remove unused variables

CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyActionTest.java

@@ -3,8 +3,6 @@ package lcsb.mapviewer.cdplugin.copypaste;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotEquals;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.Test;
 import org.mockito.Mockito;
 
@@ -13,7 +11,6 @@ import lcsb.mapviewer.cdplugin.CdPluginFunctions;
 import lcsb.mapviewer.common.SystemClipboard;
 
 public class CopyActionTest extends CdPluginFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   private SystemClipboard cp = new SystemClipboard();
 

CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java

@@ -6,8 +6,6 @@ import static org.junit.Assert.assertNull;
 
 import java.util.Set;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -19,7 +17,6 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
 import lcsb.mapviewer.model.map.MiriamType;
 
 public class CopyPasteAbstractActionTest extends CdPluginFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Before
   public void setUp() throws Exception {

CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoFrameTest.java

@@ -6,15 +6,12 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.Test;
 
 import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 import lcsb.mapviewer.cdplugin.CdPluginFunctions;
 
 public class InfoFrameTest extends CdPluginFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Test
   public void testSetEmptySpeciesList() {

CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoPluginTest.java

@@ -5,8 +5,6 @@ import static org.junit.Assert.assertEquals;
 import java.util.Arrays;
 import java.util.List;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.Test;
 
 import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
@@ -14,7 +12,6 @@ import lcsb.mapviewer.cdplugin.CdPluginFunctions;
 
 public class InfoPluginTest extends CdPluginFunctions {
 
-  private static Logger logger = LogManager.getLogger();
 
   @Test
   public void testConstructor() {

annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java

@@ -61,24 +61,24 @@ import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
 @RunWith(SpringJUnit4ClassRunner.class)
 public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit4SpringContextTests {
 
-  private Logger logger = LogManager.getLogger();
+  protected static Logger logger = LogManager.getLogger();
 
   private static int BLOCK_SIZE = 65536;
 
   private static Map<String, Model> models = new HashMap<String, Model>();
-  
+
   @Rule
   public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
-  
+
   @Autowired
   protected PermanentDatabaseLevelCacheInterface cache;
-  
+
   @Autowired
   protected CacheTypeDao cacheTypeDao;
-  
+
   @Autowired
   protected DbUtils dbUtils;
-  
+
   private MinervaLoggerAppender appender;
 
   private String dapiLogin;

annotation/src/test/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCacheTest.java

@@ -4,8 +4,6 @@ import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -18,7 +16,6 @@ import lcsb.mapviewer.model.cache.CacheType;
 
 public class ApplicationLevelCacheTest extends AnnotationTestFunctions {
 
-  private static Logger logger = LogManager.getLogger();
 
   private boolean status;
 

annotation/src/test/java/lcsb/mapviewer/annotation/cache/BigFileCacheTest.java

@@ -22,8 +22,6 @@ import java.util.concurrent.ThreadFactory;
 import org.apache.commons.net.ftp.FTPClient;
 import org.apache.commons.net.ftp.FTPFile;
 import org.apache.commons.net.ftp.FTPReply;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -42,7 +40,6 @@ import lcsb.mapviewer.persist.dao.cache.BigFileEntryDao;
 
 public class BigFileCacheTest extends AnnotationTestFunctions {
 
-  private static Logger logger = LogManager.getLogger();
 
   private String ftpUrl = "ftp://ftp.informatik.rwth-aachen.de/README";
   private String ftpUrlPartContent = "Welcome";

annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceTest.java

@@ -8,8 +8,6 @@ import static org.mockito.Mockito.when;
 
 import java.util.List;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -22,7 +20,6 @@ import lcsb.mapviewer.model.cache.CacheType;
 import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
 
 public class CachableInterfaceTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private List<CachableInterface> interfaces;

annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheTest.java

@@ -5,8 +5,6 @@ import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
@@ -19,7 +17,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.cache.CacheType;
 
 public class GeneralCacheTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   private GeneralCache cache = new GeneralCache(null);
 

annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheWithExclusionTest.java

@@ -4,8 +4,6 @@ import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
@@ -16,7 +14,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.cache.CacheType;
 
 public class GeneralCacheWithExclusionTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @AfterClass
   public static void tearDownAfterClass() throws Exception {

annotation/src/test/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheTest.java

@@ -10,8 +10,6 @@ import static org.mockito.Mockito.when;
 import java.util.Calendar;
 
 import org.apache.commons.lang3.mutable.MutableBoolean;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -33,7 +31,6 @@ import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
 @Rollback(true)
 public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
 
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;

annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java

@@ -16,8 +16,6 @@ import java.util.List;
 import java.util.Set;
 
 import org.apache.commons.lang3.SerializationException;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.Test;
 import org.mockito.Mockito;
 import org.mockito.invocation.InvocationOnMock;
@@ -43,7 +41,6 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
 import lcsb.mapviewer.model.map.MiriamType;
 
 public class ChEMBLParserTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private GeneralCacheInterface cache;

annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java

@@ -3,8 +3,6 @@ package lcsb.mapviewer.annotation.services;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assume.assumeTrue;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -17,7 +15,6 @@ import lcsb.mapviewer.annotation.services.dapi.DrugBankParser;
 
 @ActiveProfiles("drugBankTestProfile")
 public class DrugAnnotationTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private DrugBankParser drugBankParser;

annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java

@@ -13,8 +13,6 @@ import java.io.IOException;
 import java.util.List;
 
 import org.apache.http.HttpStatus;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.Test;
 import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -30,7 +28,6 @@ import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
 
 public class MeSHParserTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private MeSHParser meshParser;

annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java

@@ -12,8 +12,6 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -35,7 +33,6 @@ import lcsb.mapviewer.persist.dao.ProjectDao;
 import lcsb.mapviewer.persist.dao.user.UserDao;
 
 public class MiRNAParserTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   protected ProjectDao projectDao;

annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java

@@ -12,8 +12,6 @@ import static org.mockito.Mockito.when;
 import java.io.IOException;
 import java.lang.reflect.Field;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -30,7 +28,6 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
 import lcsb.mapviewer.model.map.MiriamType;
 
 public class MiriamConnectorTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private MiriamConnector miriamConnector;

annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java

@@ -15,8 +15,6 @@ import java.util.Map;
 import java.util.Set;
 
 import org.apache.commons.lang3.mutable.MutableDouble;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -44,7 +42,6 @@ import lcsb.mapviewer.model.user.UserClassAnnotators;
 import lcsb.mapviewer.persist.dao.map.ModelDao;
 
 public class ModelAnnotatorTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
   private IProgressUpdater updater = new IProgressUpdater() {
     @Override
     public void setProgress(final double progress) {

annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java

@@ -13,8 +13,6 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -35,7 +33,6 @@ import lcsb.mapviewer.model.Article;
 public class PubmedParserTest extends AnnotationTestFunctions {
   @Autowired
   protected PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCacheInterface;
-  private static Logger logger = LogManager.getLogger();
   @Autowired
   private PubmedParser pubmedParser;
   private boolean status2;

annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java

@@ -10,8 +10,6 @@ import static org.mockito.Mockito.when;
 
 import java.io.IOException;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.Test;
 import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -25,7 +23,6 @@ import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
 
 public class TaxonomyBackendTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private TaxonomyBackend taxonomyBackend;

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java

@@ -8,8 +8,6 @@ import static org.mockito.Mockito.when;
 
 import java.io.IOException;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Ignore;
@@ -26,7 +24,6 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Species;
 
 public class BrendaAnnotatorTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private BrendaAnnotator brendaAnnotator;

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java

@@ -12,8 +12,6 @@ import static org.mockito.Mockito.when;
 
 import java.util.List;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -41,7 +39,6 @@ import uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem;
 import uk.ac.ebi.chebi.webapps.chebiWS.model.SearchCategory;
 
 public class ChebiAnnotatorTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private ChebiAnnotator backend;

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorImplementationsTest.java

@@ -9,8 +9,6 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.AfterClass;
 import org.junit.Test;
 import org.junit.runner.RunWith;
@@ -42,7 +40,6 @@ public class ElementAnnotatorImplementationsTest extends AnnotationTestFunctions
   private static AnnotationConfigApplicationContext applicationContext;
 
   @SuppressWarnings("unused")
-  private static Logger logger = LogManager.getLogger();
 
   @Parameter
   private String testName;

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java

@@ -10,8 +10,6 @@ import static org.mockito.Mockito.when;
 
 import java.io.IOException;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -32,7 +30,6 @@ import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 
 public class GoAnnotatorTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private GoAnnotator goAnnotator;

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java

@@ -12,8 +12,6 @@ import static org.mockito.Mockito.when;
 import java.io.IOException;
 import java.util.List;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -31,8 +29,6 @@ import lcsb.mapviewer.model.map.species.Species;
 
 public class HgncAnnotatorTest extends AnnotationTestFunctions {
 
-  private final Logger logger = LogManager.getLogger();
-
   @Autowired
   private HgncAnnotator hgncAnnotator;
 

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java

@@ -11,8 +11,6 @@ import static org.mockito.Mockito.when;
 
 import java.io.IOException;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -30,7 +28,6 @@ import lcsb.mapviewer.model.map.species.SimpleMolecule;
 import lcsb.mapviewer.model.map.species.Species;
 
 public class ReconAnnotatorTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
   @Autowired
   private ReconAnnotator reconAnnotator;
 

annotation/src/test/java/lcsb/mapviewer/annotation/services/dapi/ChemicalParserTest.java

@@ -10,8 +10,6 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.commons.lang3.math.NumberUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.Before;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -33,7 +31,6 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
   private final MiriamData parkinsonDiseaseId = new MiriamData(MiriamType.MESH_2012, "D010300");
   private final MiriamData bloodLossDisease = new MiriamData(MiriamType.MESH_2012, "D016063");
 
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private ChemicalParser chemicalParser;

annotation/src/test/java/lcsb/mapviewer/annotation/services/dapi/DrugbankParserErrorHandlingTest.java

@@ -3,8 +3,6 @@ package lcsb.mapviewer.annotation.services.dapi;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assume.assumeTrue;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.Before;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -18,7 +16,6 @@ import lcsb.mapviewer.model.map.MiriamType;
 
 @ActiveProfiles("dapiDownTestProfile")
 public class DrugbankParserErrorHandlingTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private DrugBankParser drugBankParser;

annotation/src/test/java/lcsb/mapviewer/annotation/services/dapi/DrugbankParserTest.java

@@ -10,8 +10,6 @@ import static org.junit.Assume.assumeTrue;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.Before;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -32,7 +30,6 @@ import lcsb.mapviewer.model.map.model.Model;
 @ActiveProfiles("drugBankTestProfile")
 @Rollback(true)
 public class DrugbankParserTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private DrugBankParser drugBankParser;

annotation/src/test/java/lcsb/mapviewer/annotation/services/dapi/DrugbankParserWithNoConnectionTest.java

@@ -6,8 +6,6 @@ import static org.junit.Assume.assumeTrue;
 
 import java.util.List;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.Before;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -22,7 +20,6 @@ import lcsb.mapviewer.model.map.MiriamType;
 @ActiveProfiles("dapiNotConnectedTestProfile")
 @Rollback(true)
 public class DrugbankParserWithNoConnectionTest extends AnnotationTestFunctions {
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private DrugBankParser drugBankParser;

annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java

@@ -22,8 +22,6 @@ import java.util.concurrent.Future;
 import org.apache.commons.net.ftp.FTPClient;
 import org.apache.commons.net.ftp.FTPFile;
 import org.apache.commons.net.ftp.FTPReply;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -51,7 +49,6 @@ import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeDao;
 
 public class UcscReferenceGenomeConnectorTest extends AnnotationTestFunctions {
 
-  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private UcscReferenceGenomeConnector connector;

commons/src/test/java/lcsb/mapviewer/common/CommonTestFunctions.java

@@ -2,6 +2,8 @@ package lcsb.mapviewer.common;
 
 import java.util.List;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.core.LogEvent;
 import org.junit.After;
 import org.junit.Before;
@@ -9,6 +11,8 @@ import org.junit.Rule;
 
 public class CommonTestFunctions {
 
+  protected static Logger logger = LogManager.getLogger();
+
   @Rule
   public UnitTestFailedWatcher ruleExample = new UnitTestFailedWatcher();