Commit 333fd22a authored by Piotr Gawron's avatar Piotr Gawron
Browse files

logger definition simplified

parent 59736a98
......@@ -18,7 +18,7 @@ public class CopyAction extends CopyPasteAbstractAction {
/**
* Default class logger.
*/
private final Logger logger = LogManager.getLogger(CopyAction.class.getName());
private final Logger logger = LogManager.getLogger();
/**
* Method that perform annotation of a CellDesigner species listed in
......
......@@ -28,7 +28,7 @@ public class CopyPasteAbstractAction {
* Default class logger.
*/
@SuppressWarnings("unused")
private final Logger logger = LogManager.getLogger(CopyPasteAbstractAction.class);
private final Logger logger = LogManager.getLogger();
/**
* Serializes {@link MiriamData} into string that will be stored into system
......
......@@ -32,7 +32,7 @@ public class CopyPastePlugin extends CellDesignerPlugin {
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(CopyPastePlugin.class.getName());
private Logger logger = LogManager.getLogger();
/**
* Main window of cell designer.
*/
......
......@@ -25,7 +25,7 @@ public class CopyPluginAction extends PluginAction {
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(PasteAction.class.getName());
private Logger logger = LogManager.getLogger();
/**
* Plugin that access this action.
*/
......
......@@ -22,7 +22,7 @@ public class PasteAction extends CopyPasteAbstractAction {
/**
* Default class logger.
*/
private final Logger logger = LogManager.getLogger(PasteAction.class.getName());
private final Logger logger = LogManager.getLogger();
/**
* Method that perform annotation of a CellDesigner species listed in
......
......@@ -25,7 +25,7 @@ public class PastePluginAction extends PluginAction {
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(PasteAction.class.getName());
private Logger logger = LogManager.getLogger();
/**
* Plugin that access this action.
*/
......
......@@ -59,7 +59,7 @@ public final class InfoFrame {
* Default class logger.
*/
@SuppressWarnings("unused")
private final Logger logger = LogManager.getLogger(InfoFrame.class);
private final Logger logger = LogManager.getLogger();
/**
* Instance of the JFrame representation of windows.
*/
......
......@@ -38,7 +38,7 @@ public class InfoPlugin extends CellDesignerPlugin {
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(InfoPlugin.class.getName());
private Logger logger = LogManager.getLogger();
/**
* Listener called when set of selected elements in cell designer changed.
......
......@@ -13,7 +13,7 @@ import lcsb.mapviewer.cdplugin.CdPluginFunctions;
import lcsb.mapviewer.common.SystemClipboard;
public class CopyActionTest extends CdPluginFunctions {
Logger logger = LogManager.getLogger(CopyActionTest.class);
Logger logger = LogManager.getLogger();
SystemClipboard cp = new SystemClipboard();
......
......@@ -13,7 +13,7 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.*;
public class CopyPasteAbstractActionTest extends CdPluginFunctions {
Logger logger = LogManager.getLogger(CopyPasteAbstractActionTest.class);
Logger logger = LogManager.getLogger();
@Before
public void setUp() throws Exception {
......
......@@ -12,7 +12,7 @@ import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import lcsb.mapviewer.cdplugin.CdPluginFunctions;
public class InfoFrameTest extends CdPluginFunctions {
Logger logger = LogManager.getLogger(InfoFrameTest.class);
Logger logger = LogManager.getLogger();
@Test
public void testSetEmptySpeciesList() {
......
......@@ -14,7 +14,7 @@ import lcsb.mapviewer.cdplugin.CdPluginFunctions;
public class InfoPluginTest extends CdPluginFunctions {
Logger logger = LogManager.getLogger(InfoPluginTest.class);
Logger logger = LogManager.getLogger();
@Test
public void testConstructor() {
......
......@@ -32,7 +32,7 @@ public final class ApplicationLevelCache implements QueryCacheInterface {
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(ApplicationLevelCache.class);
private static Logger logger = LogManager.getLogger();
/**
* Cached nodes stored locally and identified by string.
......
......@@ -42,7 +42,7 @@ public class BigFileCache {
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(BigFileCache.class);
private Logger logger = LogManager.getLogger();
/**
* Access class for database objects storing statuses of the files.
......
......@@ -24,7 +24,7 @@ public abstract class CachableInterface {
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(CachableInterface.class);
private static Logger logger = LogManager.getLogger();
/**
* String containing class name of the class that extends
* {@link CachableInterface}. String name is used because cache layer doesn't
......
......@@ -27,7 +27,7 @@ public class GeneralCache implements GeneralCacheInterface {
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(GeneralCache.class);
private static Logger logger = LogManager.getLogger();
/**
* Application level cache. More information can be found
......
......@@ -23,7 +23,7 @@ public class GeneralCacheWithExclusion implements GeneralCacheInterface {
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(GeneralCacheWithExclusion.class);
private Logger logger = LogManager.getLogger();
/**
* How many queries should be ignored.
......
......@@ -42,7 +42,7 @@ public class WebPageDownloader {
/**
* Default class logger.
*/
private final Logger logger = LogManager.getLogger(WebPageDownloader.class);
private final Logger logger = LogManager.getLogger();
/**
* Returns content of the web page identified by url.
......
......@@ -23,7 +23,7 @@ public class XmlSerializer<T> {
/**
* Default class logger.
*/
private final Logger logger = LogManager.getLogger(XmlSerializer.class);
private final Logger logger = LogManager.getLogger();
/**
* Class of the object that DAO works on.
......
......@@ -29,7 +29,7 @@ public class Chebi implements Serializable {
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(Chebi.class);
private static Logger logger = LogManager.getLogger();
/**
* Name of the object.
......
......@@ -28,7 +28,7 @@ public class MeSH implements Serializable {
* Default class logger.
*/
@SuppressWarnings("unused")
private static Logger logger = LogManager.getLogger(MeSH.class);
private static Logger logger = LogManager.getLogger();
/**
* short name.
......
......@@ -85,7 +85,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(ChEMBLParser.class);
private Logger logger = LogManager.getLogger();
/**
* Service used for annotation of proteins using {@link MiriamType#UNIPROT
......
......@@ -37,7 +37,7 @@ public abstract class DrugAnnotation extends CachableInterface {
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(DrugAnnotation.class);
private Logger logger = LogManager.getLogger();
/**
* Object that allows to serialize {@link Drug} elements into xml string and
......
......@@ -43,7 +43,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(MeSHParser.class);
private Logger logger = LogManager.getLogger();
/**
* Object that allows to serialize {@link MeSH} elements into xml string and
......
......@@ -87,7 +87,7 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(MiRNAParser.class);
private Logger logger = LogManager.getLogger();
/**
* Class used to access information about organisms taxonomy.
......
......@@ -36,7 +36,7 @@ public final class MiriamConnector extends CachableInterface implements IExterna
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(MiriamConnector.class);
private Logger logger = LogManager.getLogger();
XmlAnnotationParser xap = new XmlAnnotationParser();
......
......@@ -47,7 +47,7 @@ public class ModelAnnotator {
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(ModelAnnotator.class);
private static Logger logger = LogManager.getLogger();
/**
* Connector used for accessing data from miriam registry.
*/
......
......@@ -57,7 +57,7 @@ public class PubmedParser extends CachableInterface implements IExternalService
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(PubmedParser.class);
private Logger logger = LogManager.getLogger();
/**
* Object that allows to serialize {@link Article} elements into xml string and
......
......@@ -42,7 +42,7 @@ public class TaxonomyBackend extends CachableInterface implements IExternalServi
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(TaxonomyBackend.class);
private Logger logger = LogManager.getLogger();
/**
* Default constructor.
......
......@@ -29,7 +29,7 @@ public class BrendaAnnotator extends ElementAnnotator implements IExternalServic
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(BrendaAnnotator.class);
private static Logger logger = LogManager.getLogger();
/**
* Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
......
......@@ -34,7 +34,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(CazyAnnotator.class);
private static Logger logger = LogManager.getLogger();
/**
* Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
......
......@@ -59,7 +59,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(ChebiAnnotator.class);
private static Logger logger = LogManager.getLogger();
/**
* Client to chebi API.
*/
......
......@@ -32,7 +32,7 @@ public abstract class ElementAnnotator extends CachableInterface {
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(ElementAnnotator.class);
private static Logger logger = LogManager.getLogger();
/**
* List of classes that can be annotated by this {@link IElementAnnotator
......
......@@ -56,7 +56,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
/**
* Standard class logger.
*/
private final Logger logger = LogManager.getLogger(EnsemblAnnotator.class);
private final Logger logger = LogManager.getLogger();
/**
* Default constructor.
......
......@@ -47,7 +47,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
/**
* Standard class logger.
*/
private final Logger logger = LogManager.getLogger(EntrezAnnotator.class);
private final Logger logger = LogManager.getLogger();
/**
* Object that allows to serialize {@link EntrezData} elements into xml string
* and deserialize xml into {@link EntrezData} objects.
......
......@@ -38,7 +38,7 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(GoAnnotator.class);
private Logger logger = LogManager.getLogger();
/**
* Connector used for accessing data from miriam registry.
......
......@@ -39,7 +39,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
/**
* Standard class logger.
*/
private final Logger logger = LogManager.getLogger(HgncAnnotator.class);
private final Logger logger = LogManager.getLogger();
private MiriamConnector miriamConnector;
/**
......
......@@ -33,7 +33,7 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(KeggAnnotator.class);
private static Logger logger = LogManager.getLogger();
/**
* Pattern used for finding PUBMED IDs in KEGG page.
......
......@@ -36,7 +36,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(PdbAnnotator.class);
private static Logger logger = LogManager.getLogger();
/**
* Default constructor.
......
......@@ -45,7 +45,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(ReconAnnotator.class);
private static Logger logger = LogManager.getLogger();
/**
* Default constructor.
......
......@@ -30,7 +30,7 @@ public class StitchAnnotator extends ElementAnnotator implements IExternalServic
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(StitchAnnotator.class);
private static Logger logger = LogManager.getLogger();
/**
* Service used for annotation of entities using {@link MiriamType#STITCH
......
......@@ -37,7 +37,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(TairAnnotator.class);
private static Logger logger = LogManager.getLogger();
/**
* Default constructor.
......
......@@ -32,7 +32,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
/**
* Default class logger.
*/
private static Logger logger = LogManager.getLogger(UniprotAnnotator.class);
private static Logger logger = LogManager.getLogger();
/**
* Pattern used for finding hgnc symbol from uniprot info page .
......
......@@ -30,7 +30,7 @@ public abstract class AbstractReferenceGenomeConnector extends CachableInterface
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(AbstractReferenceGenomeConnector.class);
private Logger logger = LogManager.getLogger();
/**
* Utils that help to manage the sessions in custom multithreaded
......
......@@ -47,7 +47,7 @@ public class UcscReferenceGenomeConnector extends AbstractReferenceGenomeConnect
/**
* Default class logger.
*/
private Logger logger = LogManager.getLogger(UcscReferenceGenomeConnector.class);
private Logger logger = LogManager.getLogger();
/**
* Regex pattern that helps to find out organism names in source file.
......
......@@ -14,7 +14,7 @@ import lcsb.mapviewer.model.cache.CacheType;
public class ApplicationLevelCacheTest extends AnnotationTestFunctions {
Logger logger = LogManager.getLogger(ApplicationLevelCacheTest.class);
Logger logger = LogManager.getLogger();
boolean status;
......
......@@ -28,7 +28,7 @@ import lcsb.mapviewer.persist.dao.cache.BigFileEntryDao;
public class BigFileCacheTest extends AnnotationTestFunctions {
Logger logger = LogManager.getLogger(BigFileCacheTest.class);
Logger logger = LogManager.getLogger();
String ftpUrl = "ftp://ftp.informatik.rwth-aachen.de/README";
String ftpUrlPartContent = "Welcome";
......
......@@ -18,7 +18,7 @@ import lcsb.mapviewer.model.cache.CacheType;
import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
public class CachableInterfaceTest extends AnnotationTestFunctions {
Logger logger = LogManager.getLogger(CachableInterfaceTest.class);
Logger logger = LogManager.getLogger();
@Autowired
private List<CachableInterface> interfaces;
......
......@@ -13,7 +13,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.cache.CacheType;
public class GeneralCacheTest extends AnnotationTestFunctions {
Logger logger = LogManager.getLogger(GeneralCacheTest.class);
Logger logger = LogManager.getLogger();
GeneralCache cache = new GeneralCache(null);
......
......@@ -11,7 +11,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.cache.CacheType;
public class GeneralCacheWithExclusionTest extends AnnotationTestFunctions {
Logger logger = LogManager.getLogger(GeneralCacheWithExclusionTest.class);
Logger logger = LogManager.getLogger();
@AfterClass
public static void tearDownAfterClass() throws Exception {
......
......@@ -27,7 +27,7 @@ import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
@Rollback(true)
public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
Logger logger = LogManager.getLogger(PermanentDatabaseLevelCacheTest.class);
Logger logger = LogManager.getLogger();
@Autowired
private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
......
......@@ -25,7 +25,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.*;
public class ChEMBLParserTest extends AnnotationTestFunctions {
Logger logger = LogManager.getLogger(ChEMBLParserTest.class);
Logger logger = LogManager.getLogger();
@Autowired
private GeneralCacheInterface cache;
......
......@@ -20,7 +20,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.*;
public class MiriamConnectorTest extends AnnotationTestFunctions {
Logger logger = LogManager.getLogger(MiriamConnectorTest.class);
Logger logger = LogManager.getLogger();
@Autowired
MiriamConnector miriamConnector;
......
......@@ -22,7 +22,7 @@ import lcsb.mapviewer.model.user.UserClassAnnotators;
import lcsb.mapviewer.persist.dao.map.ModelDao;
public class ModelAnnotatorTest extends AnnotationTestFunctions {
Logger logger = LogManager.getLogger(ModelAnnotatorTest.class);
Logger logger = LogManager.getLogger();
IProgressUpdater updater = new IProgressUpdater() {
@Override
public void setProgress(double progress) {
......