Merge branch 'master' of https://github.com/DSpace/DSpace into DS-3904

Dockerfile.jdk8

@@ -1,5 +1,12 @@
 # This image will be published as dspace/dspace
 # See https://dspace-labs.github.io/DSpace-Docker-Images/ for usage details
+# 
+# This version is JDK8 compatible
+# - tomcat:8-jre8
+# - ANT 1.10.5
+# - maven:latest
+# - note: 
+# - default tag for branch: dspace/dspace: dspace/dspace:dspace-7_x-jdk8
 
 # Step 1 - Run Maven Build
 FROM maven as build
@@ -12,7 +19,7 @@ COPY dspace/src/main/docker/local.cfg /app/local.cfg
 RUN mvn package
 
 # Step 2 - Run Ant Deploy
-FROM tomcat:8 as ant_build
+FROM tomcat:8-jre8 as ant_build
 ARG TARGET_DIR=dspace-installer
 COPY --from=build /app /dspace-src
 WORKDIR /dspace-src/dspace/target/${TARGET_DIR}
@@ -29,7 +36,7 @@ RUN ant update_configs update_code update_webapps update_solr_indexes
 
 # Step 3 - Run tomcat
 # Create a new tomcat image that does not retain the the build directory contents
-FROM tomcat:8
+FROM tomcat:8-jre8
 COPY --from=ant_build /dspace /dspace
 EXPOSE 8080 8009
 

Dockerfile.jdk8-test

@@ -0,0 +1,64 @@
+# This image will be published as dspace/dspace
+# See https://dspace-labs.github.io/DSpace-Docker-Images/ for usage details
+# 
+# This version is JDK8 compatible
+# - tomcat:8-jre8
+# - ANT 1.10.5
+# - maven:latest
+# - note: expose /solr to any host; provide /rest over http
+# - default tag for branch: dspace/dspace: dspace/dspace:dspace-7_x-jdk8-test
+
+# Step 1 - Run Maven Build
+FROM maven as build
+WORKDIR /app
+
+# Copy the DSpace source code into the workdir (excluding .dockerignore contents)
+ADD . /app/
+COPY dspace/src/main/docker/local.cfg /app/local.cfg
+
+# Provide web.xml overrides to make webapps easier to test
+COPY dspace/src/main/docker/test/solr_web.xml /app/dspace-solr/src/main/webapp/WEB-INF/web.xml
+COPY dspace/src/main/docker/test/rest_web.xml /app/dspace-rest/src/main/webapp/WEB-INF/web.xml
+
+RUN mvn package
+
+# Step 2 - Run Ant Deploy
+FROM tomcat:8-jre8 as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /app /dspace-src
+WORKDIR /dspace-src/dspace/target/${TARGET_DIR}
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.10.5
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+
+RUN mkdir $ANT_HOME && \
+    wget -qO- "https://www.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
+
+RUN ant update_configs update_code update_webapps update_solr_indexes
+
+# Step 3 - Run tomcat
+# Create a new tomcat image that does not retain the the build directory contents
+FROM tomcat:8-jre8
+COPY --from=ant_build /dspace /dspace
+EXPOSE 8080 8009
+
+# Ant will be embedded in the final container to allow additional deployments
+ENV ANT_VERSION 1.10.5
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+
+RUN mkdir $ANT_HOME && \
+    wget -qO- "https://www.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
+
+ENV DSPACE_INSTALL=/dspace
+ENV JAVA_OPTS=-Xmx2000m
+
+RUN ln -s $DSPACE_INSTALL/webapps/solr          /usr/local/tomcat/webapps/solr    && \
+    ln -s $DSPACE_INSTALL/webapps/spring-rest   /usr/local/tomcat/webapps/spring-rest   && \
+    ln -s $DSPACE_INSTALL/webapps/rest          /usr/local/tomcat/webapps/rest    && \
+    ln -s $DSPACE_INSTALL/webapps/oai           /usr/local/tomcat/webapps/oai     && \
+    ln -s $DSPACE_INSTALL/webapps/rdf           /usr/local/tomcat/webapps/rdf     && \
+    ln -s $DSPACE_INSTALL/webapps/sword         /usr/local/tomcat/webapps/sword   && \
+    ln -s $DSPACE_INSTALL/webapps/swordv2       /usr/local/tomcat/webapps/swordv2

README.md

@@ -40,6 +40,9 @@ Please be aware that, as a Java web application, DSpace requires a database (Pos
 and a servlet container (usually Tomcat) in order to function.
 More information about these and all other prerequisites can be found in the Installation instructions above.
 
+## Dockerfile Usage
+See the [DSpace Docker Tutorial](https://dspace-labs.github.io/DSpace-Docker-Images/).
+
 ## Contributing
 
 DSpace is a community built and supported project. We do not have a centralized development or support team, 

dspace-api/pom.xml

@@ -351,6 +351,24 @@
             <groupId>org.apache.jena</groupId>
             <artifactId>apache-jena-libs</artifactId>
             <type>pom</type>
+            <exclusions>
+                <exclusion>
+                    <groupId>com.fasterxml.jackson.core</groupId>
+                    <artifactId>jackson-core</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>com.fasterxml.jackson.core</groupId>
+                    <artifactId>jackson-databind</artifactId>
+	        </exclusion>
+		<exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>commons-cli</groupId>
@@ -364,10 +382,6 @@
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-collections4</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-collections4</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-dbcp2</artifactId>
@@ -382,8 +396,8 @@
             <artifactId>commons-io</artifactId>
         </dependency>
         <dependency>
-            <groupId>commons-lang</groupId>
+            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-lang</artifactId>
+            <artifactId>commons-lang3</artifactId>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
@@ -399,7 +413,7 @@
         </dependency>
         <dependency>
             <groupId>javax.servlet</groupId>
-            <artifactId>servlet-api</artifactId>
+            <artifactId>javax.servlet-api</artifactId>
             <scope>provided</scope>
         </dependency>
         <dependency>
@@ -417,8 +431,16 @@
             <artifactId>jdom</artifactId>
         </dependency>
         <dependency>
-            <groupId>log4j</groupId>
+            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j</artifactId>
+            <artifactId>log4j-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-1.2-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-core</artifactId>
         </dependency>
         <dependency>
             <groupId>oro</groupId>
@@ -530,6 +552,10 @@
                 <exclusion>
                     <groupId>org.mockito</groupId>
                     <artifactId>mockito-core</artifactId>
+	        </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
                 </exclusion>
             </exclusions>
         </dependency>
@@ -547,6 +573,10 @@
                 <exclusion>
                     <groupId>org.mockito</groupId>
                     <artifactId>mockito-core</artifactId>
+	        </exclusion>
+		<exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
                 </exclusion>
             </exclusions>
         </dependency>
@@ -575,8 +605,8 @@
         </dependency>
 
         <dependency>
-            <groupId>commons-configuration</groupId>
+            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-configuration</artifactId>
+            <artifactId>commons-configuration2</artifactId>
         </dependency>
         <dependency>
             <groupId>com.maxmind.geoip2</groupId>
@@ -615,7 +645,6 @@
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>
-            <version>19.0</version>
         </dependency>
 
 

dspace-api/src/main/java/org/dspace/administer/CreateAdministrator.java

@@ -15,7 +15,7 @@ import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.PosixParser;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.I18nUtil;

dspace-api/src/main/java/org/dspace/administer/RegistryLoader.java

@@ -17,7 +17,7 @@ import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.apache.xpath.XPathAPI;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.BitstreamFormat;
@@ -47,7 +47,7 @@ public class RegistryLoader {
     /**
      * log4j category
      */
-    private static Logger log = Logger.getLogger(RegistryLoader.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(RegistryLoader.class);
 
     protected static BitstreamFormatService bitstreamFormatService = ContentServiceFactory.getInstance()
                                                                                           .getBitstreamFormatService();

dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImport.java

@@ -25,8 +25,8 @@ import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.cli.PosixParser;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authority.AuthorityValue;
 import org.dspace.authority.factory.AuthorityServiceFactory;
 import org.dspace.authority.service.AuthorityValueService;
@@ -92,7 +92,7 @@ public class MetadataImport {
     /**
      * Logger
      */
-    protected static final Logger log = Logger.getLogger(MetadataImport.class);
+    protected static final Logger log = org.apache.logging.log4j.LogManager.getLogger(MetadataImport.class);
 
     protected final AuthorityValueService authorityValueService;
 

dspace-api/src/main/java/org/dspace/app/checker/ChecksumChecker.java

@@ -23,7 +23,8 @@ import org.apache.commons.cli.OptionBuilder;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.cli.PosixParser;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.checker.BitstreamDispatcher;
 import org.dspace.checker.CheckerCommand;
 import org.dspace.checker.HandleDispatcher;
@@ -48,7 +49,7 @@ import org.dspace.core.Utils;
  * @author Nathan Sarr
  */
 public final class ChecksumChecker {
-    private static final Logger LOG = Logger.getLogger(ChecksumChecker.class);
+    private static final Logger LOG = LogManager.getLogger(ChecksumChecker.class);
 
     private static final BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();
 

dspace-api/src/main/java/org/dspace/app/itemexport/ItemExportServiceImpl.java

@@ -32,8 +32,8 @@ import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
 import javax.mail.MessagingException;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.itemexport.service.ItemExportService;
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
@@ -98,7 +98,7 @@ public class ItemExportServiceImpl implements ItemExportService {
     /**
      * log4j logger
      */
-    private Logger log = Logger.getLogger(ItemExportServiceImpl.class);
+    private Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemExportServiceImpl.class);
 
     protected ItemExportServiceImpl() {
 

dspace-api/src/main/java/org/dspace/app/itemimport/ItemImportServiceImpl.java

@@ -55,10 +55,10 @@ import gr.ekt.bteio.loaders.OAIPMHDataLoader;
 import org.apache.commons.collections4.ComparatorUtils;
 import org.apache.commons.io.FileDeleteStrategy;
 import org.apache.commons.io.FileUtils;
-import org.apache.commons.lang.RandomStringUtils;
+import org.apache.commons.lang3.RandomStringUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.exception.ExceptionUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.apache.xpath.XPathAPI;
 import org.dspace.app.itemimport.service.ItemImportService;
 import org.dspace.app.util.LocalSchemaFilenameFilter;
@@ -124,7 +124,7 @@ import org.xml.sax.SAXException;
  * allow the registration of files (bitstreams) into DSpace.
  */
 public class ItemImportServiceImpl implements ItemImportService, InitializingBean {
-    private final Logger log = Logger.getLogger(ItemImportServiceImpl.class);
+    private final Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemImportServiceImpl.class);
 
     @Autowired(required = true)
     protected AuthorizeService authorizeService;

dspace-api/src/main/java/org/dspace/app/itemupdate/ItemArchive.java

@@ -30,7 +30,7 @@ import javax.xml.transform.TransformerConfigurationException;
 import javax.xml.transform.TransformerException;
 import javax.xml.transform.TransformerFactory;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.LocalSchemaFilenameFilter;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.DSpaceObject;
@@ -47,7 +47,7 @@ import org.w3c.dom.Document;
  * Encapsulates the Item in the context of the DSpace Archive Format
  */
 public class ItemArchive {
-    private static final Logger log = Logger.getLogger(ItemArchive.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemArchive.class);
 
     public static final String DUBLIN_CORE_XML = "dublin_core.xml";
 

dspace-api/src/main/java/org/dspace/app/itemupdate/MetadataUtilities.java

@@ -28,7 +28,7 @@ import javax.xml.transform.TransformerException;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.xpath.XPathAPI;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Item;

dspace-api/src/main/java/org/dspace/app/mediafilter/ExcelFilter.java

@@ -11,7 +11,7 @@ import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.apache.poi.POITextExtractor;
 import org.apache.poi.extractor.ExtractorFactory;
 import org.apache.poi.hssf.extractor.ExcelExtractor;
@@ -36,7 +36,7 @@ import org.dspace.content.Item;
  */
 public class ExcelFilter extends MediaFilter {
 
-    private static Logger log = Logger.getLogger(ExcelFilter.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ExcelFilter.class);
 
     public String getFilteredName(String oldFilename) {
         return oldFilename + ".txt";

dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterCLITool.java

@@ -22,7 +22,7 @@ import org.apache.commons.cli.Option;
 import org.apache.commons.cli.OptionBuilder;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.PosixParser;
-import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.lang3.ArrayUtils;
 import org.dspace.app.mediafilter.factory.MediaFilterServiceFactory;
 import org.dspace.app.mediafilter.service.MediaFilterService;
 import org.dspace.content.Collection;

dspace-api/src/main/java/org/dspace/app/mediafilter/PDFFilter.java

@@ -16,7 +16,7 @@ import java.io.InputStream;
 import java.io.OutputStreamWriter;
 import java.io.Writer;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.text.PDFTextStripper;
 import org.dspace.content.Item;
@@ -30,7 +30,7 @@ import org.dspace.core.ConfigurationManager;
  */
 public class PDFFilter extends MediaFilter {
 
-    private static Logger log = Logger.getLogger(PDFFilter.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(PDFFilter.class);
 
     @Override
     public String getFilteredName(String oldFilename) {

dspace-api/src/main/java/org/dspace/app/mediafilter/PowerPointFilter.java

@@ -10,7 +10,7 @@ package org.dspace.app.mediafilter;
 import java.io.ByteArrayInputStream;
 import java.io.InputStream;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.apache.poi.POITextExtractor;
 import org.apache.poi.extractor.ExtractorFactory;
 import org.apache.poi.hslf.extractor.PowerPointExtractor;
@@ -23,7 +23,7 @@ import org.dspace.content.Item;
  */
 public class PowerPointFilter extends MediaFilter {
 
-    private static Logger log = Logger.getLogger(PowerPointFilter.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(PowerPointFilter.class);
 
     @Override
     public String getFilteredName(String oldFilename) {

dspace-api/src/main/java/org/dspace/app/mediafilter/WordFilter.java

@@ -11,7 +11,7 @@ import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Item;
 import org.textmining.extraction.TextExtractor;
 import org.textmining.extraction.word.WordTextExtractorFactory;
@@ -24,7 +24,7 @@ import org.textmining.extraction.word.WordTextExtractorFactory;
  */
 public class WordFilter extends MediaFilter {
 
-    private static Logger log = Logger.getLogger(WordFilter.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(WordFilter.class);
 
     @Override
     public String getFilteredName(String oldFilename) {

dspace-api/src/main/java/org/dspace/app/requestitem/RequestItemHelpdeskStrategy.java

@@ -9,8 +9,8 @@ package org.dspace.app.requestitem;
 
 import java.sql.SQLException;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Item;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
@@ -31,7 +31,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  */
 public class RequestItemHelpdeskStrategy extends RequestItemSubmitterStrategy {
 
-    private Logger log = Logger.getLogger(RequestItemHelpdeskStrategy.class);
+    private Logger log = org.apache.logging.log4j.LogManager.getLogger(RequestItemHelpdeskStrategy.class);
 
     @Autowired(required = true)
     protected EPersonService ePersonService;

dspace-api/src/main/java/org/dspace/app/requestitem/RequestItemMetadataStrategy.java

@@ -10,7 +10,7 @@ package org.dspace.app.requestitem;
 import java.sql.SQLException;
 import java.util.List;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.dspace.content.Item;
 import org.dspace.content.MetadataValue;
 import org.dspace.content.service.ItemService;

dspace-api/src/main/java/org/dspace/app/requestitem/RequestItemServiceImpl.java

@@ -10,7 +10,7 @@ package org.dspace.app.requestitem;
 import java.sql.SQLException;
 import java.util.Date;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.requestitem.dao.RequestItemDAO;
 import org.dspace.app.requestitem.service.RequestItemService;
 import org.dspace.content.Bitstream;
@@ -28,7 +28,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  */
 public class RequestItemServiceImpl implements RequestItemService {
 
-    private final Logger log = Logger.getLogger(RequestItemServiceImpl.class);
+    private final Logger log = org.apache.logging.log4j.LogManager.getLogger(RequestItemServiceImpl.class);
 
     @Autowired(required = true)
     protected RequestItemDAO requestItemDAO;

dspace-api/src/main/java/org/dspace/app/sfx/SFXFileReaderServiceImpl.java

@@ -15,8 +15,8 @@ import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.sfx.service.SFXFileReaderService;
 import org.dspace.content.DCPersonName;
 import org.dspace.content.Item;
@@ -58,7 +58,7 @@ public class SFXFileReaderServiceImpl implements SFXFileReaderService {
     /**
      * log4j logger
      */
-    private final Logger log = Logger.getLogger(SFXFileReaderServiceImpl.class);
+    private final Logger log = org.apache.logging.log4j.LogManager.getLogger(SFXFileReaderServiceImpl.class);
 
     protected SFXFileReaderServiceImpl() {
     }

dspace-api/src/main/java/org/dspace/app/sherpa/SHERPAResponse.java

@@ -13,7 +13,7 @@ import java.util.List;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.dspace.app.util.XMLUtils;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;

dspace-api/src/main/java/org/dspace/app/sherpa/SHERPAService.java

@@ -7,7 +7,7 @@
  */
 package org.dspace.app.sherpa;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.http.HttpEntity;
 import org.apache.http.HttpResponse;
 import org.apache.http.HttpStatus;
@@ -16,7 +16,7 @@ import org.apache.http.client.methods.HttpGet;
 import org.apache.http.client.utils.URIBuilder;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClientBuilder;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.core.ConfigurationManager;
 
 public class SHERPAService {
@@ -29,7 +29,7 @@ public class SHERPAService {
     /**
      * log4j category
      */
-    private static final Logger log = Logger.getLogger(SHERPAService.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(SHERPAService.class);
 
     public SHERPAService() {
         HttpClientBuilder builder = HttpClientBuilder.create();

dspace-api/src/main/java/org/dspace/app/sherpa/submit/SHERPASubmitService.java

@@ -11,8 +11,8 @@ import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Set;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.sherpa.SHERPAResponse;
 import org.dspace.app.sherpa.SHERPAService;
 import org.dspace.content.Item;
@@ -27,7 +27,7 @@ public class SHERPASubmitService {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(SHERPASubmitService.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(SHERPASubmitService.class);
 
     public void setConfiguration(SHERPASubmitConfigurationService configuration) {
         this.configuration = configuration;

dspace-api/src/main/java/org/dspace/app/sitemap/GenerateSitemaps.java

@@ -27,9 +27,9 @@ import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.cli.PosixParser;
-import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.lang3.ArrayUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
 import org.dspace.content.Item;
@@ -52,7 +52,7 @@ public class GenerateSitemaps {
     /**
      * Logger
      */
-    private static Logger log = Logger.getLogger(GenerateSitemaps.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(GenerateSitemaps.class);
 
     private static final CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
     private static final CollectionService collectionService =

dspace-api/src/main/java/org/dspace/app/statistics/StatisticsLoader.java

@@ -21,7 +21,7 @@ import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.apache.commons.lang.time.DateUtils;
+import org.apache.commons.lang3.time.DateUtils;
 import org.dspace.core.ConfigurationManager;
 
 /**

dspace-api/src/main/java/org/dspace/app/util/DCInput.java

@@ -13,7 +13,7 @@ import java.util.Map;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.dspace.content.MetadataSchema;
 import org.dspace.core.Utils;
 import org.slf4j.Logger;
@@ -63,6 +63,12 @@ public class DCInput {
      */
     private String label = null;
 
+    /**
+     * a style instruction to apply to the input. The exact way to use the style value is UI depending that receive the
+     * value from the REST API as is
+     */
+    private String style = null;
+
     /**
      * the input type
      */
@@ -199,7 +205,7 @@ public class DCInput {
                 typeBind.add(type.trim());
             }
         }
-
+        style = fieldMap.get("style");
     }
 
     /**
@@ -262,7 +268,7 @@ public class DCInput {
     }
 
     /**
-     * Get the DC element for this form row.
+     * Get the DC element for this form field.
      *
      * @return the DC element
      */
@@ -271,7 +277,7 @@ public class DCInput {
     }
 
     /**
-     * Get the DC namespace prefix for this form row.
+     * Get the DC namespace prefix for this form field.
      *
      * @return the DC namespace prefix
      */
@@ -290,7 +296,7 @@ public class DCInput {
     }
 
     /**
-     * Is there a required string for this form row?
+     * Is there a required string for this form field?
      *
      * @return true if a required string is set
      */
@@ -299,7 +305,7 @@ public class DCInput {
     }
 
     /**
-     * Get the DC qualifier for this form row.
+     * Get the DC qualifier for this form field.
      *
      * @return the DC qualifier
      */
@@ -308,7 +314,7 @@ public class DCInput {
     }
 
     /**
-     * Get the language for this form row.
+     * Get the language for this form field.
      *
      * @return the language state
      */
@@ -317,7 +323,7 @@ public class DCInput {
     }
 
     /**
-     * Get the hint for this form row, formatted for an HTML table
+     * Get the hint for this form field
      *
      * @return the hints
      */
@@ -326,7 +332,7 @@ public class DCInput {
     }
 
     /**
-     * Get the label for this form row.
+     * Get the label for this form field.
      *
      * @return the label
      */
@@ -334,6 +340,15 @@ public class DCInput {
         return label;
     }
 
+    /**
+     * Get the style for this form field
+     * 
+     * @return the style
+     */
+    public String getStyle() {
+        return style;
+    }
+
     /**
      * Get the name of the pairs type
      *

dspace-api/src/main/java/org/dspace/app/util/DCInputSet.java

@@ -25,25 +25,26 @@ public class DCInputSet {
     /**
      * the inputs ordered by row position
      */
-    private DCInput[] inputs = null;
+    private DCInput[][] inputs = null;
 
     /**
      * constructor
      *
      * @param formName       form name
-     * @param headings
      * @param mandatoryFlags
-     * @param fields         fields
+     * @param rows           the rows
      * @param listMap        map
      */
-    public DCInputSet(String formName,
+    public DCInputSet(String formName, List<List<Map<String, String>>> rows, Map<String, List<String>> listMap) {
-                      List<Map<String, String>> fields, Map<String, List<String>> listMap) {
         this.formName = formName;
-        this.inputs = new DCInput[fields.size()];
+        this.inputs = new DCInput[rows.size()][];
         for (int i = 0; i < inputs.length; i++) {
-            Map<String, String> field = fields.get(i);
+            List<Map<String, String>> fields = rows.get(i);
-            inputs[i] = new DCInput(field, listMap);
+            inputs[i] = new DCInput[fields.size()];
-
+            for (int j = 0; j < inputs[i].length; j++) {
+                Map<String, String> field = rows.get(i).get(j);
+                inputs[i][j] = new DCInput(field, listMap);
+            }
         }
     }
 
@@ -71,7 +72,7 @@ public class DCInputSet {
      * @return an array containing the fields
      */
 
-    public DCInput[] getFields() {
+    public DCInput[][] getFields() {
         return inputs;
     }
 
@@ -104,10 +105,12 @@ public class DCInputSet {
      */
     public boolean isFieldPresent(String fieldName) {
         for (int i = 0; i < inputs.length; i++) {
-            DCInput field = inputs[i];
+            for (int j = 0; j < inputs[i].length; j++) {
-            String fullName = field.getFieldName();
+                DCInput field = inputs[i][j];
-            if (fullName.equals(fieldName)) {
+                String fullName = field.getFieldName();
-                return true;
+                if (fullName.equals(fieldName)) {
+                    return true;
+                }
             }
         }
         return false;
@@ -127,11 +130,13 @@ public class DCInputSet {
             documentType = "";
         }
         for (int i = 0; i < inputs.length; i++) {
-            DCInput field = inputs[i];
+            for (int j = 0; j < inputs[i].length; j++) {
-            String fullName = field.getFieldName();
+                DCInput field = inputs[i][j];
-            if (fullName.equals(fieldName)) {
+                String fullName = field.getFieldName();
-                if (field.isAllowedFor(documentType)) {
+                if (fullName.equals(fieldName)) {
-                    return true;
+                    if (field.isAllowedFor(documentType)) {
+                        return true;
+                    }
                 }
             }
         }

dspace-api/src/main/java/org/dspace/app/util/DCInputsReader.java

@@ -74,7 +74,7 @@ public class DCInputsReader {
      * Reference to the forms definitions map, computed from the forms
      * definition file
      */
-    private Map<String, List<Map<String, String>>> formDefns = null;
+    private Map<String, List<List<Map<String, String>>>> formDefns = null;
 
     /**
      * Reference to the value-pairs map, computed from the forms definition file
@@ -115,7 +115,7 @@ public class DCInputsReader {
 
     private void buildInputs(String fileName)
         throws DCInputsReaderException {
-        formDefns = new HashMap<String, List<Map<String, String>>>();
+        formDefns = new HashMap<String, List<List<Map<String, String>>>>();
         valuePairs = new HashMap<String, List<String>>();
 
         String uri = "file:" + new File(fileName).getAbsolutePath();
@@ -212,7 +212,7 @@ public class DCInputsReader {
             return lastInputSet;
         }
         // cache miss - construct new DCInputSet
-        List<Map<String, String>> pages = formDefns.get(formName);
+        List<List<Map<String, String>>> pages = formDefns.get(formName);
         if (pages == null) {
             throw new DCInputsReaderException("Missing the " + formName + " form");
         }
@@ -292,8 +292,8 @@ public class DCInputsReader {
 
     /**
      * Process the form-definitions section of the XML file. Each element is
-     * formed thusly: <form name="formname">...pages...</form> Each pages
+     * formed thusly: <form name="formname">...row...</form> Each rows
-     * subsection is formed: <page number="#"> ...fields... </page> Each field
+     * subsection is formed: <row> ...fields... </row> Each field
      * is formed from: dc-element, dc-qualifier, label, hint, input-type name,
      * required text, and repeatable flag.
      */
@@ -311,26 +311,24 @@ public class DCInputsReader {
                 if (formName == null) {
                     throw new SAXException("form element has no name attribute");
                 }
-                List<Map<String, String>> fields = new ArrayList<Map<String, String>>(); // the form contains fields
+                List<List<Map<String, String>>> rows = new ArrayList<List<Map<String, String>>>(); // the form
-                formDefns.put(formName, fields);
+                // contains rows of fields
+                formDefns.put(formName, rows);
                 NodeList pl = nd.getChildNodes();
                 int lenpg = pl.getLength();
                 for (int j = 0; j < lenpg; j++) {
                     Node npg = pl.item(j);
-
+                    if (npg.getNodeName().equals("row")) {
-                    if (npg.getNodeName().equals("field")) {
+                        List<Map<String, String>> fields = new ArrayList<Map<String, String>>(); // the fields in the
-                        // process each field definition
+                        // row
-                        Map<String, String> field = new HashMap<String, String>();
+                        // process each row definition
-                        processField(formName, npg, field);
+                        processRow(formName, j, npg, fields);
-                        fields.add(field);
+                        rows.add(fields);
-                        // we omit the duplicate validation, allowing multiple
-                        // fields definition for
-                        // the same metadata and different visibility/type-bind
                     }
                 }
                 // sanity check number of fields
-                if (fields.size() < 1) {
+                if (rows.size() < 1) {
-                    throw new DCInputsReaderException("Form " + formName + " has no fields");
+                    throw new DCInputsReaderException("Form " + formName + " has no rows");
                 }
             }
         }
@@ -339,6 +337,48 @@ public class DCInputsReader {
         }
     }
 
+    /**
+     * Process parts of a row
+     */
+    private void processRow(String formName, int rowIdx, Node n, List<Map<String, String>> fields)
+        throws SAXException, DCInputsReaderException {
+
+        NodeList pl = n.getChildNodes();
+        int lenpg = pl.getLength();
+        for (int j = 0; j < lenpg; j++) {
+            Node npg = pl.item(j);
+
+            if (npg.getNodeName().equals("field")) {
+                // process each field definition
+                Map<String, String> field = new HashMap<String, String>();
+                processField(formName, npg, field);
+                fields.add(field);
+                String key = field.get(PAIR_TYPE_NAME);
+                if (StringUtils
+                    .isNotBlank(key)) {
+                    String schema = field.get("dc-schema");
+                    String element = field.get("dc-element");
+                    String qualifier = field
+                        .get("dc-qualifier");
+                    String metadataField = schema + "."
+                        + element;
+                    if (StringUtils.isNotBlank(qualifier)) {
+                        metadataField += "." + qualifier;
+                    }
+                }
+
+                // we omit the duplicate validation, allowing multiple
+                // fields definition for
+                // the same metadata and different visibility/type-bind
+            }
+        }
+        // sanity check number of fields
+        if (fields.size() < 1) {
+            throw new DCInputsReaderException("Form " + formName + "row " + rowIdx + " has no fields");
+        }
+    }
+
+
     /**
      * Process parts of a field
      * At the end, make sure that input-types 'qualdrop_value' and
@@ -537,26 +577,29 @@ public class DCInputsReader {
         Iterator<String> ki = formDefns.keySet().iterator();
         while (ki.hasNext()) {
             String idName = ki.next();
-            List<Map<String, String>> fields = formDefns.get(idName);
+            List<List<Map<String, String>>> rows = formDefns.get(idName);
-            for (int i = 0; i < fields.size(); i++) {
+            for (int j = 0; j < rows.size(); j++) {
-                Map<String, String> fld = fields.get(i);
+                List<Map<String, String>> fields = rows.get(j);
-                // verify reference in certain input types
+                for (int i = 0; i < fields.size(); i++) {
-                String type = fld.get("input-type");
+                    Map<String, String> fld = fields.get(i);
-                if (type.equals("dropdown")
+                    // verify reference in certain input types
-                    || type.equals("qualdrop_value")
+                    String type = fld.get("input-type");
-                    || type.equals("list")) {
+                    if (type.equals("dropdown")
-                    String pairsName = fld.get(PAIR_TYPE_NAME);
+                        || type.equals("qualdrop_value")
-                    List<String> v = valuePairs.get(pairsName);
+                        || type.equals("list")) {
-                    if (v == null) {
+                        String pairsName = fld.get(PAIR_TYPE_NAME);
-                        String errString = "Cannot find value pairs for " + pairsName;
+                        List<String> v = valuePairs.get(pairsName);
-                        throw new DCInputsReaderException(errString);
+                        if (v == null) {
+                            String errString = "Cannot find value pairs for " + pairsName;
+                            throw new DCInputsReaderException(errString);
+                        }
                     }
-                }
 
-                // we omit the "required" and "visibility" validation, provided this must be checked in the
+                    // we omit the "required" and "visibility" validation, provided this must be checked in the
-                // processing class
+                    // processing class
-                // only when it makes sense (if the field isn't visible means that it is not applicable, therefore it
+                    // only when it makes sense (if the field isn't visible means that it is not applicable,
-                // can't be required)
+                    // therefore it can't be required)
+                }
             }
         }
     }
@@ -639,4 +682,5 @@ public class DCInputsReader {
         }
         throw new DCInputsReaderException("No field configuration found!");
     }
+
 }

dspace-api/src/main/java/org/dspace/app/util/DSpaceContextListener.java

@@ -16,14 +16,14 @@ import java.util.Enumeration;
 import javax.servlet.ServletContextEvent;
 import javax.servlet.ServletContextListener;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 
 /**
  * Class to initialize / cleanup resources used by DSpace when the web application
  * is started or stopped.
  */
 public class DSpaceContextListener implements ServletContextListener {
-    private static Logger log = Logger.getLogger(DSpaceContextListener.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DSpaceContextListener.class);
 
     /**
      * Initialize any resources required by the application.

dspace-api/src/main/java/org/dspace/app/util/DailyFileAppender.java

@@ -1,299 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.UnknownHostException;
-import java.text.SimpleDateFormat;
-import java.util.Calendar;
-import java.util.Date;
-
-import org.apache.commons.lang.time.DateUtils;
-import org.apache.log4j.FileAppender;
-import org.apache.log4j.helpers.LogLog;
-import org.apache.log4j.spi.LoggingEvent;
-
-/**
- * Special log appender for log4j. Adds the current date (ie. year-mon) to
- * the end of the file name, so that rolling on to the next log is simply
- * a case of starting a new one - no renaming of old logs.
- *
- * This is advisable if you are using Windows, and have multiple applications
- * (ie. dspace, dspace-oai, dspace-sword) that all want to write to the same log file,
- * as each would otherwise try to rename the old files during rollover.
- *
- * An example log4j.properties (one log per month, retains three months of logs)
- *
- * log4j.rootCategory=INFO, A1
- * log4j.appender.A1=org.dspace.app.util.DailyFileAppender
- * log4j.appender.A1.File=@@log.dir@@/dspace.log
- * log4j.appender.A1.DatePattern=yyyy-MM
- * log4j.appender.A1.MaxLogs=3
- * log4j.appender.A1.layout=org.apache.log4j.PatternLayout
- * log4j.appender.A1.layout.ConversionPattern=%d %-5p %c @ %m%n
- */
-public class DailyFileAppender extends FileAppender {
-    /**
-     * The fixed date pattern to be used if one is not specified.
-     */
-    private static final String DATE_PATTERN = "yyyy-MM-dd";
-
-    /**
-     * The folder under which daily folders are created. This can be a absolute path
-     * or relative path also.
-     * e.g. JavaLogs/CPRILog or F:/LogFiles/CPRILog
-     */
-    private String mstrFileName;
-
-    /**
-     * Used internally and contains the name of the date derived from current system date.
-     */
-    private Date mstrDate = new Date(System.currentTimeMillis());
-
-    /**
-     * Holds the user specified DatePattern,
-     */
-    private String mstrDatePattern = DATE_PATTERN;
-
-    private boolean mMonthOnly = false;
-
-    /**
-     * The date formatter object used for parsing the user specified DatePattern.
-     */
-    private SimpleDateFormat mobjSDF;
-
-    private boolean mWithHostName = false;
-
-    private int mMaxLogs = 0;
-
-    /**
-     * Default constructor. This is required as the appender class is dynamically
-     * loaded.
-     */
-    public DailyFileAppender() {
-        super();
-    }
-
-    /* (non-Javadoc)
-     * @see org.apache.log4j.FileAppender#activateOptions()
-     */
-    @Override
-    public void activateOptions() {
-        setFileName();
-        cleanupOldFiles();
-        super.activateOptions();
-    }
-
-    /*------------------------------------------------------------------------------
-     * Getters
-     *----------------------------------------------------------------------------*/
-    public String getDatePattern() {
-        return this.mstrDatePattern;
-    }
-
-    @Override
-    public String getFile() {
-        return this.mstrFileName;
-    }
-
-    public boolean getWithHost() {
-        return mWithHostName;
-    }
-
-    public int getMaxLogs() {
-        return mMaxLogs;
-    }
-
-    /*------------------------------------------------------------------------------
-     * Setters
-     *----------------------------------------------------------------------------*/
-    public void setDatePattern(String pstrPattern) {
-        this.mstrDatePattern = checkPattern(pstrPattern);
-        if (mstrDatePattern.contains("dd") || mstrDatePattern.contains("DD")) {
-            mMonthOnly = false;
-        } else {
-            mMonthOnly = true;
-        }
-    }
-
-    @Override
-    public void setFile(String file) {
-        // Trim spaces from both ends. The users probably does not want
-        // trailing spaces in file names.
-        String val = file.trim();
-        mstrFileName = val;
-    }
-
-    public void setWithHost(boolean wh) {
-        mWithHostName = wh;
-    }
-
-    public void setMaxLogs(int ml) {
-        mMaxLogs = ml;
-    }
-
-    /*------------------------------------------------------------------------------
-     * Methods
-     *----------------------------------------------------------------------------*/
-    /* (non-Javadoc)
-     * @see org.apache.log4j.WriterAppender#subAppend(org.apache.log4j.spi.LoggingEvent)
-     */
-    @Override
-    protected void subAppend(LoggingEvent pobjEvent) {
-        Date dtNow = new Date(System.currentTimeMillis());
-
-        boolean rollover = false;
-
-        if (mMonthOnly) {
-            Calendar now = Calendar.getInstance();
-            Calendar cur = Calendar.getInstance();
-            now.setTime(dtNow);
-            cur.setTime(mstrDate);
-            rollover = !(now.get(Calendar.YEAR) == cur.get(Calendar.YEAR) && now.get(Calendar.MONTH) == cur
-                .get(Calendar.MONTH));
-        } else {
-            rollover = !(DateUtils.isSameDay(dtNow, mstrDate));
-        }
-
-        if (rollover) {
-            try {
-                rollOver(dtNow);
-            } catch (IOException IOEx) {
-                LogLog.error("rollOver() failed!", IOEx);
-            }
-        }
-
-        super.subAppend(pobjEvent);
-    }
-
-    /*------------------------------------------------------------------------------
-     * Helpers
-     *----------------------------------------------------------------------------*/
-
-    /**
-     * The helper function to validate the DatePattern.
-     *
-     * @param pstrPattern The DatePattern to be validated.
-     * @return The validated date pattern or defautlt DATE_PATTERN
-     */
-    private String checkPattern(String pstrPattern) {
-        String strRet = null;
-        SimpleDateFormat objFmt = new SimpleDateFormat(DATE_PATTERN);
-
-        try {
-            this.mobjSDF = new SimpleDateFormat(pstrPattern);
-            strRet = pstrPattern;
-        } catch (NullPointerException NPExIgnore) {
-            LogLog.error("Invalid DatePattern " + pstrPattern, NPExIgnore);
-            this.mobjSDF = objFmt;
-            strRet = DATE_PATTERN;
-        } catch (IllegalArgumentException IlArgExIgnore) {
-            LogLog.error("Invalid DatePattern " + pstrPattern, IlArgExIgnore);
-            this.mobjSDF = objFmt;
-            strRet = DATE_PATTERN;
-        } finally {
-            objFmt = null;
-        }
-        return strRet;
-    }
-
-    /**
-     * This function is responsible for performing the actual file rollover.
-     *
-     * @param pstrName The name of the new folder based on current system date.
-     * @throws IOException if IO error
-     */
-    private static boolean deletingFiles = false;
-
-    private void cleanupOldFiles() {
-        // If we need to delete log files
-        if (mMaxLogs > 0 && !deletingFiles) {
-            deletingFiles = true;
-
-            // Determine the final file extension with the hostname
-            String hostFileExt = null;
-            try {
-                hostFileExt = "." + java.net.InetAddress.getLocalHost().getHostName();
-            } catch (UnknownHostException e) {
-                LogLog.error("Unable to retrieve host name");
-            }
-
-            try {
-                // Array to hold the logs we are going to keep
-                File[] logsToKeep = new File[mMaxLogs];
-
-                // Get a 'master' file handle, and the parent directory from it
-                File logMaster = new File(mstrFileName);
-                File logDir = logMaster.getParentFile();
-                if (logDir.isDirectory()) {
-                    // Iterate all the files in that directory
-                    File[] logArr = logDir.listFiles();
-                    for (File curLog : logArr) {
-                        LogLog.debug("Comparing '" + curLog.getAbsolutePath() + "' to '" + mstrFileName + "'");
-                        String name = curLog.getAbsolutePath();
-
-                        // First, see if we are not using hostname, or the log file ends with this host
-                        if (!mWithHostName || (hostFileExt != null && name.endsWith(hostFileExt))) {
-                            // Check that the file is indeed one we want (contains the master file name)
-                            if (name.contains(mstrFileName)) {
-                                // Iterate through the array of logs we are keeping
-                                for (int i = 0; curLog != null && i < logsToKeep.length; i++) {
-                                    // Have we exhausted the 'to keep' array?
-                                    if (logsToKeep[i] == null) {
-                                        // Empty space, retain this log file
-                                        logsToKeep[i] = curLog;
-                                        curLog = null;
-                                    } else if (logsToKeep[i].getName().compareTo(curLog.getName()) < 0) {
-                                        // If the 'kept' file is older than the current one
-                                        // Replace tested entry with current file
-                                        File temp = logsToKeep[i];
-                                        logsToKeep[i] = curLog;
-                                        curLog = temp;
-                                    }
-                                }
-
-                                // If we have a 'current' entry at this point, it's a log we don't want
-                                if (curLog != null) {
-                                    LogLog.debug("Deleting log " + curLog.getName());
-                                    if (!curLog.delete()) {
-                                        LogLog.error("Unable to delete log file");
-                                    }
-                                }
-                            }
-                        }
-                    }
-                }
-            } catch (Exception e) {
-                // Don't worry about exceptions
-            } finally {
-                deletingFiles = false;
-            }
-        }
-    }
-
-    private void rollOver(Date dtNow) throws IOException {
-        mstrDate = dtNow;
-        setFileName();
-        this.setFile(fileName, true, bufferedIO, bufferSize);
-
-        cleanupOldFiles();
-    }
-
-    private void setFileName() {
-        fileName = mstrFileName + "." + mobjSDF.format(mstrDate);
-
-        if (mWithHostName) {
-            try {
-                fileName += "." + java.net.InetAddress.getLocalHost().getHostName();
-            } catch (UnknownHostException e) {
-                LogLog.error("Unable to retrieve host name");
-            }
-        }
-    }
-}

dspace-api/src/main/java/org/dspace/app/util/GoogleBitstreamComparator.java

@@ -12,7 +12,7 @@ import java.util.Comparator;
 import java.util.HashMap;
 import java.util.Map;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Bitstream;
 import org.dspace.content.BitstreamFormat;
 import org.dspace.content.factory.ContentServiceFactory;
@@ -24,7 +24,7 @@ import org.dspace.core.Context;
  */
 public class GoogleBitstreamComparator implements Comparator<Bitstream> {
 
-    private final static Logger log = Logger.getLogger(GoogleBitstreamComparator.class);
+    private final static Logger log = org.apache.logging.log4j.LogManager.getLogger(GoogleBitstreamComparator.class);
 
     HashMap<String, Integer> priorityMap = new HashMap<>();
 

dspace-api/src/main/java/org/dspace/app/util/GoogleMetadata.java

@@ -26,7 +26,7 @@ import java.util.Properties;
 
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.ListMultimap;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.factory.AuthorizeServiceFactory;
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
@@ -51,7 +51,7 @@ import org.jdom.Element;
 @SuppressWarnings("deprecation")
 public class GoogleMetadata {
 
-    private final static Logger log = Logger.getLogger(GoogleMetadata.class);
+    private final static Logger log = org.apache.logging.log4j.LogManager.getLogger(GoogleMetadata.class);
 
     protected static final String GOOGLE_PREFIX = "google.";
 

dspace-api/src/main/java/org/dspace/app/util/MetadataExposureServiceImpl.java

@@ -14,7 +14,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.service.MetadataExposureService;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.core.Context;
@@ -58,7 +58,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  * @version $Revision: 3734 $
  */
 public class MetadataExposureServiceImpl implements MetadataExposureService {
-    protected Logger log = Logger.getLogger(MetadataExposureServiceImpl.class);
+    protected Logger log = org.apache.logging.log4j.LogManager.getLogger(MetadataExposureServiceImpl.class);
 
     protected Map<String, Set<String>> hiddenElementSets = null;
     protected Map<String, Map<String, Set<String>>> hiddenElementMaps = null;

dspace-api/src/main/java/org/dspace/app/util/OpenSearchServiceImpl.java

@@ -20,7 +20,7 @@ import com.sun.syndication.feed.module.opensearch.OpenSearchModule;
 import com.sun.syndication.feed.module.opensearch.entity.OSQuery;
 import com.sun.syndication.feed.module.opensearch.impl.OpenSearchModuleImpl;
 import com.sun.syndication.io.FeedException;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.service.OpenSearchService;
 import org.dspace.content.DSpaceObject;
 import org.dspace.core.Constants;
@@ -54,7 +54,7 @@ import org.w3c.dom.Document;
  * @author Richard Rodgers
  */
 public class OpenSearchServiceImpl implements OpenSearchService, InitializingBean {
-    private static final Logger log = Logger.getLogger(OpenSearchServiceImpl.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(OpenSearchServiceImpl.class);
 
     // are open search queries enabled?
     protected boolean enabled = false;

dspace-api/src/main/java/org/dspace/app/util/OptimizeSelectCollection.java

@@ -11,7 +11,7 @@ import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Collection;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.CollectionService;
@@ -28,7 +28,7 @@ import org.springframework.util.StopWatch;
  * Invocation: dsrun org.dspace.app.util.OptimizeSelectCollection
  */
 public class OptimizeSelectCollection {
-    private static final Logger log = Logger.getLogger(OptimizeSelectCollection.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(OptimizeSelectCollection.class);
     private static Context context;
 
     private static ArrayList<EPerson> brokenPeople;

dspace-api/src/main/java/org/dspace/app/util/SubmissionConfig.java

@@ -12,7 +12,7 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 
 /**
  * Class representing a single Item Submission config definition, organized into
@@ -44,7 +44,7 @@ public class SubmissionConfig implements Serializable {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(SubmissionConfig.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(SubmissionConfig.class);
 
     /**
      * Constructs a new Submission Configuration object, based on the XML

dspace-api/src/main/java/org/dspace/app/util/SubmissionConfigReader.java

@@ -19,7 +19,7 @@ import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.FactoryConfigurationError;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Collection;
 import org.dspace.content.DSpaceObject;
 import org.dspace.core.Context;
@@ -71,7 +71,7 @@ public class SubmissionConfigReader {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(SubmissionConfigReader.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(SubmissionConfigReader.class);
 
     /**
      * The fully qualified pathname of the directory containing the Item Submission Configuration file

dspace-api/src/main/java/org/dspace/app/util/SyndicationFeed.java

@@ -34,9 +34,9 @@ import com.sun.syndication.feed.synd.SyndPerson;
 import com.sun.syndication.feed.synd.SyndPersonImpl;
 import com.sun.syndication.io.FeedException;
 import com.sun.syndication.io.SyndFeedOutput;
-import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.lang3.ArrayUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
 import org.dspace.content.Collection;
@@ -69,7 +69,7 @@ import org.w3c.dom.Document;
  * @author Larry Stone
  */
 public class SyndicationFeed {
-    protected final Logger log = Logger.getLogger(SyndicationFeed.class);
+    protected final Logger log = org.apache.logging.log4j.LogManager.getLogger(SyndicationFeed.class);
 
 
     /**

dspace-api/src/main/java/org/dspace/app/util/Util.java

@@ -23,8 +23,8 @@ import java.util.UUID;
 import javax.servlet.http.HttpServletRequest;
 
 import org.apache.commons.collections4.ListUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Collection;
 import org.dspace.content.Item;
 import org.dspace.content.MetadataValue;
@@ -44,7 +44,7 @@ public class Util {
     // cache for source version result
     private static String sourceVersion = null;
 
-    private static Logger log = Logger.getLogger(Util.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(Util.class);
 
     /**
      * Default constructor. Must be protected as org.dspace.xmlworkflow.WorkflowUtils extends it
@@ -418,11 +418,12 @@ public class Util {
 
         List<DCInputSet> inputSets = inputsReader.getInputsByCollectionHandle(col_handle);
 
+        // Replace the values of Metadatum[] with the correct ones in case
+        // of
+        // controlled vocabularies
+        String currentField = Utils.standardize(schema, element, qualifier, ".");
+
         for (DCInputSet inputSet : inputSets) {
-            // Replace the values of Metadatum[] with the correct ones in case
-            // of
-            // controlled vocabularies
-            String currentField = Utils.standardize(schema, element, qualifier, ".");
 
             if (inputSet != null) {
 
@@ -430,19 +431,20 @@ public class Util {
 
                 for (int p = 0; p < fieldsNums; p++) {
 
-                    DCInput[] inputs = inputSet.getFields();
+                    DCInput[][] inputs = inputSet.getFields();
 
                     if (inputs != null) {
 
                         for (int i = 0; i < inputs.length; i++) {
-                            String inputField = Utils.standardize(inputs[i].getSchema(), inputs[i].getElement(),
+                            for (int j = 0; j < inputs[i].length; j++) {
-                                                                  inputs[i].getQualifier(), ".");
+                                String inputField = Utils
-                            if (currentField.equals(inputField)) {
+                                    .standardize(inputs[i][j].getSchema(), inputs[i][j].getElement(),
-
+                                                 inputs[i][j].getQualifier(), ".");
-                                myInputs = inputs[i];
+                                if (currentField.equals(inputField)) {
-                                myInputsFound = true;
+                                    myInputs = inputs[i][j];
-                                break;
+                                    myInputsFound = true;
-
+                                    break;
+                                }
                             }
                         }
                     }
@@ -480,13 +482,17 @@ public class Util {
         Set<String> fromFieldName = new HashSet<>();
         Set<String> toFieldName = new HashSet<>();
         for (DCInputSet ff : from) {
-            for (DCInput fdc : ff.getFields()) {
+            for (DCInput[] fdcrow : ff.getFields()) {
-                fromFieldName.add(fdc.getFieldName());
+                for (DCInput fdc : fdcrow) {
+                    fromFieldName.add(fdc.getFieldName());
+                }
             }
         }
         for (DCInputSet tt : to) {
-            for (DCInput tdc : tt.getFields()) {
+            for (DCInput[] tdcrow : tt.getFields()) {
-                toFieldName.add(tdc.getFieldName());
+                for (DCInput tdc : tdcrow) {
+                    toFieldName.add(tdc.getFieldName());
+                }
             }
         }
 

dspace-api/src/main/java/org/dspace/app/util/WebAppServiceImpl.java

@@ -18,7 +18,7 @@ import org.apache.http.HttpStatus;
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpHead;
 import org.apache.http.impl.client.DefaultHttpClient;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.dao.WebAppDAO;
 import org.dspace.app.util.service.WebAppService;
 import org.dspace.core.Context;
@@ -33,7 +33,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  */
 public class WebAppServiceImpl implements WebAppService {
 
-    private final Logger log = Logger.getLogger(WebAppServiceImpl.class);
+    private final Logger log = org.apache.logging.log4j.LogManager.getLogger(WebAppServiceImpl.class);
 
     @Autowired(required = true)
     protected WebAppDAO webAppDAO;

dspace-api/src/main/java/org/dspace/app/util/XMLUtils.java

@@ -11,7 +11,7 @@ import java.util.ArrayList;
 import java.util.LinkedList;
 import java.util.List;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.w3c.dom.Element;
 import org.w3c.dom.NodeList;
 

dspace-api/src/main/java/org/dspace/authenticate/IPAuthentication.java

@@ -17,14 +17,15 @@ import java.util.UUID;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
+import org.dspace.core.factory.CoreServiceFactory;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.eperson.service.GroupService;
+import org.dspace.service.ClientInfoService;
 import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
@@ -49,7 +50,7 @@ public class IPAuthentication implements AuthenticationMethod {
     /**
      * Our logger
      */
-    private static Logger log = Logger.getLogger(IPAuthentication.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(IPAuthentication.class);
 
     /**
      * Whether to look for x-forwarded headers for logging IP addresses
@@ -67,6 +68,7 @@ public class IPAuthentication implements AuthenticationMethod {
     protected List<IPMatcher> ipNegativeMatchers;
 
     protected GroupService groupService;
+    protected ClientInfoService clientInfoService;
 
 
     /**
@@ -91,6 +93,7 @@ public class IPAuthentication implements AuthenticationMethod {
         ipMatcherGroupIDs = new HashMap<>();
         ipMatcherGroupNames = new HashMap<>();
         groupService = EPersonServiceFactory.getInstance().getGroupService();
+        clientInfoService = CoreServiceFactory.getInstance().getClientInfoService();
 
         List<String> propNames = DSpaceServicesFactory.getInstance().getConfigurationService()
                                                       .getPropertyKeys("authentication-ip");
@@ -169,18 +172,7 @@ public class IPAuthentication implements AuthenticationMethod {
         List<Group> groups = new ArrayList<Group>();
 
         // Get the user's IP address
-        String addr = request.getRemoteAddr();
+        String addr = clientInfoService.getClientIp(request);
-        if (useProxies == null) {
-            useProxies = ConfigurationManager.getBooleanProperty("useProxies", false);
-        }
-        if (useProxies && request.getHeader("X-Forwarded-For") != null) {
-            /* This header is a comma delimited list */
-            for (String xfip : request.getHeader("X-Forwarded-For").split(",")) {
-                if (!request.getHeader("X-Forwarded-For").contains(addr)) {
-                    addr = xfip.trim();
-                }
-            }
-        }
 
         for (IPMatcher ipm : ipMatchers) {
             try {

dspace-api/src/main/java/org/dspace/authenticate/IPMatcher.java

@@ -10,7 +10,7 @@ package org.dspace.authenticate;
 import java.net.Inet6Address;
 import java.net.UnknownHostException;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 
 /**
  * <p>
@@ -38,7 +38,7 @@ import org.apache.log4j.Logger;
  * @version $Revision$
  */
 public class IPMatcher {
-    private static Logger log = Logger.getLogger(IPMatcher.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(IPMatcher.class);
 
     /**
      * Network to match

dspace-api/src/main/java/org/dspace/authenticate/LDAPAuthentication.java

@@ -28,8 +28,8 @@ import javax.naming.ldap.StartTlsResponse;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authenticate.factory.AuthenticateServiceFactory;
 import org.dspace.authenticate.service.AuthenticationService;
 import org.dspace.authorize.AuthorizeException;
@@ -61,7 +61,7 @@ public class LDAPAuthentication
     /**
      * log4j category
      */
-    private static Logger log = Logger.getLogger(LDAPAuthentication.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(LDAPAuthentication.class);
 
     protected AuthenticationService authenticationService = AuthenticateServiceFactory.getInstance()
                                                                                       .getAuthenticationService();

dspace-api/src/main/java/org/dspace/authenticate/PasswordAuthentication.java

@@ -15,7 +15,7 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
 import org.dspace.eperson.EPerson;
@@ -49,7 +49,7 @@ public class PasswordAuthentication
     /**
      * log4j category
      */
-    private static Logger log = Logger.getLogger(PasswordAuthentication.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(PasswordAuthentication.class);
 
 
     /**

dspace-api/src/main/java/org/dspace/authenticate/ShibAuthentication.java

@@ -23,8 +23,8 @@ import java.util.UUID;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authenticate.factory.AuthenticateServiceFactory;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.MetadataField;
@@ -70,7 +70,7 @@ public class ShibAuthentication implements AuthenticationMethod {
     /**
      * log4j category
      */
-    private static Logger log = Logger.getLogger(ShibAuthentication.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ShibAuthentication.class);
 
     /**
      * Additional metadata mappings

dspace-api/src/main/java/org/dspace/authenticate/X509Authentication.java

@@ -29,8 +29,8 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import javax.servlet.http.HttpSession;
 
-import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.lang3.ArrayUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authenticate.factory.AuthenticateServiceFactory;
 import org.dspace.authenticate.service.AuthenticationService;
 import org.dspace.authorize.AuthorizeException;
@@ -105,7 +105,7 @@ public class X509Authentication implements AuthenticationMethod {
     /**
      * log4j category
      */
-    private static Logger log = Logger.getLogger(X509Authentication.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(X509Authentication.class);
 
     /**
      * public key of CA to check client certs against.

dspace-api/src/main/java/org/dspace/authority/AuthoritySolrServiceImpl.java

@@ -12,7 +12,7 @@ import java.net.MalformedURLException;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.apache.solr.client.solrj.SolrQuery;
 import org.apache.solr.client.solrj.SolrServerException;
 import org.apache.solr.client.solrj.impl.HttpSolrServer;
@@ -30,7 +30,7 @@ import org.dspace.core.ConfigurationManager;
  */
 public class AuthoritySolrServiceImpl implements AuthorityIndexingService, AuthoritySearchService {
 
-    private static final Logger log = Logger.getLogger(AuthoritySolrServiceImpl.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthoritySolrServiceImpl.class);
 
     protected AuthoritySolrServiceImpl() {
 

dspace-api/src/main/java/org/dspace/authority/AuthorityTypes.java

@@ -12,7 +12,7 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 
 /**
  * This class contains a list of active authority types.
@@ -32,7 +32,7 @@ public class AuthorityTypes {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(AuthorityTypes.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthorityTypes.class);
 
     protected List<AuthorityValue> types = new ArrayList<AuthorityValue>();
 

dspace-api/src/main/java/org/dspace/authority/AuthorityValue.java

@@ -14,8 +14,8 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.apache.solr.common.SolrDocument;
 import org.apache.solr.common.SolrInputDocument;
 import org.dspace.authorize.AuthorizeException;
@@ -234,7 +234,7 @@ public class AuthorityValue {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(AuthorityValue.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthorityValue.class);
 
     @Override
     public String toString() {

dspace-api/src/main/java/org/dspace/authority/AuthorityValueServiceImpl.java

@@ -13,8 +13,8 @@ import java.util.List;
 import java.util.Map;
 import java.util.UUID;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.apache.solr.client.solrj.SolrQuery;
 import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.common.SolrDocument;
@@ -34,7 +34,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  */
 public class AuthorityValueServiceImpl implements AuthorityValueService {
 
-    private final Logger log = Logger.getLogger(AuthorityValueServiceImpl.class);
+    private final Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthorityValueServiceImpl.class);
 
     @Autowired(required = true)
     protected AuthorityTypes authorityTypes;

dspace-api/src/main/java/org/dspace/authority/PersonAuthorityValue.java

@@ -12,8 +12,8 @@ import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.lang.ObjectUtils;
+import org.apache.commons.lang3.ObjectUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.solr.common.SolrDocument;
 import org.apache.solr.common.SolrInputDocument;
 

dspace-api/src/main/java/org/dspace/authority/UpdateAuthorities.java

@@ -19,7 +19,7 @@ import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.cli.PosixParser;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authority.factory.AuthorityServiceFactory;
 import org.dspace.authority.service.AuthorityValueService;
 import org.dspace.content.Item;
@@ -40,7 +40,7 @@ public class UpdateAuthorities {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(UpdateAuthorities.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(UpdateAuthorities.class);
 
     protected PrintWriter print = null;
 

dspace-api/src/main/java/org/dspace/authority/indexer/AuthorityConsumer.java

@@ -12,7 +12,7 @@ import java.util.HashSet;
 import java.util.Set;
 import java.util.UUID;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authority.factory.AuthorityServiceFactory;
 import org.dspace.authority.service.AuthorityService;
 import org.dspace.content.DSpaceObject;
@@ -33,7 +33,7 @@ import org.dspace.event.Event;
  */
 public class AuthorityConsumer implements Consumer {
 
-    private final Logger log = Logger.getLogger(AuthorityConsumer.class);
+    private final Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthorityConsumer.class);
 
     /**
      * A set of all item IDs installed which need their authority updated

dspace-api/src/main/java/org/dspace/authority/indexer/AuthorityIndexClient.java

@@ -12,7 +12,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authority.AuthorityValue;
 import org.dspace.authority.factory.AuthorityServiceFactory;
 import org.dspace.authority.service.AuthorityService;
@@ -29,7 +29,7 @@ import org.dspace.core.Context;
  */
 public class AuthorityIndexClient {
 
-    private static Logger log = Logger.getLogger(AuthorityIndexClient.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthorityIndexClient.class);
 
     protected static final AuthorityService authorityService =
         AuthorityServiceFactory.getInstance().getAuthorityService();

dspace-api/src/main/java/org/dspace/authority/indexer/DSpaceAuthorityIndexer.java

@@ -13,8 +13,8 @@ import java.util.List;
 import java.util.Map;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authority.AuthorityValue;
 import org.dspace.authority.service.AuthorityValueService;
 import org.dspace.authorize.AuthorizeException;
@@ -45,7 +45,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  */
 public class DSpaceAuthorityIndexer implements AuthorityIndexerInterface, InitializingBean {
 
-    private static final Logger log = Logger.getLogger(DSpaceAuthorityIndexer.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(DSpaceAuthorityIndexer.class);
 
     /**
      * The list of metadata fields which are to be indexed *
@@ -124,7 +124,7 @@ public class DSpaceAuthorityIndexer implements AuthorityIndexerInterface, Initia
      * This method looks at the authority of a metadata value.
      * If the authority can be found in solr, that value is reused.
      * Otherwise a new authority value will be generated that will be indexed in solr.
-     * 
+     *
      * If the authority starts with AuthorityValueGenerator.GENERATE, a specific type of AuthorityValue will be
      * generated.
      * Depending on the type this may involve querying an external REST service

dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv2.java

@@ -15,12 +15,13 @@ import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.impl.client.HttpClientBuilder;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authority.AuthorityValue;
 import org.dspace.authority.SolrAuthorityInterface;
 import org.dspace.authority.orcid.xml.XMLtoBio;
@@ -35,7 +36,7 @@ import org.orcid.jaxb.model.record_v2.Person;
  */
 public class Orcidv2 implements SolrAuthorityInterface {
 
-    private static Logger log = Logger.getLogger(Orcidv2.class);
+    private static Logger log = LogManager.getLogger(Orcidv2.class);
 
     public RESTConnector restConnector;
     private String OAUTHUrl;
@@ -46,7 +47,9 @@ public class Orcidv2 implements SolrAuthorityInterface {
     private String accessToken;
 
     /**
-     *  Initialize the accessToken that is required for all subsequent calls to ORCID
+     * Initialize the accessToken that is required for all subsequent calls to ORCID.
+     *
+     * @throws java.io.IOException passed through from HTTPclient.
      */
     public void init() throws IOException {
         if (StringUtils.isNotBlank(accessToken) && StringUtils.isNotBlank(clientSecret)) {

dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv2AuthorityValue.java

@@ -15,7 +15,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.UUID;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.solr.common.SolrDocument;
 import org.apache.solr.common.SolrInputDocument;
 import org.dspace.authority.AuthorityValue;

dspace-api/src/main/java/org/dspace/authority/orcid/xml/Converter.java

@@ -14,10 +14,9 @@ import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.Unmarshaller;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.xml.sax.SAXException;
 
-
 /**
  * @param <T> type
  * @author Antoine Snyers (antoine at atmire.com)
@@ -30,7 +29,7 @@ public abstract class Converter<T> {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(Converter.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(Converter.class);
 
     public abstract T convert(InputStream document);
 

dspace-api/src/main/java/org/dspace/authority/orcid/xml/XMLtoBio.java

@@ -12,7 +12,7 @@ import java.net.URISyntaxException;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authority.orcid.Orcidv2;
 import org.dspace.utils.DSpace;
 import org.orcid.jaxb.model.common_v2.OrcidId;
@@ -21,8 +21,6 @@ import org.orcid.jaxb.model.search_v2.Result;
 import org.orcid.jaxb.model.search_v2.Search;
 import org.xml.sax.SAXException;
 
-
-
 /**
  * @author Antoine Snyers (antoine at atmire.com)
  * @author Kevin Van de Velde (kevin at atmire dot com)
@@ -34,7 +32,7 @@ public class XMLtoBio extends Converter {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(XMLtoBio.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(XMLtoBio.class);
 
     @Override
     public List<Person> convert(InputStream xml) {

dspace-api/src/main/java/org/dspace/authority/rest/RESTConnector.java

@@ -15,7 +15,7 @@ import org.apache.http.HttpResponse;
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.impl.client.HttpClientBuilder;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 
 /**
  * @author Antoine Snyers (antoine at atmire.com)
@@ -28,7 +28,7 @@ public class RESTConnector {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(RESTConnector.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(RESTConnector.class);
 
     private String url;
 

dspace-api/src/main/java/org/dspace/authority/util/EnumUtils.java

@@ -7,8 +7,8 @@
  */
 package org.dspace.authority.util;
 
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 
 /**
  * @author Antoine Snyers (antoine at atmire.com)
@@ -21,7 +21,7 @@ public class EnumUtils {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(EnumUtils.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(EnumUtils.class);
 
     /**
      * Default constructor

dspace-api/src/main/java/org/dspace/authority/util/XMLUtils.java

@@ -17,7 +17,7 @@ import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 import javax.xml.xpath.XPathExpressionException;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.apache.xpath.XPathAPI;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -36,7 +36,7 @@ public class XMLUtils {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(XMLUtils.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(XMLUtils.class);
 
     /**
      * Default constructor

dspace-api/src/main/java/org/dspace/authorize/AuthorizeServiceImpl.java

@@ -16,7 +16,7 @@ import java.util.List;
 import java.util.UUID;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.authorize.service.ResourcePolicyService;
 import org.dspace.content.Bitstream;

dspace-api/src/main/java/org/dspace/authorize/ResourcePolicy.java

@@ -23,7 +23,7 @@ import javax.persistence.Table;
 import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
 
-import org.apache.commons.lang.ObjectUtils;
+import org.apache.commons.lang3.ObjectUtils;
 import org.dspace.content.DSpaceObject;
 import org.dspace.core.Context;
 import org.dspace.core.ReloadableEntity;

dspace-api/src/main/java/org/dspace/authorize/ResourcePolicyServiceImpl.java

@@ -15,8 +15,8 @@ import java.util.List;
 import java.util.Set;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.lang.ObjectUtils;
+import org.apache.commons.lang3.ObjectUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.dao.ResourcePolicyDAO;
 import org.dspace.authorize.service.ResourcePolicyService;
 import org.dspace.content.DSpaceObject;
@@ -38,7 +38,7 @@ public class ResourcePolicyServiceImpl implements ResourcePolicyService {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(ResourcePolicyServiceImpl.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ResourcePolicyServiceImpl.class);
 
     @Autowired(required = true)
     protected ContentServiceFactory contentServiceFactory;

dspace-api/src/main/java/org/dspace/browse/BrowseEngine.java

@@ -12,7 +12,7 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
 import org.dspace.content.Item;
@@ -34,7 +34,7 @@ public class BrowseEngine {
     /**
      * the logger for this class
      */
-    private static final Logger log = Logger.getLogger(BrowseEngine.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(BrowseEngine.class);
 
     /**
      * the browse scope which is the basis for our browse

dspace-api/src/main/java/org/dspace/browse/ItemCountDAOSolr.java

@@ -11,7 +11,7 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
 import org.dspace.content.DSpaceObject;
@@ -36,7 +36,7 @@ public class ItemCountDAOSolr implements ItemCountDAO {
     /**
      * Log4j logger
      */
-    private static Logger log = Logger.getLogger(ItemCountDAOSolr.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemCountDAOSolr.class);
 
     /**
      * DSpace context

dspace-api/src/main/java/org/dspace/browse/ItemCounter.java

@@ -9,7 +9,7 @@ package org.dspace.browse;
 
 import java.sql.SQLException;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
 import org.dspace.content.DSpaceObject;
@@ -37,7 +37,7 @@ public class ItemCounter {
     /**
      * Log4j logger
      */
-    private static Logger log = Logger.getLogger(ItemCounter.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemCounter.class);
 
     /**
      * DAO to use to store and retrieve data

dspace-api/src/main/java/org/dspace/browse/ItemListConfig.java

@@ -12,7 +12,7 @@ import java.util.HashMap;
 import java.util.Map;
 import java.util.StringTokenizer;
 
-import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.lang3.ArrayUtils;
 import org.dspace.services.ConfigurationService;
 import org.dspace.services.factory.DSpaceServicesFactory;
 

dspace-api/src/main/java/org/dspace/browse/LocaleOrderingFilter.java

@@ -12,7 +12,7 @@ import java.util.Locale;
 import com.ibm.icu.text.CollationElementIterator;
 import com.ibm.icu.text.Collator;
 import com.ibm.icu.text.RuleBasedCollator;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.text.filter.TextFilter;
 
@@ -32,7 +32,7 @@ import org.dspace.text.filter.TextFilter;
  * @author Graham Triggs
  */
 public class LocaleOrderingFilter implements TextFilter {
-    private static Logger log = Logger.getLogger(LocaleOrderingFilter.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(LocaleOrderingFilter.class);
 
     /**
      * Uses a Locale dependent Collator to generate a sort string

dspace-api/src/main/java/org/dspace/browse/SolrBrowseDAO.java

@@ -16,7 +16,7 @@ import java.util.List;
 import java.util.UUID;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.factory.AuthorizeServiceFactory;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.content.DSpaceObject;
@@ -68,7 +68,7 @@ public class SolrBrowseDAO implements BrowseDAO {
     /**
      * Log4j log
      */
-    private static final Logger log = Logger.getLogger(SolrBrowseDAO.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(SolrBrowseDAO.class);
 
     /**
      * The DSpace context

dspace-api/src/main/java/org/dspace/checker/CheckerCommand.java

@@ -13,7 +13,7 @@ import java.util.Date;
 import java.util.Map;
 
 import org.apache.commons.collections4.MapUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.checker.factory.CheckerServiceFactory;
 import org.dspace.checker.service.ChecksumHistoryService;
 import org.dspace.checker.service.ChecksumResultService;
@@ -42,7 +42,7 @@ public final class CheckerCommand {
     /**
      * Usual Log4J logger.
      */
-    private static final Logger LOG = Logger.getLogger(CheckerCommand.class);
+    private static final Logger LOG = org.apache.logging.log4j.LogManager.getLogger(CheckerCommand.class);
 
     private Context context;
 

dspace-api/src/main/java/org/dspace/checker/CheckerConsumer.java

@@ -7,7 +7,7 @@
  */
 package org.dspace.checker;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.checker.factory.CheckerServiceFactory;
 import org.dspace.checker.service.ChecksumHistoryService;
 import org.dspace.content.Bitstream;
@@ -26,7 +26,7 @@ public class CheckerConsumer implements Consumer {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(CheckerConsumer.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(CheckerConsumer.class);
 
     protected ChecksumHistoryService checksumHistoryService = CheckerServiceFactory.getInstance()
                                                                                    .getChecksumHistoryService();

dspace-api/src/main/java/org/dspace/checker/DailyReportEmailer.java

@@ -21,7 +21,7 @@ import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.cli.PosixParser;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.checker.factory.CheckerServiceFactory;
 import org.dspace.checker.service.SimpleReporterService;
 import org.dspace.core.ConfigurationManager;
@@ -43,7 +43,7 @@ public class DailyReportEmailer {
     /**
      * log4j logger.
      */
-    private static Logger log = Logger.getLogger(DailyReportEmailer.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DailyReportEmailer.class);
 
     /**
      * Default constructor.

dspace-api/src/main/java/org/dspace/checker/HandleDispatcher.java

@@ -12,7 +12,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Bitstream;
 import org.dspace.content.DSpaceObject;
 import org.dspace.content.factory.ContentServiceFactory;
@@ -35,7 +35,7 @@ public class HandleDispatcher implements BitstreamDispatcher {
     /**
      * Log 4j logger.
      */
-    private static final Logger LOG = Logger.getLogger(HandleDispatcher.class);
+    private static final Logger LOG = org.apache.logging.log4j.LogManager.getLogger(HandleDispatcher.class);
 
     protected Context context;
 

dspace-api/src/main/java/org/dspace/checker/MostRecentChecksum.java

@@ -19,8 +19,8 @@ import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
 import javax.persistence.Transient;
 
-import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.EqualsBuilder;
-import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.dspace.content.Bitstream;
 
 /**

dspace-api/src/main/java/org/dspace/checker/MostRecentChecksumServiceImpl.java

@@ -11,7 +11,7 @@ import java.sql.SQLException;
 import java.util.Date;
 import java.util.List;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.checker.dao.MostRecentChecksumDAO;
 import org.dspace.checker.service.ChecksumResultService;
 import org.dspace.checker.service.MostRecentChecksumService;
@@ -28,7 +28,8 @@ import org.springframework.beans.factory.annotation.Autowired;
  * @author kevinvandevelde at atmire.com
  */
 public class MostRecentChecksumServiceImpl implements MostRecentChecksumService {
-    private static final Logger log = Logger.getLogger(MostRecentChecksumServiceImpl.class);
+    private static final Logger log =
+            org.apache.logging.log4j.LogManager.getLogger(MostRecentChecksumServiceImpl.class);
 
     @Autowired(required = true)
     protected MostRecentChecksumDAO mostRecentChecksumDAO;

dspace-api/src/main/java/org/dspace/checker/ResultsLogger.java

@@ -12,7 +12,7 @@ import java.text.DateFormat;
 import java.text.SimpleDateFormat;
 import java.util.Date;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Bitstream;
 import org.dspace.core.Context;
 import org.dspace.core.I18nUtil;
@@ -30,7 +30,7 @@ public class ResultsLogger implements ChecksumResultsCollector {
     /**
      * Usual Log4J logger.
      */
-    private static final Logger LOG = Logger.getLogger(ResultsLogger.class);
+    private static final Logger LOG = org.apache.logging.log4j.LogManager.getLogger(ResultsLogger.class);
 
     /**
      * Utility date format.

dspace-api/src/main/java/org/dspace/checker/ResultsPruner.java

@@ -19,7 +19,7 @@ import java.util.Properties;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.checker.factory.CheckerServiceFactory;
 import org.dspace.checker.service.ChecksumHistoryService;
 import org.dspace.core.ConfigurationManager;
@@ -40,7 +40,7 @@ public final class ResultsPruner {
     /**
      * Default logger.
      */
-    private static final Logger LOG = Logger.getLogger(ResultsPruner.class);
+    private static final Logger LOG = org.apache.logging.log4j.LogManager.getLogger(ResultsPruner.class);
 
     /**
      * Factory method for the default results pruner configuration using

dspace-api/src/main/java/org/dspace/content/BitstreamFormatServiceImpl.java

@@ -12,7 +12,7 @@ import java.util.Collections;
 import java.util.List;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.content.dao.BitstreamFormatDAO;
@@ -33,7 +33,7 @@ public class BitstreamFormatServiceImpl implements BitstreamFormatService {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(BitstreamFormat.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(BitstreamFormat.class);
 
     @Autowired(required = true)
     protected BitstreamFormatDAO bitstreamFormatDAO;

dspace-api/src/main/java/org/dspace/content/BitstreamServiceImpl.java

@@ -15,8 +15,8 @@ import java.util.List;
 import java.util.UUID;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.content.dao.BitstreamDAO;
@@ -43,7 +43,7 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(BitstreamServiceImpl.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(BitstreamServiceImpl.class);
 
 
     @Autowired(required = true)
@@ -103,6 +103,8 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
         clonedBitstream.setSizeBytes(bitstream.getSizeBytes());
         clonedBitstream.setChecksum(bitstream.getChecksum());
         clonedBitstream.setChecksumAlgorithm(bitstream.getChecksumAlgorithm());
+        clonedBitstream.setFormat(bitstream.getBitstreamFormat());
+
         try {
             //Update our bitstream but turn off the authorization system since permissions
             //haven't been set at this point in time.

dspace-api/src/main/java/org/dspace/content/BundleServiceImpl.java

@@ -16,8 +16,8 @@ import java.util.List;
 import java.util.UUID;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.AuthorizeConfiguration;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.authorize.ResourcePolicy;
@@ -45,7 +45,7 @@ public class BundleServiceImpl extends DSpaceObjectServiceImpl<Bundle> implement
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(Bundle.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(Bundle.class);
 
     @Autowired(required = true)
     protected BundleDAO bundleDAO;

dspace-api/src/main/java/org/dspace/content/CollectionServiceImpl.java

@@ -20,8 +20,8 @@ import java.util.MissingResourceException;
 import java.util.UUID;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.AuthorizeUtil;
 import org.dspace.authorize.AuthorizeConfiguration;
 import org.dspace.authorize.AuthorizeException;
@@ -61,7 +61,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
     /**
      * log4j category
      */
-    private static final Logger log = Logger.getLogger(CollectionServiceImpl.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(CollectionServiceImpl.class);
 
     @Autowired(required = true)
     protected CollectionDAO collectionDAO;

dspace-api/src/main/java/org/dspace/content/Community.java

@@ -23,8 +23,8 @@ import javax.persistence.OneToOne;
 import javax.persistence.Table;
 import javax.persistence.Transient;
 
-import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.comparator.NameAscendingComparator;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.CommunityService;
@@ -52,7 +52,7 @@ public class Community extends DSpaceObject implements DSpaceObjectLegacySupport
     /**
      * log4j category
      */
-    private static final Logger log = Logger.getLogger(Community.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(Community.class);
 
     @Column(name = "community_id", insertable = false, updatable = false)
     private Integer legacyId;

dspace-api/src/main/java/org/dspace/content/CommunityServiceImpl.java

@@ -17,8 +17,8 @@ import java.util.MissingResourceException;
 import java.util.UUID;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.AuthorizeUtil;
 import org.dspace.authorize.AuthorizeConfiguration;
 import org.dspace.authorize.AuthorizeException;
@@ -51,7 +51,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
     /**
      * log4j category
      */
-    private static Logger log = Logger.getLogger(CommunityServiceImpl.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(CommunityServiceImpl.class);
 
     @Autowired(required = true)
     protected CommunityDAO communityDAO;

dspace-api/src/main/java/org/dspace/content/DCDate.java

@@ -18,7 +18,7 @@ import java.util.Locale;
 import java.util.Map;
 import java.util.TimeZone;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 
 // FIXME: Not very robust - assumes dates will always be valid
 
@@ -45,7 +45,7 @@ public class DCDate {
     /**
      * Logger
      */
-    private static Logger log = Logger.getLogger(DCDate.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DCDate.class);
 
     // UTC timezone
     private static final TimeZone utcZone = TimeZone.getTimeZone("UTC");

dspace-api/src/main/java/org/dspace/content/DSpaceObjectServiceImpl.java

@@ -17,9 +17,9 @@ import java.util.Map;
 import java.util.StringTokenizer;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.lang3.ArrayUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.authority.Choices;
 import org.dspace.content.authority.service.ChoiceAuthorityService;
@@ -48,7 +48,7 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
     /**
      * log4j category
      */
-    private static final Logger log = Logger.getLogger(DSpaceObjectServiceImpl.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(DSpaceObjectServiceImpl.class);
 
     @Autowired(required = true)
     protected ChoiceAuthorityService choiceAuthorityService;

dspace-api/src/main/java/org/dspace/content/ItemComparator.java

@@ -15,7 +15,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
 import org.dspace.sort.OrderFormat;

dspace-api/src/main/java/org/dspace/content/ItemServiceImpl.java

@@ -17,8 +17,8 @@ import java.util.List;
 import java.util.UUID;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.AuthorizeUtil;
 import org.dspace.authorize.AuthorizeConfiguration;
 import org.dspace.authorize.AuthorizeException;
@@ -63,7 +63,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
     /**
      * log4j category
      */
-    private static final Logger log = Logger.getLogger(Item.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(Item.class);
 
     @Autowired(required = true)
     protected ItemDAO itemDAO;

dspace-api/src/main/java/org/dspace/content/MetadataFieldServiceImpl.java

@@ -12,7 +12,7 @@ import java.sql.SQLException;
 import java.util.List;
 
 import org.apache.commons.collections4.CollectionUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.content.dao.MetadataFieldDAO;
@@ -33,7 +33,7 @@ public class MetadataFieldServiceImpl implements MetadataFieldService {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(MetadataFieldServiceImpl.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(MetadataFieldServiceImpl.class);
 
     @Autowired(required = true)
     protected MetadataFieldDAO metadataFieldDAO;

dspace-api/src/main/java/org/dspace/content/MetadataSchemaServiceImpl.java

@@ -10,7 +10,7 @@ package org.dspace.content;
 import java.sql.SQLException;
 import java.util.List;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.content.dao.MetadataSchemaDAO;
@@ -31,7 +31,7 @@ public class MetadataSchemaServiceImpl implements MetadataSchemaService {
     /**
      * log4j logger
      */
-    private static Logger log = Logger.getLogger(MetadataSchemaServiceImpl.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(MetadataSchemaServiceImpl.class);
 
     @Autowired(required = true)
     protected AuthorizeService authorizeService;

dspace-api/src/main/java/org/dspace/content/MetadataValueServiceImpl.java

@@ -12,7 +12,7 @@ import java.sql.SQLException;
 import java.util.Iterator;
 import java.util.List;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.content.dao.MetadataValueDAO;
@@ -33,7 +33,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  */
 public class MetadataValueServiceImpl implements MetadataValueService {
 
-    private static final Logger log = Logger.getLogger(MetadataValueServiceImpl.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(MetadataValueServiceImpl.class);
 
     @Autowired(required = true)
     protected AuthorizeService authorizeService;

dspace-api/src/main/java/org/dspace/content/WorkspaceItem.java

@@ -25,7 +25,7 @@ import javax.persistence.OneToOne;
 import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
-import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.dspace.core.Context;
 import org.dspace.core.ReloadableEntity;
 import org.dspace.eperson.EPerson;

dspace-api/src/main/java/org/dspace/content/WorkspaceItemServiceImpl.java

@@ -13,7 +13,7 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.DCInputsReaderException;
 import org.dspace.app.util.Util;
 import org.dspace.authorize.AuthorizeException;
@@ -40,7 +40,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  */
 public class WorkspaceItemServiceImpl implements WorkspaceItemService {
 
-    private static final Logger log = Logger.getLogger(WorkspaceItemServiceImpl.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(WorkspaceItemServiceImpl.class);
 
     @Autowired(required = true)
     protected WorkspaceItemDAO workspaceItemDAO;
@@ -147,6 +147,12 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
         return workspaceItemDAO.findByEPerson(context, ep);
     }
 
+    @Override
+    public List<WorkspaceItem> findByEPerson(Context context, EPerson ep, Integer limit, Integer offset)
+        throws SQLException {
+        return workspaceItemDAO.findByEPerson(context, ep, limit, offset);
+    }
+
     @Override
     public List<WorkspaceItem> findByCollection(Context context, Collection collection) throws SQLException {
         return workspaceItemDAO.findByCollection(context, collection);
@@ -231,6 +237,11 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
         return workspaceItemDAO.countRows(context);
     }
 
+    @Override
+    public int countByEPerson(Context context, EPerson ep) throws SQLException {
+        return workspaceItemDAO.countRows(context, ep);
+    }
+
     @Override
     public List<Map.Entry<Integer, Long>> getStageReachedCounts(Context context) throws SQLException {
         return workspaceItemDAO.getStageReachedCounts(context);

dspace-api/src/main/java/org/dspace/content/authority/ChoiceAuthorityServiceImpl.java

@@ -14,7 +14,7 @@ import java.util.Map;
 import java.util.Set;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.DCInput;
 import org.dspace.app.util.DCInputSet;
 import org.dspace.app.util.DCInputsReader;
@@ -49,7 +49,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  * @see ChoiceAuthority
  */
 public final class ChoiceAuthorityServiceImpl implements ChoiceAuthorityService {
-    private Logger log = Logger.getLogger(ChoiceAuthorityServiceImpl.class);
+    private Logger log = org.apache.logging.log4j.LogManager.getLogger(ChoiceAuthorityServiceImpl.class);
 
     // map of field key to authority plugin
     protected Map<String, ChoiceAuthority> controller = new HashMap<String, ChoiceAuthority>();
@@ -264,39 +264,42 @@ public final class ChoiceAuthorityServiceImpl implements ChoiceAuthorityService
         try {
             DCInputsReader dcInputsReader = new DCInputsReader();
             for (DCInputSet dcinputSet : dcInputsReader.getAllInputs(Integer.MAX_VALUE, 0)) {
-                DCInput[] dcinputs = dcinputSet.getFields();
+                DCInput[][] dcinputs = dcinputSet.getFields();
-                for (DCInput dcinput : dcinputs) {
+                for (DCInput[] dcrows : dcinputs) {
-                    if (StringUtils.isNotBlank(dcinput.getPairsType())
+                    for (DCInput dcinput : dcrows) {
-                        || StringUtils.isNotBlank(dcinput.getVocabulary())) {
+                        if (StringUtils.isNotBlank(dcinput.getPairsType())
-                        String authorityName = dcinput.getPairsType();
+                            || StringUtils.isNotBlank(dcinput.getVocabulary())) {
-                        if (StringUtils.isBlank(authorityName)) {
+                            String authorityName = dcinput.getPairsType();
-                            authorityName = dcinput.getVocabulary();
+                            if (StringUtils.isBlank(authorityName)) {
-                        }
+                                authorityName = dcinput.getVocabulary();
-                        if (!StringUtils.equals(dcinput.getInputType(), "qualdrop_value")) {
+                            }
-                            String fieldKey = makeFieldKey(dcinput.getSchema(), dcinput.getElement(),
+                            if (!StringUtils.equals(dcinput.getInputType(), "qualdrop_value")) {
-                                                           dcinput.getQualifier());
+                                String fieldKey = makeFieldKey(dcinput.getSchema(), dcinput.getElement(),
-                            ChoiceAuthority ca = controller.get(authorityName);
+                                                               dcinput.getQualifier());
-                            if (ca == null) {
+                                ChoiceAuthority ca = controller.get(authorityName);
-                                InputFormSelfRegisterWrapperAuthority ifa = new InputFormSelfRegisterWrapperAuthority();
+                                if (ca == null) {
-                                if (controller.containsKey(fieldKey)) {
+                                    InputFormSelfRegisterWrapperAuthority ifa = new
-                                    ifa = (InputFormSelfRegisterWrapperAuthority) controller.get(fieldKey);
+                                        InputFormSelfRegisterWrapperAuthority();
+                                    if (controller.containsKey(fieldKey)) {
+                                        ifa = (InputFormSelfRegisterWrapperAuthority) controller.get(fieldKey);
+                                    }
+
+                                    ChoiceAuthority ma = (ChoiceAuthority) pluginService
+                                        .getNamedPlugin(ChoiceAuthority.class, authorityName);
+                                    if (ma == null) {
+                                        log.warn("Skipping invalid configuration for " + fieldKey
+                                                     + " because named plugin not found: " + authorityName);
+                                        continue;
+                                    }
+                                    ifa.getDelegates().put(dcinputSet.getFormName(), ma);
+                                    controller.put(fieldKey, ifa);
                                 }
 
-                                ChoiceAuthority ma = (ChoiceAuthority) pluginService
+                                if (!authorities.containsKey(authorityName)) {
-                                    .getNamedPlugin(ChoiceAuthority.class, authorityName);
+                                    authorities.put(authorityName, fieldKey);
-                                if (ma == null) {
-                                    log.warn("Skipping invalid configuration for " + fieldKey
-                                                 + " because named plugin not found: " + authorityName);
-                                    continue;
                                 }
-                                ifa.getDelegates().put(dcinputSet.getFormName(), ma);
-                                controller.put(fieldKey, ifa);
-                            }
 
-                            if (!authorities.containsKey(authorityName)) {
-                                authorities.put(authorityName, fieldKey);
                             }
-
                         }
                     }
                 }

dspace-api/src/main/java/org/dspace/content/authority/Choices.java

@@ -7,7 +7,7 @@
  */
 package org.dspace.content.authority;
 
-import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.lang3.ArrayUtils;
 
 /**
  * Record class to hold a set of Choices returned by an authority in response

dspace-api/src/main/java/org/dspace/content/authority/DCInputAuthority.java

@@ -12,8 +12,8 @@ import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
 
-import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.lang3.ArrayUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.DCInputsReader;
 import org.dspace.app.util.DCInputsReaderException;
 import org.dspace.content.Collection;
@@ -42,7 +42,7 @@ import org.dspace.core.SelfNamedPlugin;
  * fields.
  */
 public class DCInputAuthority extends SelfNamedPlugin implements ChoiceAuthority {
-    private static Logger log = Logger.getLogger(DCInputAuthority.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DCInputAuthority.class);
 
     private String values[] = null;
     private String labels[] = null;

dspace-api/src/main/java/org/dspace/content/authority/DSpaceControlledVocabulary.java

@@ -16,9 +16,9 @@ import javax.xml.xpath.XPathConstants;
 import javax.xml.xpath.XPathExpressionException;
 import javax.xml.xpath.XPathFactory;
 
-import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.lang3.ArrayUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Collection;
 import org.dspace.core.SelfNamedPlugin;
 import org.dspace.services.ConfigurationService;
@@ -56,7 +56,7 @@ import org.xml.sax.InputSource;
 
 public class DSpaceControlledVocabulary extends SelfNamedPlugin implements ChoiceAuthority {
 
-    private static Logger log = Logger.getLogger(DSpaceControlledVocabulary.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DSpaceControlledVocabulary.class);
     protected static String xpathTemplate = "//node[contains(translate(@label,'ABCDEFGHIJKLMNOPQRSTUVWXYZ'," +
         "'abcdefghijklmnopqrstuvwxyz'),'%s')]";
     protected static String idTemplate = "//node[@id = '%s']";