[maven-release-plugin] prepare release dspace-7.0-preview-1

DS-4253 Avoid oom during discovery reindex

.dockerignore

@@ -0,0 +1,6 @@
+.git/
+.idea/
+.settings/
+*/target/
+dspace/modules/*/target/
+Dockerfile.*

.travis.yml

@@ -26,19 +26,20 @@ before_install:
 # Skip install stage, as we'll do it below
 install: "echo 'Skipping install stage, dependencies will be downloaded during build and test stages.'"
 
-# Two stage Build and Test
+# Build DSpace and run both Unit and Integration Tests
-# 1. Install & Unit Test APIs
-# 2. Assemble DSpace
 script:
-  # 1. [Install & Unit Test] Check source code licenses and run source code Unit Tests
+  # Summary of flags used (below):
   #     license:check           => Validate all source code license headers
   #     -Dmaven.test.skip=false => Enable DSpace Unit Tests
   #     -DskipITs=false         => Enable DSpace Integration Tests
-  #        -P !assembly            => Skip normal assembly (as it can be memory intensive)
+  #     -P !assembly            => Skip assembly of "dspace-installer" directory (as it can be memory intensive)
   #     -B                      => Maven batch/non-interactive mode (recommended for CI)
   #     -V                      => Display Maven version info before build
   #     -Dsurefire.rerunFailingTestsCount=2 => try again for flakey tests, and keep track of/report on number of retries
   - "mvn clean install license:check -Dmaven.test.skip=false -DskipITs=false -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2"
-  # 2. [Assemble DSpace] Ensure overlay & assembly process works (from [src]/dspace/)
+
-  #        -P !assembly => SKIP the actual building of [src]/dspace/dspace-installer (as it can be memory intensive)
+# After a successful build and test (see 'script'), send code coverage reports to coveralls.io
-  - "cd dspace && mvn package -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2"
+# These code coverage reports are generated by jacoco-maven-plugin (during test process above).
+after_success:
+  # Run "verify", enabling the "coveralls" profile. This sends our reports to coveralls.io (see coveralls-maven-plugin)
+  - "cd dspace && mvn verify -P coveralls"

Dockerfile.dependencies

@@ -0,0 +1,24 @@
+# This image will be published as dspace/dspace-dependencies
+# The purpose of this image is to make the build for dspace/dspace run faster 
+
+# Step 1 - Run Maven Build
+FROM maven:3-jdk-8 as build
+ARG TARGET_DIR=dspace-installer
+WORKDIR /app
+
+RUN useradd dspace \
+    && mkdir /home/dspace \
+    && chown -Rv dspace: /home/dspace
+USER dspace
+
+# Copy the DSpace source code into the workdir (excluding .dockerignore contents)
+ADD --chown=dspace . /app/
+COPY dspace/src/main/docker/local.cfg /app/local.cfg
+
+# Trigger the installation of all maven dependencies
+# Clean up the built artifacts in the same step to keep the docker image small
+RUN mvn package && mvn clean
+
+# Clear the contents of the /app directory so no artifacts are left when dspace:dspace is built
+USER root
+RUN rm -rf /app/*

Dockerfile.jdk8

@@ -0,0 +1,63 @@
+# 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:3-jdk-8
+# - note: 
+# - default tag for branch: dspace/dspace: dspace/dspace:dspace-7_x-jdk8
+
+# Step 1 - Run Maven Build
+FROM dspace/dspace-dependencies:dspace-7_x as build
+ARG TARGET_DIR=dspace-installer
+WORKDIR /app
+
+# The dspace-install directory will be written to /install
+RUN mkdir /install \
+    && chown -Rv dspace: /install \
+    && chown -Rv dspace: /app
+
+USER dspace
+
+# Copy the DSpace source code into the workdir (excluding .dockerignore contents)
+ADD --chown=dspace . /app/
+COPY dspace/src/main/docker/local.cfg /app/local.cfg
+
+# Build DSpace.  Copy the dspace-install directory to /install.  Clean up the build to keep the docker image small
+RUN mvn package && \
+  mv /app/dspace/target/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM tomcat:8-jre8 as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.10.5
+ENV ANT_HOME /tmp/ant-$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 init_installation 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
+ENV DSPACE_INSTALL=/dspace
+COPY --from=ant_build /dspace $DSPACE_INSTALL
+EXPOSE 8080 8009
+
+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

Dockerfile.jdk8-test

@@ -0,0 +1,69 @@
+# 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:3-jdk-8
+# - note: 
+# - default tag for branch: dspace/dspace: dspace/dspace:dspace-7_x-jdk8-test
+
+# Step 1 - Run Maven Build
+FROM dspace/dspace-dependencies:dspace-7_x as build
+ARG TARGET_DIR=dspace-installer
+WORKDIR /app
+
+# The dspace-install directory will be written to /install
+RUN mkdir /install \
+    && chown -Rv dspace: /install \
+    && chown -Rv dspace: /app
+
+USER dspace
+
+# Copy the DSpace source code into the workdir (excluding .dockerignore contents)
+ADD --chown=dspace . /app/
+COPY dspace/src/main/docker/local.cfg /app/local.cfg
+
+# Build DSpace.  Copy the dspace-install directory to /install.  Clean up the build to keep the docker image small
+RUN mvn package && \
+  mv /app/dspace/target/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM tomcat:8-jre8 as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.10.5
+ENV ANT_HOME /tmp/ant-$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 init_installation 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
+ENV DSPACE_INSTALL=/dspace
+COPY --from=ant_build /dspace $DSPACE_INSTALL
+EXPOSE 8080 8009
+
+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
+
+COPY dspace/src/main/docker/test/solr_web.xml $DSPACE_INSTALL/webapps/solr/WEB-INF/web.xml
+COPY dspace/src/main/docker/test/rest_web.xml $DSPACE_INSTALL/webapps/rest/WEB-INF/web.xml
+
+RUN sed -i -e "s|\${dspace.dir}|$DSPACE_INSTALL|" $DSPACE_INSTALL/webapps/solr/WEB-INF/web.xml && \
+    sed -i -e "s|\${dspace.dir}|$DSPACE_INSTALL|" $DSPACE_INSTALL/webapps/rest/WEB-INF/web.xml

LICENSES_THIRD_PARTY

@@ -366,7 +366,6 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * FindBugs-Annotations (com.google.code.findbugs:annotations:3.0.1u2 - http://findbugs.sourceforge.net/)
         * MaxMind GeoIP Legacy API (com.maxmind.geoip:geoip-api:1.3.0 - https://github.com/maxmind/geoip-api-java)
         * JHighlight (com.uwyn:jhighlight:1.0 - https://jhighlight.dev.java.net/)
-        * DSpace TM-Extractors Dependency (org.dspace.dependencies:dspace-tm-extractors:1.0.1 - http://projects.dspace.org/dspace-pom/dspace-tm-extractors)
         * A Hibernate O/RM Module (org.hibernate:hibernate-core:4.2.21.Final - http://hibernate.org)
         * A Hibernate O/RM Module (org.hibernate:hibernate-ehcache:4.2.21.Final - http://hibernate.org)
         * Hibernate Commons Annotations (org.hibernate.common:hibernate-commons-annotations:4.0.2.Final - http://hibernate.org)

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, 
@@ -76,6 +79,57 @@ install, upgrade, customize or host DSpace, then we recommend getting in touch w
 
 The DSpace Issue Tracker can be found at: https://jira.duraspace.org/projects/DS/summary
 
+## Testing
+
+### Running Tests
+
+By default, in DSpace, Unit Tests and Integration Tests are disabled. However, they are
+run automatically by [Travis CI](https://travis-ci.org/DSpace/DSpace/) for all Pull Requests and code commits.
+
+* How to run both Unit Tests (via `maven-surefire-plugin`) and Integration Tests (via `maven-failsafe-plugin`):
+  ```
+  # NOTE: while "mvn test" runs Unit Tests,
+  # Integration Tests only run for "verify" or "install" phases
+  mvn clean install -Dmaven.test.skip=false -DskipITs=false
+  ```
+* How to run just Unit Tests:
+  ```
+  mvn clean test -Dmaven.test.skip=false
+  ```
+* How to run a *single* Unit Test
+  ```
+  # Run all tests in a specific test class
+  # NOTE: testClassName is just the class name, do not include package
+  mvn clean test -Dmaven.test.skip=false -Dtest=[testClassName]
+  
+  # Run one test method in a specific test class
+  mvn clean test -Dmaven.test.skip=false -Dtest=[testClassName]#[testMethodName]
+  ```
+* How to run Integration Tests (requires running Unit tests too)
+  ```
+  mvn clean verify -Dmaven.test.skip=false -DskipITs=false
+  ```
+* How to run a *single* Integration Test (requires running Unit tests too)
+  ```
+  # Run all integration tests in a specific test class
+  # NOTE: Integration Tests only run for "verify" or "install" phases
+  # NOTE: testClassName is just the class name, do not include package
+  mvn clean verify -Dmaven.test.skip=false -DskipITs=false -Dit.test=[testClassName]
+  
+  # Run one test method in a specific test class
+  mvn clean verify -Dmaven.test.skip=false -DskipITs=false -Dit.test=[testClassName]#[testMethodName]
+  ```
+* How to run only tests of a specific DSpace module
+  ```
+  # Before you can run only one module's tests, other modules may need installing into your ~/.m2
+  cd [dspace-src]
+  mvn clean install
+  
+  # Then, move into a module subdirectory, and run the test command
+  cd [dspace-src]/dspace-spring-rest
+  # Choose your test command from the lists above
+  ```
+
 ## License
 
 DSpace source code is freely available under a standard [BSD 3-Clause license](https://opensource.org/licenses/BSD-3-Clause).

dspace-api/pom.xml

@@ -1,5 +1,4 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.dspace</groupId>
     <artifactId>dspace-api</artifactId>
@@ -13,7 +12,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.0-SNAPSHOT</version>
+        <version>7.0-preview-1</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -51,6 +50,10 @@
                 <configuration>
                     <debug>true</debug>
                     <showDeprecation>true</showDeprecation>
+                    <compilerArguments>
+                        <processor>org.hibernate.jpamodelgen.JPAMetaModelEntityProcessor</processor>
+                    </compilerArguments>
+
                 </configuration>
             </plugin>
             <plugin>
@@ -81,6 +84,7 @@
                         <exclude>**/src/test/resources/**</exclude>
                         <exclude>**/src/test/data/**</exclude>
                         <exclude>**/.gitignore</exclude>
+                        <exclude>**/src/main/resources/rebel.xml</exclude>
                         <exclude>src/test/data/dspaceFolder/config/spiders/**</exclude>
                         <exclude>src/main/java/org/apache/solr/handler/extraction/ExtractingParams.java</exclude>
                     </excludes>
@@ -307,6 +311,10 @@
             <groupId>org.hibernate</groupId>
             <artifactId>hibernate-ehcache</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.hibernate</groupId>
+            <artifactId>hibernate-jpamodelgen</artifactId>
+        </dependency>
         <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-validator-cdi</artifactId>
@@ -334,10 +342,6 @@
             <groupId>org.dspace</groupId>
             <artifactId>mets</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.dspace.dependencies</groupId>
-            <artifactId>dspace-tm-extractors</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>apache-jena-libs</artifactId>
@@ -351,6 +355,14 @@
                     <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>
@@ -361,10 +373,6 @@
             <groupId>commons-codec</groupId>
             <artifactId>commons-codec</artifactId>
         </dependency>
-        <dependency>
-            <groupId>commons-collections</groupId>
-            <artifactId>commons-collections</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-collections4</artifactId>
@@ -383,8 +391,8 @@
             <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>
@@ -400,7 +408,7 @@
         </dependency>
         <dependency>
             <groupId>javax.servlet</groupId>
-            <artifactId>servlet-api</artifactId>
+            <artifactId>javax.servlet-api</artifactId>
             <scope>provided</scope>
         </dependency>
         <dependency>
@@ -418,8 +426,16 @@
             <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>
@@ -532,6 +548,10 @@
                     <groupId>org.mockito</groupId>
                     <artifactId>mockito-core</artifactId>
 	        </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
         <dependency>
@@ -549,6 +569,10 @@
                     <groupId>org.mockito</groupId>
                     <artifactId>mockito-core</artifactId>
 	        </exclusion>
+		<exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
         <dependency>
@@ -562,7 +586,7 @@
         <dependency>
             <groupId>org.apache.solr</groupId>
             <artifactId>solr-solrj</artifactId>
-            <version>${solr.version}</version>
+            <version>${solr.client.version}</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.slf4j</groupId>
@@ -576,8 +600,8 @@
         </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>
@@ -597,7 +621,7 @@
         <dependency>
             <groupId>org.apache.lucene</groupId>
             <artifactId>lucene-core</artifactId>
-            <version>4.10.4</version>
+            <version>${solr.client.version}</version>
         </dependency>
 
         <dependency>
@@ -616,7 +640,6 @@
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>
-            <version>19.0</version>
         </dependency>
 
 
@@ -719,20 +742,19 @@
                     <groupId>joda-time</groupId>
                     <artifactId>joda-time</artifactId>
                 </exclusion>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-databind</artifactId>
-                </exclusion>
             </exclusions>
         </dependency>
-        <!-- S3 also wanted jackson... -->
+
+        <!-- For ORCID v2 integration -->
         <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
+            <groupId>org.dspace</groupId>
-            <artifactId>jackson-core</artifactId>
+            <artifactId>orcid-jaxb-api</artifactId>
+            <version>2.1.0</version>
         </dependency>
         <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
+            <groupId>org.json</groupId>
-            <artifactId>jackson-databind</artifactId>
+            <artifactId>json</artifactId>
+            <version>20180130</version>
         </dependency>
     </dependencies>
 

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

@@ -17,7 +17,7 @@ import org.apache.commons.cli.CommandLineParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.PosixParser;
-import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.collections4.CollectionUtils;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Community;
 import org.dspace.content.factory.ContentServiceFactory;
@@ -180,14 +180,10 @@ public class CommunityFiliator {
         // second test - circularity: parent's parents can't include proposed
         // child
         List<Community> parentDads = parent.getParentCommunities();
-
+        if (parentDads.contains(child)) {
-        for (int i = 0; i < parentDads.size(); i++) {
+            System.out.println("Error, circular parentage - child is parent of parent");
-            if (parentDads.get(i).getID().equals(child.getID())) {
-                System.out
-                    .println("Error, circular parentage - child is parent of parent");
             System.exit(1);
         }
-        }
 
         // everthing's OK
         communityService.addSubcommunity(c, parent, child);
@@ -210,26 +206,15 @@ public class CommunityFiliator {
         throws SQLException, AuthorizeException, IOException {
         // verify that child is indeed a child of parent
         List<Community> parentKids = parent.getSubcommunities();
-        boolean isChild = false;
+        if (!parentKids.contains(child)) {
-
+            System.out.println("Error, child community not a child of parent community");
-        for (int i = 0; i < parentKids.size(); i++) {
-            if (parentKids.get(i).getID().equals(child.getID())) {
-                isChild = true;
-
-                break;
-            }
-        }
-
-        if (!isChild) {
-            System.out
-                .println("Error, child community not a child of parent community");
             System.exit(1);
         }
 
         // OK remove the mappings - but leave the community, which will become
         // top-level
-        child.getParentCommunities().remove(parent);
+        child.removeParentCommunity(parent);
-        parent.getSubcommunities().remove(child);
+        parent.removeSubCommunity(child);
         communityService.update(c, child);
         communityService.update(c, parent);
 

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/MetadataImporter.java

@@ -21,6 +21,7 @@ import org.apache.xpath.XPathAPI;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
+import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.content.NonUniqueMetadataException;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.MetadataFieldService;
@@ -248,7 +249,7 @@ public class MetadataImporter {
 
         // If the schema is not provided default to DC
         if (schema == null) {
-            schema = MetadataSchema.DC_SCHEMA;
+            schema = MetadataSchemaEnum.DC.getName();
         }
 
 

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/administer/StructBuilder.java

@@ -21,8 +21,10 @@ import javax.xml.transform.TransformerException;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
+import org.apache.commons.cli.ParseException;
 import org.apache.xpath.XPathAPI;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Collection;
@@ -45,6 +47,7 @@ import org.xml.sax.SAXException;
  * an XML file.
  *
  * The XML file structure needs to be:
+ * <p>
  * {@code
  * <import_structure>
  * <community>
@@ -56,29 +59,31 @@ import org.xml.sax.SAXException;
  * </community>
  * </import_structure>
  * }
- * it can be arbitrarily deep, and supports all the metadata elements
+ * <p>
+ * It can be arbitrarily deep, and supports all the metadata elements
  * that make up the community and collection metadata.  See the system
- * documentation for more details
+ * documentation for more details.
  *
  * @author Richard Jones
  */
 
 public class StructBuilder {
     /**
-     * the output xml document which will contain updated information about the
+     * The output XML document which will contain updated information about the
-     * imported structure
+     * imported structure.
      */
-    private static org.jdom.Document xmlOutput = new org.jdom.Document(new Element("imported_structure"));
+    private static final org.jdom.Document xmlOutput
+            = new org.jdom.Document(new Element("imported_structure"));
 
     /**
-     * a hashtable to hold metadata for the collection being worked on
+     * A hash table to hold metadata for the collection being worked on.
      */
-    private static Map<String, String> collectionMap = new HashMap<String, String>();
+    private static final Map<String, String> collectionMap = new HashMap<>();
 
     /**
-     * a hashtable to hold metadata for the community being worked on
+     * A hash table to hold metadata for the community being worked on.
      */
-    private static Map<String, String> communityMap = new HashMap<String, String>();
+    private static final Map<String, String> communityMap = new HashMap<>();
 
     protected static CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
     protected static CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
@@ -101,19 +106,34 @@ public class StructBuilder {
      * with the handle for each imported item added as an attribute.
      *
      * @param argv the command line arguments given
-     * @throws Exception if an error occurs
+     * @throws ParserConfigurationException passed through.
+     * @throws SQLException passed through.
      */
     public static void main(String[] argv)
-        throws Exception {
+            throws ParserConfigurationException, SQLException {
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
 
         Options options = new Options();
 
-        options.addOption("f", "file", true, "file");
+        options.addOption("h", "help", false, "help");
+        options.addOption("?", "help");
+        options.addOption("f", "file", true, "input structure document");
         options.addOption("e", "eperson", true, "eperson");
-        options.addOption("o", "output", true, "output");
+        options.addOption("o", "output", true, "output structure document");
 
-        CommandLine line = parser.parse(options, argv);
+        CommandLine line = null;
+        try {
+            line = parser.parse(options, argv);
+        } catch (ParseException ex) {
+            System.err.println(ex.getMessage());
+            usage(options);
+            System.exit(1);
+        }
+
+        if (line.hasOption('h') || line.hasOption('?')) {
+            usage(options);
+            System.exit(0);
+        }
 
         String file = null;
         String eperson = null;
@@ -132,22 +152,41 @@ public class StructBuilder {
         }
 
         if (output == null || eperson == null || file == null) {
-            usage();
+            usage(options);
-            System.exit(0);
+            System.exit(1);
         }
 
         // create a context
         Context context = new Context();
 
         // set the context
+        try {
             context.setCurrentUser(ePersonService.findByEmail(context, eperson));
+        } catch (SQLException ex) {
+            System.err.format("That user could not be found:  %s%n", ex.getMessage());
+            System.exit(1);
+        }
 
         // load the XML
-        Document document = loadXML(file);
+        Document document = null;
+        try {
+            document = loadXML(file);
+        } catch (IOException ex) {
+            System.err.format("The input document could not be read:  %s%n", ex.getMessage());
+            System.exit(1);
+        } catch (SAXException ex) {
+            System.err.format("The input document could not be parsed:  %s%n", ex.getMessage());
+            System.exit(1);
+        }
 
         // run the preliminary validation, to be sure that the the XML document
         // is properly structured
+        try {
             validate(document);
+        } catch (TransformerException ex) {
+            System.err.format("The input document is invalid:  %s%n", ex.getMessage());
+            System.exit(1);
+        }
 
         // load the mappings into the member variable hashmaps
         communityMap.put("name", "name");
@@ -164,60 +203,69 @@ public class StructBuilder {
         collectionMap.put("license", "license");
         collectionMap.put("provenance", "provenance_description");
 
+        Element[] elements = new Element[]{};
+        try {
             // get the top level community list
             NodeList first = XPathAPI.selectNodeList(document, "/import_structure/community");
 
             // run the import starting with the top level communities
-        Element[] elements = handleCommunities(context, first, null);
+            elements = handleCommunities(context, first, null);
+        } catch (TransformerException ex) {
+            System.err.format("Input content not understood:  %s%n", ex.getMessage());
+            System.exit(1);
+        } catch (AuthorizeException ex) {
+            System.err.format("Not authorized:  %s%n", ex.getMessage());
+            System.exit(1);
+        }
 
         // generate the output
         Element root = xmlOutput.getRootElement();
-        for (int i = 0; i < elements.length; i++) {
+        for (Element element : elements) {
-            root.addContent(elements[i]);
+            root.addContent(element);
         }
 
         // finally write the string into the output file
-        try {
+        try (BufferedWriter out = new BufferedWriter(new FileWriter(output));) {
-            BufferedWriter out = new BufferedWriter(new FileWriter(output));
             out.write(new XMLOutputter().outputString(xmlOutput));
-            out.close();
         } catch (IOException e) {
             System.out.println("Unable to write to output file " + output);
-            System.exit(0);
+            System.exit(1);
         }
 
         context.complete();
     }
 
     /**
-     * Output the usage information
+     * Output the usage information.
      */
-    private static void usage() {
+    private static void usage(Options options) {
-        System.out.println("Usage: java StructBuilder -f <source XML file> -o <output file> -e <eperson email>");
+        HelpFormatter helper = new HelpFormatter();
-        System.out.println(
+        helper.printHelp("java StructBuilder -f <source XML file> -o <output file> -e <eperson email>",
-            "Communities will be created from the top level, and a map of communities to handles will be returned in " +
+                "Load community/collection structure from a file.",
-                "the output file");
+                options,
-        return;
+                "Communities will be created from the top level,"
+                        + " and a map of communities to handles will be returned"
+                        + " in the output file.");
     }
 
     /**
-     * Validate the XML document.  This method does not return, but if validation
+     * Validate the XML document.  This method returns if the document is valid.
-     * fails it generates an error and ceases execution
+     * If validation fails it generates an error and ceases execution.
      *
      * @param document the XML document object
      * @throws TransformerException if transformer error
      */
     private static void validate(org.w3c.dom.Document document)
         throws TransformerException {
-        StringBuffer err = new StringBuffer();
+        StringBuilder err = new StringBuilder();
         boolean trip = false;
 
-        err.append("The following errors were encountered parsing the source XML\n");
+        err.append("The following errors were encountered parsing the source XML.\n");
-        err.append("No changes have been made to the DSpace instance\n\n");
+        err.append("No changes have been made to the DSpace instance.\n\n");
 
         NodeList first = XPathAPI.selectNodeList(document, "/import_structure/community");
         if (first.getLength() == 0) {
-            err.append("-There are no top level communities in the source document");
+            err.append("-There are no top level communities in the source document.");
             System.out.println(err.toString());
             System.exit(0);
         }
@@ -236,7 +284,7 @@ public class StructBuilder {
 
     /**
      * Validate the communities section of the XML document.  This returns a string
-     * containing any errors encountered, or null if there were no errors
+     * containing any errors encountered, or null if there were no errors.
      *
      * @param communities the NodeList of communities to validate
      * @param level       the level in the XML document that we are at, for the purposes
@@ -246,7 +294,7 @@ public class StructBuilder {
      */
     private static String validateCommunities(NodeList communities, int level)
         throws TransformerException {
-        StringBuffer err = new StringBuffer();
+        StringBuilder err = new StringBuilder();
         boolean trip = false;
         String errs = null;
 
@@ -255,8 +303,9 @@ public class StructBuilder {
             NodeList name = XPathAPI.selectNodeList(n, "name");
             if (name.getLength() != 1) {
                 String pos = Integer.toString(i + 1);
-                err.append("-The level " + level + " community in position " + pos);
+                err.append("-The level ").append(level)
-                err.append(" does not contain exactly one name field\n");
+                        .append(" community in position ").append(pos)
+                        .append(" does not contain exactly one name field.\n");
                 trip = true;
             }
 
@@ -286,7 +335,7 @@ public class StructBuilder {
 
     /**
      * validate the collection section of the XML document.  This generates a
-     * string containing any errors encountered, or returns null if no errors
+     * string containing any errors encountered, or returns null if no errors.
      *
      * @param collections a NodeList of collections to validate
      * @param level       the level in the XML document for the purposes of error reporting
@@ -294,7 +343,7 @@ public class StructBuilder {
      */
     private static String validateCollections(NodeList collections, int level)
         throws TransformerException {
-        StringBuffer err = new StringBuffer();
+        StringBuilder err = new StringBuilder();
         boolean trip = false;
         String errs = null;
 
@@ -303,8 +352,9 @@ public class StructBuilder {
             NodeList name = XPathAPI.selectNodeList(n, "name");
             if (name.getLength() != 1) {
                 String pos = Integer.toString(i + 1);
-                err.append("-The level " + level + " collection in position " + pos);
+                err.append("-The level ").append(level)
-                err.append(" does not contain exactly one name field\n");
+                        .append(" collection in position ").append(pos)
+                        .append(" does not contain exactly one name field.\n");
                 trip = true;
             }
         }
@@ -363,7 +413,7 @@ public class StructBuilder {
      * created communities (e.g. the handles they have been assigned)
      */
     private static Element[] handleCommunities(Context context, NodeList communities, Community parent)
-        throws TransformerException, SQLException, Exception {
+        throws TransformerException, SQLException, AuthorizeException {
         Element[] elements = new Element[communities.getLength()];
 
         for (int i = 0; i < communities.getLength(); i++) {
@@ -390,12 +440,10 @@ public class StructBuilder {
             }
 
             // FIXME: at the moment, if the community already exists by name
-            // then this will throw a PSQLException on a duplicate key
+            // then this will throw an SQLException on a duplicate key
-            // violation
+            // violation.
-            // Ideally we'd skip this row and continue to create sub
+            // Ideally we'd skip this row and continue to create sub communities
-            // communities
+            // and so forth where they don't exist, but it's proving difficult
-            // and so forth where they don't exist, but it's proving
-            // difficult
             // to isolate the community that already exists without hitting
             // the database directly.
             communityService.update(context, community);
@@ -470,7 +518,7 @@ public class StructBuilder {
      * created collections (e.g. the handle)
      */
     private static Element[] handleCollections(Context context, NodeList collections, Community parent)
-        throws TransformerException, SQLException, AuthorizeException, IOException, Exception {
+        throws TransformerException, SQLException, AuthorizeException {
         Element[] elements = new Element[collections.getLength()];
 
         for (int i = 0; i < collections.getLength(); i++) {

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

@@ -27,6 +27,7 @@ import java.util.UUID;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import org.apache.commons.lang3.StringUtils;
 import org.dspace.authority.AuthorityValue;
 import org.dspace.authority.factory.AuthorityServiceFactory;
 import org.dspace.authority.service.AuthorityValueService;
@@ -34,6 +35,7 @@ import org.dspace.content.Collection;
 import org.dspace.content.Item;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
+import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.content.MetadataValue;
 import org.dspace.content.authority.Choices;
 import org.dspace.content.factory.ContentServiceFactory;
@@ -198,10 +200,12 @@ public class DSpaceCSV implements Serializable {
                     }
 
                     // Check that the scheme exists
+                    if (!StringUtils.equals(metadataSchema, MetadataSchemaEnum.RELATION.getName())) {
                         MetadataSchema foundSchema = metadataSchemaService.find(c, metadataSchema);
                         if (foundSchema == null) {
                             throw new MetadataImportInvalidHeadingException(clean[0],
-                                                                        MetadataImportInvalidHeadingException.SCHEMA,
+                                                                            MetadataImportInvalidHeadingException
+                                                                                .SCHEMA,
                                                                             columnCounter);
                         }
 
@@ -210,9 +214,11 @@ public class DSpaceCSV implements Serializable {
                             .findByElement(c, foundSchema, metadataElement, metadataQualifier);
                         if (foundField == null) {
                             throw new MetadataImportInvalidHeadingException(clean[0],
-                                                                        MetadataImportInvalidHeadingException.ELEMENT,
+                                                                            MetadataImportInvalidHeadingException
+                                                                                .ELEMENT,
                                                                             columnCounter);
                         }
+                    }
 
                     // Store the heading
                     headings.add(authorityPrefix + element);

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

@@ -15,6 +15,7 @@ import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.HashSet;
+import java.util.LinkedList;
 import java.util.List;
 import java.util.Set;
 import java.util.UUID;
@@ -25,22 +26,31 @@ 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;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Collection;
 import org.dspace.content.DSpaceObject;
+import org.dspace.content.Entity;
+import org.dspace.content.EntityType;
 import org.dspace.content.Item;
+import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.content.MetadataValue;
+import org.dspace.content.Relationship;
+import org.dspace.content.RelationshipType;
 import org.dspace.content.WorkspaceItem;
 import org.dspace.content.authority.Choices;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.CollectionService;
+import org.dspace.content.service.EntityService;
+import org.dspace.content.service.EntityTypeService;
 import org.dspace.content.service.InstallItemService;
 import org.dspace.content.service.ItemService;
+import org.dspace.content.service.RelationshipService;
+import org.dspace.content.service.RelationshipTypeService;
 import org.dspace.content.service.WorkspaceItemService;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Constants;
@@ -50,6 +60,7 @@ import org.dspace.eperson.EPerson;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.handle.service.HandleService;
+import org.dspace.util.UUIDUtils;
 import org.dspace.workflow.WorkflowItem;
 import org.dspace.workflow.WorkflowService;
 import org.dspace.workflow.factory.WorkflowServiceFactory;
@@ -92,7 +103,7 @@ 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;
 
@@ -101,6 +112,10 @@ public class MetadataImport {
     protected final CollectionService collectionService;
     protected final HandleService handleService;
     protected final WorkspaceItemService workspaceItemService;
+    protected final RelationshipTypeService relationshipTypeService;
+    protected final RelationshipService relationshipService;
+    protected final EntityTypeService entityTypeService;
+    protected final EntityService entityService;
 
     /**
      * Create an instance of the metadata importer. Requires a context and an array of CSV lines
@@ -120,6 +135,10 @@ public class MetadataImport {
         handleService = HandleServiceFactory.getInstance().getHandleService();
         authorityValueService = AuthorityServiceFactory.getInstance().getAuthorityValueService();
         workspaceItemService = ContentServiceFactory.getInstance().getWorkspaceItemService();
+        relationshipService = ContentServiceFactory.getInstance().getRelationshipService();
+        relationshipTypeService = ContentServiceFactory.getInstance().getRelationshipTypeService();
+        entityTypeService = ContentServiceFactory.getInstance().getEntityTypeService();
+        entityService = ContentServiceFactory.getInstance().getEntityService();
     }
 
     /**
@@ -336,7 +355,17 @@ public class MetadataImport {
                         item = wsItem.getItem();
 
                         // Add the metadata to the item
+                        List<BulkEditMetadataValue> relationships = new LinkedList<>();
                         for (BulkEditMetadataValue dcv : whatHasChanged.getAdds()) {
+                            if (StringUtils.equals(dcv.getSchema(), MetadataSchemaEnum.RELATION.getName())) {
+
+                                if (!StringUtils.equals(dcv.getElement(), "type")) {
+                                    relationships.add(dcv);
+                                } else {
+                                    handleRelationshipMetadataValueFromBulkEditMetadataValue(item, dcv);
+                                }
+
+                            } else {
                                 itemService.addMetadata(c, item, dcv.getSchema(),
                                                         dcv.getElement(),
                                                         dcv.getQualifier(),
@@ -345,7 +374,11 @@ public class MetadataImport {
                                                         dcv.getAuthority(),
                                                         dcv.getConfidence());
                             }
+                        }
 
+                        for (BulkEditMetadataValue relationship : relationships) {
+                            handleRelationshipMetadataValueFromBulkEditMetadataValue(item, relationship);
+                        }
                         // Should the workflow be used?
                         if (useWorkflow) {
                             WorkflowService workflowService = WorkflowServiceFactory.getInstance().getWorkflowService();
@@ -396,6 +429,27 @@ public class MetadataImport {
         return changes;
     }
 
+
+    /**
+     * This metod handles the BulkEditMetadataValue objects that correspond to Relationship metadatavalues
+     * @param item  The item to which this metadatavalue will belong
+     * @param dcv   The BulkEditMetadataValue to be processed
+     * @throws SQLException If something goes wrong
+     * @throws AuthorizeException   If something goes wrong
+     */
+    private void handleRelationshipMetadataValueFromBulkEditMetadataValue(Item item, BulkEditMetadataValue dcv)
+        throws SQLException, AuthorizeException {
+        LinkedList<String> values = new LinkedList<>();
+        values.add(dcv.getValue());
+        LinkedList<String> authorities = new LinkedList<>();
+        authorities.add(dcv.getAuthority());
+        LinkedList<Integer> confidences = new LinkedList<>();
+        confidences.add(dcv.getConfidence());
+        handleRelationMetadata(c, item, dcv.getSchema(), dcv.getElement(),
+                               dcv.getQualifier(),
+                               dcv.getLanguage(), values, authorities, confidences);
+    }
+
     /**
      * Compare an item metadata with a line from CSV, and optionally update the item
      *
@@ -583,9 +637,251 @@ public class MetadataImport {
                 }
             }
 
-            // Set those values
+
+            if (StringUtils.equals(schema, MetadataSchemaEnum.RELATION.getName())) {
+                List<RelationshipType> relationshipTypeList = relationshipTypeService
+                    .findByLeftOrRightLabel(c, element);
+                for (RelationshipType relationshipType : relationshipTypeList) {
+                    for (Relationship relationship : relationshipService
+                        .findByItemAndRelationshipType(c, item, relationshipType)) {
+                        relationshipService.delete(c, relationship);
+                        relationshipService.update(c, relationship);
+                    }
+                }
+                handleRelationMetadata(c, item, schema, element, qualifier, language, values, authorities, confidences);
+            } else {
                 itemService.clearMetadata(c, item, schema, element, qualifier, language);
-            itemService.addMetadata(c, item, schema, element, qualifier, language, values, authorities, confidences);
+                itemService.addMetadata(c, item, schema, element, qualifier,
+                                        language, values, authorities, confidences);
+                itemService.update(c, item);
+            }
+        }
+    }
+
+    /**
+     * This method decides whether the metadatavalue is of type relation.type or if it corresponds to
+     * a relationship and handles it accordingly to their respective methods
+     * @param c             The relevant DSpace context
+     * @param item          The item to which this metadatavalue belongs to
+     * @param schema        The schema for the metadatavalue
+     * @param element       The element for the metadatavalue
+     * @param qualifier     The qualifier for the metadatavalue
+     * @param language      The language for the metadatavalue
+     * @param values        The values for the metadatavalue
+     * @param authorities   The authorities for the metadatavalue
+     * @param confidences   The confidences for the metadatavalue
+     * @throws SQLException If something goes wrong
+     * @throws AuthorizeException   If something goes wrong
+     */
+    private void handleRelationMetadata(Context c, Item item, String schema, String element, String qualifier,
+                                        String language, List<String> values, List<String> authorities,
+                                        List<Integer> confidences) throws SQLException, AuthorizeException {
+
+        if (StringUtils.equals(element, "type") && StringUtils.isBlank(qualifier)) {
+            handleRelationTypeMetadata(c, item, schema, element, qualifier, language, values, authorities, confidences);
+
+        } else {
+            for (String value : values) {
+                handleRelationOtherMetadata(c, item, element, value);
+            }
+        }
+
+    }
+
+    /**
+     * This method takes the item, element and values to determine what relationships should be built
+     * for these parameters and calls on the method to construct them
+     * @param c         The relevant DSpace context
+     * @param item      The item that the relationships will be made for
+     * @param element   The string determining which relationshiptype is to be used
+     * @param value    The value for the relationship
+     * @throws SQLException If something goes wrong
+     * @throws AuthorizeException   If something goes wrong
+     */
+    private void handleRelationOtherMetadata(Context c, Item item, String element, String value)
+        throws SQLException, AuthorizeException {
+        Entity entity = entityService.findByItemId(c, item.getID());
+        boolean left = false;
+        List<RelationshipType> acceptableRelationshipTypes = new LinkedList<>();
+        String url = handleService.resolveToURL(c, value);
+        UUID uuid = UUIDUtils.fromString(value);
+        if (uuid == null && StringUtils.isNotBlank(url)) {
+            return;
+        }
+
+        Entity relationEntity = entityService.findByItemId(c, uuid);
+
+
+        List<RelationshipType> leftRelationshipTypesForEntity = entityService.getLeftRelationshipTypes(c, entity);
+        List<RelationshipType> rightRelationshipTypesForEntity = entityService.getRightRelationshipTypes(c, entity);
+
+        for (RelationshipType relationshipType : entityService.getAllRelationshipTypes(c, entity)) {
+            if (StringUtils.equalsIgnoreCase(relationshipType.getLeftLabel(), element)) {
+                left = handleLeftLabelEqualityRelationshipTypeElement(c, entity, relationEntity, left,
+                                                                      acceptableRelationshipTypes,
+                                                                      leftRelationshipTypesForEntity,
+                                                                      relationshipType);
+            } else if (StringUtils.equalsIgnoreCase(relationshipType.getRightLabel(), element)) {
+                left = handleRightLabelEqualityRelationshipTypeElement(c, entity, relationEntity, left,
+                                                                       acceptableRelationshipTypes,
+                                                                       rightRelationshipTypesForEntity,
+                                                                       relationshipType);
+            }
+        }
+
+        if (acceptableRelationshipTypes.size() > 1) {
+            log.error("Ambiguous relationship_types were found");
+            return;
+        }
+        if (acceptableRelationshipTypes.size() == 0) {
+            log.error("no relationship_types were found");
+            return;
+        }
+
+        //There is exactly one
+        buildRelationObject(c, item, value, left, acceptableRelationshipTypes.get(0));
+    }
+
+    /**
+     * This method creates the relationship for the item and stores it in the database
+     * @param c         The relevant DSpace context
+     * @param item      The item for which this relationship will be constructed
+     * @param value    The value for the relationship
+     * @param left      A boolean indicating whether the item is the leftItem or the rightItem
+     * @param acceptedRelationshipType   The acceptable relationship type
+     * @throws SQLException If something goes wrong
+     * @throws AuthorizeException   If something goes wrong
+     */
+    private void buildRelationObject(Context c, Item item, String value, boolean left,
+                                     RelationshipType acceptedRelationshipType)
+        throws SQLException, AuthorizeException {
+        Item leftItem = null;
+        Item rightItem = null;
+        if (left) {
+            leftItem = item;
+            rightItem = itemService.findByIdOrLegacyId(c, value);
+        } else {
+            rightItem = item;
+            leftItem = itemService.findByIdOrLegacyId(c, value);
+        }
+        RelationshipType relationshipType = acceptedRelationshipType;
+        int leftPlace = relationshipService.findLeftPlaceByLeftItem(c, leftItem) + 1;
+        int rightPlace = relationshipService.findRightPlaceByRightItem(c, rightItem) + 1;
+        Relationship persistedRelationship = relationshipService.create(c, leftItem, rightItem,
+                                                                        relationshipType, leftPlace, rightPlace);
+        relationshipService.update(c, persistedRelationship);
+    }
+
+    /**
+     * This method will add RelationshipType objects to the acceptableRelationshipTypes list
+     * if applicable and valid RelationshipType objects are found. It will also return a boolean indicating
+     * whether we're dealing with a left Relationship or not
+     * @param c                                 The relevant DSpace context
+     * @param entity                            The Entity for which the RelationshipType has to be checked
+     * @param relationEntity                    The other Entity of the Relationship
+     * @param left                              Boolean indicating whether the Relationship is left or not
+     * @param acceptableRelationshipTypes       The list of RelationshipType objects that will be added to
+     * @param rightRelationshipTypesForEntity   The list of RelationshipType objects that are possible
+     *                                          for the right entity
+     * @param relationshipType                  The RelationshipType object that we want to check whether it's
+     *                                          valid to be added or not
+     * @return                                  A boolean indicating whether the relationship is left or right, will
+     *                                          be false in this case
+     * @throws SQLException                     If something goes wrong
+     */
+    private boolean handleRightLabelEqualityRelationshipTypeElement(Context c, Entity entity, Entity relationEntity,
+                                                                    boolean left,
+                                                                    List<RelationshipType> acceptableRelationshipTypes,
+                                                                    List<RelationshipType>
+                                                                        rightRelationshipTypesForEntity,
+                                                                    RelationshipType relationshipType)
+        throws SQLException {
+        if (StringUtils.equalsIgnoreCase(entityService.getType(c, entity).getLabel(),
+                                         relationshipType.getRightType().getLabel()) &&
+            StringUtils.equalsIgnoreCase(entityService.getType(c, relationEntity).getLabel(),
+                                         relationshipType.getLeftType().getLabel())) {
+
+            for (RelationshipType rightRelationshipType : rightRelationshipTypesForEntity) {
+                if (StringUtils.equalsIgnoreCase(rightRelationshipType.getLeftType().getLabel(),
+                                                 relationshipType.getLeftType().getLabel()) ||
+                    StringUtils.equalsIgnoreCase(rightRelationshipType.getRightType().getLabel(),
+                                                 relationshipType.getLeftType().getLabel())) {
+                    left = false;
+                    acceptableRelationshipTypes.add(relationshipType);
+                }
+            }
+        }
+        return left;
+    }
+
+    /**
+     * This method will add RelationshipType objects to the acceptableRelationshipTypes list
+     * if applicable and valid RelationshipType objects are found. It will also return a boolean indicating
+     * whether we're dealing with a left Relationship or not
+     * @param c                                 The relevant DSpace context
+     * @param entity                            The Entity for which the RelationshipType has to be checked
+     * @param relationEntity                    The other Entity of the Relationship
+     * @param left                              Boolean indicating whether the Relationship is left or not
+     * @param acceptableRelationshipTypes       The list of RelationshipType objects that will be added to
+     * @param leftRelationshipTypesForEntity    The list of RelationshipType objects that are possible
+     *                                          for the left entity
+     * @param relationshipType                  The RelationshipType object that we want to check whether it's
+     *                                          valid to be added or not
+     * @return                                  A boolean indicating whether the relationship is left or right, will
+     *                                          be true in this case
+     * @throws SQLException                     If something goes wrong
+     */
+    private boolean handleLeftLabelEqualityRelationshipTypeElement(Context c, Entity entity, Entity relationEntity,
+                                                                   boolean left,
+                                                                   List<RelationshipType> acceptableRelationshipTypes,
+                                                                   List<RelationshipType>
+                                                                       leftRelationshipTypesForEntity,
+                                                                   RelationshipType relationshipType)
+        throws SQLException {
+        if (StringUtils.equalsIgnoreCase(entityService.getType(c, entity).getLabel(),
+                                         relationshipType.getLeftType().getLabel()) &&
+            StringUtils.equalsIgnoreCase(entityService.getType(c, relationEntity).getLabel(),
+                                         relationshipType.getRightType().getLabel())) {
+            for (RelationshipType leftRelationshipType : leftRelationshipTypesForEntity) {
+                if (StringUtils.equalsIgnoreCase(leftRelationshipType.getRightType().getLabel(),
+                                                 relationshipType.getRightType().getLabel()) ||
+                    StringUtils.equalsIgnoreCase(leftRelationshipType.getLeftType().getLabel(),
+                                                 relationshipType.getRightType().getLabel())) {
+                    left = true;
+                    acceptableRelationshipTypes.add(relationshipType);
+                }
+            }
+        }
+        return left;
+    }
+
+    /**
+     * This method will add the relationship.type metadata to the item if an EntityType can be found for the value in
+     * the values list.
+     * @param c             The relevant DSpace context
+     * @param item          The item to which this metadatavalue will be added
+     * @param schema        The schema for the metadatavalue to be added
+     * @param element       The element for the metadatavalue to be added
+     * @param qualifier     The qualifier for the metadatavalue to be added
+     * @param language      The language for the metadatavalue to be added
+     * @param values        The value on which we'll search for EntityType object and it's the value
+     *                      for the metadatavalue that will be created
+     * @param authorities   The authority for the metadatavalue. This will be filled with the ID
+     *                      of the found EntityType for the value if it exists
+     * @param confidences   The confidence for the metadatavalue
+     * @throws SQLException If something goes wrong
+     * @throws AuthorizeException   If something goes wrong
+     */
+    private void handleRelationTypeMetadata(Context c, Item item, String schema, String element, String qualifier,
+                                            String language, List<String> values, List<String> authorities,
+                                            List<Integer> confidences)
+        throws SQLException, AuthorizeException {
+        EntityType entityType = entityTypeService.findByEntityType(c, values.get(0));
+        if (entityType != null) {
+            authorities.add(String.valueOf(entityType.getID()));
+            itemService.clearMetadata(c, item, schema, element, qualifier, language);
+            itemService.addMetadata(c, item, schema, element, qualifier, language,
+                                    values, authorities, confidences);
             itemService.update(c, item);
         }
     }

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;
@@ -42,7 +42,7 @@ import org.dspace.content.Community;
 import org.dspace.content.DSpaceObject;
 import org.dspace.content.Item;
 import org.dspace.content.MetadataField;
-import org.dspace.content.MetadataSchema;
+import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.content.MetadataValue;
 import org.dspace.content.service.BitstreamService;
 import org.dspace.content.service.CommunityService;
@@ -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() {
 
@@ -214,7 +214,7 @@ public class ItemExportServiceImpl implements ItemExportService {
     protected void writeMetadata(Context c, String schema, Item i,
                                  File destDir, boolean migrate) throws Exception {
         String filename;
-        if (schema.equals(MetadataSchema.DC_SCHEMA)) {
+        if (schema.equals(MetadataSchemaEnum.DC.getName())) {
             filename = "dublin_core.xml";
         } else {
             filename = "metadata_" + schema + ".xml";
@@ -271,9 +271,8 @@ public class ItemExportServiceImpl implements ItemExportService {
                             ("date".equals(metadataField.getElement()) && "accessioned".equals(qualifier)) ||
                             ("date".equals(metadataField.getElement()) && "available".equals(qualifier)) ||
                             ("identifier".equals(metadataField.getElement()) && "uri".equals(qualifier) &&
-                                (dcv.getValue() != null && dcv.getValue().startsWith("http://hdl.handle.net/" +
+                                (dcv.getValue() != null && dcv.getValue().startsWith(
-                                                                                         handleService
+                                    handleService.getCanonicalPrefix() + handleService.getPrefix() + "/"))) ||
-                                                                                             .getPrefix() + "/"))) ||
                             ("description".equals(metadataField.getElement()) && "provenance".equals(qualifier)) ||
                             ("format".equals(metadataField.getElement()) && "extent".equals(qualifier)) ||
                             ("format".equals(metadataField.getElement()) && "mimetype".equals(qualifier))))) {
@@ -547,7 +546,7 @@ public class ItemExportServiceImpl implements ItemExportService {
                                 List<Bitstream> bitstreams = bundle.getBitstreams();
                                 for (Bitstream bitstream : bitstreams) {
                                     // add up the size
-                                    size += bitstream.getSize();
+                                    size += bitstream.getSizeBytes();
                                 }
                             }
                             items.add(item.getID());
@@ -574,7 +573,7 @@ public class ItemExportServiceImpl implements ItemExportService {
                             List<Bitstream> bitstreams = bundle.getBitstreams();
                             for (Bitstream bitstream : bitstreams) {
                                 // add up the size
-                                size += bitstream.getSize();
+                                size += bitstream.getSizeBytes();
                             }
                         }
                         items.add(item.getID());
@@ -593,7 +592,7 @@ public class ItemExportServiceImpl implements ItemExportService {
                     List<Bitstream> bitstreams = bundle.getBitstreams();
                     for (Bitstream bitstream : bitstreams) {
                         // add up the size
-                        size += bitstream.getSize();
+                        size += bitstream.getSizeBytes();
                     }
                 }
                 ArrayList<UUID> items = new ArrayList<>();

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

@@ -52,13 +52,13 @@ import gr.ekt.bte.core.TransformationSpec;
 import gr.ekt.bte.dataloader.FileDataLoader;
 import gr.ekt.bteio.generators.DSpaceOutputGenerator;
 import gr.ekt.bteio.loaders.OAIPMHDataLoader;
-import org.apache.commons.collections.ComparatorUtils;
+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;
@@ -74,6 +74,7 @@ import org.dspace.content.DSpaceObject;
 import org.dspace.content.Item;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
+import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.content.WorkspaceItem;
 import org.dspace.content.service.BitstreamFormatService;
 import org.dspace.content.service.BitstreamService;
@@ -124,7 +125,7 @@ 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;
@@ -677,7 +678,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
         Node schemaAttr = metadata.item(0).getAttributes().getNamedItem(
             "schema");
         if (schemaAttr == null) {
-            schema = MetadataSchema.DC_SCHEMA;
+            schema = MetadataSchemaEnum.DC.getName();
         } else {
             schema = schemaAttr.getNodeValue();
         }

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/ItemUpdate.java

@@ -31,11 +31,12 @@ import org.apache.commons.cli.PosixParser;
 import org.dspace.content.Item;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.eperson.service.EPersonService;
+import org.dspace.handle.factory.HandleServiceFactory;
+import org.dspace.handle.service.HandleService;
 
 /**
  * Provides some batch editing capabilities for items in DSpace:
@@ -78,6 +79,7 @@ public class ItemUpdate {
 
     protected static final EPersonService epersonService = EPersonServiceFactory.getInstance().getEPersonService();
     protected static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+    protected static final HandleService handleService = HandleServiceFactory.getInstance().getHandleService();
 
     static {
         filterAliases.put("ORIGINAL", "org.dspace.app.itemupdate.OriginalBitstreamFilter");
@@ -330,10 +332,7 @@ public class ItemUpdate {
             iu.setEPerson(context, iu.eperson);
             context.turnOffAuthorisationSystem();
 
-            HANDLE_PREFIX = ConfigurationManager.getProperty("handle.canonical.prefix");
+            HANDLE_PREFIX = handleService.getCanonicalPrefix();
-            if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0) {
-                HANDLE_PREFIX = "http://hdl.handle.net/";
-            }
 
             iu.processArchive(context, sourcedir, itemField, metadataIndexName, alterProvenance, isTest);
 

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

@@ -28,12 +28,13 @@ 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;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
+import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.content.MetadataValue;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
@@ -189,7 +190,7 @@ public class MetadataUtilities {
         NodeList metadata = XPathAPI.selectNodeList(document, "/dublin_core");
         Node schemaAttr = metadata.item(0).getAttributes().getNamedItem("schema");
         if (schemaAttr == null) {
-            schema = MetadataSchema.DC_SCHEMA;
+            schema = MetadataSchemaEnum.DC.getName();
         } else {
             schema = schemaAttr.getNodeValue();
         }

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/ImageMagickThumbnailFilter.java

@@ -143,7 +143,7 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter {
         // PDFs using the CMYK color system can be handled specially if
         // profiles are defined
         if (cmyk_profile != null && srgb_profile != null) {
-            Info imageInfo = new Info(f.getAbsolutePath(), true);
+            Info imageInfo = new Info(f.getAbsolutePath() + s, true);
             String imageClass = imageInfo.getImageClass();
             if (imageClass.contains("CMYK")) {
                 op.profile(cmyk_profile);

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/MediaFilterServiceImpl.java

@@ -220,7 +220,7 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
                 } catch (Exception e) {
                     String handle = myItem.getHandle();
                     List<Bundle> bundles = myBitstream.getBundles();
-                    long size = myBitstream.getSize();
+                    long size = myBitstream.getSizeBytes();
                     String checksum = myBitstream.getChecksum() + " (" + myBitstream.getChecksumAlgorithm() + ")";
                     int assetstore = myBitstream.getStoreNumber();
 
@@ -310,12 +310,11 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
         // get bitstream filename, calculate destination filename
         String newName = formatFilter.getFilteredName(source.getName());
 
-        Bitstream existingBitstream = null; // is there an existing rendition?
+        // check if destination bitstream exists
-        Bundle targetBundle = null; // bundle we're modifying
+        Bundle existingBundle = null;
-
+        Bitstream existingBitstream = null;
         List<Bundle> bundles = itemService.getBundles(item, formatFilter.getBundleName());
 
-        // check if destination bitstream exists
         if (bundles.size() > 0) {
             // only finds the last match (FIXME?)
             for (Bundle bundle : bundles) {
@@ -323,7 +322,7 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
 
                 for (Bitstream bitstream : bitstreams) {
                     if (bitstream.getName().trim().equals(newName.trim())) {
-                        targetBundle = bundle;
+                        existingBundle = bundle;
                         existingBitstream = bitstream;
                     }
                 }
@@ -345,40 +344,41 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
                                    + " (item: " + item.getHandle() + ")");
         }
 
-        InputStream destStream;
-        try {
         System.out.println("File: " + newName);
-            destStream = formatFilter.getDestinationStream(item, bitstreamService.retrieve(context, source), isVerbose);
+
+        // start filtering of the bitstream, using try with resource to close all InputStreams properly
+        try (
+                // get the source stream
+                InputStream srcStream = bitstreamService.retrieve(context, source);
+                // filter the source stream to produce the destination stream
+                // this is the hard work, check for OutOfMemoryErrors at the end of the try clause.
+                InputStream destStream = formatFilter.getDestinationStream(item, srcStream, isVerbose);
+        ) {
             if (destStream == null) {
                 if (!isQuiet) {
                     System.out.println("SKIPPED: bitstream " + source.getID()
                             + " (item: " + item.getHandle() + ") because filtering was unsuccessful");
                 }
-
-                return false;
-            }
-        } catch (OutOfMemoryError oome) {
-            System.out.println("!!! OutOfMemoryError !!!");
                 return false;
             }
 
-        // create new bundle if needed
+            Bundle targetBundle; // bundle we're modifying
             if (bundles.size() < 1) {
+                // create new bundle if needed
                 targetBundle = bundleService.create(context, item, formatFilter.getBundleName());
             } else {
-            // take the first match
+                // take the first match as we already looked out for the correct bundle name
                 targetBundle = bundles.get(0);
             }
 
+            // create bitstream to store the filter result
             Bitstream b = bitstreamService.create(context, targetBundle, destStream);
-
+            // set the name, source and description of the bitstream
-        // Now set the format and name of the bitstream
             b.setName(context, newName);
             b.setSource(context, "Written by FormatFilter " + formatFilter.getClass().getName() +
                     " on " + DCDate.getCurrent() + " (GMT).");
             b.setDescription(context, formatFilter.getDescription());
-
+            // Set the format of the bitstream
-        // Find the proper format
             BitstreamFormat bf = bitstreamFormatService.findByShortDescription(context,
                     formatFilter.getFormatString());
             bitstreamService.setFormat(context, b, bf);
@@ -398,10 +398,17 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
                 authorizeService.inheritPolicies(context, source, b);
             }
 
+            //do post-processing of the generated bitstream
+            formatFilter.postProcessBitstream(context, item, b);
+
+        } catch (OutOfMemoryError oome) {
+            System.out.println("!!! OutOfMemoryError !!!");
+        }
+
         // fixme - set date?
         // we are overwriting, so remove old bitstream
         if (existingBitstream != null) {
-            bundleService.removeBitstream(context, targetBundle, existingBitstream);
+            bundleService.removeBitstream(context, existingBundle, existingBitstream);
         }
 
         if (!isQuiet) {
@@ -409,9 +416,6 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
                                    + " (item: " + item.getHandle() + ") and created '" + newName + "'");
         }
 
-        //do post-processing of the generated bitstream
-        formatFilter.postProcessBitstream(context, item, b);
-
         return true;
     }
 

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

@@ -1,93 +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.mediafilter;
-
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-
-import org.apache.log4j.Logger;
-import org.dspace.content.Item;
-import org.textmining.extraction.TextExtractor;
-import org.textmining.extraction.word.WordTextExtractorFactory;
-
-/*
- *
- * to do: helpful error messages - can't find mediafilter.cfg - can't
- * instantiate filter - bitstream format doesn't exist.
- *
- */
-public class WordFilter extends MediaFilter {
-
-    private static Logger log = Logger.getLogger(WordFilter.class);
-
-    @Override
-    public String getFilteredName(String oldFilename) {
-        return oldFilename + ".txt";
-    }
-
-    /**
-     * @return String bundle name
-     */
-    @Override
-    public String getBundleName() {
-        return "TEXT";
-    }
-
-    /**
-     * @return String bitstreamformat
-     */
-    @Override
-    public String getFormatString() {
-        return "Text";
-    }
-
-    /**
-     * @return String description
-     */
-    @Override
-    public String getDescription() {
-        return "Extracted text";
-    }
-
-    /**
-     * @param currentItem item
-     * @param source      source input stream
-     * @param verbose     verbose mode
-     * @return InputStream the resulting input stream
-     * @throws Exception if error
-     */
-    @Override
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
-        throws Exception {
-        // get input stream from bitstream
-        // pass to filter, get string back
-        try {
-            WordTextExtractorFactory factory = new WordTextExtractorFactory();
-            TextExtractor e = factory.textExtractor(source);
-            String extractedText = e.getText();
-
-            // if verbose flag is set, print out extracted text
-            // to STDOUT
-            if (verbose) {
-                System.out.println(extractedText);
-            }
-
-            // generate an input stream with the extracted text
-            byte[] textBytes = extractedText.getBytes();
-            ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
-
-            return bais; // will this work? or will the byte array be out of scope?
-        } catch (IOException ioe) {
-            System.out.println("Invalid Word Format");
-            log.error("Error detected - Word File format not recognized: "
-                          + ioe.getMessage(), ioe);
-            throw ioe;
-        }
-    }
-}

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/requestitem/dao/impl/RequestItemDAOImpl.java

@@ -8,13 +8,15 @@
 package org.dspace.app.requestitem.dao.impl;
 
 import java.sql.SQLException;
+import javax.persistence.criteria.CriteriaBuilder;
+import javax.persistence.criteria.CriteriaQuery;
+import javax.persistence.criteria.Root;
 
 import org.dspace.app.requestitem.RequestItem;
+import org.dspace.app.requestitem.RequestItem_;
 import org.dspace.app.requestitem.dao.RequestItemDAO;
 import org.dspace.core.AbstractHibernateDAO;
 import org.dspace.core.Context;
-import org.hibernate.Criteria;
-import org.hibernate.criterion.Restrictions;
 
 /**
  * Hibernate implementation of the Database Access Object interface class for the RequestItem object.
@@ -30,9 +32,12 @@ public class RequestItemDAOImpl extends AbstractHibernateDAO<RequestItem> implem
 
     @Override
     public RequestItem findByToken(Context context, String token) throws SQLException {
-        Criteria criteria = createCriteria(context, RequestItem.class);
+        CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
-        criteria.add(Restrictions.eq("token", token));
+        CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, RequestItem.class);
-        return uniqueResult(criteria);
+        Root<RequestItem> requestItemRoot = criteriaQuery.from(RequestItem.class);
+        criteriaQuery.select(requestItemRoot);
+        criteriaQuery.where(criteriaBuilder.equal(requestItemRoot.get(RequestItem_.token), token));
+        return uniqueResult(context, criteriaQuery, false, RequestItem.class, -1, -1);
     }
 
 

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/ReportGenerator.java

@@ -28,7 +28,7 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import org.dspace.content.Item;
-import org.dspace.content.MetadataSchema;
+import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.content.MetadataValue;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
@@ -763,9 +763,10 @@ public class ReportGenerator {
         // build the referece
         // FIXME: here we have blurred the line between content and presentation
         // and it should probably be un-blurred
-        List<MetadataValue> title = itemService.getMetadata(item, MetadataSchema.DC_SCHEMA, "title", null, Item.ANY);
+        List<MetadataValue> title = itemService.getMetadata(item, MetadataSchemaEnum.DC.getName(),
+                                                            "title", null, Item.ANY);
         List<MetadataValue> author = itemService
-            .getMetadata(item, MetadataSchema.DC_SCHEMA, "contributor", "author", Item.ANY);
+            .getMetadata(item, MetadataSchemaEnum.DC.getName(), "contributor", "author", Item.ANY);
 
         StringBuffer authors = new StringBuffer();
         if (author.size() > 0) {

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

@@ -13,8 +13,8 @@ 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.content.MetadataSchemaEnum;
 import org.dspace.core.Utils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -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
      */
@@ -154,7 +160,7 @@ public class DCInput {
         // Default the schema to dublin core
         dcSchema = fieldMap.get("dc-schema");
         if (dcSchema == null) {
-            dcSchema = MetadataSchema.DC_SCHEMA;
+            dcSchema = MetadataSchemaEnum.DC.getName();
         }
 
         //check if the input have a language tag
@@ -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;
     }
 
@@ -104,12 +105,14 @@ 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++) {
+                DCInput field = inputs[i][j];
                 String fullName = field.getFieldName();
                 if (fullName.equals(fieldName)) {
                     return true;
                 }
             }
+        }
         return false;
     }
 
@@ -127,7 +130,8 @@ 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++) {
+                DCInput field = inputs[i][j];
                 String fullName = field.getFieldName();
                 if (fullName.equals(fieldName)) {
                     if (field.isAllowedFor(documentType)) {
@@ -135,6 +139,7 @@ public class DCInputSet {
                     }
                 }
             }
+        }
         return false;
     }
 

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

@@ -21,7 +21,7 @@ import javax.xml.parsers.FactoryConfigurationError;
 
 import org.apache.commons.lang3.StringUtils;
 import org.dspace.content.Collection;
-import org.dspace.content.MetadataSchema;
+import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.core.Utils;
 import org.dspace.services.factory.DSpaceServicesFactory;
 import org.w3c.dom.Document;
@@ -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.
      */
@@ -311,10 +311,40 @@ 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")) {
+                        List<Map<String, String>> fields = new ArrayList<Map<String, String>>(); // the fields in the
+                        // row
+                        // process each row definition
+                        processRow(formName, j, npg, fields);
+                        rows.add(fields);
+                    }
+                }
+                // sanity check number of fields
+                if (rows.size() < 1) {
+                    throw new DCInputsReaderException("Form " + formName + " has no rows");
+                }
+            }
+        }
+        if (numForms == 0) {
+            throw new DCInputsReaderException("No form definition found");
+        }
+    }
+
+    /**
+     * 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);
 
@@ -323,6 +353,20 @@ public class DCInputsReader {
                 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
@@ -330,15 +374,11 @@ public class DCInputsReader {
         }
         // sanity check number of fields
         if (fields.size() < 1) {
-                    throw new DCInputsReaderException("Form " + formName + " has no fields");
+            throw new DCInputsReaderException("Form " + formName + "row " + rowIdx + " has no fields");
-                }
-            }
-        }
-        if (numForms == 0) {
-            throw new DCInputsReaderException("No form definition found");
         }
     }
 
+
     /**
      * Process parts of a field
      * At the end, make sure that input-types 'qualdrop_value' and
@@ -424,7 +464,7 @@ public class DCInputsReader {
         String elem = field.get("dc-element");
         String qual = field.get("dc-qualifier");
         if ((schema == null) || (schema.equals(""))) {
-            schema = MetadataSchema.DC_SCHEMA;
+            schema = MetadataSchemaEnum.DC.getName();
         }
         String schemaTest;
 
@@ -434,7 +474,7 @@ public class DCInputsReader {
                 Map<String, String> fld = pg.get(j);
                 if ((fld.get("dc-schema") == null) ||
                     ((fld.get("dc-schema")).equals(""))) {
-                    schemaTest = MetadataSchema.DC_SCHEMA;
+                    schemaTest = MetadataSchemaEnum.DC.getName();
                 } else {
                     schemaTest = fld.get("dc-schema");
                 }
@@ -537,7 +577,9 @@ 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 j = 0; j < rows.size(); j++) {
+                List<Map<String, String>> fields = rows.get(j);
                 for (int i = 0; i < fields.size(); i++) {
                     Map<String, String> fld = fields.get(i);
                     // verify reference in certain input types
@@ -555,8 +597,9 @@ public class DCInputsReader {
 
                     // we omit the "required" and "visibility" validation, provided this must be checked in the
                     // 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<>();
 
@@ -86,7 +86,7 @@ public class GoogleBitstreamComparator implements Comparator<Bitstream> {
         if (priority1 > priority2) {
             return 1;
         } else if (priority1 == priority2) {
-            if (b1.getSize() <= b2.getSize()) {
+            if (b1.getSizeBytes() <= b2.getSizeBytes()) {
                 return 1;
             } else {
                 return -1;

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/IndexVersion.java

@@ -121,20 +121,24 @@ public class IndexVersion {
             }
 
             // Open this index directory in Lucene
-            Directory indexDir = FSDirectory.open(dir);
+            Directory indexDir = FSDirectory.open(dir.toPath());
 
             // Get info on the Lucene segment file(s) in index directory
-            SegmentInfos sis = new SegmentInfos();
+            SegmentInfos sis;
             try {
-                sis.read(indexDir);
+                sis = SegmentInfos.readLatestCommit(indexDir);
             } catch (IOException ie) {
                 // Wrap default IOException, providing more info about which directory cannot be read
                 throw new IOException("Could not read Lucene segments files in " + dir.getAbsolutePath(), ie);
             }
 
+            if (null == sis) {
+                throw new IOException("Could not read Lucene segments files in " + dir.getAbsolutePath());
+            }
+
             // If we have a valid Solr index dir, but it has no existing segments
             // then just return an empty string. It's a valid but empty index.
-            if (sis != null && sis.size() == 0) {
+            if (sis.size() == 0) {
                 return "";
             }
 

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

@@ -0,0 +1,227 @@
+/**
+ * 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.sql.SQLException;
+import java.util.LinkedList;
+import java.util.List;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+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.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.dspace.authorize.AuthorizeException;
+import org.dspace.content.EntityType;
+import org.dspace.content.RelationshipType;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.EntityTypeService;
+import org.dspace.content.service.RelationshipService;
+import org.dspace.content.service.RelationshipTypeService;
+import org.dspace.core.Context;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.SAXException;
+
+/**
+ * This script is used to initialize the database with a set of relationshiptypes that are written
+ * in an xml file that is given to this script.
+ * This XML file needs to have a proper XML structure and needs to define the variables of the RelationshipType object
+ */
+public class InitializeEntities {
+
+    private final static Logger log = LogManager.getLogger();
+
+    private RelationshipTypeService relationshipTypeService;
+    private RelationshipService relationshipService;
+    private EntityTypeService entityTypeService;
+
+    private InitializeEntities() {
+        relationshipTypeService = ContentServiceFactory.getInstance().getRelationshipTypeService();
+        relationshipService = ContentServiceFactory.getInstance().getRelationshipService();
+        entityTypeService = ContentServiceFactory.getInstance().getEntityTypeService();
+
+    }
+
+    /**
+     * The main method for this script
+     *
+     * @param argv  The commandline arguments given with this command
+     * @throws SQLException         If something goes wrong with the database
+     * @throws AuthorizeException   If something goes wrong with permissions
+     * @throws ParseException       If something goes wrong with the parsing
+     */
+    public static void main(String[] argv) throws SQLException, AuthorizeException, ParseException {
+        InitializeEntities initializeEntities = new InitializeEntities();
+        CommandLineParser parser = new PosixParser();
+        Options options = createCommandLineOptions();
+        CommandLine line = parser.parse(options,argv);
+        String fileLocation = getFileLocationFromCommandLine(line);
+        checkHelpEntered(options, line);
+        initializeEntities.run(fileLocation);
+    }
+    private static void checkHelpEntered(Options options, CommandLine line) {
+        if (line.hasOption("h")) {
+            HelpFormatter formatter = new HelpFormatter();
+            formatter.printHelp("Intialize Entities", options);
+            System.exit(0);
+        }
+    }
+    private static String getFileLocationFromCommandLine(CommandLine line) {
+        String query = line.getOptionValue("f");
+        if (StringUtils.isEmpty(query)) {
+            System.out.println("No file location was entered");
+            log.info("No file location was entered");
+            System.exit(1);
+        }
+        return query;
+    }
+
+    protected static Options createCommandLineOptions() {
+        Options options = new Options();
+        options.addOption("f", "file", true, "the location for the file containing the xml data");
+
+        return options;
+    }
+
+    private void run(String fileLocation) throws SQLException, AuthorizeException {
+        Context context = new Context();
+        context.turnOffAuthorisationSystem();
+        this.parseXMLToRelations(context, fileLocation);
+        context.complete();
+    }
+
+    private void parseXMLToRelations(Context context, String fileLocation) throws AuthorizeException {
+        try {
+            File fXmlFile = new File(fileLocation);
+            DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
+            DocumentBuilder dBuilder = null;
+            dBuilder = dbFactory.newDocumentBuilder();
+            Document doc = dBuilder.parse(fXmlFile);
+
+            doc.getDocumentElement().normalize();
+
+            NodeList nList = doc.getElementsByTagName("type");
+            List<RelationshipType> relationshipTypes = new LinkedList<>();
+            for (int i = 0; i < nList.getLength(); i++) {
+                Node nNode = nList.item(i);
+
+                if (nNode.getNodeType() == Node.ELEMENT_NODE) {
+
+                    Element eElement = (Element) nNode;
+
+                    String leftType =  eElement.getElementsByTagName("leftType").item(0).getTextContent();
+                    String rightType = eElement.getElementsByTagName("rightType").item(0).getTextContent();
+                    String leftLabel = eElement.getElementsByTagName("leftLabel").item(0).getTextContent();
+                    String rightLabel = eElement.getElementsByTagName("rightLabel").item(0).getTextContent();
+
+
+                    NodeList leftCardinalityList = eElement.getElementsByTagName("leftCardinality");
+                    NodeList rightCardinalityList = eElement.getElementsByTagName("rightCardinality");
+
+                    String leftCardinalityMin = "";
+                    String leftCardinalityMax = "";
+
+                    String rightCardinalityMin = "";
+                    String rightCardinalityMax = "";
+
+                    for (int j = 0; j < leftCardinalityList.getLength(); j++) {
+                        Node node = leftCardinalityList.item(j);
+                        leftCardinalityMin = getString(leftCardinalityMin,(Element) node, "min");
+                        leftCardinalityMax = getString(leftCardinalityMax,(Element) node, "max");
+
+                    }
+
+                    for (int j = 0; j < rightCardinalityList.getLength(); j++) {
+                        Node node = rightCardinalityList.item(j);
+                        rightCardinalityMin = getString(rightCardinalityMin,(Element) node, "min");
+                        rightCardinalityMax = getString(rightCardinalityMax,(Element) node, "max");
+
+                    }
+                    populateRelationshipType(context, leftType, rightType, leftLabel, rightLabel,
+                                             leftCardinalityMin, leftCardinalityMax,
+                                             rightCardinalityMin, rightCardinalityMax);
+
+
+                }
+            }
+        } catch (ParserConfigurationException | SAXException | IOException | SQLException e) {
+            log.error("An error occurred while parsing the XML file to relations", e);
+        }
+    }
+
+    private String getString(String leftCardinalityMin,Element node, String minOrMax) {
+        if (node.getElementsByTagName(minOrMax).getLength() > 0) {
+            leftCardinalityMin = node.getElementsByTagName(minOrMax).item(0).getTextContent();
+        }
+        return leftCardinalityMin;
+    }
+
+    private void populateRelationshipType(Context context, String leftType, String rightType, String leftLabel,
+                                          String rightLabel, String leftCardinalityMin, String leftCardinalityMax,
+                                          String rightCardinalityMin, String rightCardinalityMax)
+        throws SQLException, AuthorizeException {
+
+        EntityType leftEntityType = entityTypeService.findByEntityType(context,leftType);
+        if (leftEntityType == null) {
+            leftEntityType = entityTypeService.create(context, leftType);
+        }
+        EntityType rightEntityType = entityTypeService.findByEntityType(context, rightType);
+        if (rightEntityType == null) {
+            rightEntityType = entityTypeService.create(context, rightType);
+        }
+        Integer leftCardinalityMinInteger;
+        Integer leftCardinalityMaxInteger;
+        Integer rightCardinalityMinInteger;
+        Integer rightCardinalityMaxInteger;
+        if (StringUtils.isNotBlank(leftCardinalityMin)) {
+            leftCardinalityMinInteger = Integer.parseInt(leftCardinalityMin);
+        } else {
+            leftCardinalityMinInteger = null;
+        }
+        if (StringUtils.isNotBlank(leftCardinalityMax)) {
+            leftCardinalityMaxInteger = Integer.parseInt(leftCardinalityMax);
+        } else {
+            leftCardinalityMaxInteger = null;
+        }
+        if (StringUtils.isNotBlank(rightCardinalityMin)) {
+            rightCardinalityMinInteger = Integer.parseInt(rightCardinalityMin);
+        } else {
+            rightCardinalityMinInteger = null;
+        }
+        if (StringUtils.isNotBlank(rightCardinalityMax)) {
+            rightCardinalityMaxInteger = Integer.parseInt(rightCardinalityMax);
+        } else {
+            rightCardinalityMaxInteger = null;
+        }
+        RelationshipType relationshipType = relationshipTypeService
+            .findbyTypesAndLabels(context, leftEntityType, rightEntityType, leftLabel, rightLabel);
+        if (relationshipType == null) {
+            relationshipTypeService.create(context, leftEntityType, rightEntityType, leftLabel, rightLabel,
+                                           leftCardinalityMinInteger, leftCardinalityMaxInteger,
+                                           rightCardinalityMinInteger, rightCardinalityMaxInteger);
+        } else {
+            relationshipType.setLeftMinCardinality(leftCardinalityMinInteger);
+            relationshipType.setLeftMaxCardinality(leftCardinalityMaxInteger);
+            relationshipType.setRightMinCardinality(rightCardinalityMinInteger);
+            relationshipType.setRightMaxCardinality(rightCardinalityMaxInteger);
+            relationshipTypeService.update(context, relationshipType);
+        }
+    }
+}

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

@@ -20,11 +20,13 @@ 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;
 import org.dspace.core.Context;
+import org.dspace.discovery.IndexableObject;
 import org.dspace.handle.service.HandleService;
 import org.dspace.services.ConfigurationService;
 import org.dspace.services.factory.DSpaceServicesFactory;
@@ -33,7 +35,6 @@ import org.jdom.JDOMException;
 import org.jdom.Namespace;
 import org.jdom.output.DOMOutputter;
 import org.jdom.output.XMLOutputter;
-import org.springframework.beans.factory.InitializingBean;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.w3c.dom.Document;
 
@@ -53,20 +54,14 @@ import org.w3c.dom.Document;
  *
  * @author Richard Rodgers
  */
-public class OpenSearchServiceImpl implements OpenSearchService, InitializingBean {
+public class OpenSearchServiceImpl implements OpenSearchService {
-    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;
-    // supported results formats
-    protected List<String> formats = null;
     // Namespaces used
     protected final String osNs = "http://a9.com/-/spec/opensearch/1.1/";
 
-    // base search UI URL
+    @Autowired(required = true)
-    protected String uiUrl = null;
+    protected ConfigurationService configurationService;
-    // base search service URL
-    protected String svcUrl = null;
 
     @Autowired(required = true)
     protected HandleService handleService;
@@ -75,25 +70,35 @@ public class OpenSearchServiceImpl implements OpenSearchService, InitializingBea
     }
 
     @Override
-    public void afterPropertiesSet() throws Exception {
+    public List<String> getFormats() {
-        ConfigurationService config = DSpaceServicesFactory.getInstance().getConfigurationService();
+        List<String> formats = new ArrayList<>();
-        enabled = config.getBooleanProperty("websvc.opensearch.enable");
+        // read formats only if enabled
-        svcUrl = config.getProperty("dspace.url") + "/" +
+        if (isEnabled()) {
-            config.getProperty("websvc.opensearch.svccontext");
+            String[] fmts = configurationService.getArrayProperty("websvc.opensearch.formats");
-        uiUrl = config.getProperty("dspace.url") + "/" +
-            config.getProperty("websvc.opensearch.uicontext");
-
-        // read rest of config info if enabled
-        formats = new ArrayList<String>();
-        if (enabled) {
-            String[] fmts = config.getArrayProperty("websvc.opensearch.formats");
             formats = Arrays.asList(fmts);
         }
+        return formats;
     }
 
     @Override
-    public List<String> getFormats() {
+    public boolean isEnabled() {
-        return formats;
+        return configurationService.getBooleanProperty("websvc.opensearch.enable");
+    }
+
+    /**
+     * Get base search service URL (websvc.opensearch.svccontext)
+     */
+    protected String getBaseSearchServiceURL() {
+        return configurationService.getProperty("dspace.url") + "/" +
+            configurationService.getProperty("websvc.opensearch.svccontext");
+    }
+
+    /**
+     * Get base search UI URL (websvc.opensearch.uicontext)
+     */
+    protected String getBaseSearchUIURL() {
+        return configurationService.getProperty("dspace.url") + "/" +
+            configurationService.getProperty("websvc.opensearch.uicontext");
     }
 
     @Override
@@ -115,7 +120,7 @@ public class OpenSearchServiceImpl implements OpenSearchService, InitializingBea
     @Override
     public String getResultsString(Context context, String format, String query, int totalResults, int start,
                                    int pageSize,
-                                   DSpaceObject scope, List<DSpaceObject> results,
+                                   IndexableObject scope, List<IndexableObject> results,
                                    Map<String, String> labels) throws IOException {
         try {
             return getResults(context, format, query, totalResults, start, pageSize, scope, results, labels)
@@ -129,7 +134,7 @@ public class OpenSearchServiceImpl implements OpenSearchService, InitializingBea
     @Override
     public Document getResultsDoc(Context context, String format, String query, int totalResults, int start,
                                   int pageSize,
-                                  DSpaceObject scope, List<DSpaceObject> results, Map<String, String> labels)
+                                  IndexableObject scope, List<IndexableObject> results, Map<String, String> labels)
         throws IOException {
         try {
             return getResults(context, format, query, totalResults, start, pageSize, scope, results, labels)
@@ -141,8 +146,8 @@ public class OpenSearchServiceImpl implements OpenSearchService, InitializingBea
     }
 
     protected SyndicationFeed getResults(Context context, String format, String query, int totalResults, int start,
-                                         int pageSize,
+                                         int pageSize, IndexableObject scope,
-                                         DSpaceObject scope, List<DSpaceObject> results, Map<String, String> labels) {
+                                         List<IndexableObject> results, Map<String, String> labels) {
         // Encode results in requested format
         if ("rss".equals(format)) {
             format = "rss_2.0";
@@ -221,13 +226,13 @@ public class OpenSearchServiceImpl implements OpenSearchService, InitializingBea
             root.addContent(fav);
         }
         // service URLs
-        for (String format : formats) {
+        for (String format : getFormats()) {
             Element url = new Element("Url", ns).setAttribute("type", getContentType(format));
             StringBuilder template = new StringBuilder();
             if ("html".equals(format)) {
-                template.append(uiUrl);
+                template.append(getBaseSearchUIURL());
             } else {
-                template.append(svcUrl);
+                template.append(getBaseSearchServiceURL());
             }
             template.append("?query={searchTerms}");
             if (!"html".equals(format)) {

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;
@@ -52,6 +52,7 @@ import org.dspace.content.service.ItemService;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
+import org.dspace.discovery.IndexableObject;
 import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.services.ConfigurationService;
 import org.dspace.services.factory.DSpaceServicesFactory;
@@ -69,7 +70,7 @@ 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);
 
 
     /**
@@ -179,12 +180,12 @@ public class SyndicationFeed {
      *
      * @param request request
      * @param context context
-     * @param dso     DSpaceObject
+     * @param dso     the scope
      * @param items   array of objects
      * @param labels  label map
      */
-    public void populate(HttpServletRequest request, Context context, DSpaceObject dso,
+    public void populate(HttpServletRequest request, Context context, IndexableObject dso,
-                         List<? extends DSpaceObject> items, Map<String, String> labels) {
+                         List<IndexableObject> items, Map<String, String> labels) {
         String logoURL = null;
         String objectURL = null;
         String defaultTitle = null;
@@ -208,6 +209,7 @@ public class SyndicationFeed {
                 if (cols != null && cols.length() > 1 && cols.contains(col.getHandle())) {
                     podcastFeed = true;
                 }
+                objectURL = resolveURL(request, col);
             } else if (dso.getType() == Constants.COMMUNITY) {
                 Community comm = (Community) dso;
                 defaultTitle = comm.getName();
@@ -217,8 +219,9 @@ public class SyndicationFeed {
                 if (comms != null && comms.length() > 1 && comms.contains(comm.getHandle())) {
                     podcastFeed = true;
                 }
+                objectURL = resolveURL(request, comm);
             }
-            objectURL = resolveURL(request, dso);
+
             if (logo != null) {
                 logoURL = urlOfBitstream(request, logo);
             }
@@ -247,11 +250,11 @@ public class SyndicationFeed {
         // add entries for items
         if (items != null) {
             List<SyndEntry> entries = new ArrayList<SyndEntry>();
-            for (DSpaceObject itemDSO : items) {
+            for (IndexableObject idxObj : items) {
-                if (itemDSO.getType() != Constants.ITEM) {
+                if (idxObj.getType() != Constants.ITEM) {
                     continue;
                 }
-                Item item = (Item) itemDSO;
+                Item item = (Item) idxObj;
                 boolean hasDate = false;
                 SyndEntry entry = new SyndEntryImpl();
                 entries.add(entry);
@@ -366,7 +369,7 @@ public class SyndicationFeed {
                                 if (ArrayUtils.contains(podcastableMIMETypes, mime)) {
                                     SyndEnclosure enc = new SyndEnclosureImpl();
                                     enc.setType(bit.getFormat(context).getMIMEType());
-                                    enc.setLength(bit.getSize());
+                                    enc.setLength(bit.getSizeBytes());
                                     enc.setUrl(urlOfBitstream(request, bit));
                                     enclosures.add(enc);
                                 } else {

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

@@ -22,9 +22,9 @@ import java.util.Set;
 import java.util.UUID;
 import javax.servlet.http.HttpServletRequest;
 
-import org.apache.commons.collections.ListUtils;
+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
@@ -418,31 +418,33 @@ public class Util {
 
         List<DCInputSet> inputSets = inputsReader.getInputsByCollectionHandle(col_handle);
 
-        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, ".");
 
+        for (DCInputSet inputSet : inputSets) {
+
             if (inputSet != null) {
 
                 int fieldsNums = inputSet.getNumberFields();
 
                 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
+                                    .standardize(inputs[i][j].getSchema(), inputs[i][j].getElement(),
+                                                 inputs[i][j].getQualifier(), ".");
                                 if (currentField.equals(inputField)) {
-
+                                    myInputs = inputs[i][j];
-                                myInputs = inputs[i];
                                     myInputsFound = true;
                                     break;
-
+                                }
                             }
                         }
                     }
@@ -471,6 +473,26 @@ public class Util {
         return toReturn;
     }
 
+    /**
+     * Split a list in an array of i sub-lists uniformly sized
+     * 
+     * @param idsList the list to split
+     * @param i the number of sublists to return
+     * 
+     * @return an array of sub-lists of fixed size
+     */
+    public static <T> List<T>[] splitList(List<T> idsList, int i) {
+        int setmin = idsList.size() / i;
+        List<T>[] result = new List[i];
+        int offset = 0;
+        for (int idx = 0; idx < i - 1; idx++) {
+            result[idx] = idsList.subList(offset, offset + setmin);
+            offset += setmin;
+        }
+        result[i - 1] = idsList.subList(offset, idsList.size());
+        return result;
+    }
+
     public static List<String> differenceInSubmissionFields(Collection fromCollection, Collection toCollection)
         throws DCInputsReaderException {
         DCInputsReader reader = new DCInputsReader();
@@ -480,15 +502,19 @@ 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()) {
+                for (DCInput fdc : fdcrow) {
                     fromFieldName.add(fdc.getFieldName());
                 }
             }
+        }
         for (DCInputSet tt : to) {
-            for (DCInput tdc : tt.getFields()) {
+            for (DCInput[] tdcrow : tt.getFields()) {
+                for (DCInput tdc : tdcrow) {
                     toFieldName.add(tdc.getFieldName());
                 }
             }
+        }
 
         return ListUtils.removeAll(fromFieldName, toFieldName);
     }

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/app/util/service/OpenSearchService.java

@@ -14,6 +14,7 @@ import java.util.Map;
 
 import org.dspace.content.DSpaceObject;
 import org.dspace.core.Context;
+import org.dspace.discovery.IndexableObject;
 import org.w3c.dom.Document;
 
 /**
@@ -41,6 +42,13 @@ public interface OpenSearchService {
      */
     public List<String> getFormats();
 
+    /**
+     * Determine if the module is active
+     *
+     * @return boolean indicator if the OpenSearch module is enabled or not
+     */
+    public boolean isEnabled();
+
     /**
      * Returns a mime-type associated with passed format
      *
@@ -76,7 +84,7 @@ public interface OpenSearchService {
      * @param totalResults - the hit count
      * @param start        - start result index
      * @param pageSize     - page size
-     * @param scope        - search scope, null or community/collection handle
+     * @param scope        - search scope, null or the community/collection
      * @param results      the retreived DSpace objects satisfying search
      * @param labels       labels to apply - format specific
      * @return formatted search results
@@ -84,7 +92,7 @@ public interface OpenSearchService {
      */
     public String getResultsString(Context context, String format, String query, int totalResults, int start,
                                    int pageSize,
-                                   DSpaceObject scope, List<DSpaceObject> results,
+                                   IndexableObject scope, List<IndexableObject> results,
                                    Map<String, String> labels) throws IOException;
 
     /**
@@ -96,7 +104,7 @@ public interface OpenSearchService {
      * @param totalResults - the hit count
      * @param start        - start result index
      * @param pageSize     - page size
-     * @param scope        - search scope, null or community/collection handle
+     * @param scope        - search scope, null or the community/collection
      * @param results      the retreived DSpace objects satisfying search
      * @param labels       labels to apply - format specific
      * @return formatted search results
@@ -104,7 +112,7 @@ public interface OpenSearchService {
      */
     public Document getResultsDoc(Context context, String format, String query, int totalResults, int start,
                                   int pageSize,
-                                  DSpaceObject scope, List<DSpaceObject> results, Map<String, String> labels)
+                                  IndexableObject scope, List<IndexableObject> results, Map<String, String> labels)
         throws IOException;
 
     public DSpaceObject resolveScope(Context context, String scope) throws SQLException;

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

@@ -210,4 +210,10 @@ public interface AuthenticationMethod {
     public String loginPageURL(Context context,
                                HttpServletRequest request,
                                HttpServletResponse response);
+
+    /**
+     * Returns a short name that uniquely identifies this authentication method
+     * @return The authentication method name
+     */
+    public String getName();
 }

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

@@ -9,6 +9,7 @@ package org.dspace.authenticate;
 
 import java.sql.SQLException;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -16,15 +17,15 @@ import java.util.UUID;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.collections.ListUtils;
+import org.apache.logging.log4j.Logger;
-import org.apache.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");
@@ -164,23 +167,12 @@ public class IPAuthentication implements AuthenticationMethod {
     public List<Group> getSpecialGroups(Context context, HttpServletRequest request)
         throws SQLException {
         if (request == null) {
-            return ListUtils.EMPTY_LIST;
+            return Collections.EMPTY_LIST;
         }
         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 {
@@ -276,4 +268,9 @@ public class IPAuthentication implements AuthenticationMethod {
                                HttpServletResponse response) {
         return null;
     }
+
+    @Override
+    public String getName() {
+        return "ip";
+    }
 }

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

@@ -10,6 +10,7 @@ package org.dspace.authenticate;
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.Hashtable;
 import java.util.List;
 import javax.naming.NamingEnumeration;
@@ -27,9 +28,8 @@ import javax.naming.ldap.StartTlsResponse;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.collections.ListUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.logging.log4j.Logger;
-import org.apache.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();
@@ -136,7 +136,7 @@ public class LDAPAuthentication
                         log.warn(LogManager.getHeader(context,
                                                       "ldap_specialgroup",
                                                       "Group defined in login.specialgroup does not exist"));
-                        return ListUtils.EMPTY_LIST;
+                        return Collections.EMPTY_LIST;
                     } else {
                         return Arrays.asList(ldapGroup);
                     }
@@ -145,7 +145,7 @@ public class LDAPAuthentication
         } catch (Exception npe) {
             // The user is not an LDAP user, so we don't need to worry about them
         }
-        return ListUtils.EMPTY_LIST;
+        return Collections.EMPTY_LIST;
     }
 
     /*
@@ -639,6 +639,11 @@ public class LDAPAuthentication
         return null;
     }
 
+    @Override
+    public String getName() {
+        return "ldap";
+    }
+
     /*
      * Add authenticated users to the group defined in dspace.cfg by
      * the authentication-ldap.login.groupmap.* key.

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

@@ -9,13 +9,13 @@ package org.dspace.authenticate;
 
 import java.sql.SQLException;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.collections.ListUtils;
 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);
 
 
     /**
@@ -151,7 +151,7 @@ public class PasswordAuthentication
                                                       "password_specialgroup",
                                                       "Group defined in modules/authentication-password.cfg login" +
                                                           ".specialgroup does not exist"));
-                        return ListUtils.EMPTY_LIST;
+                        return Collections.EMPTY_LIST;
                     } else {
                         return Arrays.asList(specialGroup);
                     }
@@ -160,7 +160,7 @@ public class PasswordAuthentication
         } catch (Exception e) {
             log.error(LogManager.getHeader(context, "getSpecialGroups", ""), e);
         }
-        return ListUtils.EMPTY_LIST;
+        return Collections.EMPTY_LIST;
     }
 
     /**
@@ -242,4 +242,9 @@ public class PasswordAuthentication
                                HttpServletResponse response) {
         return null;
     }
+
+    @Override
+    public String getName() {
+        return "password";
+    }
 }

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

@@ -12,6 +12,7 @@ import java.net.URLEncoder;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -22,9 +23,8 @@ import java.util.UUID;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-import org.apache.commons.collections.ListUtils;
+import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang.StringUtils;
+import org.apache.logging.log4j.Logger;
-import org.apache.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
@@ -288,7 +288,7 @@ public class ShibAuthentication implements AuthenticationMethod {
             if (request == null ||
                 context.getCurrentUser() == null ||
                 request.getSession().getAttribute("shib.authenticated") == null) {
-                return ListUtils.EMPTY_LIST;
+                return Collections.EMPTY_LIST;
             }
 
             // If we have already calculated the special groups then return them.
@@ -404,7 +404,7 @@ public class ShibAuthentication implements AuthenticationMethod {
             return new ArrayList<>(groups);
         } catch (Throwable t) {
             log.error("Unable to validate any sepcial groups this user may belong too because of an exception.", t);
-            return ListUtils.EMPTY_LIST;
+            return Collections.EMPTY_LIST;
         }
     }
 
@@ -538,6 +538,11 @@ public class ShibAuthentication implements AuthenticationMethod {
         }
     }
 
+    @Override
+    public String getName() {
+        return "shibboleth";
+    }
+
     /**
      * Identify an existing EPerson based upon the shibboleth attributes provided on
      * the request object. There are three cases where this can occurr, each as

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

@@ -21,6 +21,7 @@ import java.security.cert.CertificateFactory;
 import java.security.cert.X509Certificate;
 import java.sql.SQLException;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.List;
 import java.util.StringTokenizer;
@@ -28,9 +29,8 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import javax.servlet.http.HttpSession;
 
-import org.apache.commons.collections.ListUtils;
+import org.apache.commons.lang3.ArrayUtils;
-import org.apache.commons.lang.ArrayUtils;
+import org.apache.logging.log4j.Logger;
-import org.apache.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.
@@ -442,7 +442,7 @@ public class X509Authentication implements AuthenticationMethod {
     public List<Group> getSpecialGroups(Context context, HttpServletRequest request)
         throws SQLException {
         if (request == null) {
-            return ListUtils.EMPTY_LIST;
+            return Collections.EMPTY_LIST;
         }
 
         Boolean authenticated = false;
@@ -472,7 +472,7 @@ public class X509Authentication implements AuthenticationMethod {
             return groups;
         }
 
-        return ListUtils.EMPTY_LIST;
+        return Collections.EMPTY_LIST;
     }
 
     /**
@@ -589,4 +589,9 @@ public class X509Authentication implements AuthenticationMethod {
                                HttpServletResponse response) {
         return loginPageURL;
     }
+
+    @Override
+    public String getName() {
+        return "x509";
+    }
 }

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

@@ -7,6 +7,7 @@
  */
 package org.dspace.authority;
 
+import java.io.IOException;
 import java.net.MalformedURLException;
 import java.util.List;
 
@@ -22,7 +23,8 @@ import org.apache.solr.client.solrj.response.QueryResponse;
  */
 public interface AuthoritySearchService {
 
-    public QueryResponse search(SolrQuery query) throws SolrServerException, MalformedURLException;
+    public QueryResponse search(SolrQuery query)
+            throws SolrServerException, MalformedURLException, IOException;
 
     public List<String> getAllIndexedMetadataFields() throws Exception;
 

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

@@ -46,17 +46,11 @@ public class AuthorityServiceImpl implements AuthorityService {
         }
 
         for (AuthorityIndexerInterface indexerInterface : indexers) {
-
+            List<AuthorityValue> authorityValues = indexerInterface.getAuthorityValues(context , item);
-            indexerInterface.init(context, item);
+            for (AuthorityValue authorityValue : authorityValues) {
-            while (indexerInterface.hasMore()) {
+                indexingService.indexContent(authorityValue);
-                AuthorityValue authorityValue = indexerInterface.nextValue();
-                if (authorityValue != null) {
-                    indexingService.indexContent(authorityValue, true);
             }
         }
-            //Close up
-            indexerInterface.close();
-        }
         //Commit to our server
         indexingService.commit();
     }

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

@@ -12,10 +12,10 @@ 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;
+import org.apache.solr.client.solrj.impl.HttpSolrClient;
 import org.apache.solr.client.solrj.response.FacetField;
 import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.common.SolrInputDocument;
@@ -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() {
 
@@ -39,16 +39,17 @@ public class AuthoritySolrServiceImpl implements AuthorityIndexingService, Autho
     /**
      * Non-Static CommonsHttpSolrServer for processing indexing events.
      */
-    protected HttpSolrServer solr = null;
+    protected HttpSolrClient solr = null;
 
-    protected HttpSolrServer getSolr() throws MalformedURLException, SolrServerException {
+    protected HttpSolrClient getSolr()
+            throws MalformedURLException, SolrServerException, IOException {
         if (solr == null) {
 
             String solrService = ConfigurationManager.getProperty("solr.authority.server");
 
             log.debug("Solr authority URL: " + solrService);
 
-            solr = new HttpSolrServer(solrService);
+            solr = new HttpSolrClient.Builder(solrService).build();
             solr.setBaseURL(solrService);
 
             SolrQuery solrQuery = new SolrQuery().setQuery("*:*");
@@ -60,7 +61,7 @@ public class AuthoritySolrServiceImpl implements AuthorityIndexingService, Autho
     }
 
     @Override
-    public void indexContent(AuthorityValue value, boolean force) {
+    public void indexContent(AuthorityValue value) {
         SolrInputDocument doc = value.getSolrInputDocument();
 
         try {
@@ -129,7 +130,8 @@ public class AuthoritySolrServiceImpl implements AuthorityIndexingService, Autho
     }
 
     @Override
-    public QueryResponse search(SolrQuery query) throws SolrServerException, MalformedURLException {
+    public QueryResponse search(SolrQuery query)
+            throws SolrServerException, MalformedURLException, IOException {
         return getSolr().query(query);
     }
 

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/SolrAuthorityInterface.java

@@ -0,0 +1,20 @@
+/**
+ * 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.authority;
+
+import java.util.List;
+
+/**
+ * @author Jonas Van Goolen (jonas at atmire dot com)
+ */
+public interface SolrAuthorityInterface {
+
+    List<AuthorityValue> queryAuthorities(String text, int max);
+
+    AuthorityValue queryAuthorityID(String id);
+}

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

@@ -8,13 +8,17 @@
 package org.dspace.authority.indexer;
 
 import java.util.HashMap;
+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;
+import org.dspace.content.Item;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.ItemService;
 import org.dspace.core.Context;
 
 /**
@@ -25,7 +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();
@@ -33,6 +37,8 @@ public class AuthorityIndexClient {
         AuthorityServiceFactory.getInstance().getAuthorityIndexingService();
     protected static final List<AuthorityIndexerInterface> indexers =
         AuthorityServiceFactory.getInstance().getAuthorityIndexers();
+    protected static final ItemService itemService =
+        ContentServiceFactory.getInstance().getItemService();
 
     /**
      * Default constructor
@@ -64,15 +70,17 @@ public class AuthorityIndexClient {
         for (AuthorityIndexerInterface indexerInterface : indexers) {
             log.info("Initialize " + indexerInterface.getClass().getName());
             System.out.println("Initialize " + indexerInterface.getClass().getName());
-            indexerInterface.init(context, true);
+            Iterator<Item> allItems = itemService.findAll(context);
-            while (indexerInterface.hasMore()) {
+            Map<String, AuthorityValue> authorityCache = new HashMap<>();
-                AuthorityValue authorityValue = indexerInterface.nextValue();
+            while (allItems.hasNext()) {
-                if (authorityValue != null) {
+                Item item = allItems.next();
+                List<AuthorityValue> authorityValues = indexerInterface.getAuthorityValues(
+                    context, item, authorityCache);
+                for (AuthorityValue authorityValue : authorityValues) {
                     toIndexValues.put(authorityValue.getId(), authorityValue);
                 }
+                context.uncacheEntity(item);
             }
-            //Close up
-            indexerInterface.close();
         }
 
 
@@ -82,7 +90,7 @@ public class AuthorityIndexClient {
         log.info("Writing new data");
         System.out.println("Writing new data");
         for (String id : toIndexValues.keySet()) {
-            indexingService.indexContent(toIndexValues.get(id), true);
+            indexingService.indexContent(toIndexValues.get(id));
             indexingService.commit();
         }
 

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

@@ -9,6 +9,8 @@
 package org.dspace.authority.indexer;
 
 import java.sql.SQLException;
+import java.util.List;
+import java.util.Map;
 
 import org.dspace.authority.AuthorityValue;
 import org.dspace.authorize.AuthorizeException;
@@ -23,17 +25,10 @@ import org.dspace.core.Context;
  */
 public interface AuthorityIndexerInterface {
 
-    public void init(Context context, Item item);
+    public List<AuthorityValue> getAuthorityValues(Context context, Item item)
-
+            throws SQLException, AuthorizeException;
-    public void init(Context context, boolean useCache);
+    public List<AuthorityValue> getAuthorityValues(Context context, Item item, Map<String, AuthorityValue> cache)
-
+            throws SQLException, AuthorizeException;
-    public void init(Context context);
-
-    public AuthorityValue nextValue();
-
-    public boolean hasMore() throws SQLException, AuthorizeException;
-
-    public void close();
 
     public boolean isConfiguredProperly();
 }

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

@@ -19,7 +19,7 @@ import org.dspace.authority.AuthorityValue;
 public interface AuthorityIndexingService {
 
 
-    public void indexContent(AuthorityValue value, boolean force);
+    public void indexContent(AuthorityValue value);
 
     public void cleanIndex() throws Exception;
 

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

@@ -9,14 +9,12 @@ package org.dspace.authority.indexer;
 
 import java.sql.SQLException;
 import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.collections.CollectionUtils;
+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;
@@ -31,12 +29,13 @@ import org.springframework.beans.factory.annotation.Autowired;
 /**
  * DSpaceAuthorityIndexer is used in IndexClient, which is called by the AuthorityConsumer and the indexing-script.
  * <p>
- * An instance of DSpaceAuthorityIndexer is bound to a list of items.
+ * The DSpaceAuthorityIndexer will return a list of all authority values for a
- * This can be one item or all items too depending on the init() method.
+ * given item. It will return an authority value for all metadata fields defined
+ * in dspace.conf with 'authority.author.indexer.field'.
  * <p>
- * DSpaceAuthorityIndexer lets you iterate over each metadata value
+ * You have to call getAuthorityValues for every Item you want to index. But you
- * for each metadata field defined in dspace.cfg with 'authority.author.indexer.field'
+ * can supply an optional cache, to save the mapping from the metadata value to
- * for each item in the list.
+ * the new authority values for metadata fields without an authority key.
  * <p>
  *
  * @author Antoine Snyers (antoine at atmire.com)
@@ -46,25 +45,16 @@ 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);
 
-    protected Iterator<Item> itemIterator;
-    protected Item currentItem;
     /**
      * The list of metadata fields which are to be indexed *
      */
     protected List<String> metadataFields;
-    protected int currentFieldIndex;
-    protected int currentMetadataIndex;
-    protected AuthorityValue nextValue;
-    protected Context context;
     @Autowired(required = true)
     protected AuthorityValueService authorityValueService;
     @Autowired(required = true)
     protected ItemService itemService;
-    protected boolean useCache;
-    protected Map<String, AuthorityValue> cache;
-
 
     @Autowired(required = true)
     protected ConfigurationService configurationService;
@@ -80,146 +70,83 @@ public class DSpaceAuthorityIndexer implements AuthorityIndexerInterface, Initia
         }
     }
 
-
     @Override
-    public void init(Context context, Item item) {
+    public List<AuthorityValue> getAuthorityValues(Context context, Item item)
-        ArrayList<Item> itemList = new ArrayList<>();
+            throws SQLException, AuthorizeException {
-        itemList.add(item);
+        return getAuthorityValues(context, item, null);
-        this.itemIterator = itemList.iterator();
-        currentItem = this.itemIterator.next();
-        initialize(context);
     }
 
-    @Override
+    public List<AuthorityValue> getAuthorityValues(Context context, Item item, Map<String, AuthorityValue> cache)
-    public void init(Context context) {
+            throws SQLException, AuthorizeException {
-        init(context, false);
+        List<AuthorityValue> values = new ArrayList<>();
+        for (String metadataField : metadataFields) {
+            List<MetadataValue> metadataValues = itemService.getMetadataByMetadataString(item, metadataField);
+            for (MetadataValue metadataValue : metadataValues) {
+                String content = metadataValue.getValue();
+                String authorityKey = metadataValue.getAuthority();
+                 // We only want to update our item IF our UUID is not present
+                // or if we need to generate one.
+                boolean requiresItemUpdate = StringUtils.isBlank(authorityKey) ||
+                        StringUtils.startsWith(authorityKey, AuthorityValueService.GENERATE);
+                AuthorityValue value = null;
+                if (StringUtils.isBlank(authorityKey) && cache != null) {
+                    // This is a value currently without an authority. So query
+                    // the cache, if an authority is found for the exact value.
+                    value = cache.get(content);
                 }
-
+                if (value == null) {
-    @Override
+                    value = getAuthorityValue(context, metadataField, content,authorityKey);
-    public void init(Context context, boolean useCache) {
+                }
+                if (value != null) {
+                    if (requiresItemUpdate) {
+                        value.updateItem(context, item, metadataValue);
                         try {
-            this.itemIterator = itemService.findAll(context);
+                            itemService.update(context, item);
-            currentItem = this.itemIterator.next();
-        } catch (SQLException e) {
-            log.error("Error while retrieving all items in the metadata indexer");
-        }
-        initialize(context);
-        this.useCache = useCache;
-    }
-
-    protected void initialize(Context context) {
-        this.context = context;
-
-        currentFieldIndex = 0;
-        currentMetadataIndex = 0;
-        useCache = false;
-        cache = new HashMap<>();
-    }
-
-    @Override
-    public AuthorityValue nextValue() {
-        return nextValue;
-    }
-
-
-    @Override
-    public boolean hasMore() throws SQLException, AuthorizeException {
-        if (currentItem == null) {
-            return false;
-        }
-
-        // 1. iterate over the metadata values
-
-        String metadataField = metadataFields.get(currentFieldIndex);
-        List<MetadataValue> values = itemService.getMetadataByMetadataString(currentItem, metadataField);
-        if (currentMetadataIndex < values.size()) {
-            prepareNextValue(metadataField, values.get(currentMetadataIndex));
-
-            currentMetadataIndex++;
-            return true;
-        } else {
-
-            // 2. iterate over the metadata fields
-
-            if ((currentFieldIndex + 1) < metadataFields.size()) {
-                currentFieldIndex++;
-                //Reset our current metadata index since we are moving to another field
-                currentMetadataIndex = 0;
-                return hasMore();
-            } else {
-
-                // 3. iterate over the items
-                if (itemIterator.hasNext()) {
-                    currentItem = itemIterator.next();
-                    //Reset our current field index
-                    currentFieldIndex = 0;
-                    //Reset our current metadata index
-                    currentMetadataIndex = 0;
-                } else {
-                    currentItem = null;
-                }
-                return hasMore();
-            }
-        }
-    }
-
-    /**
-     * This method looks at the authority of a metadata.
-     * 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
-     *
-     * @param metadataField Is one of the fields defined in dspace.cfg to be indexed.
-     * @param value         Is one of the values of the given metadataField in one of the items being indexed.
-     * @throws SQLException       if database error
-     * @throws AuthorizeException if authorization error
-     */
-    protected void prepareNextValue(String metadataField, MetadataValue value) throws SQLException, AuthorizeException {
-
-        nextValue = null;
-
-        String content = value.getValue();
-        String authorityKey = value.getAuthority();
-        //We only want to update our item IF our UUID is not present or if we need to generate one.
-        boolean requiresItemUpdate = StringUtils.isBlank(authorityKey) || StringUtils
-            .startsWith(authorityKey, AuthorityValueService.GENERATE);
-
-        if (StringUtils.isNotBlank(authorityKey) && !authorityKey.startsWith(AuthorityValueService.GENERATE)) {
-            // !uid.startsWith(AuthorityValueGenerator.GENERATE) is not strictly necessary here but it prevents
-            // exceptions in solr
-            nextValue = authorityValueService.findByUID(context, authorityKey);
-        }
-        if (nextValue == null && StringUtils.isBlank(authorityKey) && useCache) {
-            // A metadata without authority is being indexed
-            // If there is an exact match in the cache, reuse it rather than adding a new one.
-            AuthorityValue cachedAuthorityValue = cache.get(content);
-            if (cachedAuthorityValue != null) {
-                nextValue = cachedAuthorityValue;
-            }
-        }
-        if (nextValue == null) {
-            nextValue = authorityValueService
-                .generate(context, authorityKey, content, metadataField.replaceAll("\\.", "_"));
-        }
-        if (nextValue != null && requiresItemUpdate) {
-            nextValue.updateItem(context, currentItem, value);
-            try {
-                itemService.update(context, currentItem);
                         } catch (Exception e) {
                             log.error("Error creating a metadatavalue's authority", e);
                         }
                     }
-        if (useCache) {
+                    if (cache != null) {
-            cache.put(content, nextValue);
+                        cache.put(content, value);
+                    }
+                    values.add(value);
+                } else {
+                    log.error("Error getting an authority value for " +
+                            "the metadata value \"" + content + "\" " +
+                            "in the field \"" + metadataField + "\" " +
+                            "of the item " + item.getHandle());
                 }
             }
-
+        }
-    @Override
+        return values;
-    public void close() {
+    }
-        itemIterator = null;
+    /**
-        cache.clear();
+     * 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
+     *
+     * @param context Current DSpace context
+     * @param metadataField Is one of the fields defined in dspace.cfg to be indexed.
+     * @param metadataContent Content of the current metadata value.
+     * @param metadataAuthorityKey Existing authority of the metadata value.
+     */
+    private AuthorityValue getAuthorityValue(Context context, String metadataField,
+            String metadataContent, String metadataAuthorityKey) {
+        if (StringUtils.isNotBlank(metadataAuthorityKey) &&
+                !metadataAuthorityKey.startsWith(AuthorityValueService.GENERATE)) {
+            // !uid.startsWith(AuthorityValueGenerator.GENERATE) is not strictly
+            // necessary here but it prevents exceptions in solr
+            AuthorityValue value = authorityValueService.findByUID(context, metadataAuthorityKey);
+            if (value != null) {
+                return value;
+            }
+        }
+        return authorityValueService.generate(context, metadataAuthorityKey,
+                metadataContent, metadataField.replaceAll("\\.", "_"));
     }
 
     @Override

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

@@ -1,87 +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.authority.orcid;
-
-import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.dspace.authority.AuthorityValue;
-import org.dspace.authority.orcid.model.Bio;
-import org.dspace.authority.orcid.model.Work;
-import org.dspace.authority.orcid.xml.XMLtoBio;
-import org.dspace.authority.orcid.xml.XMLtoWork;
-import org.dspace.authority.rest.RestSource;
-import org.dspace.services.factory.DSpaceServicesFactory;
-import org.w3c.dom.Document;
-
-/**
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Orcid extends RestSource {
-
-    /**
-     * log4j logger
-     */
-    private static Logger log = Logger.getLogger(Orcid.class);
-
-    private static Orcid orcid;
-
-    public static Orcid getOrcid() {
-        if (orcid == null) {
-            orcid = DSpaceServicesFactory.getInstance().getServiceManager()
-                                         .getServiceByName("OrcidSource", Orcid.class);
-        }
-        return orcid;
-    }
-
-    private Orcid(String url) {
-        super(url);
-    }
-
-    public Bio getBio(String id) {
-        Document bioDocument = restConnector.get(id + "/orcid-bio");
-        XMLtoBio converter = new XMLtoBio();
-        Bio bio = converter.convert(bioDocument).get(0);
-        bio.setOrcid(id);
-        return bio;
-    }
-
-    public List<Work> getWorks(String id) {
-        Document document = restConnector.get(id + "/orcid-works");
-        XMLtoWork converter = new XMLtoWork();
-        return converter.convert(document);
-    }
-
-    public List<Bio> queryBio(String name, int start, int rows) {
-        Document bioDocument = restConnector
-            .get("search/orcid-bio?q=" + URLEncoder.encode("\"" + name + "\"") + "&start=" + start + "&rows=" + rows);
-        XMLtoBio converter = new XMLtoBio();
-        return converter.convert(bioDocument);
-    }
-
-    @Override
-    public List<AuthorityValue> queryAuthorities(String text, int max) {
-        List<Bio> bios = queryBio(text, 0, max);
-        List<AuthorityValue> authorities = new ArrayList<AuthorityValue>();
-        for (Bio bio : bios) {
-            authorities.add(OrcidAuthorityValue.create(bio));
-        }
-        return authorities;
-    }
-
-    @Override
-    public AuthorityValue queryAuthorityID(String id) {
-        Bio bio = getBio(id);
-        return OrcidAuthorityValue.create(bio);
-    }
-}

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

@@ -1,328 +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.authority.orcid;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.UUID;
-
-import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
-import org.apache.solr.common.SolrDocument;
-import org.apache.solr.common.SolrInputDocument;
-import org.dspace.authority.AuthorityValue;
-import org.dspace.authority.AuthorityValueServiceImpl;
-import org.dspace.authority.PersonAuthorityValue;
-import org.dspace.authority.orcid.model.Bio;
-import org.dspace.authority.orcid.model.BioExternalIdentifier;
-import org.dspace.authority.orcid.model.BioName;
-import org.dspace.authority.orcid.model.BioResearcherUrl;
-
-/**
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class OrcidAuthorityValue extends PersonAuthorityValue {
-
-    /**
-     * log4j logger
-     */
-    private static Logger log = Logger.getLogger(OrcidAuthorityValue.class);
-
-    private String orcid_id;
-    private Map<String, List<String>> otherMetadata = new HashMap<String, List<String>>();
-    private boolean update; // used in setValues(Bio bio)
-
-
-    /**
-     * Creates an instance of OrcidAuthorityValue with only uninitialized fields.
-     * This is meant to be filled in with values from an existing record.
-     * To create a brand new OrcidAuthorityValue, use create()
-     */
-    public OrcidAuthorityValue() {
-    }
-
-    public OrcidAuthorityValue(SolrDocument document) {
-        super(document);
-    }
-
-    public String getOrcid_id() {
-        return orcid_id;
-    }
-
-    public void setOrcid_id(String orcid_id) {
-        this.orcid_id = orcid_id;
-    }
-
-    public Map<String, List<String>> getOtherMetadata() {
-        return otherMetadata;
-    }
-
-    public void addOtherMetadata(String label, String data) {
-        List<String> strings = otherMetadata.get(label);
-        if (strings == null) {
-            strings = new ArrayList<String>();
-        }
-        strings.add(data);
-        otherMetadata.put(label, strings);
-    }
-
-    @Override
-    public SolrInputDocument getSolrInputDocument() {
-        SolrInputDocument doc = super.getSolrInputDocument();
-        if (StringUtils.isNotBlank(getOrcid_id())) {
-            doc.addField("orcid_id", getOrcid_id());
-        }
-
-        for (String t : otherMetadata.keySet()) {
-            List<String> data = otherMetadata.get(t);
-            for (String data_entry : data) {
-                doc.addField("label_" + t, data_entry);
-            }
-        }
-        return doc;
-    }
-
-    @Override
-    public void setValues(SolrDocument document) {
-        super.setValues(document);
-        this.orcid_id = String.valueOf(document.getFieldValue("orcid_id"));
-
-        otherMetadata = new HashMap<String, List<String>>();
-        for (String fieldName : document.getFieldNames()) {
-            String labelPrefix = "label_";
-            if (fieldName.startsWith(labelPrefix)) {
-                String label = fieldName.substring(labelPrefix.length());
-                List<String> list = new ArrayList<String>();
-                Collection<Object> fieldValues = document.getFieldValues(fieldName);
-                for (Object o : fieldValues) {
-                    list.add(String.valueOf(o));
-                }
-                otherMetadata.put(label, list);
-            }
-        }
-    }
-
-    public static OrcidAuthorityValue create() {
-        OrcidAuthorityValue orcidAuthorityValue = new OrcidAuthorityValue();
-        orcidAuthorityValue.setId(UUID.randomUUID().toString());
-        orcidAuthorityValue.updateLastModifiedDate();
-        orcidAuthorityValue.setCreationDate(new Date());
-        return orcidAuthorityValue;
-    }
-
-    /**
-     * Create an authority based on a given orcid bio
-     *
-     * @param bio Bio
-     * @return OrcidAuthorityValue
-     */
-    public static OrcidAuthorityValue create(Bio bio) {
-        OrcidAuthorityValue authority = OrcidAuthorityValue.create();
-
-        authority.setValues(bio);
-
-        return authority;
-    }
-
-    public boolean setValues(Bio bio) {
-        BioName name = bio.getName();
-
-        if (updateValue(bio.getOrcid(), getOrcid_id())) {
-            setOrcid_id(bio.getOrcid());
-        }
-
-        if (updateValue(name.getFamilyName(), getLastName())) {
-            setLastName(name.getFamilyName());
-        }
-
-        if (updateValue(name.getGivenNames(), getFirstName())) {
-            setFirstName(name.getGivenNames());
-        }
-
-        if (StringUtils.isNotBlank(name.getCreditName())) {
-            if (!getNameVariants().contains(name.getCreditName())) {
-                addNameVariant(name.getCreditName());
-                update = true;
-            }
-        }
-        for (String otherName : name.getOtherNames()) {
-            if (!getNameVariants().contains(otherName)) {
-                addNameVariant(otherName);
-                update = true;
-            }
-        }
-
-        if (updateOtherMetadata("country", bio.getCountry())) {
-            addOtherMetadata("country", bio.getCountry());
-        }
-
-        for (String keyword : bio.getKeywords()) {
-            if (updateOtherMetadata("keyword", keyword)) {
-                addOtherMetadata("keyword", keyword);
-            }
-        }
-
-        for (BioExternalIdentifier externalIdentifier : bio.getBioExternalIdentifiers()) {
-            if (updateOtherMetadata("external_identifier", externalIdentifier.toString())) {
-                addOtherMetadata("external_identifier", externalIdentifier.toString());
-            }
-        }
-
-        for (BioResearcherUrl researcherUrl : bio.getResearcherUrls()) {
-            if (updateOtherMetadata("researcher_url", researcherUrl.toString())) {
-                addOtherMetadata("researcher_url", researcherUrl.toString());
-            }
-        }
-
-        if (updateOtherMetadata("biography", bio.getBiography())) {
-            addOtherMetadata("biography", bio.getBiography());
-        }
-
-        setValue(getName());
-
-        if (update) {
-            update();
-        }
-        boolean result = update;
-        update = false;
-        return result;
-    }
-
-    private boolean updateOtherMetadata(String label, String data) {
-        List<String> strings = getOtherMetadata().get(label);
-        boolean update;
-        if (strings == null) {
-            update = StringUtils.isNotBlank(data);
-        } else {
-            update = !strings.contains(data);
-        }
-        if (update) {
-            this.update = true;
-        }
-        return update;
-    }
-
-    private boolean updateValue(String incoming, String resident) {
-        boolean update = StringUtils.isNotBlank(incoming) && !incoming.equals(resident);
-        if (update) {
-            this.update = true;
-        }
-        return update;
-    }
-
-    @Override
-    public Map<String, String> choiceSelectMap() {
-
-        Map<String, String> map = super.choiceSelectMap();
-
-        map.put("orcid", getOrcid_id());
-
-        return map;
-    }
-
-    @Override
-    public String getAuthorityType() {
-        return "orcid";
-    }
-
-    @Override
-    public String generateString() {
-        String generateString = AuthorityValueServiceImpl.GENERATE + getAuthorityType() + AuthorityValueServiceImpl
-            .SPLIT;
-        if (StringUtils.isNotBlank(getOrcid_id())) {
-            generateString += getOrcid_id();
-        }
-        return generateString;
-    }
-
-
-    @Override
-    public AuthorityValue newInstance(String info) {
-        AuthorityValue authorityValue = null;
-        if (StringUtils.isNotBlank(info)) {
-            Orcid orcid = Orcid.getOrcid();
-            authorityValue = orcid.queryAuthorityID(info);
-        } else {
-            authorityValue = OrcidAuthorityValue.create();
-        }
-        return authorityValue;
-    }
-
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        OrcidAuthorityValue that = (OrcidAuthorityValue) o;
-
-        if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        return orcid_id != null ? orcid_id.hashCode() : 0;
-    }
-
-    @Override
-    public boolean hasTheSameInformationAs(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-        if (!super.hasTheSameInformationAs(o)) {
-            return false;
-        }
-
-        OrcidAuthorityValue that = (OrcidAuthorityValue) o;
-
-        if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
-            return false;
-        }
-
-        for (String key : otherMetadata.keySet()) {
-            if (otherMetadata.get(key) != null) {
-                List<String> metadata = otherMetadata.get(key);
-                List<String> otherMetadata = that.otherMetadata.get(key);
-                if (otherMetadata == null) {
-                    return false;
-                } else {
-                    HashSet<String> metadataSet = new HashSet<String>(metadata);
-                    HashSet<String> otherMetadataSet = new HashSet<String>(otherMetadata);
-                    if (!metadataSet.equals(otherMetadataSet)) {
-                        return false;
-                    }
-                }
-            } else {
-                if (that.otherMetadata.get(key) != null) {
-                    return false;
-                }
-            }
-        }
-
-        return true;
-    }
-}

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

@@ -0,0 +1,191 @@
+/**
+ * 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.authority.orcid;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URLEncoder;
+import java.util.ArrayList;
+import java.util.List;
+
+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.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;
+import org.dspace.authority.rest.RESTConnector;
+import org.json.JSONObject;
+import org.orcid.jaxb.model.record_v2.Person;
+
+/**
+ * @author Jonas Van Goolen (jonas at atmire dot com)
+ * This class contains all methods for retrieving "Person" objects calling the ORCID (version 2) endpoints.
+ * Additionally, this can also create AuthorityValues based on these returned Person objects
+ */
+public class Orcidv2 implements SolrAuthorityInterface {
+
+    private static Logger log = LogManager.getLogger(Orcidv2.class);
+
+    public RESTConnector restConnector;
+    private String OAUTHUrl;
+    private String clientId;
+
+    private String clientSecret;
+
+    private String accessToken;
+
+    /**
+     * 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)) {
+            String authenticationParameters = "?client_id=" + clientId +
+                                              "&client_secret=" + clientSecret +
+                                              "&scope=/read-public&grant_type=client_credentials";
+            HttpPost httpPost = new HttpPost(OAUTHUrl + authenticationParameters);
+            httpPost.addHeader("Accept", "application/json");
+            httpPost.addHeader("Content-Type", "application/x-www-form-urlencoded");
+
+            HttpClient httpClient = HttpClientBuilder.create().build();
+            HttpResponse getResponse = httpClient.execute(httpPost);
+
+            InputStream is = getResponse.getEntity().getContent();
+            BufferedReader streamReader = new BufferedReader(new InputStreamReader(is, "UTF-8"));
+
+            JSONObject responseObject = null;
+            String inputStr;
+            while ((inputStr = streamReader.readLine()) != null && responseObject == null) {
+                if (inputStr.startsWith("{") && inputStr.endsWith("}") && inputStr.contains("access_token")) {
+                    try {
+                        responseObject = new JSONObject(inputStr);
+                    } catch (Exception e) {
+                        //Not as valid as I'd hoped, move along
+                        responseObject = null;
+                    }
+                }
+            }
+
+            if (responseObject != null && responseObject.has("access_token")) {
+                accessToken = (String) responseObject.get("access_token");
+            }
+        }
+    }
+
+    /**
+     * Makes an instance of the Orcidv2 class based on the provided parameters.
+     * This constructor is called through the spring bean initialization
+     */
+    private Orcidv2(String url, String OAUTHUrl, String clientId, String clientSecret) {
+        this.restConnector = new RESTConnector(url);
+        this.OAUTHUrl = OAUTHUrl;
+        this.clientId = clientId;
+        this.clientSecret = clientSecret;
+    }
+
+    /**
+     * Makes an instance of the Orcidv2 class based on the provided parameters.
+     * This constructor is called through the spring bean initialization
+     */
+    private Orcidv2(String url) {
+        this.restConnector = new RESTConnector(url);
+    }
+
+    /**
+     * Makes an instance of the AuthorityValue with the given information.
+     * @param text search string
+     * @return List<AuthorityValue>
+     */
+    @Override
+    public List<AuthorityValue> queryAuthorities(String text, int max) {
+        List<Person> bios = queryBio(text, max);
+        List<AuthorityValue> result = new ArrayList<>();
+        for (Person person : bios) {
+            AuthorityValue orcidAuthorityValue = Orcidv2AuthorityValue.create(person);
+            if (orcidAuthorityValue != null) {
+                result.add(orcidAuthorityValue);
+            }
+        }
+        return result;
+    }
+
+    /**
+     * Create an AuthorityValue from a Person retrieved using the given orcid identifier.
+     * @param id orcid identifier
+     * @return AuthorityValue
+     */
+    public AuthorityValue queryAuthorityID(String id) {
+        Person person = getBio(id);
+        AuthorityValue valueFromPerson = Orcidv2AuthorityValue.create(person);
+        return valueFromPerson;
+    }
+
+    /**
+     * Retrieve a Person object based on a given orcid identifier
+     * @param id orcid identifier
+     * @return Person
+     */
+    public Person getBio(String id) {
+        log.debug("getBio called with ID=" + id);
+        if (!isValid(id)) {
+            return null;
+        }
+        InputStream bioDocument = restConnector.get(id + ((id.endsWith("/person")) ? "" : "/person"), accessToken);
+        XMLtoBio converter = new XMLtoBio();
+        Person person = converter.convertSinglePerson(bioDocument);
+        return person;
+    }
+
+
+    /**
+     * Retrieve a list of Person objects.
+     * @param text search string
+     * @param start offset to use
+     * @param rows how many rows to return
+     * @return List<Person>
+     */
+    public List<Person> queryBio(String text, int start, int rows) {
+        if (rows > 100) {
+            throw new IllegalArgumentException("The maximum number of results to retrieve cannot exceed 100.");
+        }
+
+        String searchPath = "search?q=" + URLEncoder.encode(text) + "&start=" + start + "&rows=" + rows;
+        log.debug("queryBio searchPath=" + searchPath + " accessToken=" + accessToken);
+        InputStream bioDocument = restConnector.get(searchPath, accessToken);
+        XMLtoBio converter = new XMLtoBio();
+        List<Person> bios = converter.convert(bioDocument);
+        return bios;
+    }
+
+    /**
+     * Retrieve a list of Person objects.
+     * @param text search string
+     * @param max how many rows to return
+     * @return List<Person>
+     */
+    public List<Person> queryBio(String text, int max) {
+        return queryBio(text, 0, max);
+    }
+
+    /**
+     * Check to see if the provided text has the correct ORCID syntax.
+     * Since only searching on ORCID id is allowed, this way, we filter out any queries that would return a
+     * blank result anyway
+     */
+    private boolean isValid(String text) {
+        return StringUtils.isNotBlank(text) && text.matches(Orcidv2AuthorityValue.ORCID_ID_SYNTAX);
+    }
+}

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

@@ -0,0 +1,342 @@
+/**
+ * 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.authority.orcid;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.UUID;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.solr.common.SolrDocument;
+import org.apache.solr.common.SolrInputDocument;
+import org.dspace.authority.AuthorityValue;
+import org.dspace.authority.AuthorityValueServiceImpl;
+import org.dspace.authority.PersonAuthorityValue;
+import org.dspace.utils.DSpace;
+import org.orcid.jaxb.model.common_v2.ExternalId;
+import org.orcid.jaxb.model.record_v2.ExternalIdentifiers;
+import org.orcid.jaxb.model.record_v2.KeywordType;
+import org.orcid.jaxb.model.record_v2.NameType;
+import org.orcid.jaxb.model.record_v2.Person;
+import org.orcid.jaxb.model.record_v2.ResearcherUrlType;
+
+/**
+ * @author Jonas Van Goolen (jonas at atmire dot com)
+ */
+public class Orcidv2AuthorityValue extends PersonAuthorityValue {
+
+    /*
+     * The ORCID identifier
+     */
+    private String orcid_id;
+
+    /*
+     * Map containing key-value pairs filled in by "setValues(Person person)".
+     * This represents all dynamic information of the object.
+     */
+    private Map<String, List<String>> otherMetadata = new HashMap<String, List<String>>();
+
+    /**
+     * The syntax that the ORCID id needs to conform to
+     */
+    public static final String ORCID_ID_SYNTAX = "\\d{4}-\\d{4}-\\d{4}-(\\d{3}X|\\d{4})";
+
+
+    /**
+     * Creates an instance of Orcidv2AuthorityValue with only uninitialized fields.
+     * This is meant to be filled in with values from an existing record.
+     * To create a brand new Orcidv2AuthorityValue, use create()
+     */
+    public Orcidv2AuthorityValue() {
+    }
+
+    public Orcidv2AuthorityValue(SolrDocument document) {
+        super(document);
+    }
+
+
+    public String getOrcid_id() {
+        return orcid_id;
+    }
+
+    public void setOrcid_id(String orcid_id) {
+        this.orcid_id = orcid_id;
+    }
+
+    /**
+     * Create an empty authority.
+     * @return OrcidAuthorityValue
+     */
+    public static Orcidv2AuthorityValue create() {
+        Orcidv2AuthorityValue orcidAuthorityValue = new Orcidv2AuthorityValue();
+        orcidAuthorityValue.setId(UUID.randomUUID().toString());
+        orcidAuthorityValue.updateLastModifiedDate();
+        orcidAuthorityValue.setCreationDate(new Date());
+        return orcidAuthorityValue;
+    }
+
+    /**
+     * Create an authority based on a given orcid bio
+     * @return OrcidAuthorityValue
+     */
+    public static Orcidv2AuthorityValue create(Person person) {
+        if (person == null) {
+            return null;
+        }
+        Orcidv2AuthorityValue authority = Orcidv2AuthorityValue.create();
+
+        authority.setValues(person);
+
+        return authority;
+    }
+
+    /**
+     * Initialize this instance based on a Person object
+     * @param person Person
+     */
+    protected void setValues(Person person) {
+        NameType name = person.getName();
+
+        if (!StringUtils.equals(name.getPath(), this.getOrcid_id())) {
+            this.setOrcid_id(name.getPath());
+        }
+
+        if (!StringUtils.equals(name.getFamilyName().getValue(), this.getLastName())) {
+            this.setLastName(name.getFamilyName().getValue());
+        }
+
+        if (!StringUtils.equals(name.getGivenNames().getValue(), this.getFirstName())) {
+            this.setFirstName(name.getGivenNames().getValue());
+        }
+
+        if (name.getCreditName() != null && StringUtils.isNotBlank(name.getCreditName().getValue())) {
+            if (!this.getNameVariants().contains(name.getCreditName().getValue())) {
+                this.addNameVariant(name.getCreditName().getValue());
+            }
+        }
+
+        if (person.getKeywords() != null) {
+            for (KeywordType keyword : person.getKeywords().getKeyword()) {
+                if (this.isNewMetadata("keyword", keyword.getContent())) {
+                    this.addOtherMetadata("keyword", keyword.getContent());
+                }
+            }
+        }
+
+        ExternalIdentifiers externalIdentifiers = person.getExternalIdentifiers();
+        if (externalIdentifiers != null) {
+            for (ExternalId externalIdentifier : externalIdentifiers.getExternalIdentifier()) {
+                if (this.isNewMetadata("external_identifier", externalIdentifier.getExternalIdValue())) {
+                    this.addOtherMetadata("external_identifier", externalIdentifier.getExternalIdValue());
+
+                }
+            }
+        }
+        if (person.getResearcherUrls() != null) {
+            for (ResearcherUrlType researcherUrl : person.getResearcherUrls().getResearcherUrl()) {
+                if (this.isNewMetadata("researcher_url", researcherUrl.getUrl().getValue())) {
+                    this.addOtherMetadata("researcher_url", researcherUrl.getUrl().getValue());
+                }
+            }
+
+        }
+        if (person.getBiography() != null) {
+            if (this.isNewMetadata("biography", person.getBiography().getContent())) {
+                this.addOtherMetadata("biography", person.getBiography().getContent());
+            }
+        }
+
+        this.setValue(this.getName());
+
+    }
+
+    /**
+     * Makes an instance of the AuthorityValue with the given information.
+     * @param info string info
+     * @return AuthorityValue
+     */
+    @Override
+    public AuthorityValue newInstance(String info) {
+        AuthorityValue authorityValue = null;
+        if (StringUtils.isNotBlank(info)) {
+            Orcidv2 orcid = new DSpace().getServiceManager().getServiceByName("AuthoritySource", Orcidv2.class);
+            authorityValue = orcid.queryAuthorityID(info);
+        } else {
+            authorityValue = this.create();
+        }
+        return authorityValue;
+    }
+
+    @Override
+    public void setValue(String value) {
+        super.setValue(value);
+    }
+
+    /**
+     * Check to see if the provided label / data pair is already present in the "otherMetadata" or not
+     * */
+    public boolean isNewMetadata(String label, String data) {
+        List<String> strings = getOtherMetadata().get(label);
+        boolean update;
+        if (strings == null) {
+            update = StringUtils.isNotBlank(data);
+        } else {
+            update = !strings.contains(data);
+        }
+        return update;
+    }
+
+    /**
+     * Add additional metadata to the otherMetadata map*/
+    public void addOtherMetadata(String label, String data) {
+        List<String> strings = otherMetadata.get(label);
+        if (strings == null) {
+            strings = new ArrayList<>();
+        }
+        strings.add(data);
+        otherMetadata.put(label, strings);
+    }
+
+    public Map<String, List<String>> getOtherMetadata() {
+        return otherMetadata;
+    }
+
+
+    /**
+     * Generate a solr record from this instance
+     * @return SolrInputDocument
+     */
+    @Override
+    public SolrInputDocument getSolrInputDocument() {
+        SolrInputDocument doc = super.getSolrInputDocument();
+        if (StringUtils.isNotBlank(getOrcid_id())) {
+            doc.addField("orcid_id", getOrcid_id());
+        }
+
+        for (String t : otherMetadata.keySet()) {
+            List<String> data = otherMetadata.get(t);
+            for (String data_entry : data) {
+                doc.addField("label_" + t, data_entry);
+            }
+        }
+        return doc;
+    }
+
+    /**
+     * Information that can be used the choice ui
+     * @return map
+     */
+    @Override
+    public Map<String, String> choiceSelectMap() {
+
+        Map<String, String> map = super.choiceSelectMap();
+
+        String orcid_id = getOrcid_id();
+        if (StringUtils.isNotBlank(orcid_id)) {
+            map.put("orcid", orcid_id);
+        }
+
+        return map;
+    }
+
+    @Override
+    public String getAuthorityType() {
+        return "orcid";
+    }
+
+    /**
+     * Provides a string that will allow this AuthorityType to be recognized and provides information to create a new
+     * instance to be created using public Orcidv2AuthorityValue newInstance(String info).
+     * @return see {@link org.dspace.authority.service.AuthorityValueService#GENERATE AuthorityValueService.GENERATE}
+     */
+    @Override
+    public String generateString() {
+        String generateString = AuthorityValueServiceImpl.GENERATE + getAuthorityType() +
+                                AuthorityValueServiceImpl.SPLIT;
+        if (StringUtils.isNotBlank(getOrcid_id())) {
+            generateString += getOrcid_id();
+        }
+        return generateString;
+    }
+
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) {
+            return true;
+        }
+        if (o == null || getClass() != o.getClass()) {
+            return false;
+        }
+
+        Orcidv2AuthorityValue that = (Orcidv2AuthorityValue) o;
+
+        if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
+            return false;
+        }
+
+        return true;
+    }
+
+    @Override
+    public int hashCode() {
+        return orcid_id != null ? orcid_id.hashCode() : 0;
+    }
+
+    /**
+     * The regular equals() only checks if both AuthorityValues describe the same authority.
+     * This method checks if the AuthorityValues have different information
+     * E.g. it is used to decide when lastModified should be updated.
+     * @param o object
+     * @return true or false
+     */
+    @Override
+    public boolean hasTheSameInformationAs(Object o) {
+        if (this == o) {
+            return true;
+        }
+        if (o == null || getClass() != o.getClass()) {
+            return false;
+        }
+        if (!super.hasTheSameInformationAs(o)) {
+            return false;
+        }
+
+        Orcidv2AuthorityValue that = (Orcidv2AuthorityValue) o;
+
+        if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
+            return false;
+        }
+
+        for (String key : otherMetadata.keySet()) {
+            if (otherMetadata.get(key) != null) {
+                List<String> metadata = otherMetadata.get(key);
+                List<String> otherMetadata = that.otherMetadata.get(key);
+                if (otherMetadata == null) {
+                    return false;
+                } else {
+                    HashSet<String> metadataSet = new HashSet<String>(metadata);
+                    HashSet<String> otherMetadataSet = new HashSet<String>(otherMetadata);
+                    if (!metadataSet.equals(otherMetadataSet)) {
+                        return false;
+                    }
+                }
+            } else {
+                if (that.otherMetadata.get(key) != null) {
+                    return false;
+                }
+            }
+        }
+
+        return true;
+    }
+}

dspace-api/src/main/java/org/dspace/authority/orcid/model/Bio.java

@@ -1,112 +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.authority.orcid.model;
-
-import java.util.LinkedHashSet;
-import java.util.Set;
-
-/**
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Bio {
-
-    protected String orcid;
-
-    protected BioName name;
-
-    protected String country;
-
-    protected Set<String> keywords;
-
-    protected Set<BioExternalIdentifier> bioExternalIdentifiers;
-
-    protected Set<BioResearcherUrl> researcherUrls;
-
-    protected String biography;
-
-    public Bio() {
-        this.name = new BioName();
-        keywords = new LinkedHashSet<String>();
-        bioExternalIdentifiers = new LinkedHashSet<BioExternalIdentifier>();
-        researcherUrls = new LinkedHashSet<BioResearcherUrl>();
-    }
-
-    public String getOrcid() {
-        return orcid;
-    }
-
-    public void setOrcid(String orcid) {
-        this.orcid = orcid;
-    }
-
-    public BioName getName() {
-        return name;
-    }
-
-    public void setName(BioName name) {
-        this.name = name;
-    }
-
-    public String getCountry() {
-        return country;
-    }
-
-    public void setCountry(String country) {
-        this.country = country;
-    }
-
-    public Set<String> getKeywords() {
-        return keywords;
-    }
-
-    public void addKeyword(String keyword) {
-        this.keywords.add(keyword);
-    }
-
-    public Set<BioExternalIdentifier> getBioExternalIdentifiers() {
-        return bioExternalIdentifiers;
-    }
-
-    public void addExternalIdentifier(BioExternalIdentifier externalReference) {
-        bioExternalIdentifiers.add(externalReference);
-    }
-
-    public Set<BioResearcherUrl> getResearcherUrls() {
-        return researcherUrls;
-    }
-
-    public void addResearcherUrl(BioResearcherUrl researcherUrl) {
-        researcherUrls.add(researcherUrl);
-    }
-
-    public String getBiography() {
-        return biography;
-    }
-
-    public void setBiography(String biography) {
-        this.biography = biography;
-    }
-
-    @Override
-    public String toString() {
-        return "Bio{" +
-            "orcid='" + orcid + '\'' +
-            ", name=" + name +
-            ", country='" + country + '\'' +
-            ", keywords=" + keywords +
-            ", bioExternalIdentifiers=" + bioExternalIdentifiers +
-            ", researcherUrls=" + researcherUrls +
-            ", biography='" + biography + '\'' +
-            '}';
-    }
-}
-

dspace-api/src/main/java/org/dspace/authority/orcid/model/BioExternalIdentifier.java

@@ -1,108 +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.authority.orcid.model;
-
-/**
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class BioExternalIdentifier {
-
-
-    protected String id_orcid;
-    protected String id_common_name;
-    protected String id_reference;
-    protected String id_url;
-
-    public BioExternalIdentifier(String id_orcid, String id_common_name, String id_reference, String id_url) {
-        this.id_orcid = id_orcid;
-        this.id_common_name = id_common_name;
-        this.id_reference = id_reference;
-        this.id_url = id_url;
-    }
-
-    public String getId_orcid() {
-        return id_orcid;
-    }
-
-    public void setId_orcid(String id_orcid) {
-        this.id_orcid = id_orcid;
-    }
-
-    public String getId_common_name() {
-        return id_common_name;
-    }
-
-    public void setId_common_name(String id_common_name) {
-        this.id_common_name = id_common_name;
-    }
-
-    public String getId_reference() {
-        return id_reference;
-    }
-
-    public void setId_reference(String id_reference) {
-        this.id_reference = id_reference;
-    }
-
-    public String getId_url() {
-        return id_url;
-    }
-
-    public void setId_url(String id_url) {
-        this.id_url = id_url;
-    }
-
-    @Override
-    public String toString() {
-        return "BioExternalIdentifier{" +
-            "id_orcid='" + id_orcid + '\'' +
-            ", id_common_name='" + id_common_name + '\'' +
-            ", id_reference='" + id_reference + '\'' +
-            ", id_url='" + id_url + '\'' +
-            '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        BioExternalIdentifier that = (BioExternalIdentifier) o;
-
-        if (id_common_name != null ? !id_common_name.equals(that.id_common_name) : that.id_common_name != null) {
-            return false;
-        }
-        if (id_orcid != null ? !id_orcid.equals(that.id_orcid) : that.id_orcid != null) {
-            return false;
-        }
-        if (id_reference != null ? !id_reference.equals(that.id_reference) : that.id_reference != null) {
-            return false;
-        }
-        if (id_url != null ? !id_url.equals(that.id_url) : that.id_url != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = id_orcid != null ? id_orcid.hashCode() : 0;
-        result = 31 * result + (id_common_name != null ? id_common_name.hashCode() : 0);
-        result = 31 * result + (id_reference != null ? id_reference.hashCode() : 0);
-        result = 31 * result + (id_url != null ? id_url.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/BioName.java

@@ -1,114 +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.authority.orcid.model;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class BioName {
-
-    protected String givenNames;
-    protected String familyName;
-    protected String creditName;
-    protected List<String> otherNames;
-
-    BioName() {
-        otherNames = new ArrayList<String>();
-    }
-
-    BioName(String givenNames, String familyName, String creditName, List<String> otherNames) {
-        this.givenNames = givenNames;
-        this.familyName = familyName;
-        this.creditName = creditName;
-        this.otherNames = otherNames;
-    }
-
-    public String getGivenNames() {
-        return givenNames;
-    }
-
-    public void setGivenNames(String givenNames) {
-        this.givenNames = givenNames;
-    }
-
-    public String getFamilyName() {
-        return familyName;
-    }
-
-    public void setFamilyName(String familyName) {
-        this.familyName = familyName;
-    }
-
-    public String getCreditName() {
-        return creditName;
-    }
-
-    public void setCreditName(String creditName) {
-        this.creditName = creditName;
-    }
-
-    public List<String> getOtherNames() {
-        return otherNames;
-    }
-
-    public void setOtherNames(List<String> otherNames) {
-        this.otherNames = otherNames;
-    }
-
-    @Override
-    public String toString() {
-        return "BioName{" +
-            "givenNames='" + givenNames + '\'' +
-            ", familyName='" + familyName + '\'' +
-            ", creditName='" + creditName + '\'' +
-            ", otherNames=" + otherNames +
-            '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        BioName bioName = (BioName) o;
-
-        if (creditName != null ? !creditName.equals(bioName.creditName) : bioName.creditName != null) {
-            return false;
-        }
-        if (familyName != null ? !familyName.equals(bioName.familyName) : bioName.familyName != null) {
-            return false;
-        }
-        if (givenNames != null ? !givenNames.equals(bioName.givenNames) : bioName.givenNames != null) {
-            return false;
-        }
-        if (otherNames != null ? !otherNames.equals(bioName.otherNames) : bioName.otherNames != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = givenNames != null ? givenNames.hashCode() : 0;
-        result = 31 * result + (familyName != null ? familyName.hashCode() : 0);
-        result = 31 * result + (creditName != null ? creditName.hashCode() : 0);
-        result = 31 * result + (otherNames != null ? otherNames.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/BioResearcherUrl.java

@@ -1,77 +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.authority.orcid.model;
-
-/**
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class BioResearcherUrl {
-
-    protected String name;
-    protected String url;
-
-    public BioResearcherUrl(String name, String url) {
-        this.name = name;
-        this.url = url;
-    }
-
-    public String getName() {
-        return name;
-    }
-
-    public void setName(String name) {
-        this.name = name;
-    }
-
-    public String getUrl() {
-        return url;
-    }
-
-    public void setUrl(String url) {
-        this.url = url;
-    }
-
-    @Override
-    public String toString() {
-        return "BioResearcherUrl{" +
-            "name='" + name + '\'' +
-            ", url='" + url + '\'' +
-            '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        BioResearcherUrl that = (BioResearcherUrl) o;
-
-        if (name != null ? !name.equals(that.name) : that.name != null) {
-            return false;
-        }
-        if (url != null ? !url.equals(that.url) : that.url != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = name != null ? name.hashCode() : 0;
-        result = 31 * result + (url != null ? url.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/Citation.java

@@ -1,49 +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.authority.orcid.model;
-
-/**
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Citation {
-
-    private CitationType type;
-    private String citation;
-
-    public Citation(CitationType type, String citation) {
-        this.type = type;
-        this.citation = citation;
-    }
-
-    public CitationType getType() {
-        return type;
-    }
-
-    public void setType(CitationType type) {
-        this.type = type;
-    }
-
-    public String getCitation() {
-        return citation;
-    }
-
-    public void setCitation(String citation) {
-        this.citation = citation;
-    }
-
-    @Override
-    public String toString() {
-        return "Citation{" +
-            "type=" + type +
-            ", citation='" + citation + '\'' +
-            '}';
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/CitationType.java

@@ -1,28 +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.authority.orcid.model;
-
-/**
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum CitationType {
-
-    FORMATTED_UNSPECIFIED,
-    BIBTEX,
-    FORMATTED_APA,
-    FORMATTED_HARVARD,
-    FORMATTED_IEEE,
-    FORMATTED_MLA,
-    FORMATTED_VANCOUVER,
-    FORMATTED_CHICAGO
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/Contributor.java

@@ -1,111 +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.authority.orcid.model;
-
-import java.util.Set;
-
-/**
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Contributor {
-
-    private String orcid;
-    private String creditName;
-    private String email;
-    private Set<ContributorAttribute> contributorAttributes;
-
-    public Contributor(String orcid, String creditName, String email, Set<ContributorAttribute> contributorAttributes) {
-        this.orcid = orcid;
-        this.creditName = creditName;
-        this.email = email;
-        this.contributorAttributes = contributorAttributes;
-    }
-
-    public String getOrcid() {
-        return orcid;
-    }
-
-    public void setOrcid(String orcid) {
-        this.orcid = orcid;
-    }
-
-    public String getCreditName() {
-        return creditName;
-    }
-
-    public void setCreditName(String creditName) {
-        this.creditName = creditName;
-    }
-
-    public String getEmail() {
-        return email;
-    }
-
-    public void setEmail(String email) {
-        this.email = email;
-    }
-
-    public Set<ContributorAttribute> getContributorAttributes() {
-        return contributorAttributes;
-    }
-
-    public void setContributorAttributes(Set<ContributorAttribute> contributorAttributes) {
-        this.contributorAttributes = contributorAttributes;
-    }
-
-    @Override
-    public String toString() {
-        return "Contributor{" +
-            "orcid='" + orcid + '\'' +
-            ", creditName='" + creditName + '\'' +
-            ", email='" + email + '\'' +
-            ", contributorAttributes=" + contributorAttributes +
-            '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        Contributor that = (Contributor) o;
-
-        if (contributorAttributes != null ? !contributorAttributes
-            .equals(that.contributorAttributes) : that.contributorAttributes != null) {
-            return false;
-        }
-        if (creditName != null ? !creditName.equals(that.creditName) : that.creditName != null) {
-            return false;
-        }
-        if (email != null ? !email.equals(that.email) : that.email != null) {
-            return false;
-        }
-        if (orcid != null ? !orcid.equals(that.orcid) : that.orcid != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = orcid != null ? orcid.hashCode() : 0;
-        result = 31 * result + (creditName != null ? creditName.hashCode() : 0);
-        result = 31 * result + (email != null ? email.hashCode() : 0);
-        result = 31 * result + (contributorAttributes != null ? contributorAttributes.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/ContributorAttribute.java

@@ -1,78 +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.authority.orcid.model;
-
-/**
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class ContributorAttribute {
-
-    private ContributorAttributeRole role;
-    private ContributorAttributeSequence sequence;
-
-    public ContributorAttribute(ContributorAttributeRole role, ContributorAttributeSequence sequence) {
-        this.role = role;
-        this.sequence = sequence;
-    }
-
-    public ContributorAttributeRole getRole() {
-        return role;
-    }
-
-    public void setRole(ContributorAttributeRole role) {
-        this.role = role;
-    }
-
-    public ContributorAttributeSequence getSequence() {
-        return sequence;
-    }
-
-    public void setSequence(ContributorAttributeSequence sequence) {
-        this.sequence = sequence;
-    }
-
-    @Override
-    public String toString() {
-        return "ContributorAttribute{" +
-            "role=" + role +
-            ", sequence=" + sequence +
-            '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        ContributorAttribute that = (ContributorAttribute) o;
-
-        if (role != that.role) {
-            return false;
-        }
-        if (sequence != that.sequence) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = role != null ? role.hashCode() : 0;
-        result = 31 * result + (sequence != null ? sequence.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/ContributorAttributeRole.java

@@ -1,32 +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.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118843-anatomy-of-a-contributor
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum ContributorAttributeRole {
-
-    AUTHOR,
-    ASSIGNEE,
-    EDITOR,
-    CHAIR_OR_TRANSLATOR,
-    CO_INVESTIGATOR,
-    CO_INVENTOR,
-    GRADUATE_STUDENT,
-    OTHER_INVENTOR,
-    PRINCIPAL_INVESTIGATOR,
-    POSTDOCTORAL_RESEARCHER,
-    SUPPORT_STAFF
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/ContributorAttributeSequence.java

@@ -1,23 +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.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118843-anatomy-of-a-contributor
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum ContributorAttributeSequence {
-
-    FIRST,
-    ADDITIONAL
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/Work.java

@@ -1,116 +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.authority.orcid.model;
-
-import java.util.Set;
-
-/**
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Work {
-
-    private WorkTitle workTitle;
-    private String description;
-    private Citation citation;
-    private WorkType workType;
-    private String publicationDate;
-    private WorkExternalIdentifier workExternalIdentifier;
-    private String url;
-    private Set<Contributor> contributors;
-    private String workSource;
-
-    public WorkTitle getWorkTitle() {
-        return workTitle;
-    }
-
-    public void setWorkTitle(WorkTitle workTitle) {
-        this.workTitle = workTitle;
-    }
-
-    public String getDescription() {
-        return description;
-    }
-
-    public void setDescription(String description) {
-        this.description = description;
-    }
-
-    public Citation getCitation() {
-        return citation;
-    }
-
-    public void setCitation(Citation citation) {
-        this.citation = citation;
-    }
-
-    public WorkType getWorkType() {
-        return workType;
-    }
-
-    public void setWorkType(WorkType workType) {
-        this.workType = workType;
-    }
-
-    public String getPublicationDate() {
-        return publicationDate;
-    }
-
-    public void setPublicationDate(String publicationDate) {
-        this.publicationDate = publicationDate;
-    }
-
-    public WorkExternalIdentifier getWorkExternalIdentifier() {
-        return workExternalIdentifier;
-    }
-
-    public void setWorkExternalIdentifier(WorkExternalIdentifier workExternalIdentifier) {
-        this.workExternalIdentifier = workExternalIdentifier;
-    }
-
-    public String getUrl() {
-        return url;
-    }
-
-    public void setUrl(String url) {
-        this.url = url;
-    }
-
-    public Set<Contributor> getContributors() {
-        return contributors;
-    }
-
-    public void setContributors(Set<Contributor> contributors) {
-        this.contributors = contributors;
-    }
-
-    public String getWorkSource() {
-        return workSource;
-    }
-
-    public void setWorkSource(String workSource) {
-        this.workSource = workSource;
-    }
-
-    @Override
-    public String toString() {
-        return "Work{" +
-            "workTitle=" + workTitle +
-            ", description='" + description + '\'' +
-            ", citation=" + citation +
-            ", workType=" + workType +
-            ", publicationDate='" + publicationDate + '\'' +
-            ", workExternalIdentifier=" + workExternalIdentifier +
-            ", url='" + url + '\'' +
-            ", contributors=" + contributors +
-            ", workSource='" + workSource + '\'' +
-            '}';
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkExternalIdentifier.java

@@ -1,73 +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.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118807
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class WorkExternalIdentifier {
-
-    private WorkExternalIdentifierType workExternalIdentifierType;
-    private String workExternalIdenfitierID;
-
-    public WorkExternalIdentifier(WorkExternalIdentifierType workExternalIdentifierType,
-                                  String workExternalIdenfitierID) {
-        this.workExternalIdentifierType = workExternalIdentifierType;
-        this.workExternalIdenfitierID = workExternalIdenfitierID;
-    }
-
-    public WorkExternalIdentifierType getWorkExternalIdentifierType() {
-        return workExternalIdentifierType;
-    }
-
-    public void setWorkExternalIdentifierType(WorkExternalIdentifierType workExternalIdentifierType) {
-        this.workExternalIdentifierType = workExternalIdentifierType;
-    }
-
-    @Override
-    public String toString() {
-        return "WorkExternalIdentifier{" +
-            "workExternalIdentifierType=" + workExternalIdentifierType +
-            ", workExternalIdenfitierID='" + workExternalIdenfitierID + '\'' +
-            '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        WorkExternalIdentifier that = (WorkExternalIdentifier) o;
-
-        if (workExternalIdenfitierID != null ? !workExternalIdenfitierID
-            .equals(that.workExternalIdenfitierID) : that.workExternalIdenfitierID != null) {
-            return false;
-        }
-        if (workExternalIdentifierType != that.workExternalIdentifierType) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = workExternalIdentifierType != null ? workExternalIdentifierType.hashCode() : 0;
-        result = 31 * result + (workExternalIdenfitierID != null ? workExternalIdenfitierID.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkExternalIdentifierType.java

@@ -1,42 +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.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118807
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum WorkExternalIdentifierType {
-
-    //    OTHER_ID,
-    ARXIV,
-    ASIN,
-    ASIN_TLD,
-    BIBCODE,
-    DOI,
-    EID,
-    ISBN,
-    ISSN,
-    JFM,
-    JSTOR,
-    LCCN,
-    MR,
-    OCLC,
-    OL,
-    OSTI,
-    PMC,
-    PMID,
-    RFC,
-    SSRN,
-    ZBL
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkTitle.java

@@ -1,64 +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.authority.orcid.model;
-
-import java.util.Map;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118807
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class WorkTitle {
-
-    private String title;
-    private String subtitle;
-    private Map<String, String> translatedTitles;
-
-    public WorkTitle(String title, String subtitle, Map<String, String> translatedTitles) {
-        this.title = title;
-        this.subtitle = subtitle;
-        this.translatedTitles = translatedTitles;
-    }
-
-    public String getTitle() {
-        return title;
-    }
-
-    public void setTitle(String title) {
-        this.title = title;
-    }
-
-    public String getSubtitle() {
-        return subtitle;
-    }
-
-    public void setSubtitle(String subtitle) {
-        this.subtitle = subtitle;
-    }
-
-    public String getTranslatedTitles(String languageCode) {
-        return translatedTitles.get(languageCode);
-    }
-
-    public void setTranslatedTitle(String languageCode, String translatedTitle) {
-        translatedTitles.put(languageCode, translatedTitle);
-    }
-
-    @Override
-    public String toString() {
-        return "WorkTitle{" +
-            "title='" + title + '\'' +
-            ", subtitle='" + subtitle + '\'' +
-            ", translatedTitles=" + translatedTitles +
-            '}';
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkType.java

@@ -1,57 +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.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118795
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum WorkType {
-
-    BOOK,
-    BOOK_CHAPTER,
-    BOOK_REVIEW,
-    DICTIONARY_ENTRY,
-    DISSERTATION,
-    ENCYCLOPEDIA_ARTICLE,
-    EDITED_BOOK,
-    JOURNAL_ARTICLE,
-    JOURNAL_ISSUE,
-    MAGAZINE_ARTICLE,
-    MANUAL,
-    ONLINE_RESOURCE,
-    NEWSLETTER_ARTICLE,
-    NEWSPAPER_ARTICLE,
-    REPORT,
-    RESEARCH_TOOL,
-    SUPERVISED_STUDENT_PUBLICATION,
-    TEST,
-    TRANSLATION,
-    WEBSITE,
-    CONFERENCE_ABSTRACT,
-    CONFERENCE_PAPER,
-    CONFERENCE_POSTER,
-    DISCLOSURE,
-    LICENSE,
-    PATENT,
-    REGISTERED_COPYRIGHT,
-    ARTISTIC_PERFORMANCE,
-    DATA_SET,
-    INVENTION,
-    LECTURE_SPEECH,
-    RESEARCH_TECHNIQUE,
-    SPIN_OFF_COMPANY,
-    STANDARDS_AND_POLICY,
-    TECHNICAL_STANDARD,
-    OTHER
-
-}

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

@@ -7,8 +7,15 @@
  */
 package org.dspace.authority.orcid.xml;
 
-import org.apache.log4j.Logger;
+import java.io.InputStream;
-import org.w3c.dom.Document;
+import java.net.URISyntaxException;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+
+import org.apache.logging.log4j.Logger;
+import org.xml.sax.SAXException;
 
 /**
  * @param <T> type
@@ -22,13 +29,17 @@ 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);
 
-    protected void processError(Document xml) {
+    protected Object unmarshall(InputStream input, Class<?> type) throws SAXException, URISyntaxException {
-        String errorMessage = XMLErrors.getErrorMessage(xml);
+        try {
-        log.error("The orcid-message reports an error: " + errorMessage);
+            JAXBContext context = JAXBContext.newInstance(type);
+            Unmarshaller unmarshaller = context.createUnmarshaller();
+            return unmarshaller.unmarshal(input);
+        } catch (JAXBException e) {
+            throw new RuntimeException("Unable to unmarshall orcid message" + e);
+        }
     }
-
-    public abstract T convert(Document document);
 }

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

@@ -1,77 +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.authority.orcid.xml;
-
-import javax.xml.xpath.XPathExpressionException;
-
-import org.apache.log4j.Logger;
-import org.dspace.authority.util.XMLUtils;
-import org.w3c.dom.Document;
-
-/**
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class XMLErrors {
-
-    /**
-     * log4j logger
-     */
-    private static Logger log = Logger.getLogger(XMLErrors.class);
-
-    private static final String ERROR_DESC = "/orcid-message/error-desc";
-
-    /**
-     * Default constructor
-     */
-    private XMLErrors() { }
-
-    /**
-     * Evaluates whether a given xml document contains errors or not.
-     *
-     * @param xml The given xml document
-     * @return true if the given xml document is null
-     * or if it contains errors
-     */
-    public static boolean check(Document xml) {
-
-        if (xml == null) {
-            return true;
-        }
-
-        String textContent = null;
-
-        try {
-            textContent = XMLUtils.getTextContent(xml, ERROR_DESC);
-        } catch (XPathExpressionException e) {
-            log.error("Error while checking for errors in orcid message", e);
-        }
-
-        return textContent == null;
-    }
-
-    public static String getErrorMessage(Document xml) {
-
-        if (xml == null) {
-            return "Did not receive an XML document.";
-        }
-
-        String textContent = null;
-
-        try {
-            textContent = XMLUtils.getTextContent(xml, ERROR_DESC);
-        } catch (XPathExpressionException e) {
-            log.error("Error while checking for errors in orcid message", e);
-        }
-
-        return textContent;
-    }
-
-}