsemblToEntrez2() throws Exception {
+ try {
+ MiriamData ensembl = new MiriamData(MiriamType.ENSEMBL, "ENSRNOG00000050619");
+ MiriamData entrez = ensemblAnnotator.ensemblIdToEntrezId(ensembl);
+ assertNull(entrez);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateWhenEntrezReturnWrongResponse() throws Exception {
+ WebPageDownloader downloader = ensemblAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new WrongResponseCodeIOException(null, 0));
+ ensemblAnnotator.setWebPageDownloader(mockDownloader);
+ Species proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(new MiriamData(MiriamType.ENSEMBL, "1234"));
+ ensemblAnnotator.annotateElement(proteinAlias);
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ ensemblAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = ensemblAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = ensemblAnnotator.getCache();
+ try {
+ // exclude first cached value
+ ensemblAnnotator.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
+ ensemblAnnotator.setWebPageDownloader(mockDownloader);
+ ensemblAnnotator.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ ensemblAnnotator.setWebPageDownloader(downloader);
+ ensemblAnnotator.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ ensemblAnnotator.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ ensemblAnnotator.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
index ba9a84e9c53d96492199d08b5a542ae079319263..64856c9ed81ffbef0a4605c31d72ec8711518cc5 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
@@ -6,9 +6,9 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -21,7 +21,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.cache.XmlSerializer;
@@ -36,386 +36,392 @@ import lcsb.mapviewer.model.map.species.Species;
public class EntrezAnnotatorTest extends AnnotationTestFunctions {
- @Autowired
- EntrezAnnotator entrezAnnotator;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetAnnotationsForEntrezId() throws Exception {
- try {
- MiriamData nsmf = new MiriamData(MiriamType.ENTREZ, "6647");
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(nsmf);
- entrezAnnotator.annotateElement(proteinAlias);
- assertNotNull(proteinAlias.getSymbol());
- assertNotNull(proteinAlias.getFullName());
- assertNotNull(proteinAlias.getNotes());
- assertFalse(proteinAlias.getNotes().isEmpty());
- assertTrue(proteinAlias.getMiriamData().size() > 1);
- assertTrue(proteinAlias.getSynonyms().size() > 0);
-
- boolean ensemble = false;
- boolean hgncId = false;
- boolean entrez = false;
- for (MiriamData md : proteinAlias.getMiriamData()) {
- if (MiriamType.ENSEMBL.equals(md.getDataType())) {
- ensemble = true;
- } else if (MiriamType.HGNC.equals(md.getDataType())) {
- hgncId = true;
- } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
- entrez = true;
- }
- }
-
- assertTrue("Ensemble symbol cannot be found", ensemble);
- assertTrue("Hgnc id cannot be found", hgncId);
- assertTrue("Entrez cannot be found", entrez);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testGetAnnotationsForInvalid() throws Exception {
- try {
- MiriamData nsmf = new MiriamData(MiriamType.ENTREZ, "blabla");
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(nsmf);
- entrezAnnotator.annotateElement(proteinAlias);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testCachableInterfaceInvalidate() throws Exception {
- String query = "http://google.pl/";
- try {
- String newRes = "hello";
-
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, entrezAnnotator.getCacheType(), newRes);
- String res = cache.getStringByQuery(query, entrezAnnotator.getCacheType());
- assertEquals(newRes, res);
- cache.invalidateByQuery(query, entrezAnnotator.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- res = cache.getStringByQuery(query, entrezAnnotator.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, entrezAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
- entrezAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, entrezAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- entrezAnnotator.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangedStatus() throws Exception {
- XmlSerializer<EntrezData> entrezSerializer = entrezAnnotator.getEntrezSerializer();
- try {
- @SuppressWarnings("unchecked")
- XmlSerializer<EntrezData> mockSerializer = Mockito.mock(XmlSerializer.class);
- when(mockSerializer.xmlToObject(any())).thenReturn(new EntrezData());
- entrezAnnotator.setEntrezSerializer(mockSerializer);
- assertEquals(ExternalServiceStatusType.CHANGED, entrezAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- entrezAnnotator.setEntrezSerializer(entrezSerializer);
- }
- }
-
- @Test
- public void testGetHgncFromEntrez() throws Exception {
- try {
- assertEquals(new MiriamData(MiriamType.HGNC, "11179", EntrezAnnotator.class), entrezAnnotator.getHgncIdFromEntrez(new MiriamData(MiriamType.ENTREZ, "6647", EntrezAnnotator.class)));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetHgncFromEntrezForInvalidId() throws Exception {
- try {
- assertNull(entrezAnnotator.getHgncIdFromEntrez(new MiriamData(MiriamType.ENTREZ, "664711111")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetHgncFromEntrezForInvalidId1() throws Exception {
- try {
- entrezAnnotator.getHgncIdFromEntrez(new MiriamData(MiriamType.WIKIPEDIA, "664711111"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testRefreshToHgncConversion() throws Exception {
- GeneralCacheInterface cache = entrezAnnotator.getCache();
- try {
- entrezAnnotator.setCache(null);
- assertNull(entrezAnnotator.refreshCacheQuery(EntrezAnnotator.CACHE_HGNC_ID_PREFIX + "blablabla"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- entrezAnnotator.setCache(cache);
- }
- }
-
- @Test(timeout = 60000)
- public void testRefreshToHgncConversion2() throws Exception {
- try {
- assertNotNull(entrezAnnotator.refreshCacheQuery(EntrezAnnotator.CACHE_HGNC_ID_PREFIX + "6647"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- entrezAnnotator.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- entrezAnnotator.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testRefreshEntrezData() throws Exception {
- try {
- assertNotNull(entrezAnnotator.refreshCacheQuery(EntrezAnnotator.ENTREZ_DATA_PREFIX + "6647"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = entrezAnnotator.getCache();
- try {
- // exclude first cached value
- entrezAnnotator.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
- entrezAnnotator.setWebPageDownloader(mockDownloader);
- entrezAnnotator.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- entrezAnnotator.setWebPageDownloader(downloader);
- entrezAnnotator.setCache(originalCache);
- }
- }
-
- @Test
- public void testRefreshCacheQueryWithInvalidEntrezServerResponse() throws Exception {
- WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = entrezAnnotator.getCache();
- try {
- // exclude first cached value
- entrezAnnotator.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
- entrezAnnotator.setWebPageDownloader(mockDownloader);
- entrezAnnotator.refreshCacheQuery(EntrezAnnotator.ENTREZ_DATA_PREFIX + "6647");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- entrezAnnotator.setWebPageDownloader(downloader);
- entrezAnnotator.setCache(originalCache);
- }
- }
-
- @Test
- public void testAnnotateElementWithoutId() throws Exception {
- try {
- GenericProtein proteinAlias = new GenericProtein("id");
- entrezAnnotator.annotateElement(proteinAlias);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotateElementWithTwoEntrez() throws Exception {
- try {
- Species proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(new MiriamData(MiriamType.ENTREZ, "6647"));
- proteinAlias.addMiriamData(new MiriamData(MiriamType.ENTREZ, "6648"));
- entrezAnnotator.annotateElement(proteinAlias);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseEntrezResponse() throws Exception {
- WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
- GeneralCacheInterface cache = entrezAnnotator.getCache();
- try {
- entrezAnnotator.setCache(null);
- String response = super.readFile("testFiles/annotation/entrezResponse.xml");
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn(response);
- entrezAnnotator.setWebPageDownloader(mockDownloader);
- EntrezData data = entrezAnnotator.getEntrezForMiriamData(new MiriamData(), "");
- boolean ensembl = false;
- boolean hgnc = false;
- for (MiriamData md : data.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.HGNC)) {
- hgnc = true;
- }
- if (md.getDataType().equals(MiriamType.ENSEMBL)) {
- ensembl = true;
- }
- }
- assertTrue(ensembl);
- assertTrue(hgnc);
- assertNotNull(data.getDescription());
- assertFalse(data.getDescription().isEmpty());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- entrezAnnotator.setWebPageDownloader(downloader);
- entrezAnnotator.setCache(cache);
- }
- }
-
- @Test
- public void testParseInvalidEntrezResponse() throws Exception {
- WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
- GeneralCacheInterface cache = entrezAnnotator.getCache();
- try {
- entrezAnnotator.setCache(null);
- String response = "";
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn(response);
- entrezAnnotator.setWebPageDownloader(mockDownloader);
- entrezAnnotator.getEntrezForMiriamData(new MiriamData(), "");
- fail("Exception expected");
- } catch (AnnotatorException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- entrezAnnotator.setWebPageDownloader(downloader);
- entrezAnnotator.setCache(cache);
- }
-
- }
-
- @Test
- public void testParseInvalidEntrezResponse2() throws Exception {
- WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
- GeneralCacheInterface cache = entrezAnnotator.getCache();
- try {
- entrezAnnotator.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new WrongResponseCodeIOException(null, 404));
- entrezAnnotator.setWebPageDownloader(mockDownloader);
- entrezAnnotator.getEntrezForMiriamData(new MiriamData(), "");
- fail("Exception expected");
- } catch (AnnotatorException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- entrezAnnotator.setWebPageDownloader(downloader);
- entrezAnnotator.setCache(cache);
- }
-
- }
+ @Autowired
+ EntrezAnnotator entrezAnnotator;
+
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetAnnotationsForEntrezId() throws Exception {
+ try {
+ MiriamData nsmf = new MiriamData(MiriamType.ENTREZ, "6647");
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(nsmf);
+ entrezAnnotator.annotateElement(proteinAlias);
+ assertNotNull(proteinAlias.getSymbol());
+ assertNotNull(proteinAlias.getFullName());
+ assertNotNull(proteinAlias.getNotes());
+ assertFalse(proteinAlias.getNotes().isEmpty());
+ assertTrue(proteinAlias.getMiriamData().size() > 1);
+ assertTrue(proteinAlias.getSynonyms().size() > 0);
+
+ boolean ensemble = false;
+ boolean hgncId = false;
+ boolean entrez = false;
+ for (MiriamData md : proteinAlias.getMiriamData()) {
+ if (MiriamType.ENSEMBL.equals(md.getDataType())) {
+ ensemble = true;
+ } else if (MiriamType.HGNC.equals(md.getDataType())) {
+ hgncId = true;
+ } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ entrez = true;
+ }
+ }
+
+ assertTrue("Ensemble symbol cannot be found", ensemble);
+ assertTrue("Hgnc id cannot be found", hgncId);
+ assertTrue("Entrez cannot be found", entrez);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testGetAnnotationsForInvalid() throws Exception {
+ try {
+ MiriamData nsmf = new MiriamData(MiriamType.ENTREZ, "blabla");
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(nsmf);
+ entrezAnnotator.annotateElement(proteinAlias);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testCachableInterfaceInvalidate() throws Exception {
+ String query = "http://google.pl/";
+ try {
+ String newRes = "hello";
+
+ cache.setCachedQuery(query, entrezAnnotator.getCacheType(), newRes);
+ String res = cache.getStringByQuery(query, entrezAnnotator.getCacheType());
+ assertEquals(newRes, res);
+ cache.invalidateByQuery(query, entrezAnnotator.getCacheType());
+
+ permanentDatabaseLevelCache.waitToFinishTasks();
+
+ res = cache.getStringByQuery(query, entrezAnnotator.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, entrezAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
+ entrezAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, entrezAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ entrezAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ XmlSerializer<EntrezData> entrezSerializer = entrezAnnotator.getEntrezSerializer();
+ try {
+ @SuppressWarnings("unchecked")
+ XmlSerializer<EntrezData> mockSerializer = Mockito.mock(XmlSerializer.class);
+ when(mockSerializer.xmlToObject(any())).thenReturn(new EntrezData());
+ entrezAnnotator.setEntrezSerializer(mockSerializer);
+ assertEquals(ExternalServiceStatusType.CHANGED, entrezAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ entrezAnnotator.setEntrezSerializer(entrezSerializer);
+ }
+ }
+
+ @Test
+ public void testGetHgncFromEntrez() throws Exception {
+ try {
+ assertEquals(new MiriamData(MiriamType.HGNC, "11179", EntrezAnnotator.class),
+ entrezAnnotator.getHgncIdFromEntrez(new MiriamData(MiriamType.ENTREZ, "6647", EntrezAnnotator.class)));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetHgncFromEntrezForInvalidId() throws Exception {
+ try {
+ assertNull(entrezAnnotator.getHgncIdFromEntrez(new MiriamData(MiriamType.ENTREZ, "664711111")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetHgncFromEntrezForInvalidId1() throws Exception {
+ try {
+ entrezAnnotator.getHgncIdFromEntrez(new MiriamData(MiriamType.WIKIPEDIA, "664711111"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testRefreshToHgncConversion() throws Exception {
+ GeneralCacheInterface cache = entrezAnnotator.getCache();
+ try {
+ entrezAnnotator.setCache(null);
+ assertNull(entrezAnnotator.refreshCacheQuery(EntrezAnnotator.CACHE_HGNC_ID_PREFIX + "blablabla"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ entrezAnnotator.setCache(cache);
+ }
+ }
+
+ @Test(timeout = 60000)
+ public void testRefreshToHgncConversion2() throws Exception {
+ try {
+ assertNotNull(entrezAnnotator.refreshCacheQuery(EntrezAnnotator.CACHE_HGNC_ID_PREFIX + "6647"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ entrezAnnotator.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ entrezAnnotator.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testRefreshEntrezData() throws Exception {
+ try {
+ assertNotNull(entrezAnnotator.refreshCacheQuery(EntrezAnnotator.ENTREZ_DATA_PREFIX + "6647"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = entrezAnnotator.getCache();
+ try {
+ // exclude first cached value
+ entrezAnnotator.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
+ entrezAnnotator.setWebPageDownloader(mockDownloader);
+ entrezAnnotator.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ entrezAnnotator.setWebPageDownloader(downloader);
+ entrezAnnotator.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryWithInvalidEntrezServerResponse() throws Exception {
+ WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = entrezAnnotator.getCache();
+ try {
+ // exclude first cached value
+ entrezAnnotator.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
+ entrezAnnotator.setWebPageDownloader(mockDownloader);
+ entrezAnnotator.refreshCacheQuery(EntrezAnnotator.ENTREZ_DATA_PREFIX + "6647");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ entrezAnnotator.setWebPageDownloader(downloader);
+ entrezAnnotator.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testAnnotateElementWithoutId() throws Exception {
+ try {
+ GenericProtein proteinAlias = new GenericProtein("id");
+ entrezAnnotator.annotateElement(proteinAlias);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateElementWithTwoEntrez() throws Exception {
+ try {
+ Species proteinAlias = new GenericProtein("id");
+ proteinAlias.addMiriamData(new MiriamData(MiriamType.ENTREZ, "6647"));
+ proteinAlias.addMiriamData(new MiriamData(MiriamType.ENTREZ, "6648"));
+ entrezAnnotator.annotateElement(proteinAlias);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseEntrezResponse() throws Exception {
+ WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
+ GeneralCacheInterface cache = entrezAnnotator.getCache();
+ try {
+ entrezAnnotator.setCache(null);
+ String response = super.readFile("testFiles/annotation/entrezResponse.xml");
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn(response);
+ entrezAnnotator.setWebPageDownloader(mockDownloader);
+ EntrezData data = entrezAnnotator.getEntrezForMiriamData(new MiriamData(), "");
+ boolean ensembl = false;
+ boolean hgnc = false;
+ for (MiriamData md : data.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.HGNC)) {
+ hgnc = true;
+ }
+ if (md.getDataType().equals(MiriamType.ENSEMBL)) {
+ ensembl = true;
+ }
+ }
+ assertTrue(ensembl);
+ assertTrue(hgnc);
+ assertNotNull(data.getDescription());
+ assertFalse(data.getDescription().isEmpty());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ entrezAnnotator.setWebPageDownloader(downloader);
+ entrezAnnotator.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testParseInvalidEntrezResponse() throws Exception {
+ WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
+ GeneralCacheInterface cache = entrezAnnotator.getCache();
+ try {
+ entrezAnnotator.setCache(null);
+ String response = "";
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn(response);
+ entrezAnnotator.setWebPageDownloader(mockDownloader);
+ entrezAnnotator.getEntrezForMiriamData(new MiriamData(), "");
+ fail("Exception expected");
+ } catch (AnnotatorException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ entrezAnnotator.setWebPageDownloader(downloader);
+ entrezAnnotator.setCache(cache);
+ }
+
+ }
+
+ @Test
+ public void testParseInvalidEntrezResponse2() throws Exception {
+ WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();
+ GeneralCacheInterface cache = entrezAnnotator.getCache();
+ try {
+ entrezAnnotator.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new WrongResponseCodeIOException(null, 404));
+ entrezAnnotator.setWebPageDownloader(mockDownloader);
+ entrezAnnotator.getEntrezForMiriamData(new MiriamData(), "");
+ fail("Exception expected");
+ } catch (AnnotatorException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ entrezAnnotator.setWebPageDownloader(downloader);
+ entrezAnnotator.setCache(cache);
+ }
+
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
index cda5bb5ca3fce92738a2e03566c4c3a080222c8c..bc77268d3851b5454f58e74c1e9a2fc4fdba2cf8 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
@@ -5,8 +5,8 @@ import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -20,6 +20,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
@@ -38,7 +39,7 @@ public class GoAnnotatorTest extends AnnotationTestFunctions {
GoAnnotator goAnnotator;
@Autowired
- private PermanentDatabaseLevelCacheInterface cache;
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
@Before
public void setUp() throws Exception {
@@ -102,12 +103,10 @@ public class GoAnnotatorTest extends AnnotationTestFunctions {
String query = GoAnnotator.GO_TERM_CACHE_PREFIX + "GO:0046902";
String newRes = "hello";
try {
- waitForRefreshCacheQueueToEmpty();
-
cache.setCachedQuery(query, goAnnotator.getCacheType(), newRes);
cache.invalidateByQuery(query, goAnnotator.getCacheType());
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
String res = cache.getStringByQuery(query, goAnnotator.getCacheType());
@@ -129,7 +128,8 @@ public class GoAnnotatorTest extends AnnotationTestFunctions {
goAnnotator.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
goAnnotator.setWebPageDownloader(mockDownloader);
goAnnotator.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
@@ -195,7 +195,8 @@ public class GoAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = goAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
goAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, goAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
index 6d3f84cd6d05aa240437aba9cf2bfcaffb243101..d491779e34060ec1160a8be393c9fbb2d761e40c 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
@@ -6,8 +6,8 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -22,6 +22,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
@@ -38,6 +40,9 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
@Autowired
private HgncAnnotator hgncAnnotator;
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
+
@Before
public void setUp() {
}
@@ -207,16 +212,16 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
GenericProtein bidProtein = new GenericProtein("id");
bidProtein.setName("BID");
hgncAnnotator.annotateElement(bidProtein);
-
+
GenericProtein bidMutationProtein = new GenericProtein("id2");
bidMutationProtein.setName("BID (p15)");
hgncAnnotator.annotateElement(bidMutationProtein);
-
- assertEquals(bidProtein.getSymbol(),bidMutationProtein.getSymbol());
- assertEquals(bidProtein.getFormerSymbols(),bidMutationProtein.getFormerSymbols());
- assertEquals(bidProtein.getFullName(),bidMutationProtein.getFullName());
- assertEquals(bidProtein.getMiriamData(),bidMutationProtein.getMiriamData());
- assertEquals(bidProtein.getSynonyms(),bidMutationProtein.getSynonyms());
+
+ assertEquals(bidProtein.getSymbol(), bidMutationProtein.getSymbol());
+ assertEquals(bidProtein.getFormerSymbols(), bidMutationProtein.getFormerSymbols());
+ assertEquals(bidProtein.getFullName(), bidMutationProtein.getFullName());
+ assertEquals(bidProtein.getMiriamData(), bidMutationProtein.getMiriamData());
+ assertEquals(bidProtein.getSynonyms(), bidMutationProtein.getSynonyms());
} catch (Exception e) {
e.printStackTrace();
@@ -260,14 +265,12 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
try {
String newRes = "hello";
- waitForRefreshCacheQueueToEmpty();
-
cache.setCachedQuery(query, hgncAnnotator.getCacheType(), newRes);
String res = cache.getStringByQuery(query, hgncAnnotator.getCacheType());
assertEquals(newRes, res);
cache.invalidateByQuery(query, hgncAnnotator.getCacheType());
- waitForRefreshCacheQueueToEmpty();
+ permanentDatabaseLevelCache.waitToFinishTasks();
res = cache.getStringByQuery(query, hgncAnnotator.getCacheType());
@@ -520,7 +523,8 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
hgncAnnotator.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
hgncAnnotator.setWebPageDownloader(mockDownloader);
hgncAnnotator.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
@@ -539,7 +543,8 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = hgncAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
hgncAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, hgncAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java b/reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java
index 7696b1a875297b9c71529b3a12fb0eac400edf9c..80019a0fd68c3ad7aadcabeee1842ba42338426c 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/ReactomeTestFunctions.java
@@ -27,15 +27,6 @@ import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
-import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
-
import org.apache.log4j.Logger;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
@@ -49,209 +40,211 @@ import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
+import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
+
@Transactional(value = "txManager")
@Rollback(false)
@ContextConfiguration(locations = { "/applicationContext-annotation.xml", //
- "/applicationContext-reactome.xml", //
- "/applicationContext-persist.xml", //
- "/test-applicationContext.xml", //
- "/test-dataSource.xml", //
+ "/applicationContext-reactome.xml", //
+ "/applicationContext-persist.xml", //
+ "/test-applicationContext.xml", //
+ "/test-dataSource.xml", //
})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class ReactomeTestFunctions {
- private Logger logger = Logger.getLogger(ReactomeTestFunctions.class);
-
- @Autowired
- protected PermanentDatabaseLevelCacheInterface cache;
-
- @Autowired
- protected DataSourceUpdater rc;
-
- @Autowired
- protected DbUtils dbUtils;
-
- @Autowired
- protected ReactomeQueryUtil rcu;
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- private static Map<String, Model> models = new HashMap<String, Model>();
-
- protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
- if (!fromCache) {
- logger.debug("File without cache: " + fileName);
- return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- }
- Model result = ReactomeTestFunctions.models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: " + fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- ReactomeTestFunctions.models.put(fileName, result);
- }
- return result;
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- URLConnection urlConn = url.openConnection();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- }
-
- protected void waitForRefreshCacheQueueToEmpty() throws InterruptedException {
- while (cache.refreshIsBusy()) {
- logger.debug("Waiting for refresh queue to empty. " + cache.getRefreshPendingQueueSize() + " pending. " + cache.getRefreshExecutingTasksSize()
- + " tasks are executed.");
- Thread.sleep(100);
- }
- }
+ private Logger logger = Logger.getLogger(ReactomeTestFunctions.class);
+
+ @Autowired
+ protected PermanentDatabaseLevelCacheInterface cache;
+
+ @Autowired
+ protected DataSourceUpdater rc;
+
+ @Autowired
+ protected DbUtils dbUtils;
+
+ @Autowired
+ protected ReactomeQueryUtil rcu;
+
+ protected String readFile(String file) throws IOException {
+ StringBuilder stringBuilder = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ try {
+ String line = null;
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ } finally {
+ reader.close();
+ }
+
+ return stringBuilder.toString();
+ }
+
+ protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+ }
+
+ protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+ File file = new File(fileName);
+ InputStream inputStream = new FileInputStream(file);
+ Reader reader = null;
+ try {
+ reader = new InputStreamReader(inputStream, "UTF-8");
+ InputSource is = new InputSource(reader);
+
+ Document result = getXmlDocumentFromInputSource(is);
+ inputStream.close();
+ return result;
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
+ DocumentBuilder db;
+ try {
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser");
+ }
+ Document doc = null;
+ try {
+ doc = db.parse(stream);
+ } catch (SAXException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ return doc;
+ }
+
+ private static Map<String, Model> models = new HashMap<String, Model>();
+
+ protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
+ if (!fromCache) {
+ logger.debug("File without cache: " + fileName);
+ return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+ }
+ Model result = ReactomeTestFunctions.models.get(fileName);
+ if (result == null) {
+ logger.debug("File to cache: " + fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+ ReactomeTestFunctions.models.put(fileName, result);
+ }
+ return result;
+ }
+
+ protected String createTmpFileName() {
+ try {
+ File f = File.createTempFile("prefix", ".txt");
+ String filename = f.getName();
+ f.delete();
+ return filename;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ protected String nodeToString(Node node) {
+ return nodeToString(node, false);
+ }
+
+ protected String nodeToString(Node node, boolean includeHeadNode) {
+ if (node == null)
+ return null;
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ protected boolean equalFiles(String fileA, String fileB) throws IOException {
+ int BLOCK_SIZE = 65536;
+ FileInputStream inputStreamA = new FileInputStream(fileA);
+ FileInputStream inputStreamB = new FileInputStream(fileB);
+ // vary BLOCK_SIZE to suit yourself.
+ // it should probably a factor or multiple of the size of a disk
+ // sector/cluster.
+ // Note that your max heap size may need to be adjused
+ // if you have a very big block size or lots of these comparators.
+
+ // assume inputStreamA and inputStreamB are streams from your two files.
+ byte[] streamABlock = new byte[BLOCK_SIZE];
+ byte[] streamBBlock = new byte[BLOCK_SIZE];
+ boolean match = true;
+ int bytesReadA = 0;
+ int bytesReadB = 0;
+ do {
+ bytesReadA = inputStreamA.read(streamABlock);
+ bytesReadB = inputStreamB.read(streamBBlock);
+ match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+ } while (match && (bytesReadA > -1));
+ inputStreamA.close();
+ inputStreamB.close();
+ return match;
+ }
+
+ public File createTempDirectory() throws IOException {
+ final File temp;
+
+ temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+ if (!(temp.delete())) {
+ throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+ }
+
+ if (!(temp.mkdir())) {
+ throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+ }
+
+ return (temp);
+ }
+
+ protected String getWebpage(String accessUrl) throws IOException {
+ String inputLine;
+ StringBuilder tmp = new StringBuilder();
+ URL url = new URL(accessUrl);
+ URLConnection urlConn = url.openConnection();
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+ while ((inputLine = in.readLine()) != null) {
+ tmp.append(inputLine);
+ }
+ in.close();
+ return tmp.toString();
+ }
+
}
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java
index 65aed9ba0998833b2d56e8b96f926dc0ccf244f6..cfc792e5f612d0caad2fad0009e871be3fb2ccb6 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java
@@ -12,7 +12,15 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.w3c.dom.Node;
+
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.model.cache.CacheType;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
@@ -24,171 +32,165 @@ import lcsb.mapviewer.reactome.model.ReactomeReaction;
import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.w3c.dom.Node;
-
public class ReactomeConnectorTest extends ReactomeTestFunctions {
- Logger logger = Logger.getLogger(ReactomeConnectorTest.class);
-
- CacheType reactomeCacheType;
-
- @Autowired
- private GeneralCacheInterface cache;
-
- @Before
- public void setUp() throws Exception {
- reactomeCacheType = rc.getCacheType();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetEntities() throws Exception {
- try {
- List<ReactomePhysicalEntity> list = rc.getEntitiesForName("GAK", true);
- assertNotNull(list);
- assertTrue("Too few elements on the list: " + list.size(), list.size() > 1);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetReactions() throws Exception {
- try {
- List<ReactomeReactionlikeEvent> list = rc.getReactionsForEntityId(162704);
- assertNotNull(list);
- assertTrue("Too few elements on the list: " + list.size(), list.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetNodeForId() {
- try {
- Node node = rc.getFullNodeForDbId(1385634);
- assertNotNull(node);
- assertEquals("referenceDatabase", node.getNodeName());
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testGetTypeForId() {
- try {
- Class<?> clazz = rc.getTypeForDbId(109624);
- assertNotNull(clazz);
- assertEquals(clazz.getName(), ReactomeReaction.class.getName());
-
- clazz = rc.getTypeForDbId(70154);
- assertNotNull(clazz);
- assertEquals(clazz.getName(), ReactomeInstanceEdit.class.getName());
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testGetObjectsForIds() {
- try {
- List<Integer> ids = new ArrayList<Integer>();
- ids.add(3896801);
- ids.add(549119);
-
- Map<Integer, ReactomeDatabaseObject> objects = rc.getFullObjectsForDbIds(ids);
- assertEquals(2, objects.keySet().size());
- ReactomeDatabaseObject object = objects.get(3896801);
- assertNotNull(object);
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testGetObjectsForIds2() {
- try {
- List<Integer> ids = new ArrayList<Integer>();
- ids.add(2671814);
- ids.add(2562550);
- ids.add(2562550);
- ids.add(2562550);
-
- Map<Integer, ReactomeDatabaseObject> objects = rc.getFullObjectsForDbIds(ids);
- assertEquals(2, objects.keySet().size());
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testGetEntitiesForChebiId() throws Exception {
- try {
- Set<MiriamData> ids = new HashSet<MiriamData>();
- ids.add(new MiriamData(MiriamType.CHEBI, "CHEBI:15378"));
- List<ReactomePhysicalEntity> list = rc.getEntitiesForChebiId(ids, false);
- assertNotNull(list);
- assertTrue(list.size() > 0);
- assertTrue(list.get(0) instanceof ReactomeSimpleEntity);
- ReactomeSimpleEntity entity = (ReactomeSimpleEntity) list.get(0);
- assertNotNull(entity);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSimpleObjectListByQuery() throws Exception {
- try {
- String query = "name=GAK";
- List<ReactomeDatabaseObject> list = rc.getSimpleObjectListByQuery(query, ReactomePhysicalEntity.class);
- assertNotNull(list);
- assertTrue(list.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test(timeout = 15000)
- public void testCachableInterfaceByParams() throws Exception {
- String url = "http://reactome.org/ReactomeRESTfulAPI/RESTfulWS/listByQuery/DatabaseObjects";
- String query = "identifier=2562550\n" + url;
- String newRes = "hello";
- try {
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, reactomeCacheType, newRes);
- cache.invalidateByQuery(query, reactomeCacheType);
-
- waitForRefreshCacheQueueToEmpty();
-
- String res = cache.getStringByQuery(query, reactomeCacheType);
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(ReactomeConnectorTest.class);
+
+ CacheType reactomeCacheType;
+
+ @Autowired
+ private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
+
+ @Autowired
+ private GeneralCacheInterface cache;
+
+ @Before
+ public void setUp() throws Exception {
+ reactomeCacheType = rc.getCacheType();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetEntities() throws Exception {
+ try {
+ List<ReactomePhysicalEntity> list = rc.getEntitiesForName("GAK", true);
+ assertNotNull(list);
+ assertTrue("Too few elements on the list: " + list.size(), list.size() > 1);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetReactions() throws Exception {
+ try {
+ List<ReactomeReactionlikeEvent> list = rc.getReactionsForEntityId(162704);
+ assertNotNull(list);
+ assertTrue("Too few elements on the list: " + list.size(), list.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetNodeForId() {
+ try {
+ Node node = rc.getFullNodeForDbId(1385634);
+ assertNotNull(node);
+ assertEquals("referenceDatabase", node.getNodeName());
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testGetTypeForId() {
+ try {
+ Class<?> clazz = rc.getTypeForDbId(109624);
+ assertNotNull(clazz);
+ assertEquals(clazz.getName(), ReactomeReaction.class.getName());
+
+ clazz = rc.getTypeForDbId(70154);
+ assertNotNull(clazz);
+ assertEquals(clazz.getName(), ReactomeInstanceEdit.class.getName());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testGetObjectsForIds() {
+ try {
+ List<Integer> ids = new ArrayList<Integer>();
+ ids.add(3896801);
+ ids.add(549119);
+
+ Map<Integer, ReactomeDatabaseObject> objects = rc.getFullObjectsForDbIds(ids);
+ assertEquals(2, objects.keySet().size());
+ ReactomeDatabaseObject object = objects.get(3896801);
+ assertNotNull(object);
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testGetObjectsForIds2() {
+ try {
+ List<Integer> ids = new ArrayList<Integer>();
+ ids.add(2671814);
+ ids.add(2562550);
+ ids.add(2562550);
+ ids.add(2562550);
+
+ Map<Integer, ReactomeDatabaseObject> objects = rc.getFullObjectsForDbIds(ids);
+ assertEquals(2, objects.keySet().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testGetEntitiesForChebiId() throws Exception {
+ try {
+ Set<MiriamData> ids = new HashSet<MiriamData>();
+ ids.add(new MiriamData(MiriamType.CHEBI, "CHEBI:15378"));
+ List<ReactomePhysicalEntity> list = rc.getEntitiesForChebiId(ids, false);
+ assertNotNull(list);
+ assertTrue(list.size() > 0);
+ assertTrue(list.get(0) instanceof ReactomeSimpleEntity);
+ ReactomeSimpleEntity entity = (ReactomeSimpleEntity) list.get(0);
+ assertNotNull(entity);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSimpleObjectListByQuery() throws Exception {
+ try {
+ String query = "name=GAK";
+ List<ReactomeDatabaseObject> list = rc.getSimpleObjectListByQuery(query, ReactomePhysicalEntity.class);
+ assertNotNull(list);
+ assertTrue(list.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test(timeout = 15000)
+ public void testCachableInterfaceByParams() throws Exception {
+ String url = "http://reactome.org/ReactomeRESTfulAPI/RESTfulWS/listByQuery/DatabaseObjects";
+ String query = "identifier=2562550\n" + url;
+ String newRes = "hello";
+ try {
+ cache.setCachedQuery(query, reactomeCacheType, newRes);
+ cache.invalidateByQuery(query, reactomeCacheType);
+
+ permanentDatabaseLevelCache.waitToFinishTasks();
+
+ String res = cache.getStringByQuery(query, reactomeCacheType);
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}