fields must be private

CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java

@@ -20,7 +20,7 @@ public class CdPluginFunctions {
   @Rule
   public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
 
-  String rdfString = "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
+  private String rdfString = "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
       + "<rdf:Description rdf:about=\"#s3\">\n"
       + "<bqmodel:is>\n"
       + "<rdf:Bag>\n"

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

@@ -13,9 +13,9 @@ import lcsb.mapviewer.cdplugin.CdPluginFunctions;
 import lcsb.mapviewer.common.SystemClipboard;
 
 public class CopyActionTest extends CdPluginFunctions {
-  Logger logger = LogManager.getLogger();
+  private static Logger logger = LogManager.getLogger();
 
-  SystemClipboard cp = new SystemClipboard();
+  private SystemClipboard cp = new SystemClipboard();
 
   @Test
   public void testCopyFromSpecies() {

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

@@ -19,7 +19,7 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
 import lcsb.mapviewer.model.map.MiriamType;
 
 public class CopyPasteAbstractActionTest extends CdPluginFunctions {
-  Logger logger = LogManager.getLogger();
+  private static Logger logger = LogManager.getLogger();
 
   @Before
   public void setUp() throws Exception {

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

@@ -15,7 +15,7 @@ import lcsb.mapviewer.common.SystemClipboard;
 
 public class CopyPastePluginTest extends CdPluginFunctions {
 
-  SystemClipboard cp = new SystemClipboard();
+  private SystemClipboard cp = new SystemClipboard();
 
   @Test
   public void testConstructor() {

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

@@ -17,7 +17,7 @@ import lcsb.mapviewer.common.SystemClipboard;
 
 public class PasteActionTest extends CdPluginFunctions {
 
-  SystemClipboard cp = new SystemClipboard();
+  private SystemClipboard cp = new SystemClipboard();
 
   @Test
   public void testPerformAnnotationOnSpecies() {

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

@@ -14,7 +14,7 @@ import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 import lcsb.mapviewer.cdplugin.CdPluginFunctions;
 
 public class InfoFrameTest extends CdPluginFunctions {
-  Logger logger = LogManager.getLogger();
+  private static Logger logger = LogManager.getLogger();
 
   @Test
   public void testSetEmptySpeciesList() {

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

@@ -14,7 +14,7 @@ import lcsb.mapviewer.cdplugin.CdPluginFunctions;
 
 public class InfoPluginTest extends CdPluginFunctions {
 
-  Logger logger = LogManager.getLogger();
+  private static Logger logger = LogManager.getLogger();
 
   @Test
   public void testConstructor() {

annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java

@@ -43,7 +43,7 @@ public final class MiriamConnector extends CachableInterface implements IExterna
    */
   private Logger logger = LogManager.getLogger();
   
-  XmlAnnotationParser xap = new XmlAnnotationParser();
+  private XmlAnnotationParser xap = new XmlAnnotationParser();
 
   /**
    * Default class constructor. Prevent initialization.

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbBestMappingEntry.java

@@ -9,16 +9,16 @@ import lcsb.mapviewer.model.map.species.field.Structure;
  *
  */
 public class PdbBestMappingEntry {
-  public String chainId;
-  public String experimentalMethod;
-  public String pdbId;
-  public int start;
-  public int end;
-  public int unpEnd;
-  public double coverage;
-  public int unpStart;
-  public double resolution;
-  public int taxId;
+  private String chainId;
+  private String experimentalMethod;
+  private String pdbId;
+  private int start;
+  private int end;
+  private int unpEnd;
+  private double coverage;
+  private int unpStart;
+  private double resolution;
+  private int taxId;
 
   public Structure convertToStructure() {
 

annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/ChemicalParser.java

@@ -44,7 +44,7 @@ public class ChemicalParser {
 
   private ChemicalEntityDtoConverter chemicalEntityDtoConverter;
 
-  ObjectMapper objectMapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,
+  private ObjectMapper objectMapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,
       false);
 
   @Autowired

annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/DrugBankParser.java

@@ -46,7 +46,7 @@ public class DrugBankParser extends DrugAnnotation implements IExternalService {
 
   private ChemicalEntityDtoConverter chemicalEntityDtoConverter;
 
-  ObjectMapper objectMapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,
+  private ObjectMapper objectMapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,
       false);
 
   @Autowired

annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/dto/DapiDatabase.java

 package lcsb.mapviewer.annotation.services.dapi.dto;
 
 public class DapiDatabase {
-  public String name;
+  private String name;
 
   public DapiDatabase(final String name) {
     this.name = name;
   }
+
+  public String getName() {
+    return name;
+  }
 }

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

@@ -18,9 +18,9 @@ import lcsb.mapviewer.model.cache.CacheType;
 
 public class ApplicationLevelCacheTest extends AnnotationTestFunctions {
 
-  Logger logger = LogManager.getLogger();
+  private static Logger logger = LogManager.getLogger();
 
-  boolean status;
+  private boolean status;
 
   @Before
   public void setUp() throws Exception {

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

@@ -42,15 +42,15 @@ import lcsb.mapviewer.persist.dao.cache.BigFileEntryDao;
 
 public class BigFileCacheTest extends AnnotationTestFunctions {
 
-  Logger logger = LogManager.getLogger();
+  private static Logger logger = LogManager.getLogger();
 
-  String ftpUrl = "ftp://ftp.informatik.rwth-aachen.de/README";
-  String ftpUrlPartContent = "Welcome";
+  private String ftpUrl = "ftp://ftp.informatik.rwth-aachen.de/README";
+  private String ftpUrlPartContent = "Welcome";
 
-  String httpUrl = "https://www.google.pl/humans.txt";
+  private String httpUrl = "https://www.google.pl/humans.txt";
 
   @Autowired
-  BigFileCache bigFileCache;
+  private BigFileCache bigFileCache;
 
   @Before
   public void setUp() throws Exception {

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

@@ -22,7 +22,7 @@ import lcsb.mapviewer.model.cache.CacheType;
 import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
 
 public class CachableInterfaceTest extends AnnotationTestFunctions {
-  Logger logger = LogManager.getLogger();
+  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private List<CachableInterface> interfaces;

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

@@ -19,12 +19,12 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.cache.CacheType;
 
 public class GeneralCacheTest extends AnnotationTestFunctions {
-  Logger logger = LogManager.getLogger();
+  private static Logger logger = LogManager.getLogger();
 
-  GeneralCache cache = new GeneralCache(null);
+  private GeneralCache cache = new GeneralCache(null);
 
   @Autowired
-  PermanentDatabaseLevelCacheInterface databaseLevelCache;
+  private PermanentDatabaseLevelCacheInterface databaseLevelCache;
 
   @AfterClass
   public static void tearDownAfterClass() throws Exception {

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

@@ -16,7 +16,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.cache.CacheType;
 
 public class GeneralCacheWithExclusionTest extends AnnotationTestFunctions {
-  Logger logger = LogManager.getLogger();
+  private static Logger logger = LogManager.getLogger();
 
   @AfterClass
   public static void tearDownAfterClass() throws Exception {

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

@@ -9,8 +9,8 @@ package lcsb.mapviewer.annotation.cache;
  */
 public final class MockCacheInterface extends CachableInterface {
 
-  public static RuntimeException exceptionToThrow = null;
-  public static Error errorToThrow;
+  protected static RuntimeException exceptionToThrow = null;
+  protected static Error errorToThrow;
 
   /**
    * Defsault constructor.

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

@@ -33,7 +33,7 @@ import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
 @Rollback(true)
 public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
 
-  Logger logger = LogManager.getLogger();
+  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;

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

@@ -43,7 +43,7 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
 import lcsb.mapviewer.model.map.MiriamType;
 
 public class ChEMBLParserTest extends AnnotationTestFunctions {
-  Logger logger = LogManager.getLogger();
+  private static Logger logger = LogManager.getLogger();
 
   @Autowired
   private GeneralCacheInterface cache;