[maven-release-plugin] prepare release dspace-7.0-beta1

DS-4303: Disable "dspace-rest" from default build. Add more deprecation warnings

.dockerignore

@@ -0,0 +1,11 @@
+.git/
+.idea/
+.settings/
+*/target/
+dspace/modules/*/target/
+Dockerfile.*
+dspace/src/main/docker/dspace-postgres-pgcrypto
+dspace/src/main/docker/dspace-postgres-pgcrypto-curl
+dspace/src/main/docker/solr
+dspace/src/main/docker/README.md
+dspace/src/main/docker-compose/

.gitignore

@@ -41,4 +41,4 @@ nb-configuration.xml
 .DS_Store
 
 ##Ignore JRebel project configuration
-rebel.xml
+rebel.xml

.travis.yml

@@ -1,14 +1,15 @@
 language: java
 sudo: false
+dist: trusty
 
-env: 
+env:
   # Give Maven 1GB of memory to work with
   - MAVEN_OPTS=-Xmx1024M
 
 jdk:
-  # DS-3384 Oracle JDK 8 has DocLint enabled by default.
+  # DS-3384 Oracle JDK has DocLint enabled by default.
   # Let's use this to catch any newly introduced DocLint issues.
-  - oraclejdk8
+  - oraclejdk11
 
 ## Should we run into any problems with oraclejdk8 on Travis, we may try the following workaround.
 ## https://docs.travis-ci.com/user/languages/java#Testing-Against-Multiple-JDKs
@@ -18,7 +19,6 @@ jdk:
 #    packages:
 #      - oracle-java8-installer
 
-# Install prerequisites for building Mirage2 more rapidly
 before_install:
   # Remove outdated settings.xml from Travis builds. Workaround for https://github.com/travis-ci/travis-ci/issues/4629
   - rm ~/.m2/settings.xml
@@ -26,19 +26,21 @@ 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
-# 1. Install & Unit Test APIs
-# 2. Assemble DSpace
+# Build DSpace and run both Unit and Integration Tests
 script:
-  # 1. [Install & Unit Test] Check source code licenses and run source code Unit Tests
-  #        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)
-  #        -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)
-  - "cd dspace && mvn package -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2"
+  # 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
+  #     -Pdspace-rest          => Enable optional dspace-rest module as part of build
+  #     -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 -Pdspace-rest -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2"
+
+# After a successful build and test (see 'script'), send code coverage reports to coveralls.io
+# 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

@@ -0,0 +1,63 @@
+# This image will be published as dspace/dspace
+# See https://github.com/DSpace/DSpace/tree/master/dspace/src/main/docker for usage details
+#
+# This version is JDK11 compatible
+# - tomcat:8-jdk11
+# - ANT 1.10.7
+# - maven:3-jdk-11 (see dspace-dependencies)
+# - note: default tag for branch: dspace/dspace: dspace/dspace:dspace-7_x
+
+# 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 (note: this build doesn't include the optional, deprecated "dspace-rest" webapp)
+# Copy the dspace-install directory to /install.  Clean up the build to keep the docker image small
+RUN mvn package && \
+  mv /app/dspace/target/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM tomcat:8-jdk11 as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.10.7
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+
+RUN mkdir $ANT_HOME && \
+    wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
+
+RUN ant init_installation update_configs update_code update_webapps
+
+# Step 3 - Run tomcat
+# Create a new tomcat image that does not retain the the build directory contents
+FROM tomcat:8-jdk11
+ENV DSPACE_INSTALL=/dspace
+COPY --from=ant_build /dspace $DSPACE_INSTALL
+EXPOSE 8080 8009
+
+ENV JAVA_OPTS=-Xmx2000m
+
+# Run the "server" webapp off the /server path (e.g. http://localhost:8080/server/)
+RUN ln -s $DSPACE_INSTALL/webapps/server   /usr/local/tomcat/webapps/server
+# If you wish to run "server" webapp off the ROOT path, then comment out the above RUN, and uncomment the below RUN.
+# You also MUST update the URL in dspace/src/main/docker/local.cfg
+# Please note that server webapp should only run on one path at a time.
+#RUN mv /usr/local/tomcat/webapps/ROOT /usr/local/tomcat/webapps/ROOT.bk && \
+#    ln -s $DSPACE_INSTALL/webapps/server   /usr/local/tomcat/webapps/ROOT

Dockerfile.cli

@@ -0,0 +1,53 @@
+# This image will be published as dspace/dspace-cli
+# See https://github.com/DSpace/DSpace/tree/master/dspace/src/main/docker for usage details
+#
+# This version is JDK11 compatible
+# - openjdk:11
+# - ANT 1.10.7
+# - maven:3-jdk-11 (see dspace-dependencies)
+# - note: default tag for branch: dspace/dspace-cli: dspace/dspace-cli:dspace-7_x
+
+# 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/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM openjdk:11 as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.10.7
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+
+RUN mkdir $ANT_HOME && \
+    wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
+
+RUN ant init_installation update_configs update_code
+
+# Step 3 - Run jdk
+# Create a new tomcat image that does not retain the the build directory contents
+FROM openjdk:11
+ENV DSPACE_INSTALL=/dspace
+COPY --from=ant_build /dspace $DSPACE_INSTALL
+
+ENV JAVA_OPTS=-Xmx1000m

Dockerfile.dependencies

@@ -0,0 +1,27 @@
+# This image will be published as dspace/dspace-dependencies
+# The purpose of this image is to make the build for dspace/dspace run faster
+#
+# This version is JDK11 compatible
+# - maven:3-jdk-11
+
+# Step 1 - Run Maven Build
+FROM maven:3-jdk-11 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
+RUN mvn package
+
+# Clear the contents of the /app directory (including all maven builds), so no artifacts remain.
+# This ensures when dspace:dspace is built, it will just the Maven local cache (.m2) for dependencies
+USER root
+RUN rm -rf /app/*

Dockerfile.test

@@ -0,0 +1,72 @@
+# This image will be published as dspace/dspace
+# See https://github.com/DSpace/DSpace/tree/master/dspace/src/main/docker for usage details
+#
+# This version is JDK11 compatible
+# - tomcat:8-jdk11
+# - ANT 1.10.7
+# - maven:3-jdk-11 (see dspace-dependencies)
+# - note: default tag for branch: dspace/dspace: dspace/dspace:dspace-7_x-test
+#
+# This image is meant for TESTING/DEVELOPMENT ONLY as it deploys the old v6 REST API under HTTP (not HTTPS)
+
+# 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 (including the optional, deprecated "dspace-rest" webapp)
+# Copy the dspace-install directory to /install.  Clean up the build to keep the docker image small
+RUN mvn package -Pdspace-rest && \
+  mv /app/dspace/target/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM tomcat:8-jdk11 as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.10.7
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+
+RUN mkdir $ANT_HOME && \
+    wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
+
+RUN ant init_installation update_configs update_code update_webapps
+
+# Step 3 - Run tomcat
+# Create a new tomcat image that does not retain the the build directory contents
+FROM tomcat:8-jdk11
+ENV DSPACE_INSTALL=/dspace
+COPY --from=ant_build /dspace $DSPACE_INSTALL
+EXPOSE 8080 8009
+
+ENV JAVA_OPTS=-Xmx2000m
+
+# Run the "server" webapp off the /server path (e.g. http://localhost:8080/server/)
+# and the v6.x (deprecated) REST API off the "/rest" path
+RUN ln -s $DSPACE_INSTALL/webapps/server   /usr/local/tomcat/webapps/server   && \
+    ln -s $DSPACE_INSTALL/webapps/rest          /usr/local/tomcat/webapps/rest
+# If you wish to run "server" webapp off the ROOT path, then comment out the above RUN, and uncomment the below RUN.
+# You also MUST update the URL in dspace/src/main/docker/local.cfg
+# Please note that server webapp should only run on one path at a time.
+#RUN mv /usr/local/tomcat/webapps/ROOT /usr/local/tomcat/webapps/ROOT.bk && \
+#    ln -s $DSPACE_INSTALL/webapps/server   /usr/local/tomcat/webapps/ROOT && \
+#    ln -s $DSPACE_INSTALL/webapps/rest          /usr/local/tomcat/webapps/rest
+
+# Overwrite the v6.x (deprecated) REST API's web.xml, so that we can run it on HTTP (defaults to requiring HTTPS)
+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/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

@@ -3,21 +3,21 @@
 
 [![Build Status](https://travis-ci.org/DSpace/DSpace.png?branch=master)](https://travis-ci.org/DSpace/DSpace)
 
-[DSpace Documentation](https://wiki.duraspace.org/display/DSDOC/) | 
+[DSpace Documentation](https://wiki.duraspace.org/display/DSDOC/) |
 [DSpace Releases](https://github.com/DSpace/DSpace/releases) |
-[DSpace Wiki](https://wiki.duraspace.org/display/DSPACE/Home) | 
+[DSpace Wiki](https://wiki.duraspace.org/display/DSPACE/Home) |
 [Support](https://wiki.duraspace.org/display/DSPACE/Support)
 
-DSpace open source software is a turnkey repository application used by more than 
+DSpace open source software is a turnkey repository application used by more than
 2,000 organizations and institutions worldwide to provide durable access to digital resources.
 For more information, visit http://www.dspace.org/
 
 ***
 :warning: **Work on DSpace 7 has begun on our `master` branch.** This means that there is temporarily NO user interface on this `master` branch. DSpace 7 will feature a new, unified [Angular](https://angular.io/) user interface, along with an enhanced, rebuilt REST API. The latest status of this work can be found on the [DSpace 7 UI Working Group](https://wiki.duraspace.org/display/DSPACE/DSpace+7+UI+Working+Group) page.  Additionally, the codebases can be found in the following places:
-  * DSpace 7 REST API work is occurring on the [`master` branch](https://github.com/DSpace/DSpace/tree/master/dspace-spring-rest) of this repository.
+  * DSpace 7 REST API work is occurring on the [`master` branch](https://github.com/DSpace/DSpace/tree/master/dspace-server-webapp) of this repository.
      * The REST Contract is being documented at https://github.com/DSpace/Rest7Contract
   * DSpace 7 Angular UI work is occurring at https://github.com/DSpace/dspace-angular
-  
+
 **If you would like to get involved in our DSpace 7 development effort, we welcome new contributors.** Just join one of our meetings or get in touch via Slack. See the [DSpace 7 UI Working Group](https://wiki.duraspace.org/display/DSPACE/DSpace+7+UI+Working+Group) wiki page for more info.
 
 **If you are looking for the ongoing maintenance work for DSpace 6 (or prior releases)**, you can find that work on the corresponding maintenance branch (e.g. [`dspace-6_x`](https://github.com/DSpace/DSpace/tree/dspace-6_x)) in this repository.
@@ -31,18 +31,21 @@ Past releases are all available via GitHub at https://github.com/DSpace/DSpace/r
 
 ## Documentation / Installation
 
-Documentation for each release may be viewed online or downloaded via our [Documentation Wiki](https://wiki.duraspace.org/display/DSDOC/). 
+Documentation for each release may be viewed online or downloaded via our [Documentation Wiki](https://wiki.duraspace.org/display/DSDOC/).
 
 The latest DSpace Installation instructions are available at:
 https://wiki.duraspace.org/display/DSDOC6x/Installing+DSpace
 
-Please be aware that, as a Java web application, DSpace requires a database (PostgreSQL or Oracle) 
+Please be aware that, as a Java web application, DSpace requires a database (PostgreSQL or Oracle)
 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.
 
+## Running DSpace 7 in Docker
+See [Running DSpace 7 with Docker Compose](dspace/src/main/docker-compose/README.md)
+
 ## Contributing
 
-DSpace is a community built and supported project. We do not have a centralized development or support team, 
+DSpace is a community built and supported project. We do not have a centralized development or support team,
 but have a dedicated group of volunteers who help us improve the software, documentation, resources, etc.
 
 We welcome contributions of any type. Here's a few basic guides that provide suggestions for contributing to DSpace:
@@ -68,14 +71,65 @@ Great Q&A is also available under the [DSpace tag on Stackoverflow](http://stack
 
 Additional support options are listed at https://wiki.duraspace.org/display/DSPACE/Support
 
-DSpace also has an active service provider network. If you'd rather hire a service provider to 
-install, upgrade, customize or host DSpace, then we recommend getting in touch with one of our 
+DSpace also has an active service provider network. If you'd rather hire a service provider to
+install, upgrade, customize or host DSpace, then we recommend getting in touch with one of our
 [Registered Service Providers](http://www.dspace.org/service-providers).
 
 ## Issue Tracker
 
 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-server-webapp
+  # 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).

docker-compose-cli.yml

@@ -0,0 +1,25 @@
+version: "3.7"
+
+services:
+  dspace-cli:
+    image: "${DOCKER_OWNER:-dspace}/dspace-cli:${DSPACE_VER:-dspace-7_x}"
+    container_name: dspace-cli
+    build:
+      context: .
+      dockerfile: Dockerfile.cli
+    #environment:
+    volumes:
+    - ./dspace/src/main/docker-compose/local.cfg:/dspace/config/local.cfg
+    - assetstore:/dspace/assetstore
+    entrypoint: /dspace/bin/dspace
+    command: help
+    networks:
+      - dspacenet
+    tty: true
+    stdin_open: true
+
+volumes:
+  assetstore:
+
+networks:
+  dspacenet:

docker-compose.yml

@@ -0,0 +1,69 @@
+version: '3.7'
+networks:
+  dspacenet:
+services:
+  dspace:
+    container_name: dspace
+    image: "${DOCKER_OWNER:-dspace}/dspace:${DSPACE_VER:-dspace-7_x-test}"
+    build:
+      context: .
+      dockerfile: Dockerfile.test
+    depends_on:
+    - dspacedb
+    networks:
+      dspacenet:
+    ports:
+    - published: 8080
+      target: 8080
+    stdin_open: true
+    tty: true
+    volumes:
+    - assetstore:/dspace/assetstore
+    - ./dspace/src/main/docker-compose/local.cfg:/dspace/config/local.cfg
+    # Ensure that the database is ready BEFORE starting tomcat
+    # 1. While a TCP connection to dspacedb port 5432 is not available, continue to sleep
+    # 2. Then, run database migration to init database tables
+    # 3. Finally, start Tomcat
+    entrypoint:
+    - /bin/bash
+    - '-c'
+    - |
+      while (!</dev/tcp/dspacedb/5432) > /dev/null 2>&1; do sleep 1; done;
+      /dspace/bin/dspace database migrate
+      catalina.sh run
+  dspacedb:
+    container_name: dspacedb
+    environment:
+      PGDATA: /pgdata
+    image: dspace/dspace-postgres-pgcrypto
+    networks:
+      dspacenet:
+    ports:
+    - published: 5432
+      target: 5432
+    stdin_open: true
+    tty: true
+    volumes:
+    - pgdata:/pgdata
+  dspacesolr:
+    container_name: dspacesolr
+    image: dspace/dspace-solr
+    networks:
+      dspacenet:
+    ports:
+    - published: 8983
+      target: 8983
+    stdin_open: true
+    tty: true
+    volumes:
+    - solr_authority:/opt/solr/server/solr/authority/data
+    - solr_oai:/opt/solr/server/solr/oai/data
+    - solr_search:/opt/solr/server/solr/search/data
+    - solr_statistics:/opt/solr/server/solr/statistics/data
+volumes:
+  assetstore:
+  pgdata:
+  solr_authority:
+  solr_oai:
+  solr_search:
+  solr_statistics:

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"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<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">
     <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-beta1</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -51,6 +50,33 @@
                 <configuration>
                     <debug>true</debug>
                     <showDeprecation>true</showDeprecation>
+                    <annotationProcessorPaths>
+                        <!-- Enable Hibernate's Metamodel Generator to generate metadata model classes
+                             (ending in _ suffix) for more type-safe Criteria queries -->
+                        <path>
+                            <groupId>org.hibernate</groupId>
+                            <artifactId>hibernate-jpamodelgen</artifactId>
+                            <version>${hibernate.version}</version>
+                        </path>
+                        <!-- Enable JAXB -->
+                        <path>
+                            <groupId>javax.xml.bind</groupId>
+                            <artifactId>jaxb-api</artifactId>
+                            <version>${jaxb-api.version}</version>
+                        </path>
+                        <!-- Enable Commons Annotations -->
+                        <path>
+                            <groupId>javax.annotation</groupId>
+                            <artifactId>javax.annotation-api</artifactId>
+                            <version>${javax-annotation.version}</version>
+                        </path>
+                        <!-- Enable http://errorprone.info -->
+                        <path>
+                            <groupId>com.google.errorprone</groupId>
+                            <artifactId>error_prone_core</artifactId>
+                            <version>${errorprone.version}</version>
+                        </path>
+                    </annotationProcessorPaths>
                 </configuration>
             </plugin>
             <plugin>
@@ -81,8 +107,8 @@
                         <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>
                 </configuration>
             </plugin>
@@ -90,7 +116,7 @@
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>build-helper-maven-plugin</artifactId>
-                <version>1.9.1</version>
+                <version>3.0.0</version>
                 <executions>
                     <execution>
                         <phase>validate</phase>
@@ -158,7 +184,6 @@
                          install of DSpace, against which Tests can be run. -->
                     <plugin>
                         <artifactId>maven-dependency-plugin</artifactId>
-                        <version>2.8</version>
                         <configuration>
                             <outputDirectory>${project.build.directory}/testing</outputDirectory>
                             <artifactItems>
@@ -193,7 +218,7 @@
                          (see: http://gmaven.codehaus.org/Executing+Groovy+Code )
                          We are generating a OS-agnostic version (agnostic.build.dir) of
                          the ${project.build.directory} property (full path of target dir).
-                         This is needed by the FileWeaver & Surefire plugins (see below)
+                         This is needed by the Surefire & Failsafe plugins (see below)
                          to initialize the Unit Test environment's dspace.cfg file.
                          Otherwise, the Unit Test Framework will not work on Windows OS.
                          This Groovy code was mostly borrowed from:
@@ -202,19 +227,17 @@
                     <plugin>
                         <groupId>org.codehaus.gmaven</groupId>
                         <artifactId>groovy-maven-plugin</artifactId>
-                        <version>2.0</version>
                         <executions>
                             <execution>
                                 <id>setproperty</id>
-                                <phase>generate-test-resources
-                                </phase> <!-- XXX I think this should be 'initialize' - MHW -->
+                                <phase>initialize</phase>
                                 <goals>
                                     <goal>execute</goal>
                                 </goals>
                                 <configuration>
                                     <source>
                                         project.properties['agnostic.build.dir'] = project.build.directory.replace(File.separator, '/');
-                                        println("Initializing Maven property 'agnostic.build.dir' to: " + project.properties['agnostic.build.dir']);
+                                        log.info("Initializing Maven property 'agnostic.build.dir' to: {}", project.properties['agnostic.build.dir']);
                                     </source>
                                 </configuration>
                             </execution>
@@ -227,6 +250,7 @@
                         <configuration>
                             <systemPropertyVariables>
                                 <!-- Specify the dspace.dir to use for test environment -->
+                                <!-- ${agnostic.build.dir} is set dynamically by groovy-maven-plugin above -->
                                 <!-- This system property is loaded by AbstractDSpaceTest to initialize the test environment -->
                                 <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
                                 <!-- Turn off any DSpace logging -->
@@ -235,51 +259,13 @@
                         </configuration>
                     </plugin>
 
-
-                    <plugin>
-                        <groupId>org.codehaus.mojo</groupId>
-                        <artifactId>xml-maven-plugin</artifactId>
-                        <version>1.0.1</version>
-                        <executions>
-                            <execution>
-                                <id>validate-ALL-xml-and-xsl</id>
-                                <phase>process-test-resources</phase>
-                                <goals>
-                                    <goal>validate</goal>
-                                </goals>
-                            </execution>
-                        </executions>
-                        <configuration>
-                            <validationSets>
-                                <!-- validate ALL XML and XSL config files in the testing folder -->
-                                <validationSet>
-                                    <dir>${agnostic.build.dir}/testing</dir>
-                                    <includes>
-                                        <include>**/*.xml</include>
-                                        <include>**/*.xsl</include>
-                                        <include>**/*.xconf</include>
-                                    </includes>
-                                </validationSet>
-                                <!-- validate ALL XML and XSL files throughout the project -->
-                                <validationSet>
-                                    <dir>${root.basedir}</dir>
-                                    <includes>
-                                        <include>**/*.xml</include>
-                                        <include>**/*.xsl</include>
-                                        <include>**/*.xmap</include>
-                                    </includes>
-                                </validationSet>
-                            </validationSets>
-                        </configuration>
-                    </plugin>
-
-
                     <!-- Run Integration Testing! This plugin just kicks off the tests (when enabled). -->
                     <plugin>
                         <artifactId>maven-failsafe-plugin</artifactId>
                         <configuration>
                             <systemPropertyVariables>
                                 <!-- Specify the dspace.dir to use for test environment -->
+                                <!-- ${agnostic.build.dir} is set dynamically by groovy-maven-plugin above -->
                                 <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
                                 <!-- Turn off any DSpace logging -->
                                 <dspace.log.init.disable>true</dspace.log.init.disable>
@@ -293,25 +279,21 @@
     </profiles>
 
     <dependencies>
-        <dependency>
-            <groupId>org.hibernate</groupId>
-            <artifactId>hibernate-core</artifactId>
-            <exclusions>
-                <exclusion>
-                    <groupId>org.jboss.logging</groupId>
-                    <artifactId>jboss-logging</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
+
         <dependency>
             <groupId>org.hibernate</groupId>
             <artifactId>hibernate-ehcache</artifactId>
         </dependency>
         <dependency>
-           <groupId>org.hibernate</groupId>
-           <artifactId>hibernate-validator-cdi</artifactId>
-           <version>${hibernate-validator.version}</version>
+            <groupId>org.hibernate</groupId>
+            <artifactId>hibernate-jpamodelgen</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.hibernate.validator</groupId>
+            <artifactId>hibernate-validator-cdi</artifactId>
+            <version>${hibernate-validator.version}</version>
+        </dependency>
+
         <dependency>
             <groupId>org.springframework</groupId>
             <artifactId>spring-orm</artifactId>
@@ -326,6 +308,16 @@
             <groupId>org.dspace</groupId>
             <artifactId>handle</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.eclipse.jetty.aggregate</groupId>
+            <artifactId>jetty-all</artifactId>
+            <exclusions>
+                <exclusion>
+                    <artifactId>javax.servlet</artifactId>
+                    <groupId>org.eclipse.jetty.orbit</groupId>
+                </exclusion>
+            </exclusions>
+        </dependency>
         <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>jargon</artifactId>
@@ -334,37 +326,15 @@
             <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>
             <type>pom</type>
-            <exclusions>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-core</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-databind</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <dependency>
-            <groupId>commons-cli</groupId>
-            <artifactId>commons-cli</artifactId>
         </dependency>
         <dependency>
             <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 +353,8 @@
             <artifactId>commons-io</artifactId>
         </dependency>
         <dependency>
-            <groupId>commons-lang</groupId>
-            <artifactId>commons-lang</artifactId>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-lang3</artifactId>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
@@ -400,7 +370,7 @@
         </dependency>
         <dependency>
             <groupId>javax.servlet</groupId>
-            <artifactId>servlet-api</artifactId>
+            <artifactId>javax.servlet-api</artifactId>
             <scope>provided</scope>
         </dependency>
         <dependency>
@@ -417,10 +387,6 @@
             <groupId>org.jdom</groupId>
             <artifactId>jdom</artifactId>
         </dependency>
-        <dependency>
-            <groupId>log4j</groupId>
-            <artifactId>log4j</artifactId>
-        </dependency>
         <dependency>
             <groupId>oro</groupId>
             <artifactId>oro</artifactId>
@@ -433,18 +399,6 @@
             <groupId>org.apache.pdfbox</groupId>
             <artifactId>fontbox</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcprov-jdk15</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcmail-jdk15</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.poi</groupId>
-            <artifactId>poi</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-scratchpad</artifactId>
@@ -464,12 +418,6 @@
         <dependency>
             <groupId>xerces</groupId>
             <artifactId>xercesImpl</artifactId>
-            <exclusions>
-                <exclusion>
-                    <groupId>xml-apis</groupId>
-                    <artifactId>xml-apis</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <dependency>
             <groupId>xml-apis</groupId>
@@ -491,11 +439,6 @@
             <groupId>org.dspace</groupId>
             <artifactId>dspace-services</artifactId>
         </dependency>
-        <dependency> <!-- Keep jmockit before junit -->
-            <groupId>org.jmockit</groupId>
-            <artifactId>jmockit</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
@@ -516,69 +459,38 @@
             <artifactId>mockito-core</artifactId>
             <scope>test</scope>
         </dependency>
-
+        <dependency>
+            <groupId>org.springframework</groupId>
+            <artifactId>spring-test</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>org.rometools</groupId>
             <artifactId>rome-modules</artifactId>
             <version>1.0</version>
         </dependency>
-        <dependency>
-            <groupId>gr.ekt.bte</groupId>
-            <artifactId>bte-core</artifactId>
-            <version>0.9.3.5</version>
-            <exclusions>
-                <!-- A more recent version is retrieved from another dependency -->
-                <exclusion>
-                    <groupId>org.mockito</groupId>
-                    <artifactId>mockito-core</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
         <dependency>
             <groupId>gr.ekt.bte</groupId>
             <artifactId>bte-io</artifactId>
             <version>0.9.3.5</version>
             <exclusions>
-                <!-- A more recent version is retrieved from another dependency -->
                 <exclusion>
-                    <groupId>org.apache.commons</groupId>
-                    <artifactId>commons-lang3</artifactId>
-                </exclusion>
-                <!-- A more recent version is retrieved from another dependency -->
-                <exclusion>
-                    <groupId>org.mockito</groupId>
-                    <artifactId>mockito-core</artifactId>
+                    <groupId>net.bytebuddy</groupId>
+                    <artifactId>byte-buddy</artifactId>
                 </exclusion>
             </exclusions>
         </dependency>
-        <dependency>
-            <groupId>org.apache.httpcomponents</groupId>
-            <artifactId>httpcore</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.apache.solr</groupId>
-            <artifactId>solr-solrj</artifactId>
-            <version>${solr.version}</version>
-            <exclusions>
-                <exclusion>
-                    <groupId>org.slf4j</groupId>
-                    <artifactId>jcl-over-slf4j</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.slf4j</groupId>
-                    <artifactId>slf4j-api</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
 
         <dependency>
-            <groupId>commons-configuration</groupId>
-            <artifactId>commons-configuration</artifactId>
+            <groupId>org.apache.solr</groupId>
+            <artifactId>solr-cell</artifactId>
+            <version>${solr.client.version}</version>
         </dependency>
+
         <dependency>
             <groupId>com.maxmind.geoip2</groupId>
             <artifactId>geoip2</artifactId>
@@ -594,12 +506,6 @@
             <version>2.1.7</version>
         </dependency>
 
-        <dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-core</artifactId>
-            <version>4.10.4</version>
-        </dependency>
-
         <dependency>
             <groupId>com.coverity.security</groupId>
             <artifactId>coverity-escapers</artifactId>
@@ -616,7 +522,6 @@
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>
-            <version>19.0</version>
         </dependency>
 
 
@@ -625,11 +530,6 @@
             <artifactId>postgresql</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-api</artifactId>
-        </dependency>
-
         <dependency>
             <groupId>jdbm</groupId>
             <artifactId>jdbm</artifactId>
@@ -691,19 +591,44 @@
             <type>jar</type>
         </dependency>
 
+        <!-- JAXB API and implementation (no longer bundled as of Java 11) -->
+        <dependency>
+            <groupId>javax.xml.bind</groupId>
+            <artifactId>jaxb-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jaxb</groupId>
+            <artifactId>jaxb-runtime</artifactId>
+        </dependency>
+
+        <!-- Apache Axiom -->
         <dependency>
             <groupId>org.apache.ws.commons.axiom</groupId>
             <artifactId>axiom-impl</artifactId>
-            <!-- NOTE: SWORDv2 needs 1.2.14, required by Abdera: https://abdera.apache.org/ -->
-            <version>1.2.14</version>
+            <version>${axiom.version}</version>
+            <exclusions>
+                <!-- Exclude Geronimo as it is NOT necessary when using javax.activation (which we use)
+                     See: https://ws.apache.org/axiom/userguide/ch04.html#d0e732 -->
+                <exclusion>
+                    <groupId>org.apache.geronimo.specs</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
-
         <dependency>
             <groupId>org.apache.ws.commons.axiom</groupId>
             <artifactId>axiom-api</artifactId>
-            <!-- NOTE: SWORDv2 needs 1.2.14, required by Abdera: https://abdera.apache.org/ -->
-            <version>1.2.14</version>
+            <version>${axiom.version}</version>
+            <exclusions>
+                <!-- Exclude Geronimo as it is NOT necessary when using javax.activation (which we use)
+                     See: https://ws.apache.org/axiom/userguide/ch04.html#d0e732 -->
+                <exclusion>
+                    <groupId>org.apache.geronimo.specs</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
+
         <dependency>
             <groupId>org.glassfish.jersey.core</groupId>
             <artifactId>jersey-client</artifactId>
@@ -714,26 +639,54 @@
             <groupId>com.amazonaws</groupId>
             <artifactId>aws-java-sdk-s3</artifactId>
             <version>1.10.50</version>
-            <exclusions>
-                <exclusion>
-                    <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>
-            <artifactId>jackson-core</artifactId>
+            <groupId>org.dspace</groupId>
+            <artifactId>orcid-jaxb-api</artifactId>
+            <version>2.1.0</version>
         </dependency>
         <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-databind</artifactId>
+            <groupId>org.json</groupId>
+            <artifactId>json</artifactId>
+            <version>20180130</version>
         </dependency>
+
+        <!-- Used for Solr core export/import -->
+        <dependency>
+            <groupId>com.opencsv</groupId>
+            <artifactId>opencsv</artifactId>
+            <version>4.5</version>
+        </dependency>
+
+        <!-- Email templating -->
+        <dependency>
+            <groupId>org.apache.velocity</groupId>
+            <artifactId>velocity-engine-core</artifactId>
+            <version>2.0</version>
+            <type>jar</type>
+        </dependency>
+
+        <dependency>
+            <groupId>org.xmlunit</groupId>
+            <artifactId>xmlunit-matchers</artifactId>
+            <version>2.6.3</version>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.hibernate.javax.persistence</groupId>
+            <artifactId>hibernate-jpa-2.1-api</artifactId>
+            <version>1.0.0.Final</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.bcel</groupId>
+            <artifactId>bcel</artifactId>
+            <version>6.4.0</version>
+        </dependency>
+
     </dependencies>
 
 </project>

dspace-api/src/main/java/org/apache/solr/handler/extraction/ExtractingParams.java

@@ -1,163 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements.  See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License.  You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.apache.solr.handler.extraction;
-
-
-/**
- * The various Solr Parameters names to use when extracting content.
- **/
-public interface ExtractingParams {
-
-    /**
-     * Map all generated attribute names to field names with lowercase and underscores.
-     */
-    public static final String LOWERNAMES = "lowernames";
-
-    /**
-     * if true, ignore TikaException (give up to extract text but index meta data)
-     */
-    public static final String IGNORE_TIKA_EXCEPTION = "ignoreTikaException";
-
-
-    /**
-     * The param prefix for mapping Tika metadata to Solr fields.
-     * <p>
-     * To map a field, add a name like:
-     * <pre>fmap.title=solr.title</pre>
-     *
-     * In this example, the tika "title" metadata value will be added to a Solr field named "solr.title"
-     */
-    public static final String MAP_PREFIX = "fmap.";
-
-    /**
-     * The boost value for the name of the field.  The boost can be specified by a name mapping.
-     * <p>
-     * For example
-     * <pre>
-     * map.title=solr.title
-     * boost.solr.title=2.5
-     * </pre>
-     * will boost the solr.title field for this document by 2.5
-     */
-    public static final String BOOST_PREFIX = "boost.";
-
-    /**
-     * Pass in literal values to be added to the document, as in
-     * <pre>
-     *  literal.myField=Foo
-     * </pre>
-     */
-    public static final String LITERALS_PREFIX = "literal.";
-
-
-    /**
-     * Restrict the extracted parts of a document to be indexed
-     * by passing in an XPath expression.  All content that satisfies the XPath expr.
-     * will be passed to the {@link org.apache.solr.handler.extraction.SolrContentHandler}.
-     * <p>
-     * See Tika's docs for what the extracted document looks like.
-     *
-     * @see #CAPTURE_ELEMENTS
-     */
-    public static final String XPATH_EXPRESSION = "xpath";
-
-
-    /**
-     * Only extract and return the content, do not index it.
-     */
-    public static final String EXTRACT_ONLY = "extractOnly";
-
-    /**
-     * Content output format if extractOnly is true. Default is "xml", alternative is "text".
-     */
-    public static final String EXTRACT_FORMAT = "extractFormat";
-
-    /**
-     * Capture attributes separately according to the name of the element, instead of just adding them to the string
-     * buffer
-     */
-    public static final String CAPTURE_ATTRIBUTES = "captureAttr";
-
-    /**
-     * Literal field values will by default override other values such as metadata and content. Set this to false to
-     * revert to pre-4.0 behaviour
-     */
-    public static final String LITERALS_OVERRIDE = "literalsOverride";
-
-    /**
-     * Capture the specified fields (and everything included below it that isn't capture by some other capture field)
-     * separately from the default.  This is different
-     * then the case of passing in an XPath expression.
-     * <p>
-     * The Capture field is based on the localName returned to the
-     * {@link org.apache.solr.handler.extraction.SolrContentHandler}
-     * by Tika, not to be confused by the mapped field.  The field name can then
-     * be mapped into the index schema.
-     * <p>
-     * For instance, a Tika document may look like:
-     * <pre>
-     *  &lt;html&gt;
-     *    ...
-     *    &lt;body&gt;
-     *      &lt;p&gt;some text here.  &lt;div&gt;more text&lt;/div&gt;&lt;/p&gt;
-     *      Some more text
-     *    &lt;/body&gt;
-     * </pre>
-     * By passing in the p tag, you could capture all P tags separately from the rest of the t
-     * Thus, in the example, the capture of the P tag would be: "some text here.  more text"
-     */
-    public static final String CAPTURE_ELEMENTS = "capture";
-
-    /**
-     * The type of the stream.  If not specified, Tika will use mime type detection.
-     */
-    public static final String STREAM_TYPE = "stream.type";
-
-
-    /**
-     * Optional.  The file name. If specified, Tika can take this into account while
-     * guessing the MIME type.
-     */
-    public static final String RESOURCE_NAME = "resource.name";
-
-    /**
-     * Optional. The password for this resource. Will be used instead of the rule based password lookup mechanisms
-     */
-    public static final String RESOURCE_PASSWORD = "resource.password";
-
-    /**
-     * Optional.  If specified, the prefix will be prepended to all Metadata, such that it would be possible
-     * to setup a dynamic field to automatically capture it
-     */
-    public static final String UNKNOWN_FIELD_PREFIX = "uprefix";
-
-    /**
-     * Optional.  If specified and the name of a potential field cannot be determined, the default Field specified
-     * will be used instead.
-     */
-    public static final String DEFAULT_FIELD = "defaultField";
-
-    /**
-     * Optional. If specified, loads the file as a source for password lookups for Tika encrypted documents.
-     * <p>
-     * File format is Java properties format with one key=value per line.
-     * The key is evaluated as a regex against the file name, and the value is the password
-     * The rules are evaluated top-bottom, i.e. the first match will be used
-     * If you want a fallback password to be always used, supply a .*=&lt;defaultmypassword&gt; at the end
-     */
-    public static final String PASSWORD_MAP_FILE = "passwordsFile";
-}

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;
@@ -180,13 +180,9 @@ public class CommunityFiliator {
         // second test - circularity: parent's parents can't include proposed
         // child
         List<Community> parentDads = parent.getParentCommunities();
-
-        for (int i = 0; i < parentDads.size(); i++) {
-            if (parentDads.get(i).getID().equals(child.getID())) {
-                System.out
-                    .println("Error, circular parentage - child is parent of parent");
-                System.exit(1);
-            }
+        if (parentDads.contains(child)) {
+            System.out.println("Error, circular parentage - child is parent of parent");
+            System.exit(1);
         }
 
         // everthing's OK
@@ -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;
-
-        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");
+        if (!parentKids.contains(child)) {
+            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);
-        parent.getSubcommunities().remove(child);
+        child.removeParentCommunity(parent);
+        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

@@ -7,12 +7,16 @@
  */
 package org.dspace.administer;
 
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.io.PrintWriter;
 import java.sql.SQLException;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
@@ -21,12 +25,18 @@ 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.Option;
 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;
 import org.dspace.content.Community;
+import org.dspace.content.Item;
+import org.dspace.content.MetadataSchemaEnum;
+import org.dspace.content.MetadataValue;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.CollectionService;
 import org.dspace.content.service.CommunityService;
@@ -34,6 +44,7 @@ import org.dspace.core.Context;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.eperson.service.EPersonService;
 import org.jdom.Element;
+import org.jdom.output.Format;
 import org.jdom.output.XMLOutputter;
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
@@ -45,44 +56,51 @@ import org.xml.sax.SAXException;
  * an XML file.
  *
  * The XML file structure needs to be:
- * {@code
+ * <pre>{@code
  * <import_structure>
- * <community>
- * <name>....</name>
- * <community>...</community>
- * <collection>
- * <name>....</name>
- * </collection>
- * </community>
+ *   <community>
+ *     <name>....</name>
+ *     <community>...</community>
+ *     <collection>
+ *       <name>....</name>
+ *     </collection>
+ *   </community>
  * </import_structure>
- * }
- * it can be arbitrarily deep, and supports all the metadata elements
+ * }</pre>
+ * <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
-     * imported structure
+    /** Name of the root element for the document to be imported. */
+    static final String INPUT_ROOT = "import_structure";
+
+    /*
+     * Name of the root element for the document produced by importing.
+     * Community and collection elements are annotated with their identifiers.
      */
-    private static org.jdom.Document xmlOutput = new org.jdom.Document(new Element("imported_structure"));
+    static final String RESULT_ROOT = "imported_structure";
 
     /**
-     * a hashtable to hold metadata for the collection being worked on
+     * A 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 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();
-    protected static EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
+    protected static CommunityService communityService
+            = ContentServiceFactory.getInstance().getCommunityService();
+    protected static CollectionService collectionService
+            = ContentServiceFactory.getInstance().getCollectionService();
+    protected static EPersonService ePersonService
+            = EPersonServiceFactory.getInstance().getEPersonService();
 
     /**
      * Default constructor
@@ -91,63 +109,156 @@ public class StructBuilder {
 
     /**
      * Main method to be run from the command line to import a structure into
-     * DSpace
+     * DSpacee or export existing structure to a file.The command is of the form:
      *
-     * This is of the form:
+     * <p>{@code StructBuilder -f [XML source] -e [administrator email] -o [output file]}
      *
-     * {@code StructBuilder -f [xml source] -e [administrator email] -o [output file]}
+     * <p>to import, or
      *
-     * The output file will contain exactly the same as the source xml document, but
-     * with the handle for each imported item added as an attribute.
+     * <p>{@code StructBuilder -x -e [administrator email] -o [output file]}</p>
      *
-     * @param argv the command line arguments given
-     * @throws Exception if an error occurs
+     * <p>to export.  The output will contain exactly the same as the source XML
+     * document, but with the Handle for each imported item added as an attribute.
+     *
+     *
+     * @param argv command line arguments.
+     * @throws ParserConfigurationException passed through.
+     * @throws SQLException passed through.
+     * @throws FileNotFoundException if input or output could not be opened.
+     * @throws TransformerException if the input document is invalid.
      */
     public static void main(String[] argv)
-        throws Exception {
-        CommandLineParser parser = new PosixParser();
-
+            throws ParserConfigurationException, SQLException,
+            FileNotFoundException, IOException, TransformerException {
+        // Define command line options.
         Options options = new Options();
 
-        options.addOption("f", "file", true, "file");
-        options.addOption("e", "eperson", true, "eperson");
-        options.addOption("o", "output", true, "output");
+        options.addOption("h", "help", false, "Print this help message.");
+        options.addOption("?", "help");
+        options.addOption("x", "export", false, "Export the current structure as XML.");
 
-        CommandLine line = parser.parse(options, argv);
+        options.addOption(Option.builder("e").longOpt("eperson")
+                .desc("User who is manipulating the repository's structure.")
+                .hasArg().argName("eperson").required().build());
 
-        String file = null;
-        String eperson = null;
-        String output = null;
+        options.addOption(Option.builder("f").longOpt("file")
+                .desc("File of new structure information.")
+                .hasArg().argName("input").build());
 
-        if (line.hasOption('f')) {
-            file = line.getOptionValue('f');
+        options.addOption(Option.builder("o").longOpt("output")
+                .desc("File to receive the structure map ('-' for standard out).")
+                .hasArg().argName("output").required().build());
+
+        // Parse the command line.
+        CommandLineParser parser = new DefaultParser();
+        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('e')) {
-            eperson = line.getOptionValue('e');
-        }
-
-        if (line.hasOption('o')) {
-            output = line.getOptionValue('o');
-        }
-
-        if (output == null || eperson == null || file == null) {
-            usage();
+        // If the user asked for help, give it and exit.
+        if (line.hasOption('h') || line.hasOption('?')) {
+            giveHelp(options);
             System.exit(0);
         }
 
+        // Otherwise, analyze the command.
+        // Must be import or export.
+        if (!(line.hasOption('f') || line.hasOption('x'))) {
+            giveHelp(options);
+            System.exit(1);
+        }
+
+        // Open the output stream.
+        String output = line.getOptionValue('o');
+        OutputStream outputStream;
+        if ("-".equals(output)) {
+            outputStream = System.out;
+        } else {
+            outputStream = new FileOutputStream(output);
+        }
+
         // create a context
         Context context = new Context();
 
-        // set the context
-        context.setCurrentUser(ePersonService.findByEmail(context, eperson));
+        // set the context.
+        String eperson = line.getOptionValue('e');
+        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);
+        }
+
+        // Export? Import?
+        if (line.hasOption('x')) { // export
+            exportStructure(context, outputStream);
+        } else { // Must be import
+            String input = line.getOptionValue('f');
+            if (null == input) {
+                usage(options);
+                System.exit(1);
+            }
+
+            InputStream inputStream;
+            if ("-".equals(input)) {
+                inputStream = System.in;
+            } else {
+                inputStream = new FileInputStream(input);
+            }
+
+            importStructure(context, inputStream, outputStream);
+            // save changes from import
+            context.complete();
+        }
+        System.exit(0);
+    }
+
+    /**
+     * Import new Community/Collection structure.
+     *
+     * @param context
+     * @param input XML which describes the new communities and collections.
+     * @param output input, annotated with the new objects' identifiers.
+     * @throws IOException
+     * @throws ParserConfigurationException
+     * @throws SAXException
+     * @throws TransformerException
+     * @throws SQLException
+     */
+    static void importStructure(Context context, InputStream input, OutputStream output)
+            throws IOException, ParserConfigurationException, SQLException, TransformerException {
 
         // load the XML
-        Document document = loadXML(file);
+        Document document = null;
+        try {
+            document = loadXML(input);
+        } 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
-        validate(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);
+        }
+
+        // Check for 'identifier' attributes -- possibly output by this class.
+        NodeList identifierNodes = XPathAPI.selectNodeList(document, "//*[@identifier]");
+        if (identifierNodes.getLength() > 0) {
+            System.err.println("The input document has 'identifier' attributes, which will be ignored.");
+        }
 
         // load the mappings into the member variable hashmaps
         communityMap.put("name", "name");
@@ -164,62 +275,190 @@ public class StructBuilder {
         collectionMap.put("license", "license");
         collectionMap.put("provenance", "provenance_description");
 
-        // get the top level community list
-        NodeList first = XPathAPI.selectNodeList(document, "/import_structure/community");
+        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);
+            // run the import starting with the top level communities
+            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++) {
-            root.addContent(elements[i]);
+        final Element root = new Element(RESULT_ROOT);
+
+        for (Element element : elements) {
+            root.addContent(element);
         }
 
-        // finally write the string into the output file
+        // finally write the string into the output file.
+        final org.jdom.Document xmlOutput = new org.jdom.Document(root);
         try {
-            BufferedWriter out = new BufferedWriter(new FileWriter(output));
-            out.write(new XMLOutputter().outputString(xmlOutput));
-            out.close();
+            new XMLOutputter().output(xmlOutput, output);
         } catch (IOException e) {
-            System.out.println("Unable to write to output file " + output);
-            System.exit(0);
+            System.out.printf("Unable to write to output file %s:  %s%n",
+                    output, e.getMessage());
+            System.exit(1);
+        }
+    }
+
+    /**
+     * Add a single community, and its children, to the Document.
+     *
+     * @param community
+     * @return a fragment representing this Community.
+     */
+    private static Element exportACommunity(Community community) {
+        // Export this Community.
+        Element element = new Element("community");
+        element.setAttribute("identifier", community.getHandle());
+        element.addContent(new Element("name").setText(community.getName()));
+        element.addContent(new Element("description")
+                .setText(communityService.getMetadataFirstValue(community,
+                        MetadataSchemaEnum.DC.getName(), "description", "abstract", Item.ANY)));
+        element.addContent(new Element("intro")
+                .setText(communityService.getMetadataFirstValue(community,
+                        MetadataSchemaEnum.DC.getName(), "description", null, Item.ANY)));
+        element.addContent(new Element("copyright")
+                .setText(communityService.getMetadataFirstValue(community,
+                        MetadataSchemaEnum.DC.getName(), "rights", null, Item.ANY)));
+        element.addContent(new Element("sidebar")
+                .setText(communityService.getMetadataFirstValue(community,
+                        MetadataSchemaEnum.DC.getName(), "description", "tableofcontents", Item.ANY)));
+
+        // Export this Community's Community children.
+        for (Community subCommunity : community.getSubcommunities()) {
+            element.addContent(exportACommunity(subCommunity));
         }
 
-        context.complete();
+        // Export this Community's Collection children.
+        for (Collection collection : community.getCollections()) {
+            element.addContent(exportACollection(collection));
+        }
+
+        return element;
     }
 
     /**
-     * Output the usage information
+     * Add a single Collection to the Document.
+     *
+     * @param collection
+     * @return a fragment representing this Collection.
      */
-    private static void usage() {
-        System.out.println("Usage: java StructBuilder -f <source XML file> -o <output file> -e <eperson email>");
-        System.out.println(
-            "Communities will be created from the top level, and a map of communities to handles will be returned in " +
-                "the output file");
-        return;
+    private static Element exportACollection(Collection collection) {
+        // Export this Collection.
+        Element element = new Element("collection");
+        element.setAttribute("identifier", collection.getHandle());
+        element.addContent(new Element("name").setText(collection.getName()));
+        element.addContent(new Element("description")
+                .setText(collectionService.getMetadataFirstValue(collection,
+                        MetadataSchemaEnum.DC.getName(), "description", "abstract", Item.ANY)));
+        element.addContent(new Element("intro")
+                .setText(collectionService.getMetadataFirstValue(collection,
+                        MetadataSchemaEnum.DC.getName(), "description", null, Item.ANY)));
+        element.addContent(new Element("copyright")
+                .setText(collectionService.getMetadataFirstValue(collection,
+                        MetadataSchemaEnum.DC.getName(), "rights", null, Item.ANY)));
+        element.addContent(new Element("sidebar")
+                .setText(collectionService.getMetadataFirstValue(collection,
+                        MetadataSchemaEnum.DC.getName(), "description", "tableofcontents", Item.ANY)));
+        element.addContent(new Element("license")
+                .setText(collectionService.getMetadataFirstValue(collection,
+                        MetadataSchemaEnum.DC.getName(), "rights", "license", Item.ANY)));
+        // Provenance is special:  multivalued
+        for (MetadataValue value : collectionService.getMetadata(collection,
+                MetadataSchemaEnum.DC.getName(), "provenance", null, Item.ANY)) {
+            element.addContent(new Element("provenance")
+                    .setText(value.getValue()));
+        }
+
+        return element;
     }
 
     /**
-     * Validate the XML document.  This method does not return, but if validation
-     * fails it generates an error and ceases execution
+     * Write out the existing Community/Collection structure.
+     */
+    static void exportStructure(Context context, OutputStream output) {
+        // Build a document from the Community/Collection hierarchy.
+        Element rootElement = new Element(INPUT_ROOT);  // To be read by importStructure, perhaps
+
+        List<Community> communities = null;
+        try {
+            communities = communityService.findAllTop(context);
+        } catch (SQLException ex) {
+            System.out.printf("Unable to get the list of top-level communities:  %s%n",
+                    ex.getMessage());
+            System.exit(1);
+        }
+
+        for (Community community : communities) {
+            rootElement.addContent(exportACommunity(community));
+        }
+
+        // Now write the structure out.
+        org.jdom.Document xmlOutput = new org.jdom.Document(rootElement);
+        try {
+            XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat());
+            outputter.output(xmlOutput, output);
+        } catch (IOException e) {
+            System.out.printf("Unable to write to output file %s:  %s%n",
+                    output, e.getMessage());
+            System.exit(1);
+        }
+    }
+
+    /**
+     * Output the usage information.
+     */
+    private static void usage(Options options) {
+        HelpFormatter helper = new HelpFormatter();
+        try (PrintWriter writer = new PrintWriter(System.out);) {
+            helper.printUsage(writer, 80/* FIXME Magic */,
+                    "structure-builder", options);
+        }
+    }
+
+    /**
+     * Help the user more.
+     */
+    private static void giveHelp(Options options) {
+        HelpFormatter formatter = new HelpFormatter();
+        formatter.printHelp("struct-builder",
+                "Import or export Community/Collection structure.",
+                options,
+                "When importing (-f), communities will be created from the "
+                    + "top level, and a map of communities to handles will "
+                    + "be returned in the output file.  When exporting (-x),"
+                    + "the current structure will be written to the map file.",
+                true);
+    }
+
+    /**
+     * Validate the XML document.  This method returns if the document is valid.
+     * 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("No changes have been made to the DSpace instance\n\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");
 
         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);
+            System.exit(1);
         }
 
         String errs = validateCommunities(first, 1);
@@ -230,13 +469,13 @@ public class StructBuilder {
 
         if (trip) {
             System.out.println(err.toString());
-            System.exit(0);
+            System.exit(1);
         }
     }
 
     /**
      * 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 +485,7 @@ 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 +494,9 @@ 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(" does not contain exactly one name field\n");
+                err.append("-The level ").append(level)
+                        .append(" community in position ").append(pos)
+                        .append(" does not contain exactly one name field.\n");
                 trip = true;
             }
 
@@ -286,7 +526,7 @@ 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 +534,7 @@ 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 +543,9 @@ 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(" does not contain exactly one name field\n");
+                err.append("-The level ").append(level)
+                        .append(" collection in position ").append(pos)
+                        .append(" does not contain exactly one name field.\n");
                 trip = true;
             }
         }
@@ -317,17 +558,17 @@ public class StructBuilder {
     }
 
     /**
-     * Load in the XML from file.
+     * Load the XML document from input.
      *
-     * @param filename the filename to load from
-     * @return the DOM representation of the XML file
+     * @param input the filename to load from.
+     * @return the DOM representation of the XML input.
      */
-    private static org.w3c.dom.Document loadXML(String filename)
+    private static org.w3c.dom.Document loadXML(InputStream input)
         throws IOException, ParserConfigurationException, SAXException {
         DocumentBuilder builder = DocumentBuilderFactory.newInstance()
                                                         .newDocumentBuilder();
 
-        org.w3c.dom.Document document = builder.parse(new File(filename));
+        org.w3c.dom.Document document = builder.parse(input);
 
         return document;
     }
@@ -338,7 +579,7 @@ public class StructBuilder {
      * @param node the node from which we want to extract the string value
      * @return the string value of the node
      */
-    public static String getStringValue(Node node) {
+    private static String getStringValue(Node node) {
         String value = node.getNodeValue();
 
         if (node.hasChildNodes()) {
@@ -363,7 +604,7 @@ 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 +631,10 @@ public class StructBuilder {
             }
 
             // FIXME: at the moment, if the community already exists by name
-            // then this will throw a PSQLException on a duplicate key
-            // violation
-            // Ideally we'd skip this row and continue to create sub
-            // communities
-            // and so forth where they don't exist, but it's proving
-            // difficult
+            // then this will throw an SQLException on a duplicate key
+            // violation.
+            // Ideally we'd skip this row and continue to create sub communities
+            // 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 +709,7 @@ 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/BulkEditChange.java

@@ -19,6 +19,7 @@ import org.dspace.content.Item;
  * @author Stuart Lewis
  */
 public class BulkEditChange {
+
     /**
      * The item these changes relate to
      */

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;
@@ -168,6 +170,9 @@ public class DSpaceCSV implements Serializable {
                 if ("collection".equals(element)) {
                     // Store the heading
                     headings.add(element);
+                }   else if ("rowName".equals(element)) {
+                    // Store the heading
+                    headings.add(element);
                 } else if ("action".equals(element)) { // Store the action
                     // Store the heading
                     headings.add(element);
@@ -198,20 +203,24 @@ public class DSpaceCSV implements Serializable {
                     }
 
                     // Check that the scheme exists
-                    MetadataSchema foundSchema = metadataSchemaService.find(c, metadataSchema);
-                    if (foundSchema == null) {
-                        throw new MetadataImportInvalidHeadingException(clean[0],
-                                                                        MetadataImportInvalidHeadingException.SCHEMA,
-                                                                        columnCounter);
-                    }
+                    if (!StringUtils.equals(metadataSchema, MetadataSchemaEnum.RELATION.getName())) {
+                        MetadataSchema foundSchema = metadataSchemaService.find(c, metadataSchema);
+                        if (foundSchema == null) {
+                            throw new MetadataImportInvalidHeadingException(clean[0],
+                                                                            MetadataImportInvalidHeadingException
+                                                                                .SCHEMA,
+                                                                            columnCounter);
+                        }
 
-                    // Check that the metadata element exists in the schema
-                    MetadataField foundField = metadataFieldService
-                        .findByElement(c, foundSchema, metadataElement, metadataQualifier);
-                    if (foundField == null) {
-                        throw new MetadataImportInvalidHeadingException(clean[0],
-                                                                        MetadataImportInvalidHeadingException.ELEMENT,
-                                                                        columnCounter);
+                        // Check that the metadata element exists in the schema
+                        MetadataField foundField = metadataFieldService
+                            .findByElement(c, foundSchema, metadataElement, metadataQualifier);
+                        if (foundField == null) {
+                            throw new MetadataImportInvalidHeadingException(clean[0],
+                                                                            MetadataImportInvalidHeadingException
+                                                                                .ELEMENT,
+                                                                            columnCounter);
+                        }
                     }
 
                     // Store the heading

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

@@ -14,10 +14,14 @@ import java.io.InputStreamReader;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.UUID;
+import javax.annotation.Nullable;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
@@ -25,22 +29,33 @@ 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.log4j.Logger;
+import org.apache.commons.lang3.StringUtils;
+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.Item;
+import org.dspace.content.MetadataField;
+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.MetadataFieldService;
+import org.dspace.content.service.MetadataValueService;
+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;
@@ -89,10 +104,49 @@ public class MetadataImport {
      */
     protected static final String AC_PREFIX = "authority.controlled.";
 
+    /**
+     * Map of field:value to csv row number, used to resolve indirect entity target references.
+     *
+     * @see #populateRefAndRowMap(DSpaceCSVLine, UUID)
+     */
+    protected Map<String, Set<Integer>> csvRefMap = new HashMap<>();
+
+    /**
+     * Map of csv row number to UUID, used to resolve indirect entity target references.
+     *
+     * @see #populateRefAndRowMap(DSpaceCSVLine, UUID)
+     */
+    protected HashMap<Integer, UUID> csvRowMap = new HashMap<>();
+
+    /**
+     * Map of UUIDs to their entity types.
+     *
+     * @see #populateRefAndRowMap(DSpaceCSVLine, UUID)
+     */
+    protected static HashMap<UUID, String> entityTypeMap = new HashMap<>();
+
+    /**
+     * Map of UUIDs to their relations that are referenced within any import with their referers.
+     *
+     * @see #populateEntityRelationMap(String, String, String)
+     */
+    protected static HashMap<String, HashMap<String, ArrayList<String>>> entityRelationMap = new HashMap<>();
+
+
+    /**
+     * Collection of errors generated during relation validation process.
+     */
+    protected ArrayList<String> relationValidationErrors = new ArrayList<>();
+
+    /**
+     * Counter of rows proccssed in a CSV.
+     */
+    protected Integer rowCount = 1;
+
     /**
      * 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 +155,10 @@ 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 +178,10 @@ 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();
     }
 
     /**
@@ -131,7 +193,7 @@ public class MetadataImport {
      * @param workflowNotify If the workflows should be used, whether to send notifications or not
      * @param useTemplate    Use collection template if create new item
      * @return An array of BulkEditChange elements representing the items that have changed
-     * @throws MetadataImportException if something goes wrong
+     * @throws MetadataImportException  if something goes wrong
      */
     public List<BulkEditChange> runImport(boolean change,
                                           boolean useWorkflow,
@@ -146,7 +208,11 @@ public class MetadataImport {
             c.setMode(Context.Mode.BATCH_EDIT);
 
             // Process each change
+            rowCount = 1;
             for (DSpaceCSVLine line : toImport) {
+                // Resolve target references to other items
+                populateRefAndRowMap(line, line.getID());
+                line = resolveEntityRefs(line);
                 // Get the DSpace item to compare with
                 UUID id = line.getID();
 
@@ -159,7 +225,7 @@ public class MetadataImport {
                 WorkflowItem wfItem = null;
                 Item item = null;
 
-                // Is this a new item?
+                // Is this an existing item?
                 if (id != null) {
                     // Get the item
                     item = itemService.find(c, id);
@@ -196,9 +262,8 @@ public class MetadataImport {
                                     }
                                 }
                             }
-
                             // Compare
-                            compare(item, fromCSV, change, md, whatHasChanged, line);
+                            compareAndUpdate(item, fromCSV, change, md, whatHasChanged, line);
                         }
                     }
 
@@ -259,7 +324,7 @@ public class MetadataImport {
                     BulkEditChange whatHasChanged = new BulkEditChange();
                     for (String md : line.keys()) {
                         // Get the values we already have
-                        if (!"id".equals(md)) {
+                        if (!"id".equals(md) && !"rowName".equals(md)) {
                             // Get the values from the CSV
                             String[] fromCSV = line.get(md).toArray(new String[line.get(md).size()]);
 
@@ -337,14 +402,23 @@ public class MetadataImport {
 
                         // Add the metadata to the item
                         for (BulkEditMetadataValue dcv : whatHasChanged.getAdds()) {
-                            itemService.addMetadata(c, item, dcv.getSchema(),
-                                                    dcv.getElement(),
-                                                    dcv.getQualifier(),
-                                                    dcv.getLanguage(),
-                                                    dcv.getValue(),
-                                                    dcv.getAuthority(),
-                                                    dcv.getConfidence());
+                            if (!StringUtils.equals(dcv.getSchema(), MetadataSchemaEnum.RELATION.getName())) {
+                                itemService.addMetadata(c, item, dcv.getSchema(),
+                                        dcv.getElement(),
+                                        dcv.getQualifier(),
+                                        dcv.getLanguage(),
+                                        dcv.getValue(),
+                                        dcv.getAuthority(),
+                                        dcv.getConfidence());
+                            }
                         }
+                        //Add relations after all metadata has been processed
+                        for (BulkEditMetadataValue dcv : whatHasChanged.getAdds()) {
+                            if (StringUtils.equals(dcv.getSchema(), MetadataSchemaEnum.RELATION.getName())) {
+                                addRelationship(c, item, dcv.getElement(), dcv.getValue());
+                            }
+                        }
+
 
                         // Should the workflow be used?
                         if (useWorkflow) {
@@ -368,8 +442,6 @@ public class MetadataImport {
                             }
                         }
 
-                        // Commit changes to the object
-//                        c.commit();
                         whatHasChanged.setItem(item);
                     }
 
@@ -383,6 +455,9 @@ public class MetadataImport {
                     c.uncacheEntity(wfItem);
                     c.uncacheEntity(item);
                 }
+                populateRefAndRowMap(line, item == null ? null : item.getID());
+                // keep track of current rows processed
+                rowCount++;
             }
 
             c.setMode(originalMode);
@@ -393,11 +468,14 @@ public class MetadataImport {
         }
 
         // Return the changes
+        if (!change ) {
+            validateExpressedRelations();
+        }
         return changes;
     }
 
     /**
-     * Compare an item metadata with a line from CSV, and optionally update the item
+     * Compare an item metadata with a line from CSV, and optionally update the item.
      *
      * @param item    The current item metadata
      * @param fromCSV The metadata from the CSV file
@@ -407,10 +485,11 @@ public class MetadataImport {
      * @param line    line in CSV file
      * @throws SQLException       if there is a problem accessing a Collection from the database, from its handle
      * @throws AuthorizeException if there is an authorization problem with permissions
+     * @throws MetadataImportException custom exception for error handling within metadataimport
      */
-    protected void compare(Item item, String[] fromCSV, boolean change,
-                           String md, BulkEditChange changes, DSpaceCSVLine line)
-        throws SQLException, AuthorizeException {
+    protected void compareAndUpdate(Item item, String[] fromCSV, boolean change,
+                                    String md, BulkEditChange changes, DSpaceCSVLine line)
+        throws SQLException, AuthorizeException, MetadataImportException {
         // Log what metadata element we're looking at
         String all = "";
         for (String part : fromCSV) {
@@ -420,8 +499,8 @@ public class MetadataImport {
         log.debug(LogManager.getHeader(c, "metadata_import",
                                        "item_id=" + item.getID() + ",fromCSV=" + all));
 
-        // Don't compare collections  or actions
-        if (("collection".equals(md)) || ("action".equals(md))) {
+        // Don't compare collections or actions or rowNames
+        if (("collection".equals(md)) || ("action".equals(md)) || ("rowName".equals(md))) {
             return;
         }
 
@@ -583,13 +662,131 @@ public class MetadataImport {
                 }
             }
 
-            // Set those values
-            itemService.clearMetadata(c, item, schema, element, qualifier, language);
-            itemService.addMetadata(c, item, schema, element, qualifier, language, values, authorities, confidences);
-            itemService.update(c, item);
+            if (StringUtils.equals(schema, MetadataSchemaEnum.RELATION.getName())) {
+                List<RelationshipType> relationshipTypeList = relationshipTypeService
+                    .findByLeftwardOrRightwardTypeName(c, element);
+                for (RelationshipType relationshipType : relationshipTypeList) {
+                    for (Relationship relationship : relationshipService
+                        .findByItemAndRelationshipType(c, item, relationshipType)) {
+                        relationshipService.delete(c, relationship);
+                        relationshipService.update(c, relationship);
+                    }
+                }
+                addRelationships(c, item, element, values);
+            } else {
+                itemService.clearMetadata(c, item, schema, element, qualifier, language);
+                itemService.addMetadata(c, item, schema, element, qualifier,
+                                        language, values, authorities, confidences);
+                itemService.update(c, item);
+            }
         }
     }
 
+    /**
+     *
+     * Adds multiple relationships with a matching typeName to an item.
+     *
+     * @param c             The relevant DSpace context
+     * @param item          The item to which this metadatavalue belongs to
+     * @param typeName       The element for the metadatavalue
+     * @param values to iterate over
+     * @throws SQLException If something goes wrong
+     * @throws AuthorizeException   If something goes wrong
+     */
+    private void addRelationships(Context c, Item item, String typeName, List<String> values)
+            throws SQLException, AuthorizeException,
+                                        MetadataImportException {
+        for (String value : values) {
+            addRelationship(c, item, typeName, value);
+        }
+    }
+
+    /**
+     * Gets an existing entity from a target reference.
+     *
+     * @param context the context to use.
+     * @param targetReference the target reference which may be a UUID, metadata reference, or rowName reference.
+     * @return the entity, which is guaranteed to exist.
+     * @throws MetadataImportException if the target reference is badly formed or refers to a non-existing item.
+     */
+    private Entity getEntity(Context context, String targetReference) throws MetadataImportException {
+        Entity entity = null;
+        UUID uuid = resolveEntityRef(context, targetReference);
+        // At this point, we have a uuid, so we can get an entity
+        try {
+            entity = entityService.findByItemId(context, uuid);
+            if (entity.getItem() == null) {
+                throw new IllegalArgumentException("No item found in repository with uuid: " + uuid);
+            }
+            return entity;
+        } catch (SQLException sqle) {
+            throw new MetadataImportException("Unable to find entity using reference: " + targetReference, sqle);
+        }
+    }
+
+    /**
+     *
+     * Creates a relationship for the given item
+     *
+     * @param c         The relevant DSpace context
+     * @param item      The item that the relationships will be made for
+     * @param typeName     The relationship typeName
+     * @param value    The value for the relationship
+     * @throws SQLException If something goes wrong
+     * @throws AuthorizeException   If something goes wrong
+     */
+    private void addRelationship(Context c, Item item, String typeName, String value)
+        throws SQLException, AuthorizeException, MetadataImportException {
+        if (value.isEmpty()) {
+            return;
+        }
+        boolean left = false;
+
+        // Get entity from target reference
+        Entity relationEntity = getEntity(c, value);
+        // Get relationship type of entity and item
+        String relationEntityRelationshipType = itemService.getMetadata(relationEntity.getItem(),
+                "relationship", "type",
+                null, Item.ANY).get(0).getValue();
+        String itemRelationshipType = itemService.getMetadata(item, "relationship", "type",
+                null, Item.ANY).get(0).getValue();
+
+        // Get the correct RelationshipType based on typeName
+        List<RelationshipType> relType = relationshipTypeService.findByLeftwardOrRightwardTypeName(c, typeName);
+        RelationshipType foundRelationshipType = matchRelationshipType(relType,
+                relationEntityRelationshipType, itemRelationshipType, typeName);
+
+        if (foundRelationshipType == null) {
+            throw new MetadataImportException("Error on CSV row " + rowCount + ":" + "\n" +
+                    "No Relationship type found for:\n" +
+                    "Target type: " + relationEntityRelationshipType + "\n" +
+                    "Origin referer type: " + itemRelationshipType + "\n" +
+                    "with typeName: " + typeName);
+        }
+
+        if (foundRelationshipType.getLeftwardType().equalsIgnoreCase(typeName)) {
+            left = true;
+        }
+
+        // Placeholder items for relation placing
+        Item leftItem = null;
+        Item rightItem = null;
+        if (left) {
+            leftItem = item;
+            rightItem = relationEntity.getItem();
+        } else {
+            leftItem = relationEntity.getItem();
+            rightItem = item;
+        }
+
+        // Create the relationship
+        int leftPlace = relationshipService.findNextLeftPlaceByLeftItem(c, leftItem);
+        int rightPlace = relationshipService.findNextRightPlaceByRightItem(c, rightItem);
+        Relationship persistedRelationship = relationshipService.create(c, leftItem, rightItem,
+                foundRelationshipType, leftPlace, rightPlace);
+        relationshipService.update(c, persistedRelationship);
+    }
+
     /**
      * Compare changes between an items owning collection and mapped collections
      * and what is in the CSV file
@@ -1078,6 +1275,8 @@ public class MetadataImport {
                           "notify - when adding new items using a workflow, send notification emails");
         options.addOption("t", "template", false,
                           "template - when adding new items, use the collection template (if it exists)");
+        options.addOption("v", "validate-only", false,
+                          "validate - just validate the csv, don't run the import");
         options.addOption("h", "help", false, "help");
 
         // Parse the command line arguments
@@ -1175,7 +1374,9 @@ public class MetadataImport {
         MetadataImport importer = new MetadataImport(c, csv);
         List<BulkEditChange> changes;
 
-        if (!line.hasOption('s')) {
+        boolean validateOnly = line.hasOption('v');
+
+        if (!line.hasOption('s') || validateOnly) {
             // See what has changed
             try {
                 changes = importer.runImport(false, useWorkflow, workflowNotify, useTemplate);
@@ -1189,7 +1390,7 @@ public class MetadataImport {
             int changeCounter = displayChanges(changes, false);
 
             // If there were changes, ask if we should execute them
-            if (changeCounter > 0) {
+            if (!validateOnly && changeCounter > 0) {
                 try {
                     // Ask the user if they want to make the changes
                     System.out.println("\n" + changeCounter + " item(s) will be changed\n");
@@ -1214,7 +1415,7 @@ public class MetadataImport {
 
         try {
             // If required, make the change
-            if (change) {
+            if (change && !validateOnly) {
                 try {
                     // Make the changes
                     changes = importer.runImport(true, useWorkflow, workflowNotify, useTemplate);
@@ -1226,9 +1427,6 @@ public class MetadataImport {
 
                 // Display the changes
                 displayChanges(changes, true);
-
-                // Commit the change to the DB
-//                c.commit();
             }
 
             // Finsh off and tidy up
@@ -1241,4 +1439,418 @@ public class MetadataImport {
             System.exit(1);
         }
     }
+
+    /**
+     * Gets a copy of the given csv line with all entity target references resolved to UUID strings.
+     * Keys being iterated over represent metadatafields or special columns to be processed.
+     *
+     * @param line the csv line to process.
+     * @return a copy, with all references resolved.
+     * @throws MetadataImportException if there is an error resolving any entity target reference.
+     */
+    public DSpaceCSVLine resolveEntityRefs(DSpaceCSVLine line) throws MetadataImportException {
+        DSpaceCSVLine newLine = new DSpaceCSVLine(line.getID());
+        UUID originId = evaluateOriginId(line.getID());
+        for (String key : line.keys()) {
+            // If a key represents a relation field attempt to resolve the target reference from the csvRefMap
+            if (key.split("\\.")[0].equalsIgnoreCase("relation")) {
+                if (line.get(key).size() > 0) {
+                    for (String val : line.get(key)) {
+                        // Attempt to resolve the relation target reference
+                        // These can be a UUID, metadata target reference or rowName target reference
+                        String uuid = resolveEntityRef(c, val).toString();
+                        newLine.add(key, uuid);
+                        //Entity refs have been resolved / placeholdered
+                        //Populate the EntityRelationMap
+                        populateEntityRelationMap(uuid, key, originId.toString());
+                    }
+                }
+            } else {
+                if (line.get(key).size() > 1) {
+                    for (String value : line.get(key)) {
+                        newLine.add(key, value);
+                    }
+                } else {
+                    if (line.get(key).size() > 0) {
+                        newLine.add(key, line.get(key).get(0));
+                    }
+                }
+            }
+        }
+
+        return newLine;
+    }
+
+    /**
+     * Populate the entityRelationMap with all target references and it's asscoiated typeNames
+     * to their respective origins
+     *
+     * @param refUUID the target reference UUID for the relation
+     * @param relationField the field of the typeNames to relate from
+     */
+    private void populateEntityRelationMap(String refUUID, String relationField, String originId) {
+        HashMap<String, ArrayList<String>> typeNames = null;
+        if (entityRelationMap.get(refUUID) == null) {
+            typeNames = new HashMap<>();
+            ArrayList<String> originIds = new ArrayList<>();
+            originIds.add(originId);
+            typeNames.put(relationField, originIds);
+            entityRelationMap.put(refUUID, typeNames);
+        } else {
+            typeNames = entityRelationMap.get(refUUID);
+            if (typeNames.get(relationField) == null) {
+                ArrayList<String> originIds = new ArrayList<>();
+                originIds.add(originId);
+                typeNames.put(relationField, originIds);
+            } else {
+                ArrayList<String> originIds =  typeNames.get(relationField);
+                originIds.add(originId);
+                typeNames.put(relationField, originIds);
+            }
+            entityRelationMap.put(refUUID, typeNames);
+        }
+    }
+
+    /**
+     * Populates the csvRefMap, csvRowMap, and entityTypeMap for the given csv line.
+     *
+     * The csvRefMap is an index that keeps track of which rows have a specific value for
+     * a specific metadata field or the special "rowName" column. This is used to help resolve indirect
+     * entity target references in the same CSV.
+     *
+     * The csvRowMap is a row number to UUID map, and contains an entry for every row that has
+     * been processed so far which has a known (minted) UUID for its item. This is used to help complete
+     * the resolution after the row number has been determined.
+     *
+     * @param line the csv line.
+     * @param uuid the uuid of the item, which may be null if it has not been minted yet.
+     */
+    private void populateRefAndRowMap(DSpaceCSVLine line, @Nullable UUID uuid) {
+        if (uuid != null) {
+            csvRowMap.put(rowCount, uuid);
+        } else {
+            csvRowMap.put(rowCount, new UUID(0, rowCount));
+        }
+        for (String key : line.keys()) {
+            if (key.contains(".") && !key.split("\\.")[0].equalsIgnoreCase("relation") ||
+                    key.equalsIgnoreCase("rowName")) {
+                for (String value : line.get(key)) {
+                    String valueKey = key + ":" + value;
+                    Set<Integer> rowNums = csvRefMap.get(valueKey);
+                    if (rowNums == null) {
+                        rowNums = new HashSet<>();
+                        csvRefMap.put(valueKey, rowNums);
+                    }
+                    rowNums.add(rowCount);
+                }
+            }
+            //Populate entityTypeMap
+            if (key.equalsIgnoreCase("relationship.type") && line.get(key).size() > 0) {
+                if (uuid == null) {
+                    entityTypeMap.put(new UUID(0, rowCount), line.get(key).get(0));
+                } else {
+                    entityTypeMap.put(uuid, line.get(key).get(0));
+                }
+            }
+        }
+    }
+
+    /**
+     * Gets the UUID of the item indicated by the given target reference,
+     * which may be a direct UUID string, a row reference
+     * of the form rowName:VALUE, or a metadata value reference of the form schema.element[.qualifier]:VALUE.
+     *
+     * The reference may refer to a previously-processed item in the CSV or an item in the database.
+     *
+     * @param context the context to use.
+     * @param reference the target reference which may be a UUID, metadata reference, or rowName reference.
+     * @return the uuid.
+     * @throws MetadataImportException if the target reference is malformed or ambiguous (refers to multiple items).
+     */
+    private UUID resolveEntityRef(Context context, String reference) throws MetadataImportException {
+        // value reference
+        UUID uuid = null;
+        if (!reference.contains(":")) {
+            // assume it's a UUID
+            try {
+                return UUID.fromString(reference);
+            } catch (IllegalArgumentException e) {
+                throw new MetadataImportException("Error in CSV row " + rowCount +  ":\n" +
+                        "Not a UUID or indirect entity reference: '" + reference + "'");
+            }
+        } else if (!reference.startsWith("rowName:") ) { // Not a rowName ref; so it's a metadata value reference
+            MetadataValueService metadataValueService = ContentServiceFactory.getInstance().getMetadataValueService();
+            MetadataFieldService metadataFieldService =
+                    ContentServiceFactory.getInstance().getMetadataFieldService();
+            int i = reference.indexOf(":");
+            String mfValue = reference.substring(i + 1);
+            String mf[] = reference.substring(0, i).split("\\.");
+            if (mf.length < 2) {
+                throw new MetadataImportException("Error in CSV row " + rowCount +  ":\n" +
+                        "Bad metadata field in reference: '" + reference
+                        + "' (expected syntax is schema.element[.qualifier])");
+            }
+            String schema = mf[0];
+            String element = mf[1];
+            String qualifier = mf.length == 2 ? null : mf[2];
+            try {
+                MetadataField mfo = metadataFieldService.findByElement(context, schema, element, qualifier);
+                Iterator<MetadataValue> mdv = metadataValueService.findByFieldAndValue(context, mfo, mfValue);
+                if (mdv.hasNext()) {
+                    MetadataValue mdvVal = mdv.next();
+                    uuid = mdvVal.getDSpaceObject().getID();
+                    if (mdv.hasNext()) {
+                        throw new MetadataImportException("Error in CSV row " + rowCount +  ":\n" +
+                                "Ambiguous reference; multiple matches in db: " + reference);
+                    }
+                }
+            } catch (SQLException e) {
+                throw new MetadataImportException("Error in CSV row " + rowCount +  ":\n" +
+                        "Error looking up item by metadata reference: " + reference, e);
+            }
+        }
+        // Lookup UUIDs that may have already been processed into the csvRefMap
+        // See populateRefAndRowMap() for how the csvRefMap is populated
+        // See getMatchingCSVUUIDs() for how the reference param is sourced from the csvRefMap
+        Set<UUID> csvUUIDs = getMatchingCSVUUIDs(reference);
+        if (csvUUIDs.size() > 1) {
+            throw new MetadataImportException("Error in CSV row " + rowCount +  ":\n" +
+                    "Ambiguous reference; multiple matches in csv: " + reference);
+        } else if (csvUUIDs.size() == 1) {
+            UUID csvUUID = csvUUIDs.iterator().next();
+            if (csvUUID.equals(uuid)) {
+                return uuid; // one match from csv and db (same item)
+            } else if (uuid != null) {
+                throw new MetadataImportException("Error in CSV row " + rowCount +  ":\n" +
+                        "Ambiguous reference; multiple matches in db and csv: " + reference);
+            } else {
+                return csvUUID; // one match from csv
+            }
+        } else { // size == 0; the reference does not exist throw an error
+            if (uuid == null) {
+                throw new MetadataImportException("Error in CSV row " + rowCount +  ":\n" +
+                        "No matches found for reference: " + reference
+                        + "\nKeep in mind you can only reference entries that are listed before " +
+                        "this one within the CSV.");
+            } else {
+                return uuid; // one match from db
+            }
+        }
+    }
+
+    /**
+     * Gets the set of matching lines as UUIDs that have already been processed given a metadata value.
+     *
+     * @param mdValueRef the metadataValue reference to search for.
+     * @return the set of matching lines as UUIDs.
+     */
+    private Set<UUID> getMatchingCSVUUIDs(String mdValueRef) {
+        Set<UUID> set = new HashSet<>();
+        if (csvRefMap.containsKey(mdValueRef)) {
+            for (Integer rowNum : csvRefMap.get(mdValueRef)) {
+                set.add(getUUIDForRow(rowNum));
+            }
+        }
+        return set;
+    }
+
+    /**
+     * Gets the UUID of the item of a given row in the CSV, if it has been minted.
+     * If the UUID has not yet been minted, gets a UUID representation of the row
+     * (a UUID whose numeric value equals the row number).
+     *
+     * @param rowNum the row number.
+     * @return the UUID of the item
+     */
+    private UUID getUUIDForRow(int rowNum) {
+        if (csvRowMap.containsKey(rowNum)) {
+            return csvRowMap.get(rowNum);
+        } else {
+            return new UUID(0, rowNum);
+        }
+    }
+
+    /**
+     * Return a UUID of the origin in process or a placeholder for the origin to be evaluated later
+     *
+     * @param originId UUID of the origin
+     * @return the UUID of the item or UUID placeholder
+     */
+    private UUID evaluateOriginId(@Nullable UUID originId) {
+        if (originId != null) {
+            return originId;
+        } else {
+            return new UUID(0, rowCount);
+        }
+    }
+
+    /**
+     * Validate every relation modification expressed in the CSV.
+     *
+     */
+    private void validateExpressedRelations() throws MetadataImportException {
+        for (String targetUUID : entityRelationMap.keySet()) {
+            String targetType = null;
+            try {
+                // Get the type of reference. Attempt lookup in processed map first before looking in archive.
+                if (entityTypeMap.get(UUID.fromString(targetUUID)) != null) {
+                    targetType = entityTypeService.
+                            findByEntityType(c, entityTypeMap.get(UUID.fromString(targetUUID))).getLabel();
+                } else {
+                    // Target item may be archived; check there.
+                    // Add to errors if Realtionship.type cannot be derived
+                    Item targetItem = null;
+                    if (itemService.find(c, UUID.fromString(targetUUID)) != null) {
+                        targetItem = itemService.find(c, UUID.fromString(targetUUID));
+                        List<MetadataValue> relTypes = itemService.
+                                getMetadata(targetItem, "relationship", "type", null, Item.ANY);
+                        String relTypeValue = null;
+                        if (relTypes.size() > 0) {
+                            relTypeValue = relTypes.get(0).getValue();
+                            targetType = entityTypeService.findByEntityType(c, relTypeValue).getLabel();
+                        } else {
+                            relationValidationErrors.add("Cannot resolve Entity type for target UUID: " +
+                                    targetUUID);
+                        }
+                    } else {
+                        relationValidationErrors.add("Cannot resolve Entity type for target UUID: " +
+                                targetUUID);
+                    }
+                }
+                if (targetType == null) {
+                    continue;
+                }
+                // Get typeNames for each origin referer of this target.
+                for (String typeName : entityRelationMap.get(targetUUID).keySet()) {
+                    // Resolve Entity Type for each origin referer.
+                    for (String originRefererUUID : entityRelationMap.get(targetUUID).get(typeName)) {
+                        // Evaluate row number for origin referer.
+                        String originRow = "N/A";
+                        if (csvRowMap.containsValue(UUID.fromString(originRefererUUID))) {
+                            for (int key : csvRowMap.keySet()) {
+                                if (csvRowMap.get(key).toString().equalsIgnoreCase(originRefererUUID)) {
+                                    originRow = key + "";
+                                    break;
+                                }
+                            }
+                        }
+                        String originType = "";
+                        // Validate target type and origin type pairing with typeName or add to errors.
+                        // Attempt lookup in processed map first before looking in archive.
+                        if (entityTypeMap.get(UUID.fromString(originRefererUUID)) != null) {
+                            originType = entityTypeMap.get(UUID.fromString(originRefererUUID));
+                            validateTypesByTypeByTypeName(targetType, originType, typeName, originRow);
+                        } else {
+                            // Origin item may be archived; check there.
+                            // Add to errors if Realtionship.type cannot be derived.
+                            Item originItem = null;
+                            if (itemService.find(c, UUID.fromString(targetUUID)) != null) {
+                                originItem = itemService.find(c, UUID.fromString(originRefererUUID));
+                                List<MetadataValue> relTypes = itemService.
+                                        getMetadata(originItem, "relationship", "type", null, Item.ANY);
+                                String relTypeValue = null;
+                                if (relTypes.size() > 0) {
+                                    relTypeValue = relTypes.get(0).getValue();
+                                    originType = entityTypeService.findByEntityType(c, relTypeValue).getLabel();
+                                    validateTypesByTypeByTypeName(targetType, originType, typeName, originRow);
+                                } else {
+                                    relationValidationErrors.add("Error on CSV row " + originRow + ":" + "\n" +
+                                            "Cannot resolve Entity type for reference: "
+                                            + originRefererUUID);
+                                }
+
+                            } else {
+                                relationValidationErrors.add("Error on CSV row " + originRow + ":" + "\n" +
+                                        "Cannot resolve Entity type for reference: "
+                                        + originRefererUUID + " in row: " + originRow );
+                            }
+                        }
+                    }
+                }
+
+            } catch (SQLException sqle) {
+                throw new MetadataImportException("Error interacting with database!", sqle);
+            }
+
+        } // If relationValidationErrors is empty all described relationships are valid.
+        if (!relationValidationErrors.isEmpty()) {
+            StringBuilder errors = new StringBuilder();
+            for (String error : relationValidationErrors) {
+                errors.append(error + "\n");
+            }
+            throw new MetadataImportException("Error validating relationships: \n" + errors);
+        }
+    }
+
+    /**
+     * Generates a list of potenital Relationship Types given a typeName and attempts to match the given
+     * targetType and originType to a Relationship Type in the list.
+     *
+     * @param targetType entity type of target.
+     * @param originType entity type of origin referer.
+     * @param typeName left or right typeName of the respective Relationship.
+     * @return the UUID of the item.
+     */
+    private void validateTypesByTypeByTypeName(String targetType, String originType, String typeName, String originRow)
+            throws MetadataImportException {
+        try {
+            RelationshipType foundRelationshipType = null;
+            List<RelationshipType> relationshipTypeList = relationshipTypeService.
+                    findByLeftwardOrRightwardTypeName(c, typeName.split("\\.")[1]);
+            // Validate described relationship form the CSV.
+            foundRelationshipType = matchRelationshipType(relationshipTypeList, targetType, originType, typeName);
+            if (foundRelationshipType == null) {
+                relationValidationErrors.add("Error on CSV row " + originRow + ":" + "\n" +
+                        "No Relationship type found for:\n" +
+                        "Target type: " + targetType + "\n" +
+                        "Origin referer type: " + originType + "\n" +
+                        "with typeName: " + typeName + " for type: " + originType);
+            }
+        } catch (SQLException sqle) {
+            throw new MetadataImportException("Error interacting with database!", sqle);
+        }
+    }
+
+    /**
+     * Matches two Entity types to a Relationship Type from a set of Relationship Types.
+     *
+     * @param relTypes set of Relationship Types.
+     * @param targetType entity type of target.
+     * @param originType entity type of origin referer.
+     * @return null or matched Relationship Type.
+     */
+    private RelationshipType matchRelationshipType(List<RelationshipType> relTypes,
+                                                   String targetType, String originType, String originTypeName) {
+        RelationshipType foundRelationshipType = null;
+        if (originTypeName.split("\\.").length > 1) {
+            originTypeName = originTypeName.split("\\.")[1];
+        }
+        for (RelationshipType relationshipType : relTypes) {
+            // Is origin type leftward or righward
+            boolean isLeft = false;
+            if (relationshipType.getLeftType().getLabel().equalsIgnoreCase(originType)) {
+                isLeft = true;
+            }
+            if (isLeft) {
+                // Validate typeName reference
+                if (!relationshipType.getLeftwardType().equalsIgnoreCase(originTypeName)) {
+                    continue;
+                }
+                if (relationshipType.getLeftType().getLabel().equalsIgnoreCase(originType) &&
+                        relationshipType.getRightType().getLabel().equalsIgnoreCase(targetType)) {
+                    foundRelationshipType = relationshipType;
+                }
+            } else {
+                if (!relationshipType.getRightwardType().equalsIgnoreCase(originTypeName)) {
+                    continue;
+                }
+                if (relationshipType.getLeftType().getLabel().equalsIgnoreCase(targetType) &&
+                        relationshipType.getRightType().getLabel().equalsIgnoreCase(originType)) {
+                    foundRelationshipType = relationshipType;
+                }
+            }
+        }
+        return foundRelationshipType;
+    }
+
 }

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/harvest/Harvest.java

@@ -272,9 +272,8 @@ public class Harvest {
                         targetCollection = (Collection) dso;
                     }
                 } else {
-                    // not a handle, try and treat it as an integer collection database ID
-                    System.out.println("Looking up by id: " + collectionID + ", parsed as '" + Integer
-                        .parseInt(collectionID) + "', " + "in context: " + context);
+                    // not a handle, try and treat it as an collection database UUID
+                    System.out.println("Looking up by UUID: " + collectionID + ", " + "in context: " + context);
                     targetCollection = collectionService.find(context, UUID.fromString(collectionID));
                 }
             }
@@ -460,7 +459,7 @@ public class Harvest {
         List<String> errors;
 
         System.out.print("Testing basic PMH access:  ");
-        errors = OAIHarvester.verifyOAIharvester(server, set,
+        errors = harvestedCollectionService.verifyOAIharvester(server, set,
                                                  (null != metadataFormat) ? metadataFormat : "dc", false);
         if (errors.isEmpty()) {
             System.out.println("OK");
@@ -471,7 +470,7 @@ public class Harvest {
         }
 
         System.out.print("Testing ORE support:  ");
-        errors = OAIHarvester.verifyOAIharvester(server, set,
+        errors = harvestedCollectionService.verifyOAIharvester(server, set,
                                                  (null != metadataFormat) ? metadataFormat : "dc", true);
         if (errors.isEmpty()) {
             System.out.println("OK");

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.log4j.Logger;
+import org.apache.commons.lang3.StringUtils;
+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/" +
-                                                                                         handleService
-                                                                                             .getPrefix() + "/"))) ||
+                                (dcv.getValue() != null && dcv.getValue().startsWith(
+                                    handleService.getCanonicalPrefix() + handleService.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<>();
@@ -930,7 +929,7 @@ public class ItemExportServiceImpl implements ItemExportService {
             Locale supportedLocale = I18nUtil.getEPersonLocale(eperson);
             Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "export_success"));
             email.addRecipient(eperson.getEmail());
-            email.addArgument(ConfigurationManager.getProperty("dspace.url") + "/exportdownload/" + fileName);
+            email.addArgument(ConfigurationManager.getProperty("dspace.ui.url") + "/exportdownload/" + fileName);
             email.addArgument(ConfigurationManager.getProperty("org.dspace.app.itemexport.life.span.hours"));
 
             email.send();
@@ -948,7 +947,7 @@ public class ItemExportServiceImpl implements ItemExportService {
             Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "export_error"));
             email.addRecipient(eperson.getEmail());
             email.addArgument(error);
-            email.addArgument(ConfigurationManager.getProperty("dspace.url") + "/feedback");
+            email.addArgument(ConfigurationManager.getProperty("dspace.ui.url") + "/feedback");
 
             email.send();
         } catch (Exception e) {

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.lang.StringUtils;
+import org.apache.commons.lang3.RandomStringUtils;
+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();
         }
@@ -1796,7 +1797,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
             Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "bte_batch_import_error"));
             email.addRecipient(eperson.getEmail());
             email.addArgument(error);
-            email.addArgument(ConfigurationManager.getProperty("dspace.url") + "/feedback");
+            email.addArgument(ConfigurationManager.getProperty("dspace.ui.url") + "/feedback");
 
             email.send();
         } catch (Exception e) {

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");
-            if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0) {
-                HANDLE_PREFIX = "http://hdl.handle.net/";
-            }
+            HANDLE_PREFIX = handleService.getCanonicalPrefix();
 
             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/launcher/ScriptLauncher.java

@@ -13,6 +13,12 @@ import java.lang.reflect.Method;
 import java.util.List;
 import java.util.TreeMap;
 
+import org.apache.commons.cli.ParseException;
+import org.apache.log4j.Logger;
+import org.dspace.scripts.DSpaceRunnable;
+import org.dspace.scripts.factory.ScriptServiceFactory;
+import org.dspace.scripts.handler.DSpaceRunnableHandler;
+import org.dspace.scripts.handler.impl.CommandLineDSpaceRunnableHandler;
 import org.dspace.servicemanager.DSpaceKernelImpl;
 import org.dspace.servicemanager.DSpaceKernelInit;
 import org.dspace.services.RequestService;
@@ -27,6 +33,9 @@ import org.jdom.input.SAXBuilder;
  * @author Mark Diggory
  */
 public class ScriptLauncher {
+
+    private static final Logger log = Logger.getLogger(ScriptLauncher.class);
+
     /**
      * The service manager kernel
      */
@@ -76,8 +85,9 @@ public class ScriptLauncher {
         }
 
         // Look up command in the configuration, and execute.
-        int status;
-        status = runOneCommand(commandConfigs, args);
+
+        CommandLineDSpaceRunnableHandler commandLineDSpaceRunnableHandler = new CommandLineDSpaceRunnableHandler();
+        int status = handleScript(args, commandConfigs, commandLineDSpaceRunnableHandler, kernelImpl);
 
         // Destroy the service kernel if it is still alive
         if (kernelImpl != null) {
@@ -86,6 +96,50 @@ public class ScriptLauncher {
         }
 
         System.exit(status);
+
+    }
+
+    /**
+     * This method will take the arguments from a commandline input and it'll find the script that the first argument
+     * refers to and it'll execute this script.
+     * It can return a 1 or a 0 depending on whether the script failed or passed respectively
+     * @param args                  The arguments for the script and the script as first one in the array
+     * @param commandConfigs        The Document
+     * @param dSpaceRunnableHandler The DSpaceRunnableHandler for this execution
+     * @param kernelImpl            The relevant DSpaceKernelImpl
+     * @return                      A 1 or 0 depending on whether the script failed or passed respectively
+     */
+    public static int handleScript(String[] args, Document commandConfigs,
+                                       DSpaceRunnableHandler dSpaceRunnableHandler,
+                                       DSpaceKernelImpl kernelImpl) {
+        int status;
+        DSpaceRunnable script = ScriptServiceFactory.getInstance().getScriptService().getScriptForName(args[0]);
+        if (script != null) {
+            status = executeScript(args, dSpaceRunnableHandler, script);
+        } else {
+            status = runOneCommand(commandConfigs, args, kernelImpl);
+        }
+        return status;
+    }
+
+    /**
+     * This method will simply execute the script
+     * @param args                  The arguments of the script with the script name as first place in the array
+     * @param dSpaceRunnableHandler The relevant DSpaceRunnableHandler
+     * @param script                The script to be executed
+     * @return                      A 1 or 0 depending on whether the script failed or passed respectively
+     */
+    private static int executeScript(String[] args, DSpaceRunnableHandler dSpaceRunnableHandler,
+                                     DSpaceRunnable script) {
+        try {
+            script.initialize(args, dSpaceRunnableHandler);
+            script.run();
+            return 0;
+        } catch (ParseException e) {
+            script.printHelp();
+            e.printStackTrace();
+            return 1;
+        }
     }
 
     protected static int runOneCommand(Document commandConfigs, String[] args) {
@@ -98,7 +152,7 @@ public class ScriptLauncher {
      * @param commandConfigs  Document
      * @param args the command line arguments given
      */
-    public static int runOneCommand(Document commandConfigs, String[] args, DSpaceKernelImpl kernelImpl) {
+    protected static int runOneCommand(Document commandConfigs, String[] args, DSpaceKernelImpl kernelImpl) {
         String request = args[0];
         Element root = commandConfigs.getRootElement();
         List<Element> commands = root.getChildren("command");

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?
-        Bundle targetBundle = null; // bundle we're modifying
-
+        // check if destination bitstream exists
+        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;
                     }
                 }
@@ -345,63 +344,71 @@ 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);
+        System.out.println("File: " + newName);
+
+        // 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");
+                            + " (item: " + item.getHandle() + ") because filtering was unsuccessful");
                 }
-
                 return false;
             }
+
+            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 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
+            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
+            BitstreamFormat bf = bitstreamFormatService.findByShortDescription(context,
+                    formatFilter.getFormatString());
+            bitstreamService.setFormat(context, b, bf);
+            bitstreamService.update(context, b);
+
+            //Set permissions on the derivative bitstream
+            //- First remove any existing policies
+            authorizeService.removeAllPolicies(context, b);
+
+            //- Determine if this is a public-derivative format
+            if (publicFiltersClasses.contains(formatFilter.getClass().getSimpleName())) {
+                //- Set derivative bitstream to be publicly accessible
+                Group anonymous = groupService.findByName(context, Group.ANONYMOUS);
+                authorizeService.addPolicy(context, b, Constants.READ, anonymous);
+            } else {
+                //- Inherit policies from the source bitstream
+                authorizeService.inheritPolicies(context, source, b);
+            }
+
+            //do post-processing of the generated bitstream
+            formatFilter.postProcessBitstream(context, item, b);
+
         } catch (OutOfMemoryError oome) {
             System.out.println("!!! OutOfMemoryError !!!");
-            return false;
-        }
-
-        // create new bundle if needed
-        if (bundles.size() < 1) {
-            targetBundle = bundleService.create(context, item, formatFilter.getBundleName());
-        } else {
-            // take the first match
-            targetBundle = bundles.get(0);
-        }
-
-        Bitstream b = bitstreamService.create(context, targetBundle, destStream);
-
-        // 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());
-
-        // Find the proper format
-        BitstreamFormat bf = bitstreamFormatService.findByShortDescription(context,
-                                                                           formatFilter.getFormatString());
-        bitstreamService.setFormat(context, b, bf);
-        bitstreamService.update(context, b);
-
-        //Set permissions on the derivative bitstream
-        //- First remove any existing policies
-        authorizeService.removeAllPolicies(context, b);
-
-        //- Determine if this is a public-derivative format
-        if (publicFiltersClasses.contains(formatFilter.getClass().getSimpleName())) {
-            //- Set derivative bitstream to be publicly accessible
-            Group anonymous = groupService.findByName(context, Group.ANONYMOUS);
-            authorizeService.addPolicy(context, b, Constants.READ, anonymous);
-        } else {
-            //- Inherit policies from the source bitstream
-            authorizeService.inheritPolicies(context, source, b);
         }
 
         // 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/PDFBoxThumbnail.java

@@ -11,7 +11,9 @@ import java.awt.image.BufferedImage;
 import java.io.InputStream;
 import javax.imageio.ImageIO;
 
+import org.apache.logging.log4j.Logger;
 import org.apache.pdfbox.pdmodel.PDDocument;
+import org.apache.pdfbox.pdmodel.encryption.InvalidPasswordException;
 import org.apache.pdfbox.rendering.PDFRenderer;
 import org.dspace.content.Item;
 
@@ -26,6 +28,8 @@ import org.dspace.content.Item;
  * @author Jason Sherman jsherman@usao.edu
  */
 public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFormats {
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(PDFBoxThumbnail.class);
+
     @Override
     public String getFilteredName(String oldFilename) {
         return oldFilename + ".jpg";
@@ -65,12 +69,19 @@ public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFor
     @Override
     public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
         throws Exception {
-        PDDocument doc = PDDocument.load(source);
-        PDFRenderer renderer = new PDFRenderer(doc);
-        BufferedImage buf = renderer.renderImage(0);
-//        ImageIO.write(buf, "PNG", new File("custom-render.png"));
-        doc.close();
+        BufferedImage buf;
 
+        // Render the page image.
+        try ( PDDocument doc = PDDocument.load(source); ) {
+            PDFRenderer renderer = new PDFRenderer(doc);
+            buf = renderer.renderImage(0);
+        } catch (InvalidPasswordException ex) {
+            log.error("PDF is encrypted. Cannot create thumbnail (item: {})",
+                () -> currentItem.getHandle());
+            return null;
+        }
+
+        // Generate thumbnail derivative and return as IO stream.
         JPEGFilter jpegFilter = new JPEGFilter();
         return jpegFilter.getThumb(currentItem, buf, verbose);
     }

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

@@ -16,8 +16,9 @@ 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.pdmodel.encryption.InvalidPasswordException;
 import org.apache.pdfbox.text.PDFTextStripper;
 import org.dspace.content.Item;
 import org.dspace.core.ConfigurationManager;
@@ -30,7 +31,7 @@ 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) {
@@ -95,6 +96,10 @@ public class PDFFilter extends MediaFilter {
             try {
                 pdfDoc = PDDocument.load(source);
                 pts.writeText(pdfDoc, writer);
+            } catch (InvalidPasswordException ex) {
+                log.error("PDF is encrypted. Cannot extract text (item: {})",
+                    () -> currentItem.getHandle());
+                return null;
             } finally {
                 try {
                     if (pdfDoc != null) {

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/RequestItem.java

@@ -78,7 +78,7 @@ public class RequestItem implements ReloadableEntity<Integer> {
     private Date request_date = null;
 
     @Column(name = "accept_request")
-    private Boolean accept_request = null;
+    private boolean accept_request;
 
     /**
      * Protected constructor, create object using:
@@ -88,6 +88,7 @@ public class RequestItem implements ReloadableEntity<Integer> {
     protected RequestItem() {
     }
 
+    @Override
     public Integer getID() {
         return requestitem_id;
     }

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.log4j.Logger;
+import org.apache.commons.lang3.StringUtils;
+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);
-        criteria.add(Restrictions.eq("token", token));
-        return uniqueResult(criteria);
+        CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
+        CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, RequestItem.class);
+        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.log4j.Logger;
+import org.apache.commons.lang3.StringUtils;
+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/SHERPAPublisher.java

@@ -15,6 +15,9 @@ import java.util.List;
  * @author Andrea Bollini
  */
 public class SHERPAPublisher {
+
+    private String id;
+
     private String name;
 
     private String alias;
@@ -49,7 +52,7 @@ public class SHERPAPublisher {
 
     private String dateupdated;
 
-    public SHERPAPublisher(String name, String alias, String homeurl,
+    public SHERPAPublisher(String id, String name, String alias, String homeurl,
                            String prearchiving, List<String> prerestriction,
                            String postarchiving, List<String> postrestriction,
                            String pubarchiving, List<String> pubrestriction,
@@ -57,6 +60,8 @@ public class SHERPAPublisher {
                            String paidaccessname, String paidaccessnotes,
                            List<String[]> copyright, String romeocolour, String datedded,
                            String dateupdated) {
+        this.id = id;
+
         this.name = name;
 
         this.alias = alias;
@@ -160,4 +165,11 @@ public class SHERPAPublisher {
         return dateupdated;
     }
 
+    /**
+     * Generic getter for the id
+     * @return the id value of this SHERPAPublisher
+     */
+    public String getId() {
+        return id;
+    }
 }

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

@@ -13,7 +13,8 @@ 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.apache.logging.log4j.Logger;
 import org.dspace.app.util.XMLUtils;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -24,7 +25,9 @@ import org.w3c.dom.Element;
  * @author Andrea Bollini
  */
 public class SHERPAResponse {
-    private boolean error;
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(SHERPAResponse.class);
+
+    private int numHits;
 
     private String message;
 
@@ -57,12 +60,13 @@ public class SHERPAResponse {
             Element publishersElement = XMLUtils.getSingleElement(xmlRoot,
                                                                   "publishers");
 
-            message = XMLUtils.getElementValue(headersElement, "message");
-
-            if (StringUtils.isNotBlank(message)) {
-                error = true;
-                return;
+            String numhitsString = XMLUtils.getElementValue(headersElement, "numhits");
+            if (StringUtils.isNotBlank(numhitsString)) {
+                numHits = Integer.parseInt(numhitsString);
+            } else {
+                numHits = 0;
             }
+            message = XMLUtils.getElementValue(headersElement, "message");
 
             license = XMLUtils.getElementValue(headersElement, "license");
             licenseURL = XMLUtils.getElementValue(headersElement, "licenseurl");
@@ -112,9 +116,8 @@ public class SHERPAResponse {
 
                     Element copyrightlinksElement = XMLUtils.getSingleElement(
                         publisherElement, "copyrightlinks");
-
                     publishers
-                        .add(new SHERPAPublisher(XMLUtils.getElementValue(
+                        .add(new SHERPAPublisher(publisherElement.getAttribute("id"), XMLUtils.getElementValue(
                             publisherElement, "name"),
                                                  XMLUtils.getElementValue(publisherElement,
                                                                           "alias"), XMLUtils.getElementValue(
@@ -162,17 +165,12 @@ public class SHERPAResponse {
                 }
             }
         } catch (Exception e) {
-            error = true;
+            log.error("Error parsing SHERPA API Response", e);
         }
     }
 
     public SHERPAResponse(String message) {
         this.message = message;
-        this.error = true;
-    }
-
-    public boolean isError() {
-        return error;
     }
 
     public String getMessage() {
@@ -198,4 +196,8 @@ public class SHERPAResponse {
     public List<SHERPAPublisher> getPublishers() {
         return publishers;
     }
+
+    public int getNumHits() {
+        return numHits;
+    }
 }

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.log4j.Logger;
+import org.apache.commons.lang3.StringUtils;
+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.lang.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.commons.lang3.ArrayUtils;
+import org.apache.commons.lang3.StringUtils;
+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 =
@@ -152,11 +152,11 @@ public class GenerateSitemaps {
      */
     public static void generateSitemaps(boolean makeHTMLMap,
                                         boolean makeSitemapOrg) throws SQLException, IOException {
-        String sitemapStem = configurationService.getProperty("dspace.url")
+        String sitemapStem = configurationService.getProperty("dspace.ui.url")
             + "/sitemap";
-        String htmlMapStem = configurationService.getProperty("dspace.url")
+        String htmlMapStem = configurationService.getProperty("dspace.ui.url")
             + "/htmlmap";
-        String handleURLStem = configurationService.getProperty("dspace.url")
+        String handleURLStem = configurationService.getProperty("dspace.ui.url")
             + "/handle/";
 
         File outputDir = new File(configurationService.getProperty("sitemap.dir"));
@@ -293,7 +293,7 @@ public class GenerateSitemaps {
                 .getProperty("http.proxy.port"));
         }
 
-        String sitemapURL = configurationService.getProperty("dspace.url")
+        String sitemapURL = configurationService.getProperty("dspace.ui.url")
             + "/sitemap";
 
         URL url = new URL(engineURL + URLEncoder.encode(sitemapURL, "UTF-8"));

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

@@ -33,6 +33,7 @@ import org.apache.commons.lang3.StringUtils;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
+import org.dspace.core.Utils;
 import org.dspace.discovery.DiscoverQuery;
 import org.dspace.discovery.SearchServiceException;
 import org.dspace.discovery.SearchUtils;
@@ -581,9 +582,9 @@ public class LogAnalyser {
         }
 
         // now do the host name and url lookup
-        hostName = ConfigurationManager.getProperty("dspace.hostname").trim();
+        hostName = Utils.getHostName(ConfigurationManager.getProperty("dspace.ui.url"));
         name = ConfigurationManager.getProperty("dspace.name").trim();
-        url = ConfigurationManager.getProperty("dspace.url").trim();
+        url = ConfigurationManager.getProperty("dspace.ui.url").trim();
         if ((url != null) && (!url.endsWith("/"))) {
             url = url + "/";
         }

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/Stat.java

@@ -15,7 +15,7 @@ package org.dspace.app.statistics;
  *
  * @author Richard Jones
  */
-public class Stat implements Comparable {
+public class Stat implements Comparable<Stat> {
     // FIXME: this class is functional but a bit messy, and should be neatened
     // up and completed
 
@@ -132,17 +132,17 @@ public class Stat implements Comparable {
 
 
     /**
-     * compare the current object to the given object returning -1 if o is less
-     * than the current object, 0 if they are the same, and +1 if o is greater
-     * than the current object.
+     * Compare the current Stat to the given Stat returning -1 if o is less
+     * than the current Stat, 0 if they are the same, and +1 if o is greater
+     * than the current Stat.
      *
-     * @param o the object to compare to the current one
+     * @param stat the Stat object to compare to the current one
      * @return +1, 0, -1 if o is less than, equal to, or greater than the
      * current object value.
      */
     @Override
-    public int compareTo(Object o) {
-        int objectValue = ((Stat) o).getValue();
+    public int compareTo(Stat stat) {
+        int objectValue = stat.getValue();
 
         if (objectValue < this.getValue()) {
             return -1;

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/AbstractDSpaceWebapp.java

@@ -50,16 +50,16 @@ abstract public class AbstractDSpaceWebapp
     /**
      * Construct a particular kind of DSpace application.
      *
-     * @param kind what kind of application is this?  (XMLUI, JSPUI, etc.)
+     * @param kind what kind of application is this?
      */
     public AbstractDSpaceWebapp(String kind) {
         this.kind = kind;
 
         started = new Date();
 
-        url = ConfigurationManager.getProperty("dspace.url");
+        url = ConfigurationManager.getProperty("dspace.ui.url");
         if (null == url) {
-            throw new IllegalStateException("dspace.url is undefined");
+            throw new IllegalStateException("dspace.ui.url is undefined");
         }
     }
 

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

@@ -34,12 +34,6 @@ import org.dspace.core.Context;
  */
 public class AuthorizeUtil {
 
-    private static final AuthorizeService authorizeService =
-        AuthorizeServiceFactory.getInstance().getAuthorizeService();
-    private static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-    private static final CollectionService collectionService =
-        ContentServiceFactory.getInstance().getCollectionService();
-
     /**
      * Default constructor
      */
@@ -95,8 +89,9 @@ public class AuthorizeUtil {
      */
     public static void authorizeManageItemPolicy(Context context, Item item)
         throws AuthorizeException, SQLException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         if (AuthorizeConfiguration.canItemAdminManagePolicies()) {
-            authorizeService.authorizeAction(context, item, Constants.ADMIN);
+            AuthorizeServiceFactory.getInstance().getAuthorizeService().authorizeAction(context, item, Constants.ADMIN);
         } else if (AuthorizeConfiguration.canCollectionAdminManageItemPolicies()) {
             authorizeService.authorizeAction(context, item
                 .getOwningCollection(), Constants.ADMIN);
@@ -124,6 +119,7 @@ public class AuthorizeUtil {
      */
     public static void authorizeManageCollectionPolicy(Context context,
                                                        Collection collection) throws AuthorizeException, SQLException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         if (AuthorizeConfiguration.canCollectionAdminManagePolicies()) {
             authorizeService.authorizeAction(context, collection,
                                              Constants.ADMIN);
@@ -151,6 +147,7 @@ public class AuthorizeUtil {
      */
     public static void authorizeManageCommunityPolicy(Context context,
                                                       Community community) throws AuthorizeException, SQLException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         if (AuthorizeConfiguration.canCommunityAdminManagePolicies()) {
             authorizeService.authorizeAction(context, community,
                                              Constants.ADMIN);
@@ -171,6 +168,7 @@ public class AuthorizeUtil {
      */
     public static void requireAdminRole(Context context)
         throws AuthorizeException, SQLException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         if (!authorizeService.isAdmin(context)) {
             throw new AuthorizeException(
                 "Only system admin are allowed to perform this action");
@@ -191,6 +189,8 @@ public class AuthorizeUtil {
      */
     public static void authorizeManageCCLicense(Context context, Item item)
         throws AuthorizeException, SQLException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
+        ItemService itemService = ContentServiceFactory.getInstance().getItemService();
         try {
             authorizeService.authorizeAction(context, item, Constants.ADD);
             authorizeService.authorizeAction(context, item, Constants.REMOVE);
@@ -224,6 +224,8 @@ public class AuthorizeUtil {
      */
     public static void authorizeManageTemplateItem(Context context,
                                                    Collection collection) throws AuthorizeException, SQLException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
+        CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
         boolean isAuthorized = collectionService.canEditBoolean(context, collection, false);
 
         if (!isAuthorized
@@ -258,6 +260,7 @@ public class AuthorizeUtil {
      */
     public static void authorizeManageSubmittersGroup(Context context,
                                                       Collection collection) throws AuthorizeException, SQLException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         if (AuthorizeConfiguration.canCollectionAdminManageSubmitters()) {
             authorizeService.authorizeAction(context, collection,
                                              Constants.ADMIN);
@@ -285,6 +288,7 @@ public class AuthorizeUtil {
      */
     public static void authorizeManageWorkflowsGroup(Context context,
                                                      Collection collection) throws AuthorizeException, SQLException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         if (AuthorizeConfiguration.canCollectionAdminManageWorkflows()) {
             authorizeService.authorizeAction(context, collection,
                                              Constants.ADMIN);
@@ -313,6 +317,7 @@ public class AuthorizeUtil {
      */
     public static void authorizeManageAdminGroup(Context context,
                                                  Collection collection) throws AuthorizeException, SQLException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         if (AuthorizeConfiguration.canCollectionAdminManageAdminGroup()) {
             authorizeService.authorizeAction(context, collection,
                                              Constants.ADMIN);
@@ -341,6 +346,7 @@ public class AuthorizeUtil {
      */
     public static void authorizeRemoveAdminGroup(Context context,
                                                  Collection collection) throws AuthorizeException, SQLException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         List<Community> parentCommunities = collection.getCommunities();
         if (AuthorizeConfiguration
             .canCommunityAdminManageCollectionAdminGroup()
@@ -368,6 +374,7 @@ public class AuthorizeUtil {
      */
     public static void authorizeManageAdminGroup(Context context,
                                                  Community community) throws AuthorizeException, SQLException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         if (AuthorizeConfiguration.canCommunityAdminManageAdminGroup()) {
             authorizeService.authorizeAction(context, community,
                                              Constants.ADMIN);
@@ -392,6 +399,7 @@ public class AuthorizeUtil {
      */
     public static void authorizeRemoveAdminGroup(Context context,
                                                  Community community) throws SQLException, AuthorizeException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         List<Community> parentCommunities = community.getParentCommunities();
         Community parentCommunity = null;
         if (0 < parentCommunities.size()) {
@@ -458,6 +466,7 @@ public class AuthorizeUtil {
     public static void authorizeWithdrawItem(Context context, Item item)
         throws SQLException, AuthorizeException {
         boolean authorized = false;
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         if (AuthorizeConfiguration.canCollectionAdminPerformItemWithdrawn()) {
             authorized = authorizeService.authorizeActionBoolean(context, item
                 .getOwningCollection(), Constants.ADMIN);
@@ -492,6 +501,7 @@ public class AuthorizeUtil {
      */
     public static void authorizeReinstateItem(Context context, Item item)
         throws SQLException, AuthorizeException {
+        AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         List<Collection> colls = item.getCollections();
 
         for (Collection coll : colls) {

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

@@ -0,0 +1,58 @@
+/**
+ * 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 net.sf.ehcache.Cache;
+import net.sf.ehcache.CacheManager;
+import org.dspace.core.Context;
+import org.dspace.servicemanager.DSpaceKernelImpl;
+import org.dspace.servicemanager.DSpaceKernelInit;
+import org.dspace.services.CachingService;
+
+/**
+ * List all EhCache CacheManager and Cache instances.
+ *
+ * <p>This is a debugging tool, not used in the daily operation of DSpace.
+ * Just run it from the installed instance using
+ * {@code bin/dspace dsrun org.dspace.app.util.CacheSnooper}
+ * to check that the cache configuration is what you expect it to be,
+ * given your configuration.
+ *
+ * <p>This was created to prove a specific cache configuration patch,
+ * but I leave it here in the hope that it may be useful to others.
+ *
+ * @author Mark H. Wood <mwood@iupui.edu>
+ */
+public class CacheSnooper {
+    private CacheSnooper() { }
+
+    public static void main(String[] argv) {
+        // Ensure that the DSpace kernel is started.
+        DSpaceKernelImpl kernel = DSpaceKernelInit.getKernel(null);
+
+        // Ensure that the services cache manager is started.
+        CachingService serviceCaches = kernel.getServiceManager()
+                .getServiceByName(null, CachingService.class);
+
+        // Ensure that the database layer is started.
+        Context ctx = new Context();
+
+        // List those caches!
+        for (CacheManager manager : CacheManager.ALL_CACHE_MANAGERS) {
+            System.out.format("CacheManager:  %s%n", manager);
+            for (String cacheName : manager.getCacheNames()) {
+                Cache cache = manager.getCache(cacheName);
+                System.out.format("       Cache:  '%s'; maxHeap:  %d; maxDisk:  %d%n",
+                        cacheName,
+                        cache.getCacheConfiguration().getMaxEntriesLocalHeap(),
+                        cache.getCacheConfiguration().getMaxEntriesLocalDisk());
+            }
+        }
+    }
+}

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.dspace.content.MetadataSchema;
+import org.apache.commons.lang3.StringUtils;
+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
      */
@@ -83,6 +89,11 @@ public class DCInput {
      */
     private boolean repeatable = false;
 
+    /**
+     * should name-variants be used?
+     */
+    private boolean nameVariants = false;
+
     /**
      * 'hint' text to display
      */
@@ -128,6 +139,12 @@ public class DCInput {
      */
     private List<String> typeBind = null;
 
+    private boolean isRelationshipField = false;
+    private boolean isMetadataField = false;
+    private String relationshipType = null;
+    private String searchConfiguration = null;
+    private String filter;
+
     /**
      * The scope of the input sets, this restricts hidden metadata fields from
      * view during workflow processing.
@@ -154,7 +171,7 @@ 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
@@ -171,6 +188,9 @@ public class DCInput {
         String repStr = fieldMap.get("repeatable");
         repeatable = "true".equalsIgnoreCase(repStr)
             || "yes".equalsIgnoreCase(repStr);
+        String nameVariantsString = fieldMap.get("name-variants");
+        nameVariants = (StringUtils.isNotBlank(nameVariantsString)) ?
+                nameVariantsString.equalsIgnoreCase("true") : false;
         label = fieldMap.get("label");
         inputType = fieldMap.get("input-type");
         // these types are list-controlled
@@ -199,7 +219,12 @@ public class DCInput {
                 typeBind.add(type.trim());
             }
         }
-
+        style = fieldMap.get("style");
+        isRelationshipField = fieldMap.containsKey("relationship-type");
+        isMetadataField = fieldMap.containsKey("dc-schema");
+        relationshipType = fieldMap.get("relationship-type");
+        searchConfiguration = fieldMap.get("search-configuration");
+        filter = fieldMap.get("filter");
     }
 
     /**
@@ -252,6 +277,15 @@ public class DCInput {
         return isRepeatable();
     }
 
+    /**
+     * Get the nameVariants flag for this row
+     *
+     * @return the nameVariants flag
+     */
+    public boolean areNameVariantsAllowed() {
+        return nameVariants;
+    }
+
     /**
      * Get the input type for this row
      *
@@ -262,7 +296,7 @@ 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 +305,7 @@ 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 +324,7 @@ 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 +333,7 @@ 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 +342,7 @@ public class DCInput {
     }
 
     /**
-     * Get the language for this form row.
+     * Get the language for this form field.
      *
      * @return the language state
      */
@@ -317,7 +351,7 @@ 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 +360,7 @@ public class DCInput {
     }
 
     /**
-     * Get the label for this form row.
+     * Get the label for this form field.
      *
      * @return the label
      */
@@ -334,6 +368,15 @@ 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
      *
@@ -466,6 +509,18 @@ public class DCInput {
         return Utils.standardize(this.getSchema(), this.getElement(), this.getQualifier(), ".");
     }
 
+    public String getRelationshipType() {
+        return relationshipType;
+    }
+
+    public String getSearchConfiguration() {
+        return searchConfiguration;
+    }
+
+    public String getFilter() {
+        return filter;
+    }
+
     public boolean isQualdropValue() {
         if ("qualdrop_value".equals(getInputType())) {
             return true;
@@ -490,4 +545,22 @@ public class DCInput {
 
         return true;
     }
+
+    /**
+     * Verify whether the current field contains an entity relationship
+     * This also implies a relationship type is defined for this field
+     * The field can contain both an entity relationship and a metadata field simultaneously
+     */
+    public boolean isRelationshipField() {
+        return isRelationshipField;
+    }
+
+    /**
+     * Verify whether the current field contains a metadata field
+     * This also implies a field type is defined for this field
+     * The field can contain both an entity relationship and a metadata field simultaneously
+     */
+    public boolean isMetadataField() {
+        return isMetadataField;
+    }
 }

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,
-                      List<Map<String, String>> fields, Map<String, List<String>> listMap) {
+    public DCInputSet(String formName, List<List<Map<String, String>>> rows, 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);
-            inputs[i] = new DCInput(field, listMap);
-
+            List<Map<String, String>> fields = rows.get(i);
+            inputs[i] = new DCInput[fields.size()];
+            for (int j = 0; j < inputs[i].length; j++) {
+                Map<String, String> field = rows.get(i).get(j);
+                inputs[i][j] = new DCInput(field, listMap);
+            }
         }
     }
 
@@ -71,7 +72,7 @@ public class DCInputSet {
      * @return an array containing the fields
      */
 
-    public DCInput[] getFields() {
+    public DCInput[][] getFields() {
         return inputs;
     }
 
@@ -104,10 +105,12 @@ public class DCInputSet {
      */
     public boolean isFieldPresent(String fieldName) {
         for (int i = 0; i < inputs.length; i++) {
-            DCInput field = inputs[i];
-            String fullName = field.getFieldName();
-            if (fullName.equals(fieldName)) {
-                return true;
+            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;
@@ -127,11 +130,13 @@ public class DCInputSet {
             documentType = "";
         }
         for (int i = 0; i < inputs.length; i++) {
-            DCInput field = inputs[i];
-            String fullName = field.getFieldName();
-            if (fullName.equals(fieldName)) {
-                if (field.isAllowedFor(documentType)) {
-                    return true;
+            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)) {
+                        return true;
+                    }
                 }
             }
         }

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
-     * subsection is formed: <page number="#"> ...fields... </page> Each field
+     * formed thusly: <form name="formname">...row...</form> Each rows
+     * subsection is formed: <row> ...fields... </row> Each field
      * is formed from: dc-element, dc-qualifier, label, hint, input-type name,
      * required text, and repeatable flag.
      */
@@ -311,26 +311,24 @@ public class DCInputsReader {
                 if (formName == null) {
                     throw new SAXException("form element has no name attribute");
                 }
-                List<Map<String, String>> fields = new ArrayList<Map<String, String>>(); // the form contains fields
-                formDefns.put(formName, fields);
+                List<List<Map<String, String>>> rows = new ArrayList<List<Map<String, String>>>(); // the form
+                // 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("field")) {
-                        // process each field definition
-                        Map<String, String> field = new HashMap<String, String>();
-                        processField(formName, npg, field);
-                        fields.add(field);
-                        // we omit the duplicate validation, allowing multiple
-                        // fields definition for
-                        // the same metadata and different visibility/type-bind
+                    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 (fields.size() < 1) {
-                    throw new DCInputsReaderException("Form " + formName + " has no fields");
+                if (rows.size() < 1) {
+                    throw new DCInputsReaderException("Form " + formName + " has no rows");
                 }
             }
         }
@@ -339,6 +337,52 @@ public class DCInputsReader {
         }
     }
 
+    /**
+     * Process parts of a row
+     */
+    private void processRow(String formName, int rowIdx, Node n, List<Map<String, String>> fields)
+        throws SAXException, DCInputsReaderException {
+
+        NodeList pl = n.getChildNodes();
+        int lenpg = pl.getLength();
+        for (int j = 0; j < lenpg; j++) {
+            Node npg = pl.item(j);
+
+            if (npg.getNodeName().equals("field")) {
+                // process each field definition
+                Map<String, String> field = new HashMap<String, String>();
+                processField(formName, npg, field);
+                fields.add(field);
+                String key = field.get(PAIR_TYPE_NAME);
+                if (StringUtils
+                    .isNotBlank(key)) {
+                    String schema = field.get("dc-schema");
+                    String element = field.get("dc-element");
+                    String qualifier = field
+                        .get("dc-qualifier");
+                    String metadataField = schema + "."
+                        + element;
+                    if (StringUtils.isNotBlank(qualifier)) {
+                        metadataField += "." + qualifier;
+                    }
+                }
+                // we omit the duplicate validation, allowing multiple
+                // fields definition for
+                // the same metadata and different visibility/type-bind
+            } else if (StringUtils.equalsIgnoreCase(npg.getNodeName(), "relation-field")) {
+                Map<String, String> relationField = new HashMap<>();
+                processField(formName, npg, relationField);
+                fields.add(relationField);
+            }
+
+        }
+        // sanity check number of fields
+        if (fields.size() < 1) {
+            throw new DCInputsReaderException("Form " + formName + "row " + rowIdx + " has no fields");
+        }
+    }
+
+
     /**
      * Process parts of a field
      * At the end, make sure that input-types 'qualdrop_value' and
@@ -356,19 +400,7 @@ public class DCInputsReader {
                 String value = getValue(nd);
                 field.put(tagName, value);
                 if (tagName.equals("input-type")) {
-                    if (value.equals("dropdown")
-                        || value.equals("qualdrop_value")
-                        || value.equals("list")) {
-                        String pairTypeName = getAttribute(nd, PAIR_TYPE_NAME);
-                        if (pairTypeName == null) {
-                            throw new SAXException("Form " + formName + ", field " +
-                                                       field.get("dc-element") +
-                                                       "." + field.get("dc-qualifier") +
-                                                       " has no name attribute");
-                        } else {
-                            field.put(PAIR_TYPE_NAME, pairTypeName);
-                        }
-                    }
+                    handleInputTypeTagName(formName, field, nd, value);
                 } else if (tagName.equals("vocabulary")) {
                     String closedVocabularyString = getAttribute(nd, "closed");
                     field.put("closedVocabulary", closedVocabularyString);
@@ -384,17 +416,30 @@ public class DCInputsReader {
                             field.put(PAIR_TYPE_NAME, pairTypeName);
                         }
                     }
+                } else if (StringUtils.equalsIgnoreCase(tagName, "linked-metadata-field")) {
+                    for (int j = 0; j < nd.getChildNodes().getLength(); j ++) {
+                        Node nestedNode = nd.getChildNodes().item(j);
+                        String nestedTagName = nestedNode.getNodeName();
+                        String nestedValue = getValue(nestedNode);
+                        field.put(nestedTagName, nestedValue);
+                        if (nestedTagName.equals("input-type")) {
+                            handleInputTypeTagName(formName, field, nestedNode, nestedValue);
+                        }
+                    }
                 }
             }
         }
         String missing = null;
-        if (field.get("dc-element") == null) {
+        String nodeName = n.getNodeName();
+        if (field.get("dc-element") == null &&
+                (nodeName.equals("field") || field.containsKey("linked-metadata-field"))) {
             missing = "dc-element";
         }
         if (field.get("label") == null) {
             missing = "label";
         }
-        if (field.get("input-type") == null) {
+        if (field.get("input-type") == null &&
+                (nodeName.equals("field") || field.containsKey("linked-metadata-field"))) {
             missing = "input-type";
         }
         if (missing != null) {
@@ -402,7 +447,7 @@ public class DCInputsReader {
             throw new SAXException(msg);
         }
         String type = field.get("input-type");
-        if (type.equals("twobox") || type.equals("qualdrop_value")) {
+        if (StringUtils.isNotBlank(type) && (type.equals("twobox") || type.equals("qualdrop_value"))) {
             String rpt = field.get("repeatable");
             if ((rpt == null) ||
                 ((!rpt.equalsIgnoreCase("yes")) &&
@@ -413,6 +458,23 @@ public class DCInputsReader {
         }
     }
 
+    private void handleInputTypeTagName(String formName, Map<String, String> field, Node nd, String value)
+        throws SAXException {
+        if (value.equals("dropdown")
+            || value.equals("qualdrop_value")
+            || value.equals("list")) {
+            String pairTypeName = getAttribute(nd, PAIR_TYPE_NAME);
+            if (pairTypeName == null) {
+                throw new SAXException("Form " + formName + ", field " +
+                                           field.get("dc-element") +
+                                           "." + field.get("dc-qualifier") +
+                                           " has no name attribute");
+            } else {
+                field.put(PAIR_TYPE_NAME, pairTypeName);
+            }
+        }
+    }
+
     /**
      * Check that this is the only field with the name dc-element.dc-qualifier
      * If there is a duplicate, return an error message, else return null;
@@ -424,7 +486,7 @@ 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 +496,7 @@ 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");
                 }
@@ -537,26 +599,29 @@ public class DCInputsReader {
         Iterator<String> ki = formDefns.keySet().iterator();
         while (ki.hasNext()) {
             String idName = ki.next();
-            List<Map<String, String>> fields = formDefns.get(idName);
-            for (int i = 0; i < fields.size(); i++) {
-                Map<String, String> fld = fields.get(i);
-                // verify reference in certain input types
-                String type = fld.get("input-type");
-                if (type.equals("dropdown")
-                    || type.equals("qualdrop_value")
-                    || type.equals("list")) {
-                    String pairsName = fld.get(PAIR_TYPE_NAME);
-                    List<String> v = valuePairs.get(pairsName);
-                    if (v == null) {
-                        String errString = "Cannot find value pairs for " + pairsName;
-                        throw new DCInputsReaderException(errString);
+            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
+                    String type = fld.get("input-type");
+                    if (StringUtils.isNotBlank(type) && (type.equals("dropdown")
+                        || type.equals("qualdrop_value")
+                        || type.equals("list"))) {
+                        String pairsName = fld.get(PAIR_TYPE_NAME);
+                        List<String> v = valuePairs.get(pairsName);
+                        if (v == null) {
+                            String errString = "Cannot find value pairs for " + pairsName;
+                            throw new DCInputsReaderException(errString);
+                        }
                     }
-                }
 
-                // we omit the "required" and "visibility" validation, provided this must be checked in the
-                // processing class
-                // only when it makes sense (if the field isn't visible means that it is not applicable, therefore it
-                // can't be required)
+                    // 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 can't be required)
+                }
             }
         }
     }
@@ -639,4 +704,5 @@ 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.";
 
@@ -889,7 +889,7 @@ public class GoogleMetadata {
             Bitstream bitstream = findLinkableFulltext(item);
             if (bitstream != null) {
                 StringBuilder path = new StringBuilder();
-                path.append(ConfigurationManager.getProperty("dspace.url"));
+                path.append(ConfigurationManager.getProperty("dspace.ui.url"));
 
                 if (item.getHandle() != null) {
                     path.append("/bitstream/");

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 +1,245 @@
+/**
+ * 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 leftwardType = eElement.getElementsByTagName("leftwardType").item(0).getTextContent();
+                    String rightwardType = eElement.getElementsByTagName("rightwardType").item(0).getTextContent();
+                    Node copyToLeftNode = eElement.getElementsByTagName("copyToLeft").item(0);
+                    Boolean copyToLeft;
+                    if (copyToLeftNode == null) {
+                        copyToLeft = false;
+                    } else {
+                        copyToLeft = Boolean.valueOf(copyToLeftNode.getTextContent());
+
+                    }
+                    Node copyToRightNode = eElement.getElementsByTagName("copyToRight").item(0);
+                    Boolean copyToRight;
+                    if (copyToRightNode == null) {
+                        copyToRight = false;
+                    } else {
+                        copyToRight = Boolean.valueOf(copyToRightNode.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, leftwardType, rightwardType,
+                                             leftCardinalityMin, leftCardinalityMax,
+                                             rightCardinalityMin, rightCardinalityMax, copyToLeft, copyToRight);
+
+
+                }
+            }
+        } 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 leftwardType,
+                                          String rightwardType, String leftCardinalityMin, String leftCardinalityMax,
+                                          String rightCardinalityMin, String rightCardinalityMax,
+                                          Boolean copyToLeft, Boolean copyToRight)
+        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
+            .findbyTypesAndTypeName(context, leftEntityType, rightEntityType, leftwardType, rightwardType);
+        if (relationshipType == null) {
+            relationshipTypeService.create(context, leftEntityType, rightEntityType, leftwardType, rightwardType,
+                                           leftCardinalityMinInteger, leftCardinalityMaxInteger,
+                                           rightCardinalityMinInteger, rightCardinalityMaxInteger,
+                                           copyToLeft, copyToRight);
+        } else {
+            relationshipType.setCopyToLeft(copyToLeft);
+            relationshipType.setCopyToRight(copyToRight);
+            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 {
-    private static final Logger log = Logger.getLogger(OpenSearchServiceImpl.class);
+public class OpenSearchServiceImpl implements OpenSearchService {
+    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
-    protected String uiUrl = null;
-    // base search service URL
-    protected String svcUrl = null;
+    @Autowired(required = true)
+    protected ConfigurationService configurationService;
 
     @Autowired(required = true)
     protected HandleService handleService;
@@ -75,25 +70,35 @@ public class OpenSearchServiceImpl implements OpenSearchService, InitializingBea
     }
 
     @Override
-    public void afterPropertiesSet() throws Exception {
-        ConfigurationService config = DSpaceServicesFactory.getInstance().getConfigurationService();
-        enabled = config.getBooleanProperty("websvc.opensearch.enable");
-        svcUrl = config.getProperty("dspace.url") + "/" +
-            config.getProperty("websvc.opensearch.svccontext");
-        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");
+    public List<String> getFormats() {
+        List<String> formats = new ArrayList<>();
+        // read formats only if enabled
+        if (isEnabled()) {
+            String[] fmts = configurationService.getArrayProperty("websvc.opensearch.formats");
             formats = Arrays.asList(fmts);
         }
+        return formats;
     }
 
     @Override
-    public List<String> getFormats() {
-        return formats;
+    public boolean isEnabled() {
+        return configurationService.getBooleanProperty("websvc.opensearch.enable");
+    }
+
+    /**
+     * Get base search service URL (websvc.opensearch.svccontext)
+     */
+    protected String getBaseSearchServiceURL() {
+        return configurationService.getProperty("dspace.server.url") + "/" +
+            configurationService.getProperty("websvc.opensearch.svccontext");
+    }
+
+    /**
+     * Get base search UI URL (websvc.opensearch.uicontext)
+     */
+    protected String getBaseSearchUIURL() {
+        return configurationService.getProperty("dspace.server.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,
-                                         DSpaceObject scope, List<DSpaceObject> results, Map<String, String> labels) {
+                                         int pageSize, IndexableObject scope,
+                                         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.lang.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.commons.lang3.ArrayUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.Logger;
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
 import org.dspace.content.Collection;
@@ -50,8 +50,11 @@ import org.dspace.content.service.CollectionService;
 import org.dspace.content.service.CommunityService;
 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.discovery.indexobject.IndexableCollection;
+import org.dspace.discovery.indexobject.IndexableCommunity;
+import org.dspace.discovery.indexobject.IndexableItem;
 import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.services.ConfigurationService;
 import org.dspace.services.factory.DSpaceServicesFactory;
@@ -69,7 +72,7 @@ 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 +182,12 @@ 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,
-                         List<? extends DSpaceObject> items, Map<String, String> labels) {
+    public void populate(HttpServletRequest request, Context context, IndexableObject dso,
+                         List<IndexableObject> items, Map<String, String> labels) {
         String logoURL = null;
         String objectURL = null;
         String defaultTitle = null;
@@ -199,8 +202,8 @@ public class SyndicationFeed {
             logoURL = ConfigurationManager.getProperty("webui.feed.logo.url");
         } else {
             Bitstream logo = null;
-            if (dso.getType() == Constants.COLLECTION) {
-                Collection col = (Collection) dso;
+            if (dso instanceof IndexableCollection) {
+                Collection col = ((IndexableCollection) dso).getIndexedObject();
                 defaultTitle = col.getName();
                 feed.setDescription(collectionService.getMetadata(col, "short_description"));
                 logo = col.getLogo();
@@ -208,8 +211,9 @@ public class SyndicationFeed {
                 if (cols != null && cols.length() > 1 && cols.contains(col.getHandle())) {
                     podcastFeed = true;
                 }
-            } else if (dso.getType() == Constants.COMMUNITY) {
-                Community comm = (Community) dso;
+                objectURL = resolveURL(request, col);
+            } else if (dso instanceof IndexableCommunity) {
+                Community comm = ((IndexableCommunity) dso).getIndexedObject();
                 defaultTitle = comm.getName();
                 feed.setDescription(communityService.getMetadata(comm, "short_description"));
                 logo = comm.getLogo();
@@ -217,8 +221,9 @@ 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 +252,11 @@ public class SyndicationFeed {
         // add entries for items
         if (items != null) {
             List<SyndEntry> entries = new ArrayList<SyndEntry>();
-            for (DSpaceObject itemDSO : items) {
-                if (itemDSO.getType() != Constants.ITEM) {
+            for (IndexableObject idxObj : items) {
+                if (!(idxObj instanceof IndexableItem)) {
                     continue;
                 }
-                Item item = (Item) itemDSO;
+                Item item = ((IndexableItem) idxObj).getIndexedObject();
                 boolean hasDate = false;
                 SyndEntry entry = new SyndEntryImpl();
                 entries.add(entry);
@@ -366,7 +371,7 @@ 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 {
@@ -526,11 +531,9 @@ public class SyndicationFeed {
         if (dso == null) {
             if (baseURL == null) {
                 if (request == null) {
-                    baseURL = ConfigurationManager.getProperty("dspace.url");
+                    baseURL = ConfigurationManager.getProperty("dspace.ui.url");
                 } else {
-                    baseURL = (request.isSecure()) ? "https://" : "http://";
-                    baseURL += ConfigurationManager.getProperty("dspace.hostname");
-                    baseURL += ":" + request.getServerPort();
+                    baseURL = ConfigurationManager.getProperty("dspace.ui.url");
                     baseURL += request.getContextPath();
                 }
             }

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.lang.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.commons.collections4.ListUtils;
+import org.apache.commons.lang3.StringUtils;
+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
@@ -360,9 +360,13 @@ public class Util {
             InputStream cis = null;
             try {
                 cis = Util.class.getResourceAsStream("/META-INF/maven/org.dspace/dspace-api/pom.properties");
+                if (cis == null) {
+                    // pom.properties will not exist when running tests
+                    return "unknown";
+                }
                 constants.load(cis);
             } catch (Exception e) {
-                log.error(e.getMessage(), e);
+                log.error("Could not open dspace-api's pom.properties", e);
             } finally {
                 if (cis != null) {
                     try {
@@ -418,11 +422,12 @@ public class Util {
 
         List<DCInputSet> inputSets = inputsReader.getInputsByCollectionHandle(col_handle);
 
+        // Replace the values of Metadatum[] with the correct ones in case
+        // of
+        // controlled vocabularies
+        String currentField = Utils.standardize(schema, element, qualifier, ".");
+
         for (DCInputSet inputSet : inputSets) {
-            // Replace the values of Metadatum[] with the correct ones in case
-            // of
-            // controlled vocabularies
-            String currentField = Utils.standardize(schema, element, qualifier, ".");
 
             if (inputSet != null) {
 
@@ -430,19 +435,20 @@ public class Util {
 
                 for (int p = 0; p < fieldsNums; p++) {
 
-                    DCInput[] inputs = inputSet.getFields();
+                    DCInput[][] inputs = inputSet.getFields();
 
                     if (inputs != null) {
 
                         for (int i = 0; i < inputs.length; i++) {
-                            String inputField = Utils.standardize(inputs[i].getSchema(), inputs[i].getElement(),
-                                                                  inputs[i].getQualifier(), ".");
-                            if (currentField.equals(inputField)) {
-
-                                myInputs = inputs[i];
-                                myInputsFound = true;
-                                break;
-
+                            for (int j = 0; j < inputs[i].length; j++) {
+                                String inputField = Utils
+                                    .standardize(inputs[i][j].getSchema(), inputs[i][j].getElement(),
+                                                 inputs[i][j].getQualifier(), ".");
+                                if (currentField.equals(inputField)) {
+                                    myInputs = inputs[i][j];
+                                    myInputsFound = true;
+                                    break;
+                                }
                             }
                         }
                     }
@@ -471,6 +477,26 @@ 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();
@@ -480,13 +506,17 @@ public class Util {
         Set<String> fromFieldName = new HashSet<>();
         Set<String> toFieldName = new HashSet<>();
         for (DCInputSet ff : from) {
-            for (DCInput fdc : ff.getFields()) {
-                fromFieldName.add(fdc.getFieldName());
+            for (DCInput[] fdcrow : ff.getFields()) {
+                for (DCInput fdc : fdcrow) {
+                    fromFieldName.add(fdc.getFieldName());
+                }
             }
         }
         for (DCInputSet tt : to) {
-            for (DCInput tdc : tt.getFields()) {
-                toFieldName.add(tdc.getFieldName());
+            for (DCInput[] tdcrow : tt.getFields()) {
+                for (DCInput tdc : tdcrow) {
+                    toFieldName.add(tdc.getFieldName());
+                }
             }
         }
 

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

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

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

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

dspace-api/src/main/java/org/dspace/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.log4j.Logger;
-import org.dspace.core.ConfigurationManager;
+import org.apache.logging.log4j.Logger;
 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();
-        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();
-                }
-            }
-        }
+        String addr = clientInfoService.getClientIp(request);
 
         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.lang.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authenticate.factory.AuthenticateServiceFactory;
 import org.dspace.authenticate.service.AuthenticationService;
 import org.dspace.authorize.AuthorizeException;
@@ -61,7 +61,7 @@ public class LDAPAuthentication
     /**
      * log4j category
      */
-    private static Logger log = Logger.getLogger(LDAPAuthentication.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(LDAPAuthentication.class);
 
     protected AuthenticationService authenticationService = AuthenticateServiceFactory.getInstance()
                                                                                       .getAuthenticationService();
@@ -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.lang.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authenticate.factory.AuthenticateServiceFactory;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.MetadataField;
@@ -70,7 +70,7 @@ public class ShibAuthentication implements AuthenticationMethod {
     /**
      * log4j category
      */
-    private static Logger log = Logger.getLogger(ShibAuthentication.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ShibAuthentication.class);
 
     /**
      * Additional metadata mappings
@@ -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.lang.ArrayUtils;
-import org.apache.log4j.Logger;
+import org.apache.commons.lang3.ArrayUtils;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authenticate.factory.AuthenticateServiceFactory;
 import org.dspace.authenticate.service.AuthenticationService;
 import org.dspace.authorize.AuthorizeException;
@@ -105,7 +105,7 @@ public class X509Authentication implements AuthenticationMethod {
     /**
      * log4j category
      */
-    private static Logger log = Logger.getLogger(X509Authentication.class);
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(X509Authentication.class);
 
     /**
      * public key of CA to check client certs against.
@@ -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

@@ -46,16 +46,10 @@ public class AuthorityServiceImpl implements AuthorityService {
         }
 
         for (AuthorityIndexerInterface indexerInterface : indexers) {
-
-            indexerInterface.init(context, item);
-            while (indexerInterface.hasMore()) {
-                AuthorityValue authorityValue = indexerInterface.nextValue();
-                if (authorityValue != null) {
-                    indexingService.indexContent(authorityValue, true);
-                }
+            List<AuthorityValue> authorityValues = indexerInterface.getAuthorityValues(context , item);
+            for (AuthorityValue authorityValue : authorityValues) {
+                indexingService.indexContent(authorityValue);
             }
-            //Close up
-            indexerInterface.close();
         }
         //Commit to our server
         indexingService.commit();

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

@@ -12,10 +12,11 @@ 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.SolrClient;
 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 +31,7 @@ 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() {
 
@@ -39,28 +40,31 @@ public class AuthoritySolrServiceImpl implements AuthorityIndexingService, Autho
     /**
      * Non-Static CommonsHttpSolrServer for processing indexing events.
      */
-    protected HttpSolrServer solr = null;
+    protected SolrClient solr = null;
 
-    protected HttpSolrServer getSolr() throws MalformedURLException, SolrServerException {
+    protected SolrClient 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.setBaseURL(solrService);
+            HttpSolrClient solrServer = new HttpSolrClient.Builder(solrService).build();
+            solrServer.setBaseURL(solrService);
 
             SolrQuery solrQuery = new SolrQuery().setQuery("*:*");
 
-            solr.query(solrQuery);
+            solrServer.query(solrQuery);
+
+            solr = solrServer;
         }
 
         return solr;
     }
 
     @Override
-    public void indexContent(AuthorityValue value, boolean force) {
+    public void indexContent(AuthorityValue value) {
         SolrInputDocument doc = value.getSolrInputDocument();
 
         try {
@@ -129,7 +133,8 @@ 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

@@ -8,14 +8,15 @@
 package org.dspace.authority;
 
 import java.sql.SQLException;
+import java.text.DateFormat;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.Logger;
 import org.apache.solr.common.SolrDocument;
 import org.apache.solr.common.SolrInputDocument;
 import org.dspace.authorize.AuthorizeException;
@@ -23,6 +24,7 @@ import org.dspace.content.Item;
 import org.dspace.content.MetadataValue;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.core.Context;
+import org.dspace.util.SolrUtils;
 import org.joda.time.DateTime;
 import org.joda.time.format.DateTimeFormatter;
 import org.joda.time.format.ISODateTimeFormat;
@@ -34,8 +36,6 @@ import org.joda.time.format.ISODateTimeFormat;
  * @author Mark Diggory (markd at atmire dot com)
  */
 public class AuthorityValue {
-
-
     /**
      * The id of the record in solr
      */
@@ -150,12 +150,13 @@ public class AuthorityValue {
     public SolrInputDocument getSolrInputDocument() {
 
         SolrInputDocument doc = new SolrInputDocument();
+        DateFormat solrDateFormatter = SolrUtils.getDateFormatter();
         doc.addField("id", getId());
         doc.addField("field", getField());
         doc.addField("value", getValue());
         doc.addField("deleted", isDeleted());
-        doc.addField("creation_date", getCreationDate());
-        doc.addField("last_modified_date", getLastModified());
+        doc.addField("creation_date", solrDateFormatter.format(getCreationDate()));
+        doc.addField("last_modified_date", solrDateFormatter.format(getLastModified()));
         doc.addField("authority_type", getAuthorityType());
         return doc;
     }
@@ -196,12 +197,12 @@ public class AuthorityValue {
      * @return map
      */
     public Map<String, String> choiceSelectMap() {
-        return new HashMap<String, String>();
+        return new HashMap<>();
     }
 
 
     public List<DateTimeFormatter> getDateFormatters() {
-        List<DateTimeFormatter> list = new ArrayList<DateTimeFormatter>();
+        List<DateTimeFormatter> list = new ArrayList<>();
         list.add(ISODateTimeFormat.dateTime());
         list.add(ISODateTimeFormat.dateTimeNoMillis());
         return list;
@@ -234,7 +235,7 @@ 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.log4j.Logger;
+import org.apache.commons.lang3.StringUtils;
+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

@@ -11,9 +11,9 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 
-import org.apache.commons.lang.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;
 
@@ -140,8 +140,8 @@ public class PersonAuthorityValue extends AuthorityValue {
     @Override
     public void setValues(SolrDocument document) {
         super.setValues(document);
-        this.firstName = ObjectUtils.toString(document.getFieldValue("first_name"));
-        this.lastName = ObjectUtils.toString(document.getFieldValue("last_name"));
+        this.firstName = Objects.toString(document.getFieldValue("first_name"), "");
+        this.lastName = Objects.toString(document.getFieldValue("last_name"), "");
         nameVariants = new ArrayList<String>();
         Collection<Object> document_name_variant = document.getFieldValues("name_variant");
         if (document_name_variant != null) {

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/factory/AuthorityServiceFactory.java

@@ -35,6 +35,7 @@ public abstract class AuthorityServiceFactory {
 
     public abstract AuthorityService getAuthorityService();
 
+
     public abstract List<AuthorityIndexerInterface> getAuthorityIndexers();
 
     public static AuthorityServiceFactory getInstance() {

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);
-            while (indexerInterface.hasMore()) {
-                AuthorityValue authorityValue = indexerInterface.nextValue();
-                if (authorityValue != null) {
+            Iterator<Item> allItems = itemService.findAll(context);
+            Map<String, AuthorityValue> authorityCache = new HashMap<>();
+            while (allItems.hasNext()) {
+                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 void init(Context context, boolean useCache);
-
-    public void init(Context context);
-
-    public AuthorityValue nextValue();
-
-    public boolean hasMore() throws SQLException, AuthorizeException;
-
-    public void close();
+    public List<AuthorityValue> getAuthorityValues(Context context, Item item)
+            throws SQLException, AuthorizeException;
+    public List<AuthorityValue> getAuthorityValues(Context context, Item item, Map<String, AuthorityValue> cache)
+            throws SQLException, AuthorizeException;
 
     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.lang.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.lang3.StringUtils;
+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.
- * This can be one item or all items too depending on the init() method.
+ * The DSpaceAuthorityIndexer will return a list of all authority values for a
+ * 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
- * for each metadata field defined in dspace.cfg with 'authority.author.indexer.field'
- * for each item in the list.
+ * You have to call getAuthorityValues for every Item you want to index. But you
+ * can supply an optional cache, to save the mapping from the metadata value to
+ * 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) {
-        ArrayList<Item> itemList = new ArrayList<>();
-        itemList.add(item);
-        this.itemIterator = itemList.iterator();
-        currentItem = this.itemIterator.next();
-        initialize(context);
+    public List<AuthorityValue> getAuthorityValues(Context context, Item item)
+            throws SQLException, AuthorizeException {
+        return getAuthorityValues(context, item, null);
     }
 
-    @Override
-    public void init(Context context) {
-        init(context, false);
-    }
-
-    @Override
-    public void init(Context context, boolean useCache) {
-        try {
-            this.itemIterator = itemService.findAll(context);
-            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;
+    public List<AuthorityValue> getAuthorityValues(Context context, Item item, Map<String, AuthorityValue> cache)
+            throws SQLException, AuthorizeException {
+        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) {
+                    value = getAuthorityValue(context, metadataField, content,authorityKey);
+                }
+                if (value != null) {
+                    if (requiresItemUpdate) {
+                        value.updateItem(context, item, metadataValue);
+                        try {
+                            itemService.update(context, item);
+                        } catch (Exception e) {
+                            log.error("Error creating a metadatavalue's authority", e);
+                        }
+                    }
+                    if (cache != null) {
+                        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());
                 }
-                return hasMore();
             }
         }
+        return values;
     }
-
     /**
-     * This method looks at the authority of a metadata.
+     * 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 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
+     * @param metadataContent Content of the current metadata value.
+     * @param metadataAuthorityKey Existing authority of the metadata value.
      */
-    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;
+    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;
             }
         }
-        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) {
-            cache.put(content, nextValue);
-        }
-    }
-
-    @Override
-    public void close() {
-        itemIterator = null;
-        cache.clear();
+        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/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;
-    }
-}