Replaced System.out.println, System.err.println and printStackTrace with a logger (ref #223)

dmp-backend/data/src/main/java/eu/eudat/data/converters/DateToUTCConverter.java

@@ -1,5 +1,7 @@
 package eu.eudat.data.converters;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.format.datetime.DateFormatter;
 
 import javax.persistence.AttributeConverter;
@@ -15,6 +17,7 @@ import java.util.TimeZone;
  */
 @Converter
 public class DateToUTCConverter implements AttributeConverter<Date, Date> {
+    private static final Logger logger = LoggerFactory.getLogger(DateToUTCConverter.class);
 
     @Override
     public Date convertToDatabaseColumn(Date attribute) {
@@ -25,7 +28,7 @@ public class DateToUTCConverter implements AttributeConverter<Date, Date> {
             String date = formatterIST.format(attribute);
             return formatterIST.parse(date);
         } catch (ParseException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
         return null;
     }
@@ -39,7 +42,7 @@ public class DateToUTCConverter implements AttributeConverter<Date, Date> {
             String date = formatterIST.format(dbData);
             return formatterIST.parse(date);
         } catch (ParseException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
         return null;
     }

dmp-backend/data/src/main/java/eu/eudat/data/query/definition/Query.java

@@ -3,8 +3,11 @@ package eu.eudat.data.query.definition;
 import eu.eudat.data.dao.criteria.Criteria;
 import eu.eudat.queryable.QueryableList;
 import eu.eudat.queryable.queryableentity.DataEntity;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public abstract class Query<C extends Criteria<T>, T extends DataEntity> implements CriteriaQuery<C, T> {
+    private static final Logger logger = LoggerFactory.getLogger(Query.class);
     private C criteria;
     private QueryableList<T> query;
 
@@ -33,10 +36,8 @@ public abstract class Query<C extends Criteria<T>, T extends DataEntity> impleme
                 q.setCriteria(criteria);
                 q.setQuery(query);
                 return q;
-            } catch (InstantiationException e) {
+            } catch (InstantiationException | IllegalAccessException e) {
-                e.printStackTrace();
+                logger.error (e.getMessage(), e);
-            } catch (IllegalAccessException e) {
-                e.printStackTrace();
             }
             return null;
         }

dmp-backend/elastic/src/main/java/eu/eudat/elastic/entities/Dataset.java

@@ -1,6 +1,8 @@
 package eu.eudat.elastic.entities;
 
 import org.elasticsearch.common.xcontent.XContentBuilder;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.util.LinkedList;
@@ -11,6 +13,7 @@ import java.util.Map;
  * Created by ikalyvas on 7/5/2018.
  */
 public class Dataset implements ElasticEntity<Dataset> {
+    private static final Logger logger = LoggerFactory.getLogger(Dataset.class);
 
     private String id;
     private List<Tag> tags = new LinkedList<>();
@@ -40,7 +43,7 @@ public class Dataset implements ElasticEntity<Dataset> {
             try {
                 x.toElasticEntity(builder);
             } catch (IOException e) {
-                e.printStackTrace();
+                logger.error(e.getMessage(), e);
             }
         });
         builder.endArray();

dmp-backend/elastic/src/main/java/eu/eudat/elastic/repository/ElasticRepository.java

@@ -6,6 +6,8 @@ import eu.eudat.elastic.entities.ElasticEntity;
 import org.elasticsearch.client.Client;
 import org.elasticsearch.client.RestClient;
 import org.elasticsearch.client.RestHighLevelClient;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 
@@ -13,6 +15,7 @@ import java.io.IOException;
  * Created by ikalyvas on 7/5/2018.
  */
 public abstract class ElasticRepository<T extends ElasticEntity,C extends Criteria> implements Repository<T,C> {
+    private static final Logger logger = LoggerFactory.getLogger(ElasticRepository.class);
     private RestHighLevelClient client;
 
     public RestHighLevelClient getClient() {
@@ -29,7 +32,7 @@ public abstract class ElasticRepository<T extends ElasticEntity,C extends Criter
         try {
             item = mapper.readValue(value, tClass);
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
         return item;
     }

dmp-backend/queryable/src/main/java/eu/eudat/queryable/jpa/hibernatequeryablelist/QueryableHibernateList.java

@@ -7,6 +7,8 @@ import eu.eudat.queryable.jpa.predicates.*;
 import eu.eudat.queryable.queryableentity.DataEntity;
 import eu.eudat.queryable.types.FieldSelectionType;
 import eu.eudat.queryable.types.SelectionField;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.scheduling.annotation.Async;
 
 import javax.persistence.EntityManager;
@@ -18,6 +20,7 @@ import java.util.concurrent.CompletableFuture;
 import java.util.stream.Collectors;
 
 public class QueryableHibernateList<T extends DataEntity> implements QueryableList<T> {
+	private static final Logger logger = LoggerFactory.getLogger(QueryableHibernateList.class);
 
 	private Collector collector = new Collector();
 	private EntityManager manager;
@@ -264,7 +267,7 @@ public class QueryableHibernateList<T extends DataEntity> implements QueryableLi
 			try {
 				return (T) this.tClass.newInstance().buildFromTuple(groupedResults.get(x.get("id")), this.fields, "");
 			} catch (InstantiationException | IllegalAccessException e) {
-				e.printStackTrace();
+				logger.error(e.getMessage(), e);
 			}
 			return null;
 		}).collect(Collectors.toList()));

dmp-backend/web/src/main/java/eu/eudat/cache/ResponsesCache.java

@@ -2,6 +2,8 @@ package eu.eudat.cache;
 
 
 import com.google.common.cache.CacheBuilder;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.cache.CacheManager;
 import org.springframework.cache.annotation.EnableCaching;
 import org.springframework.cache.guava.GuavaCache;
@@ -17,6 +19,7 @@ import java.util.concurrent.TimeUnit;
 @Component
 @EnableCaching
 public class ResponsesCache {
+    private static final Logger logger = LoggerFactory.getLogger(ResponsesCache.class);
 
     public static long HOW_MANY = 30;
     public static TimeUnit TIME_UNIT = TimeUnit.MINUTES;
@@ -24,7 +27,7 @@ public class ResponsesCache {
 
     @Bean
     public CacheManager cacheManager() {
-        System.out.print("Loading ResponsesCache...");
+        logger.info("Loading ResponsesCache...");
         SimpleCacheManager simpleCacheManager = new SimpleCacheManager();
         List<GuavaCache> caches = new ArrayList<GuavaCache>();
         caches.add(new GuavaCache("repositories", CacheBuilder.newBuilder().expireAfterAccess(HOW_MANY, TIME_UNIT).build()));
@@ -38,7 +41,7 @@ public class ResponsesCache {
         caches.add(new GuavaCache("researchers", CacheBuilder.newBuilder().expireAfterAccess(HOW_MANY, TIME_UNIT).build()));
         caches.add(new GuavaCache("externalDatasets", CacheBuilder.newBuilder().expireAfterAccess(HOW_MANY, TIME_UNIT).build()));
         simpleCacheManager.setCaches(caches);
-        System.out.println("OK");
+        logger.info("OK");
         return simpleCacheManager;
     }
 

dmp-backend/web/src/main/java/eu/eudat/configurations/dynamicfunder/DynamicFunderConfigurationDevelImpl.java

@@ -4,6 +4,8 @@ import eu.eudat.configurations.dynamicfunder.entities.Configuration;
 import eu.eudat.configurations.dynamicfunder.entities.Property;
 import eu.eudat.models.data.dynamicfields.Dependency;
 import eu.eudat.models.data.dynamicfields.DynamicField;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.context.annotation.Profile;
 import org.springframework.core.env.Environment;
 import org.springframework.stereotype.Service;
@@ -19,6 +21,7 @@ import java.util.List;
 @Service("dynamicFunderConfiguration")
 @Profile("devel")
 public class DynamicFunderConfigurationDevelImpl implements DynamicFunderConfiguration {
+	private static final Logger logger = LoggerFactory.getLogger(DynamicFunderConfigurationDevelImpl.class);
 
 	private Configuration configuration;
 	private List<DynamicField> fields;
@@ -32,7 +35,7 @@ public class DynamicFunderConfigurationDevelImpl implements DynamicFunderConfigu
 	public Configuration getConfiguration() {
 		if (this.configuration != null) return this.configuration;
 		String fileUrl = this.environment.getProperty("configuration.dynamicFunderUrl");
-		System.out.println("Loaded also config file: " + fileUrl);
+		logger.info("Loaded also config file: " + fileUrl);
 		String current = null;
 		InputStream is = null;
 		try {
@@ -43,13 +46,12 @@ public class DynamicFunderConfigurationDevelImpl implements DynamicFunderConfigu
 			is = new URL("file:///"+ current + "/web/src/main/resources/FunderConfiguration.xml").openStream();
 			this.configuration = (Configuration) jaxbUnmarshaller.unmarshal(is);
 		} catch (Exception ex) {
-			ex.printStackTrace();
+			logger.error("Cannot find in folder" + current, ex);
-			System.out.println("Cannot find in folder" + current);
 		} finally {
 			try {
 				if (is != null) is.close();
 			} catch (IOException e) {
-				System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
+				logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
 			}
 		}
 		return this.configuration;

dmp-backend/web/src/main/java/eu/eudat/configurations/dynamicfunder/DynamicFunderConfigurationProdImpl.java

@@ -4,6 +4,8 @@ import eu.eudat.configurations.dynamicfunder.entities.Configuration;
 import eu.eudat.configurations.dynamicfunder.entities.Property;
 import eu.eudat.models.data.dynamicfields.Dependency;
 import eu.eudat.models.data.dynamicfields.DynamicField;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.context.annotation.Profile;
 import org.springframework.core.env.Environment;
 import org.springframework.stereotype.Service;
@@ -20,6 +22,7 @@ import java.util.List;
 @Service("dynamicFunderConfiguration")
 @Profile({ "production", "staging" })
 public class DynamicFunderConfigurationProdImpl implements DynamicFunderConfiguration {
+	private static final Logger logger = LoggerFactory.getLogger(DynamicFunderConfigurationProdImpl.class);
 
 	private Configuration configuration;
 	private List<DynamicField> fields;
@@ -33,7 +36,7 @@ public class DynamicFunderConfigurationProdImpl implements DynamicFunderConfigur
 	public Configuration getConfiguration() {
 		if (this.configuration != null) return this.configuration;
 		String fileUrl = this.environment.getProperty("configuration.dynamicFunderUrl");
-		System.out.println("Loaded also config file: " + fileUrl);
+		logger.info("Loaded also config file: " + fileUrl);
 		String current = null;
 		InputStream is = null;
 		try {
@@ -44,13 +47,12 @@ public class DynamicFunderConfigurationProdImpl implements DynamicFunderConfigur
 			is = new URL(Paths.get(fileUrl).toUri().toURL().toString()).openStream();
 			this.configuration = (Configuration) jaxbUnmarshaller.unmarshal(is);
 		} catch (Exception ex) {
-			ex.printStackTrace();
+			logger.error("Cannot find in folder" + current, ex);
-			System.out.println("Cannot find in folder" + current);
 		} finally {
 			try {
 				if (is != null) is.close();
 			} catch (IOException e) {
-				System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
+				logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
 			}
 		}
 		return this.configuration;

dmp-backend/web/src/main/java/eu/eudat/configurations/dynamicgrant/DynamicGrantConfigurationDevelImpl.java

@@ -4,6 +4,8 @@ import eu.eudat.configurations.dynamicgrant.entities.Configuration;
 import eu.eudat.configurations.dynamicgrant.entities.Property;
 import eu.eudat.models.data.dynamicfields.Dependency;
 import eu.eudat.models.data.dynamicfields.DynamicField;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Profile;
 import org.springframework.core.env.Environment;
@@ -24,6 +26,7 @@ import java.util.List;
 @Service("dynamicGrantConfiguration")
 @Profile("devel")
 public class DynamicGrantConfigurationDevelImpl implements DynamicGrantConfiguration {
+    private static final Logger logger = LoggerFactory.getLogger(DynamicGrantConfigurationDevelImpl.class);
 
     private Configuration configuration;
 
@@ -40,7 +43,7 @@ public class DynamicGrantConfigurationDevelImpl implements DynamicGrantConfigura
     public Configuration getConfiguration() {
         if (this.configuration != null) return this.configuration;
         String fileUrl = this.environment.getProperty("configuration.dynamicGrantUrl");
-        System.out.println("Loaded also config file: " + fileUrl);
+        logger.info("Loaded also config file: " + fileUrl);
         String current = null;
         InputStream is = null;
         try {
@@ -51,13 +54,12 @@ public class DynamicGrantConfigurationDevelImpl implements DynamicGrantConfigura
             is = new URL("file:///"+ current + "/web/src/main/resources/GrantConfiguration.xml").openStream();
             this.configuration = (Configuration) jaxbUnmarshaller.unmarshal(is);
         } catch (Exception ex) {
-            ex.printStackTrace();
+            logger.error("Cannot find in folder" + current, ex);
-            System.out.println("Cannot find in folder" + current);
         } finally {
             try {
                 if (is != null) is.close();
             } catch (IOException e) {
-                System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
+                logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
             }
         }
         return this.configuration;

dmp-backend/web/src/main/java/eu/eudat/configurations/dynamicgrant/DynamicGrantConfigurationProdImpl.java

@@ -4,6 +4,8 @@ import eu.eudat.configurations.dynamicgrant.entities.Configuration;
 import eu.eudat.configurations.dynamicgrant.entities.Property;
 import eu.eudat.models.data.dynamicfields.Dependency;
 import eu.eudat.models.data.dynamicfields.DynamicField;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Profile;
 import org.springframework.core.env.Environment;
@@ -24,6 +26,7 @@ import java.util.List;
 @Service("dynamicGrantConfiguration")
 @Profile({ "production", "staging" })
 public class DynamicGrantConfigurationProdImpl implements DynamicGrantConfiguration {
+    private static final Logger logger = LoggerFactory.getLogger(DynamicGrantConfigurationProdImpl.class);
 
     private Configuration configuration;
 
@@ -40,7 +43,7 @@ public class DynamicGrantConfigurationProdImpl implements DynamicGrantConfigurat
     public Configuration getConfiguration() {
         if (this.configuration != null) return this.configuration;
         String fileUrl = this.environment.getProperty("configuration.dynamicGrantUrl");
-        System.out.println("Loaded also config file: " + fileUrl);
+        logger.info("Loaded also config file: " + fileUrl);
         String current = null;
         InputStream is = null;
         try {
@@ -51,13 +54,12 @@ public class DynamicGrantConfigurationProdImpl implements DynamicGrantConfigurat
             is = new URL(Paths.get(fileUrl).toUri().toURL().toString()).openStream();
             this.configuration = (Configuration) jaxbUnmarshaller.unmarshal(is);
         } catch (Exception ex) {
-            ex.printStackTrace();
+            logger.error("Cannot find in folder" + current, ex);
-            System.out.println("Cannot find in folder" + current);
         } finally {
             try {
                 if (is != null) is.close();
             } catch (IOException e) {
-                System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
+                logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
             }
         }
         return this.configuration;

dmp-backend/web/src/main/java/eu/eudat/configurations/dynamicproject/DynamicProjectConfigurationDevelImpl.java

@@ -4,6 +4,8 @@ import eu.eudat.configurations.dynamicproject.entities.Configuration;
 import eu.eudat.configurations.dynamicproject.entities.Property;
 import eu.eudat.models.data.dynamicfields.Dependency;
 import eu.eudat.models.data.dynamicfields.DynamicField;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Profile;
 import org.springframework.core.env.Environment;
@@ -20,6 +22,7 @@ import java.util.List;
 @Service("dynamicProjectConfiguration")
 @Profile("devel")
 public class DynamicProjectConfigurationDevelImpl implements DynamicProjectConfiguration{
+	private static final Logger logger = LoggerFactory.getLogger(DynamicProjectConfigurationDevelImpl.class);
 
 	private Configuration configuration;
 	private List<DynamicField> fields;
@@ -34,7 +37,7 @@ public class DynamicProjectConfigurationDevelImpl implements DynamicProjectConfi
 	public Configuration getConfiguration() {
 		if (this.configuration != null) return this.configuration;
 		String fileUrl = this.environment.getProperty("configuration.dynamicProjectUrl");
-		System.out.println("Loaded also config file: " + fileUrl);
+		logger.info("Loaded also config file: " + fileUrl);
 		String current = null;
 		InputStream is = null;
 		try {
@@ -45,13 +48,12 @@ public class DynamicProjectConfigurationDevelImpl implements DynamicProjectConfi
 			is = new URL("file:///"+ current + "/web/src/main/resources/ProjectConfiguration.xml").openStream();
 			this.configuration = (Configuration) jaxbUnmarshaller.unmarshal(is);
 		} catch (Exception ex) {
-			ex.printStackTrace();
+			logger.error("Cannot find in folder" + current, ex);
-			System.out.println("Cannot find in folder" + current);
 		} finally {
 			try {
 				if (is != null) is.close();
 			} catch (IOException e) {
-				System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
+				logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
 			}
 		}
 		return this.configuration;

dmp-backend/web/src/main/java/eu/eudat/configurations/dynamicproject/DynamicProjectConfigurationProdImpl.java

@@ -4,6 +4,8 @@ import eu.eudat.configurations.dynamicproject.entities.Configuration;
 import eu.eudat.configurations.dynamicproject.entities.Property;
 import eu.eudat.models.data.dynamicfields.Dependency;
 import eu.eudat.models.data.dynamicfields.DynamicField;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Profile;
 import org.springframework.core.env.Environment;
@@ -21,6 +23,7 @@ import java.util.List;
 @Service("dynamicProjectConfiguration")
 @Profile({ "production", "staging" })
 public class DynamicProjectConfigurationProdImpl implements DynamicProjectConfiguration{
+	private static final Logger logger = LoggerFactory.getLogger(DynamicProjectConfigurationProdImpl.class);
 
 	private Configuration configuration;
 
@@ -37,7 +40,7 @@ public class DynamicProjectConfigurationProdImpl implements DynamicProjectConfig
 	public Configuration getConfiguration() {
 		if (this.configuration != null) return this.configuration;
 		String fileUrl = this.environment.getProperty("configuration.dynamicProjectUrl");
-		System.out.println("Loaded also config file: " + fileUrl);
+		logger.info("Loaded also config file: " + fileUrl);
 		String current = null;
 		InputStream is = null;
 		try {
@@ -48,13 +51,12 @@ public class DynamicProjectConfigurationProdImpl implements DynamicProjectConfig
 			is = new URL(Paths.get(fileUrl).toUri().toURL().toString()).openStream();
 			this.configuration = (Configuration) jaxbUnmarshaller.unmarshal(is);
 		} catch (Exception ex) {
-			ex.printStackTrace();
+			logger.error("Cannot find in folder" + current, ex);
-			System.out.println("Cannot find in folder" + current);
 		} finally {
 			try {
 				if (is != null) is.close();
 			} catch (IOException e) {
-				System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
+				logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
 			}
 		}
 		return this.configuration;

dmp-backend/web/src/main/java/eu/eudat/controllers/ContactEmail.java

@@ -5,6 +5,8 @@ import eu.eudat.models.data.ContactEmail.ContactEmailModel;
 import eu.eudat.models.data.helpers.responses.ResponseItem;
 import eu.eudat.models.data.security.Principal;
 import eu.eudat.types.ApiMessageCode;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;
@@ -15,6 +17,7 @@ import javax.transaction.Transactional;
 @CrossOrigin
 @RequestMapping(value = "api/contactEmail")
 public class ContactEmail {
+	private static final Logger logger = LoggerFactory.getLogger(ContactEmail.class);
 
 	private ContactEmailManager contactEmailManager;
 
@@ -31,7 +34,7 @@ public class ContactEmail {
 			this.contactEmailManager.sendContactEmail(contactEmailModel, principal);
 			return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem().status(ApiMessageCode.SUCCESS_MESSAGE));
 		} catch (Exception ex) {
-			ex.printStackTrace();
+			logger.error(ex.getMessage(), ex);
 			return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem().status(ApiMessageCode.ERROR_MESSAGE).message(ex.getMessage()));
 		}
 	}

dmp-backend/web/src/main/java/eu/eudat/controllers/DMPs.java

@@ -29,6 +29,8 @@ import eu.eudat.models.data.security.Principal;
 import eu.eudat.query.DMPQuery;
 import eu.eudat.types.ApiMessageCode;
 import eu.eudat.types.Authorities;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.env.Environment;
 import org.springframework.http.HttpHeaders;
@@ -55,6 +57,7 @@ import java.util.UUID;
 @CrossOrigin
 @RequestMapping(value = {"/api/dmps/"})
 public class DMPs extends BaseController {
+    private static final Logger logger = LoggerFactory.getLogger(DMPs.class);
 
     private DynamicGrantConfiguration dynamicGrantConfiguration;
     private Environment environment;
@@ -195,7 +198,7 @@ public class DMPs extends BaseController {
         String name = file.getName().substring(0, file.getName().length() - 5);
         File pdffile = datasetManager.convertToPDF(file, environment, name);
         InputStream resource = new FileInputStream(pdffile);
-        System.out.println("Mime Type of " + file.getName() + " is " +
+        logger.info("Mime Type of " + file.getName() + " is " +
                 new MimetypesFileTypeMap().getContentType(file));
         HttpHeaders responseHeaders = new HttpHeaders();
         responseHeaders.setContentLength(pdffile.length());
@@ -269,7 +272,7 @@ public class DMPs extends BaseController {
             String zenodoDOI = this.dataManagementPlanManager.createZenodoDoi(UUID.fromString(id), principal, configLoader);
             return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<String>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Successfully created DOI for Data Datamanagement Plan in question.").payload(zenodoDOI));
         } catch (Exception e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
             return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<String>().status(ApiMessageCode.ERROR_MESSAGE).message(e.getMessage()));
         }
     }

dmp-backend/web/src/main/java/eu/eudat/controllers/DatasetWizardController.java

@@ -19,6 +19,8 @@ import eu.eudat.models.data.security.Principal;
 import eu.eudat.models.data.user.composite.PagedDatasetProfile;
 import eu.eudat.types.ApiMessageCode;
 import org.apache.poi.util.IOUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.env.Environment;
 import org.springframework.http.HttpHeaders;
@@ -44,6 +46,7 @@ import static eu.eudat.types.Authorities.ANONYMOUS;
 @CrossOrigin
 @RequestMapping(value = {"api/datasetwizard"})
 public class DatasetWizardController extends BaseController {
+    private static final Logger logger = LoggerFactory.getLogger(DatasetWizardController.class);
 
     private Environment environment;
     private DatasetManager datasetManager;
@@ -191,7 +194,7 @@ public class DatasetWizardController extends BaseController {
                 return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem().status(ApiMessageCode.NO_MESSAGE).message("Import was unsuccessful."));
             }
         } catch (Exception e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
             return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem().status(ApiMessageCode.NO_MESSAGE).message("Import was unsuccessful."));
         }
     }

dmp-backend/web/src/main/java/eu/eudat/controllers/controllerhandler/ControllerErrorHandler.java

@@ -4,11 +4,12 @@ import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.ObjectWriter;
 import com.fasterxml.jackson.databind.SerializationFeature;
-import eu.eudat.core.logger.Logger;
 import eu.eudat.core.models.exception.ApiExceptionLoggingModel;
 import eu.eudat.models.data.helpers.responses.ResponseItem;
 import eu.eudat.models.data.security.Principal;
 import eu.eudat.types.ApiMessageCode;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpStatus;
 import org.springframework.web.bind.annotation.ControllerAdvice;
@@ -27,13 +28,14 @@ import java.util.Map;
 @ControllerAdvice
 @Priority(5)
 public class ControllerErrorHandler {
+    private static final Logger logger = LoggerFactory.getLogger(ControllerErrorHandler.class);
 
-    private Logger logger;
+//    private Logger logger;
 
-    @Autowired
+    /*@Autowired
     public ControllerErrorHandler(Logger logger) {
         this.logger = logger;
-    }
+    }*/
 
     @ExceptionHandler(Exception.class)
     @ResponseStatus(HttpStatus.BAD_REQUEST)
@@ -49,12 +51,11 @@ public class ControllerErrorHandler {
             exceptionMap.put("exception", json);
             apiExceptionLoggingModel.setData(ow.writeValueAsString(exceptionMap));
         } catch (JsonProcessingException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
         apiExceptionLoggingModel.setMessage(ex.getMessage());
         apiExceptionLoggingModel.setType(LoggingType.ERROR);
-        ex.printStackTrace();
+        logger.error(ex.getMessage(), ex);
-        this.logger.error(apiExceptionLoggingModel);
         return new ResponseItem<Exception>().message(ex.getMessage()).status(ApiMessageCode.DEFAULT_ERROR_MESSAGE);
     }
 }

dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java

@@ -50,6 +50,8 @@ import org.apache.poi.xwpf.usermodel.XWPFDocument;
 import org.apache.poi.xwpf.usermodel.XWPFParagraph;
 import org.apache.poi.xwpf.usermodel.XWPFRun;
 import org.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.env.Environment;
 import org.springframework.core.io.FileSystemResource;
@@ -76,6 +78,7 @@ import java.util.stream.Collectors;
 
 @Component
 public class DataManagementPlanManager {
+    private static final Logger logger = LoggerFactory.getLogger(DataManagementPlanManager.class);
 
     private ApiContext apiContext;
     private DatasetManager datasetManager;
@@ -309,7 +312,7 @@ public class DataManagementPlanManager {
                     try {
                         wordBuilder.build(document, pagedDatasetProfile, visibilityRuleService);
                     } catch (IOException e) {
-                        e.printStackTrace();
+                        logger.error(e.getMessage(), e);
                     }
                     // Page break at the end of the Dataset.
                     XWPFParagraph parBreakDataset = document.createParagraph();
@@ -975,7 +978,7 @@ public class DataManagementPlanManager {
         try {
             mapper.writeValue(file, rdaExportModel);
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
 
         InputStream resource = new FileInputStream(file);
@@ -1033,7 +1036,7 @@ public class DataManagementPlanManager {
                 DmpImportModel dmpImportModel = (DmpImportModel) jaxbUnmarshaller.unmarshal(in);
                 dataManagementPlans.add(dmpImportModel);
             } catch (IOException | JAXBException ex) {
-                ex.printStackTrace();
+                logger.error(ex.getMessage(), ex);
             }
             // TODO Iterate through the list of dataManagementPlans.
             // Creates new dataManagementPlan to fill it with the data model that was parsed from the xml.
@@ -1096,7 +1099,7 @@ public class DataManagementPlanManager {
 
             //createOrUpdate(apiContext, dm, principal);
 
-            System.out.println(dm);
+            logger.info(dm.toString());
         }
 
         return dataManagementPlans;

dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementProfileManager.java

@@ -21,6 +21,8 @@ import eu.eudat.models.data.listingmodels.DataManagementPlanProfileListingModel;
 import eu.eudat.models.data.security.Principal;
 import eu.eudat.queryable.QueryableList;
 import eu.eudat.logic.services.ApiContext;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Component;
@@ -43,6 +45,7 @@ import org.w3c.dom.Element;
  */
 @Component
 public class DataManagementProfileManager {
+	private static final Logger logger = LoggerFactory.getLogger(DataManagementProfileManager.class);
 
     private ApiContext apiContext;
     private DatabaseRepository databaseRepository;
@@ -93,7 +96,7 @@ public class DataManagementProfileManager {
     public ResponseEntity<byte[]> getDocument(DataManagementPlanProfileListingModel dmpProfile, String label) throws IllegalAccessException, IOException, InstantiationException {
         FileEnvelope envelope = getXmlDocument(dmpProfile, label);
         InputStream resource = new FileInputStream(envelope.getFile());
-        System.out.println("Mime Type of " + envelope.getFilename() + " is " +
+        logger.info("Mime Type of " + envelope.getFilename() + " is " +
                 new MimetypesFileTypeMap().getContentType(envelope.getFile()));
         HttpHeaders responseHeaders = new HttpHeaders();
         responseHeaders.setContentLength(envelope.getFile().length());
@@ -124,7 +127,7 @@ public class DataManagementProfileManager {
         try {
             return xmlBuilder.build(convert(multiPartFile));
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
         return null;
     }

dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetManager.java

@@ -36,6 +36,8 @@ import org.apache.poi.xwpf.usermodel.XWPFDocument;
 import org.apache.poi.xwpf.usermodel.XWPFParagraph;
 import org.apache.poi.xwpf.usermodel.XWPFRun;
 import org.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.env.Environment;
 import org.springframework.core.io.FileSystemResource;
@@ -73,6 +75,7 @@ import java.util.zip.ZipInputStream;
 
 @Component
 public class DatasetManager {
+    private static final Logger logger = LoggerFactory.getLogger(DatasetManager.class);
 
     private ApiContext apiContext;
     private DatabaseRepository databaseRepository;
@@ -544,7 +547,7 @@ public class DatasetManager {
     public ResponseEntity<byte[]> getDocument(String id, VisibilityRuleService visibilityRuleService, String contentType) throws IllegalAccessException, IOException, InstantiationException {
         FileEnvelope envelope = getXmlDocument(id, visibilityRuleService);
         InputStream resource = new FileInputStream(envelope.getFile());
-        System.out.println("Mime Type of " + envelope.getFilename() + " is " +
+        logger.info("Mime Type of " + envelope.getFilename() + " is " +
                 new MimetypesFileTypeMap().getContentType(envelope.getFile()));
         HttpHeaders responseHeaders = new HttpHeaders();
         responseHeaders.setContentLength(envelope.getFile().length());
@@ -574,7 +577,7 @@ public class DatasetManager {
             DatasetImportPagedDatasetProfile datasetImport = (DatasetImportPagedDatasetProfile) jaxbUnmarshaller.unmarshal(in);
             importModel = datasetImport;
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
 
         // Checks if XML datasetProfileId GroupId matches the one selected.
@@ -585,7 +588,7 @@ public class DatasetManager {
                 throw new Exception();
             }
         } catch (Exception e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
             return null;
         }
 

dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetProfileManager.java

@@ -22,6 +22,8 @@ import eu.eudat.models.data.externaldataset.ExternalAutocompleteFieldModel;
 import eu.eudat.models.data.helpers.common.DataTableData;
 import eu.eudat.queryable.QueryableList;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.*;
 import org.springframework.stereotype.Component;
@@ -41,6 +43,7 @@ import java.io.*;
 
 @Component
 public class DatasetProfileManager {
+    private static final Logger logger = LoggerFactory.getLogger(DatasetProfileManager.class);
 
     private ApiContext apiContext;
     private DatabaseRepository databaseRepository;
@@ -119,7 +122,7 @@ public class DatasetProfileManager {
     public ResponseEntity<byte[]> getDocument(eu.eudat.models.data.user.composite.DatasetProfile datasetProfile, String label) throws IllegalAccessException, IOException, InstantiationException {
         FileEnvelope envelope = getXmlDocument(datasetProfile, label);
         InputStream resource = new FileInputStream(envelope.getFile());
-        System.out.println("Mime Type of " + envelope.getFilename() + " is " +
+        logger.info("Mime Type of " + envelope.getFilename() + " is " +
                 new MimetypesFileTypeMap().getContentType(envelope.getFile()));
         HttpHeaders responseHeaders = new HttpHeaders();
         responseHeaders.setContentLength(envelope.getFile().length());
@@ -151,7 +154,7 @@ public class DatasetProfileManager {
         try {
             return xmlBuilder.build(convert(multiPartFile));
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
         return null;
     }

dmp-backend/web/src/main/java/eu/eudat/logic/managers/DocumentManager.java

@@ -13,6 +13,8 @@ import eu.eudat.models.data.user.composite.PagedDatasetProfile;
 import org.apache.commons.io.IOUtils;
 import org.apache.poi.xwpf.usermodel.XWPFDocument;
 import org.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.core.env.Environment;
 import org.springframework.core.io.FileSystemResource;
 import org.springframework.http.*;
@@ -36,6 +38,7 @@ import java.util.zip.ZipInputStream;
  */
 @Service
 public class DocumentManager {
+    private static final Logger logger = LoggerFactory.getLogger(DocumentManager.class);
 
     private ApiContext context;
     private DatasetManager datasetManager;
@@ -104,12 +107,12 @@ public class DocumentManager {
 
         Map mediaResult = new RestTemplate().getForObject(environment.getProperty("pdf.converter.url") +
                 "/api/v1/" + queueResult.get("id"), Map.class);
-        System.out.println("Status: " + mediaResult.get("status"));
+        logger.info("Status: " + mediaResult.get("status"));
         while (!mediaResult.get("status").equals("finished")) {
             Thread.sleep(500);
             mediaResult = new RestTemplate().getForObject(environment.getProperty("pdf.converter.url") +
                     "api/v1/" + queueResult.get("id"), Map.class);
-            System.out.println("Polling");
+            logger.info("Polling");
         }
         RestTemplate restTemplate = new RestTemplate();
         restTemplate.getMessageConverters().add(new ByteArrayHttpMessageConverter());

dmp-backend/web/src/main/java/eu/eudat/logic/proxy/config/configloaders/DevelConfigLoader.java

@@ -5,6 +5,8 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.logic.proxy.config.ExternalUrls;
 import eu.eudat.logic.security.customproviders.ConfigurableProvider.entities.ConfigurableProviders;
 import org.apache.poi.xwpf.usermodel.XWPFDocument;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Profile;
 import org.springframework.core.env.Environment;
@@ -33,6 +35,7 @@ import java.util.stream.Collectors;
 @Service("configLoader")
 @Profile("devel")
 public class DevelConfigLoader implements ConfigLoader {
+    private static final Logger logger = LoggerFactory.getLogger(DevelConfigLoader.class);
 
     private ExternalUrls externalUrls;
     private List<String> rdaProperties;
@@ -45,7 +48,7 @@ public class DevelConfigLoader implements ConfigLoader {
 
     private void setExternalUrls() {
         String fileUrl = this.environment.getProperty("configuration.externalUrls");
-        System.out.println("Loaded also config file: " + fileUrl);
+        logger.info("Loaded also config file: " + fileUrl);
         InputStream is = null;
         try {
             JAXBContext jaxbContext = JAXBContext.newInstance(ExternalUrls.class);
@@ -53,13 +56,12 @@ public class DevelConfigLoader implements ConfigLoader {
             is = getClass().getClassLoader().getResource(fileUrl).openStream();
             externalUrls = (ExternalUrls) jaxbUnmarshaller.unmarshal(is);
         } catch (Exception ex) {
-            ex.printStackTrace();
+           logger.error("Cannot find resource in classpath", ex);
-            System.err.println("Cannot find resource in classpath");
         } finally {
             try {
                 if (is != null) is.close();
             } catch (IOException | NullPointerException e) {
-                System.err.println("Warning: Could not close a stream after reading from file: " + fileUrl);
+                logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
             }
         }
     }
@@ -77,7 +79,7 @@ public class DevelConfigLoader implements ConfigLoader {
             }
             reader.close();
         } catch (IOException | NullPointerException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
 
         rdaProperties = rdaList;
@@ -90,12 +92,12 @@ public class DevelConfigLoader implements ConfigLoader {
             is = getClass().getClassLoader().getResource(filePath).openStream();
             this.document = new XWPFDocument(is);
         } catch (IOException | NullPointerException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         } finally {
             try {
                 if (is != null) is.close();
             } catch (IOException e) {
-                System.err.println("Warning: Could not close a stream after reading from file: " + filePath);
+                logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
             }
         }
     }
@@ -108,19 +110,19 @@ public class DevelConfigLoader implements ConfigLoader {
             ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
             this.configurableProviders = mapper.readValue(is, ConfigurableProviders.class);
         } catch (IOException | NullPointerException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         } finally {
             try {
                 if (is != null) is.close();
             } catch (IOException e) {
-                System.err.println("Warning: Could not close a stream after reading from file: " + filePath);
+               logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
             }
         }
     }
 
     private void setKeyToSourceMap() {
         String filePath = this.environment.getProperty("configuration.externalUrls");
-        System.out.println("Loaded also config file: " + filePath);
+        logger.info("Loaded also config file: " + filePath);
         Document doc = getXmlDocumentFromFilePath(filePath);
         if (doc == null) {
             this.keyToSourceMap = null;
@@ -177,14 +179,14 @@ public class DevelConfigLoader implements ConfigLoader {
             doc = documentBuilder.parse(is);
             return doc;
         } catch (IOException | ParserConfigurationException | SAXException | NullPointerException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         } finally {
             try {
                 if (is != null) {
                     is.close();
                 }
             } catch (IOException e) {
-                System.out.println("Warning: Could not close a stream after reading from file: " + filePath);
+               logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
             }
         }
         return null;
@@ -197,7 +199,7 @@ public class DevelConfigLoader implements ConfigLoader {
         try {
             nodeList = (NodeList) xPath.compile(expression).evaluate(doc, XPathConstants.NODESET);
         } catch (XPathExpressionException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
         if (nodeList != null) {
             for (int i = 0; i < nodeList.getLength(); i++) {

dmp-backend/web/src/main/java/eu/eudat/logic/proxy/config/configloaders/ProductionConfigLoader.java

@@ -4,6 +4,8 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.logic.proxy.config.ExternalUrls;
 import eu.eudat.logic.security.customproviders.ConfigurableProvider.entities.ConfigurableProviders;
 import org.apache.poi.xwpf.usermodel.XWPFDocument;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Profile;
 import org.springframework.core.env.Environment;
@@ -34,6 +36,7 @@ import java.util.stream.Collectors;
 @Service("configLoader")
 @Profile({ "production", "staging" })
 public class ProductionConfigLoader implements ConfigLoader {
+    private static final Logger logger = LoggerFactory.getLogger(ProductionConfigLoader.class);
 
     private ExternalUrls externalUrls;
     private List<String> rdaProperties;
@@ -46,7 +49,7 @@ public class ProductionConfigLoader implements ConfigLoader {
 
     private void setExternalUrls() {
         String fileUrl = this.environment.getProperty("configuration.externalUrls");
-        System.out.println("Loaded also config file: " + fileUrl);
+        logger.info("Loaded also config file: " + fileUrl);
         String current = null;
         InputStream is = null;
         try {
@@ -57,13 +60,12 @@ public class ProductionConfigLoader implements ConfigLoader {
             externalUrls = (ExternalUrls) jaxbUnmarshaller.unmarshal(is);
 
         } catch (Exception ex) {
-            ex.printStackTrace();
+            logger.error("Cannot find in folder" + current, ex);
-            System.out.println("Cannot find in folder" + current);
         } finally {
             try {
                 if (is != null) is.close();
             } catch (IOException e) {
-                System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
+                logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
             }
         }
     }
@@ -81,7 +83,7 @@ public class ProductionConfigLoader implements ConfigLoader {
             }
             reader.close();
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
 
         rdaProperties = rdaList;
@@ -94,12 +96,12 @@ public class ProductionConfigLoader implements ConfigLoader {
             is = new URL(Paths.get(filePath).toUri().toURL().toString()).openStream();
             this.document = new XWPFDocument(is);
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         } finally {
             try {
                 if (is != null) is.close();
             } catch (IOException e) {
-                System.out.println("Warning: Could not close a stream after reading from file: " + filePath);
+                logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
             }
         }
     }
@@ -117,18 +119,18 @@ public class ProductionConfigLoader implements ConfigLoader {
                 this.configurableProviders = new ConfigurableProviders();
             }
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         } finally {
             try {
                 if (is != null) is.close();
             } catch (IOException e) {
-                System.out.println("Warning: Could not close a stream after reading from file: " + filePath);
+               logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
             }
         }
     }
     private void setKeyToSourceMap() {
         String filePath = this.environment.getProperty("configuration.externalUrls");
-        System.out.println("Loaded also config file: " + filePath);
+        logger.info("Loaded also config file: " + filePath);
         Document doc = getXmlDocumentFromFilePath(filePath);
         if (doc == null) {
             this.keyToSourceMap = null;
@@ -183,14 +185,14 @@ public class ProductionConfigLoader implements ConfigLoader {
             doc = documentBuilder.parse(is);
             return doc;
         } catch (IOException | ParserConfigurationException | SAXException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         } finally {
             try {
                 if (is != null) {
                     is.close();
                 }
             } catch (IOException e) {
-                System.out.println("Warning: Could not close a stream after reading from file: " + filePath);
+                logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
             }
         }
         return null;
@@ -203,7 +205,7 @@ public class ProductionConfigLoader implements ConfigLoader {
         try {
             nodeList = (NodeList) xPath.compile(expression).evaluate(doc, XPathConstants.NODESET);
         } catch (XPathExpressionException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
         if (nodeList != null) {
             for (int i = 0; i < nodeList.getLength(); i++) {

dmp-backend/web/src/main/java/eu/eudat/logic/proxy/fetching/RemoteFetcher.java

@@ -8,6 +8,8 @@ import eu.eudat.logic.proxy.config.*;
 import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
 import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
 import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Service;
@@ -25,6 +27,7 @@ import java.util.stream.Collectors;
 
 @Service
 public class RemoteFetcher {
+    private static final Logger logger = LoggerFactory.getLogger(RemoteFetcher.class);
 
     private ConfigLoader configLoader;
 
@@ -163,7 +166,7 @@ public class RemoteFetcher {
             try {
                 funderId = URLEncoder.encode(externalUrlCriteria.getFunderId(), "UTF-8");
             } catch (UnsupportedEncodingException e) {
-                e.printStackTrace();
+                logger.error(e.getMessage(), e);
             }
             completedPath = completedPath.replace("{funderId}", funderId);
         }
@@ -251,13 +254,13 @@ public class RemoteFetcher {
                 return results;
             }
         } catch (MalformedURLException e1) {
-            e1.printStackTrace();
+            logger.error(e1.getMessage(), e1);
         } //maybe print smth...
         catch (IOException e2) {
-            e2.printStackTrace();
+            logger.error(e2.getMessage(), e2);
         } //maybe print smth...
         catch (Exception exception) {
-            exception.printStackTrace();
+            logger.error(exception.getMessage(), exception);
         } //maybe print smth...
         finally {
         }
@@ -273,7 +276,7 @@ public class RemoteFetcher {
             internalResults = mapper.readValue(new File(filePath), new TypeReference<List<Map<String, Object>>>(){});
             return searchListMap(internalResults, query);
         } catch (Exception e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
             return new LinkedList<>();
         }
     }

dmp-backend/web/src/main/java/eu/eudat/logic/security/CustomAuthenticationProvider.java

@@ -6,6 +6,8 @@ import eu.eudat.exceptions.security.UnauthorisedException;
 import eu.eudat.models.data.login.LoginInfo;
 import eu.eudat.models.data.security.Principal;
 import eu.eudat.logic.security.validators.TokenValidatorFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
@@ -14,6 +16,7 @@ import java.security.GeneralSecurityException;
 
 @Component
 public class CustomAuthenticationProvider {
+    private static final Logger logger = LoggerFactory.getLogger(CustomAuthenticationProvider.class);
 
 
     @Autowired
@@ -25,14 +28,13 @@ public class CustomAuthenticationProvider {
             Principal principal = this.tokenValidatorFactory.getProvider(credentials.getProvider()).validateToken(credentials);
             return principal;
         } catch (NonValidTokenException e) {
-            e.printStackTrace();
+            logger.error("Could not validate a user by his token! Reason: " + e.getMessage(), e);
-            System.out.println("Could not validate a user by his token! Reason: " + e.getMessage());
             throw new UnauthorisedException("Token validation failed - Not a valid token");
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
             throw new UnauthorisedException("IO Exeption");
         } catch (NullEmailException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
             throw new NullEmailException();
         }
     }

dmp-backend/web/src/main/java/eu/eudat/logic/services/helpers/FileStorageServiceImpl.java

@@ -2,6 +2,8 @@ package eu.eudat.logic.services.helpers;
 
 import eu.eudat.exceptions.files.TempFileNotFoundException;
 import eu.eudat.models.data.files.ContentFile;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.env.Environment;
 import org.springframework.core.io.Resource;
@@ -22,6 +24,7 @@ import java.util.UUID;
  */
 @Service("fileStorageService")
 public class FileStorageServiceImpl implements FileStorageService {
+    private static final Logger logger = LoggerFactory.getLogger(FileStorageServiceImpl.class);
 
     private Environment environment;
 
@@ -68,7 +71,7 @@ public class FileStorageServiceImpl implements FileStorageService {
                 Files.createDirectory(Paths.get(environment.getProperty("files.storage.final")));
             }
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
     }
 

dmp-backend/web/src/main/java/eu/eudat/logic/services/operations/authentication/AbstractAuthenticationService.java

@@ -15,12 +15,15 @@ import eu.eudat.models.data.loginprovider.LoginProviderUser;
 import eu.eudat.models.data.security.Principal;
 import eu.eudat.types.Authorities;
 import org.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.core.env.Environment;
 import org.springframework.transaction.annotation.Transactional;
 
 import java.util.*;
 
 public abstract class AbstractAuthenticationService implements AuthenticationService {
+	private static final Logger logger = LoggerFactory.getLogger(AbstractAuthenticationService.class);
 
 	protected ApiContext apiContext;
 	protected Environment environment;
@@ -86,7 +89,7 @@ public abstract class AbstractAuthenticationService implements AuthenticationSer
 			try {
 				credential = this.autoCreateUser(credentials.getUsername(), credentials.getSecret());
 			} catch (Exception e) {
-				e.printStackTrace();
+				logger.error(e.getMessage(), e);
 				return null;
 			}
 		}

dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/ConfirmationEmailServiceImpl.java

@@ -1,9 +1,10 @@
 package eu.eudat.logic.services.utilities;
 
-import eu.eudat.core.logger.Logger;
 import eu.eudat.data.dao.entities.LoginConfirmationEmailDao;
 import eu.eudat.data.entities.LoginConfirmationEmail;
 import eu.eudat.models.data.mail.SimpleMail;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.core.env.Environment;
 import org.springframework.stereotype.Service;
 
@@ -13,11 +14,12 @@ import java.util.concurrent.CompletableFuture;
 
 @Service("ConfirmationEmailService")
 public class ConfirmationEmailServiceImpl implements ConfirmationEmailService {
-	private Logger logger;
+	private static final Logger logger = LoggerFactory.getLogger(ConfirmationEmailServiceImpl.class);
+	//private Logger logger;
 	private Environment environment;
 
-	public ConfirmationEmailServiceImpl(Logger logger, Environment environment) {
+	public ConfirmationEmailServiceImpl(/*Logger logger,*/ Environment environment) {
-		this.logger = logger;
+//		this.logger = logger;
 		this.environment = environment;
 	}
 
@@ -48,8 +50,7 @@ public class ConfirmationEmailServiceImpl implements ConfirmationEmailService {
 			try {
 				mailService.sendSimpleMail(mail);
 			} catch (Exception ex) {
-				ex.printStackTrace();
+				logger.error(ex.getMessage(), ex);
-				this.logger.error(ex, ex.getMessage());
 			}
 		});
 	}

dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/InvitationServiceImpl.java

@@ -1,6 +1,5 @@
 package eu.eudat.logic.services.utilities;
 
-import eu.eudat.core.logger.Logger;
 import eu.eudat.core.models.exception.ApiExceptionLoggingModel;
 import eu.eudat.data.dao.entities.DMPDao;
 import eu.eudat.data.dao.entities.InvitationDao;
@@ -8,6 +7,8 @@ import eu.eudat.data.entities.DMP;
 import eu.eudat.data.entities.Invitation;
 import eu.eudat.data.entities.UserInfo;
 import eu.eudat.models.data.mail.SimpleMail;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.env.Environment;
 import org.springframework.http.HttpStatus;
@@ -25,13 +26,13 @@ import java.util.stream.Collectors;
 
 @Service("invitationService")
 public class InvitationServiceImpl implements InvitationService {
-
+    private static final Logger logger = LoggerFactory.getLogger(InvitationServiceImpl.class);
-    private Logger logger;
+//    private Logger logger;
     private Environment environment;
 
     @Autowired
-    public InvitationServiceImpl(Logger logger, Environment environment) {
+    public InvitationServiceImpl(/*Logger logger,*/ Environment environment) {
-        this.logger = logger;
+//        this.logger = logger;
         this.environment = environment;
     }
 
@@ -75,8 +76,7 @@ public class InvitationServiceImpl implements InvitationService {
             try {
                 mailService.sendSimpleMail(mail);
             } catch (Exception ex) {
-                ex.printStackTrace();
+                logger.error(ex.getMessage(), ex);
-                this.logger.error(ex, ex.getMessage());
             }
         });
     }

dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/MailServiceImpl.java

@@ -2,6 +2,8 @@ package eu.eudat.logic.services.utilities;
 
 import eu.eudat.models.data.mail.SimpleMail;
 import org.apache.commons.io.IOUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
 import org.springframework.core.env.Environment;
@@ -17,6 +19,7 @@ import java.io.*;
 
 @Service("mailService")
 public class MailServiceImpl implements MailService {
+    private static final Logger logger = LoggerFactory.getLogger(MailServiceImpl.class);
 
     private Environment env;
 
@@ -54,7 +57,7 @@ public class MailServiceImpl implements MailService {
             IOUtils.copy(inputStream, writer, "UTF-8");
             return writer.toString();
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
         return "";
     }

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/builders/ModelBuilder.java

@@ -5,6 +5,8 @@ import eu.eudat.models.data.components.commons.datafield.*;
 import eu.eudat.models.data.entities.xmlmodels.modeldefinition.DatabaseModelDefinition;
 import eu.eudat.logic.utilities.interfaces.ModelDefinition;
 import eu.eudat.logic.utilities.interfaces.ViewStyleDefinition;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.w3c.dom.Element;
 
 import java.util.LinkedList;
@@ -12,15 +14,16 @@ import java.util.List;
 import java.util.Map;
 
 public class ModelBuilder {
+    private static final Logger logger = LoggerFactory.getLogger(ModelBuilder.class);
     public <U extends ModelDefinition<T>, T extends DatabaseModelDefinition> List<T> toModelDefinition(List<U> items, Class<T> clazz) {
         List<T> list = new LinkedList<T>();
         for (U item : items) {
             try {
                 list.add(item.toDatabaseDefinition(clazz.newInstance()));
             } catch (InstantiationException e) {
-                e.printStackTrace();
+                logger.error(e.getMessage(), e);
             } catch (IllegalAccessException e) {
-                e.printStackTrace();
+                logger.error(e.getMessage(), e);
             }
         }
         return list;
@@ -32,9 +35,9 @@ public class ModelBuilder {
             try {
                 list.add(item.toDatabaseDefinition(clazz.newInstance()));
             } catch (InstantiationException e) {
-                e.printStackTrace();
+                logger.error(e.getMessage(), e);
             } catch (IllegalAccessException e) {
-                e.printStackTrace();
+                logger.error(e.getMessage(), e);
             }
         }
         return list;
@@ -48,9 +51,9 @@ public class ModelBuilder {
                 modelItem.fromDatabaseDefinition(item);
                 list.add(modelItem);
             } catch (InstantiationException e) {
-                e.printStackTrace();
+                logger.error(e.getMessage(), e);
             } catch (IllegalAccessException e) {
-                e.printStackTrace();
+                logger.error(e.getMessage(), e);
             }
         }
         return list;

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/builders/XmlBuilder.java

@@ -1,5 +1,7 @@
 package eu.eudat.logic.utilities.builders;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.Node;
@@ -21,6 +23,7 @@ import java.io.StringWriter;
 
 
 public class XmlBuilder {
+    private static final Logger logger = LoggerFactory.getLogger(XmlBuilder.class);
 
     public static Document getDocument() {
         DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
@@ -31,7 +34,7 @@ public class XmlBuilder {
             return doc;
         } catch (ParserConfigurationException e) {
             // TODO Auto-generated catch block
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
             return null;
         }
     }
@@ -48,7 +51,7 @@ public class XmlBuilder {
             return writer.toString();
         } catch (TransformerException e) {
             // TODO Auto-generated catch block
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
             return null;
         }
     }
@@ -63,7 +66,7 @@ public class XmlBuilder {
             return doc;
         } catch (ParserConfigurationException | SAXException | IOException e) {
             // TODO Auto-generated catch block
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
             return null;
         }
     }

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/word/WordBuilder.java

@@ -19,6 +19,8 @@ import org.openxmlformats.schemas.wordprocessingml.x2006.main.CTAbstractNum;
 import org.openxmlformats.schemas.wordprocessingml.x2006.main.CTDecimalNumber;
 import org.openxmlformats.schemas.wordprocessingml.x2006.main.CTLvl;
 import org.openxmlformats.schemas.wordprocessingml.x2006.main.STNumberFormat;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.math.BigInteger;
@@ -27,6 +29,7 @@ import java.util.List;
 import java.util.Map;
 
 public class WordBuilder {
+    private static final Logger logger = LoggerFactory.getLogger(WordBuilder.class);
 
     private Map<ParagraphStyle, ApplierWithValue<XWPFDocument, String, XWPFParagraph>> options = new HashMap<>();
     private CTAbstractNum cTAbstractNum;
@@ -186,7 +189,7 @@ public class WordBuilder {
                         CTDecimalNumber number = paragraph.getCTP().getPPr().getNumPr().addNewIlvl();
                         number.setVal(BigInteger.valueOf(indent));
                     } catch (IOException e) {
-                        e.printStackTrace();
+                        logger.error(e.getMessage(), e);
                     }
                 }
             }

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/xml/datasetProfileXml/ImportXmlBuilderDatasetProfile.java

@@ -1,5 +1,7 @@
 package eu.eudat.logic.utilities.documents.xml.datasetProfileXml;
 import eu.eudat.logic.utilities.documents.xml.datasetProfileXml.datasetProfileModel.DatasetProfile;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
@@ -7,6 +9,7 @@ import javax.xml.bind.Unmarshaller;
 import java.io.*;
 
 public class ImportXmlBuilderDatasetProfile {
+    private static final Logger logger = LoggerFactory.getLogger(ImportXmlBuilderDatasetProfile.class);
 
     public DatasetProfile build(File xmlFile) throws IOException {
         DatasetProfile datasetProfile = new DatasetProfile();
@@ -16,7 +19,7 @@ public class ImportXmlBuilderDatasetProfile {
             Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
             datasetProfile = (DatasetProfile) unmarshaller.unmarshal(xmlFile);
         } catch (JAXBException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
 
         return datasetProfile;

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/xml/dmpXml/ImportXmlBuilderDmpProfile.java

@@ -1,6 +1,8 @@
 package eu.eudat.logic.utilities.documents.xml.dmpXml;
 
 import eu.eudat.logic.utilities.documents.xml.dmpXml.dmpProfileModel.DmpProfile;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
@@ -9,6 +11,7 @@ import java.io.File;
 import java.io.IOException;
 
 public class ImportXmlBuilderDmpProfile {
+    private static final Logger logger = LoggerFactory.getLogger(ImportXmlBuilderDmpProfile.class);
 
     public DmpProfile build(File xmlFile) throws IOException {
         DmpProfile dmpProfile = new DmpProfile();
@@ -18,7 +21,7 @@ public class ImportXmlBuilderDmpProfile {
             Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
             dmpProfile = (DmpProfile) unmarshaller.unmarshal(xmlFile);
         } catch (JAXBException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
         }
 
         return dmpProfile;

dmp-backend/web/src/main/java/eu/eudat/models/HintedModelFactory.java

@@ -1,16 +1,20 @@
 package eu.eudat.models;
 
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 public class HintedModelFactory {
+    private static final Logger logger = LoggerFactory.getLogger(HintedModelFactory.class);
 
     public static <T extends DataModel> String getHint(Class<T> clazz) {
         try {
             return clazz.newInstance().getHint();
         } catch (InstantiationException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
             return null;
         } catch (IllegalAccessException e) {
-            e.printStackTrace();
+            logger.error(e.getMessage(), e);
             return null;
         }
     }

dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/Researcher.java

@@ -2,11 +2,14 @@ package eu.eudat.models.data.dmp;
 
 import eu.eudat.models.DataModel;
 import eu.eudat.logic.utilities.helpers.LabelGenerator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.util.Date;
 import java.util.UUID;
 
 public class Researcher implements DataModel<eu.eudat.data.entities.Researcher, Researcher>, LabelGenerator {
+    private static final Logger logger = LoggerFactory.getLogger(Researcher.class);
     private String label;
     private String name;
     private String id;
@@ -104,7 +107,7 @@ public class Researcher implements DataModel<eu.eudat.data.entities.Researcher,
             try {
                 throw new Exception("Researcher has no key value");
             } catch (Exception e) {
-                e.printStackTrace();
+                logger.error(e.getMessage(), e);
             }
         }
 

dmp-backend/web/src/main/java/eu/eudat/models/data/external/ProjectsExternalSourcesModel.java

@@ -2,12 +2,15 @@ package eu.eudat.models.data.external;
 
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.util.List;
 import java.util.Map;
 
 public class ProjectsExternalSourcesModel extends ExternalListingItem<ProjectsExternalSourcesModel> {
+	private static final Logger logger = LoggerFactory.getLogger(ProjectsExternalSourcesModel.class);
 	private static final ObjectMapper mapper = new ObjectMapper();
 
 	@Override
@@ -61,7 +64,7 @@ public class ProjectsExternalSourcesModel extends ExternalListingItem<ProjectsEx
 				this.add(model);
 
 			} catch (IOException e) {
-				e.printStackTrace();
+				logger.error(e.getMessage(), e);
 			}
 		}
 		return this;

dmp-backend/web/src/main/java/eu/eudat/models/data/rda/DatasetRDAExportModel.java

@@ -9,6 +9,8 @@ import eu.eudat.logic.managers.DatasetManager;
 import eu.eudat.logic.utilities.builders.XmlBuilder;
 import org.json.JSONArray;
 import org.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
@@ -20,6 +22,7 @@ import java.util.*;
 import static java.util.stream.Collectors.groupingBy;
 
 public class DatasetRDAExportModel {
+	private static final Logger logger = LoggerFactory.getLogger(DatasetRDAExportModel.class);
 
 	private static final ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 	private Map<String, String> multiplicityIdToFieldSetId = new HashMap<>();
@@ -165,7 +168,7 @@ public class DatasetRDAExportModel {
 			String jsonResult = mapper.writeValueAsString(datasetManager.getSingle(dataset.getId().toString()).getDatasetProfileDefinition());
 			datasetDescriptionJson = new JSONObject(jsonResult);
 		} catch (JsonProcessingException e) {
-			e.printStackTrace();
+			logger.error(e.getMessage(), e);
 		}
 		setMultiplicityIdToFieldSetId(datasetDescriptionJson);
 
@@ -461,7 +464,7 @@ public class DatasetRDAExportModel {
 				valuesList.add(node.getNodeValue());
 			}
 		} catch (XPathExpressionException e) {
-			e.printStackTrace();
+			logger.error(e.getMessage(), e);
 		}
 
 		return valuesList;