[maven-release-plugin] prepare release dspace-6.4

Minor Docker fixes for 6.x. Ensure correct permissions and ensure wget installed

.dockerignore

@@ -0,0 +1,10 @@
+.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/README.md
+dspace/src/main/docker-compose/

.github/workflows/build.yml

@@ -0,0 +1,63 @@
+# DSpace 6.x Continuous Integration/Build via GitHub Actions
+# Concepts borrowed from
+# https://docs.github.com/en/free-pro-team@latest/actions/guides/building-and-testing-java-with-maven
+name: Build
+
+# Run this Build for all pushes / PRs to current branch
+on: [push, pull_request]
+
+jobs:
+  tests:
+    runs-on: ubuntu-18.04
+    env:
+      # Give Maven 1GB of memory to work with
+      # Suppress all Maven "downloading" messages in Travis logs (see https://stackoverflow.com/a/35653426)
+      # This also slightly speeds builds, as there is less logging
+      MAVEN_OPTS: "-Xmx1024M -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=warn"
+    # These are the actual CI steps to perform per job
+    steps:
+      # https://github.com/actions/checkout
+      - name: Checkout codebase
+        uses: actions/checkout@v1
+
+      # https://github.com/actions/setup-java
+      - name: Install JDK 8
+        uses: actions/setup-java@v1
+        with:
+          java-version: 8
+
+      # GitHub CI already has Node.js installed, but this gives us the correct
+      # version. GitHub CI also already has grunt installed so we don't need to
+      # install any other pre-requisites for Mirage 2.
+      - name: Install Node.js v14 (for Mirage 2)
+        uses: actions/setup-node@v3
+        with:
+          node-version: 14
+
+      # https://github.com/actions/cache
+      - name: Cache Maven dependencies
+        uses: actions/cache@v2
+        with:
+          # Cache entire ~/.m2/repository
+          path: ~/.m2/repository
+          # Cache key is hash of all pom.xml files. Therefore any changes to POMs will invalidate cache
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: ${{ runner.os }}-maven-
+
+      # [Build & 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 flaky tests, and keep track of/report on number of retries
+      - name: Run Maven Build & Test
+        run: mvn clean install license:check -Dmaven.test.skip=false -DskipITs=false -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2
+
+      # [Assemble DSpace] Ensure assembly process works (from [src]/dspace/), including Mirage 2
+      #   -Dmirage2.on=true => Build Mirage2
+      #   -Dmirage2.deps.included=false => Don't include Mirage2 build dependencies (we installed them above)
+      #   -P !assembly => SKIP the actual building of [src]/dspace/dspace-installer (as it can be memory intensive)
+      - name: Assemble DSpace & Build Mirage 2
+        run: cd dspace && mvn package -Dmirage2.on=true -Dmirage2.deps.included=false -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2

.gitignore

@@ -9,7 +9,6 @@ tags
 /bin/
 .project
 .classpath
-.checkstyle
 
 ## Ignore project files created by IntelliJ IDEA
 *.iml
@@ -26,6 +25,7 @@ dist/
 nbdist/
 nbactions.xml
 nb-configuration.xml
+META-INF/
 
 ## Ignore all *.properties file in root folder, EXCEPT build.properties (the default)
 ## KEPT FOR BACKWARDS COMPATIBILITY WITH 5.x (build.properties is now replaced with local.cfg)
@@ -39,6 +39,3 @@ nb-configuration.xml
 
 ##Mac noise
 .DS_Store
-
-##Ignore JRebel project configuration
-rebel.xml

.travis.yml

@@ -1,44 +0,0 @@
-language: java
-sudo: false
-
-env: 
-  # Give Maven 1GB of memory to work with
-  - MAVEN_OPTS=-Xmx1024M
-
-jdk:
-  # DS-3384 Oracle JDK 8 has DocLint enabled by default.
-  # Let's use this to catch any newly introduced DocLint issues.
-  - oraclejdk8
-
-## 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
-## https://github.com/travis-ci/travis-ci/issues/3259#issuecomment-130860338
-#addons:
-#  apt:
-#    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
-
-# 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
-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"

Dockerfile.cli.jdk8

@@ -0,0 +1,59 @@
+# This image will be published as dspace/dspace-cli
+# See https://dspace-labs.github.io/DSpace-Docker-Images/ for usage details
+#
+# This version is JDK8 compatible
+# - openjdk:8-jdk
+# - ANT 1.10.7
+# - maven:3-jdk-8
+# - note:
+# - default tag for branch: dspace/dspace-cli: dspace/dspace-cli:dspace-6_x
+
+# Step 1 - Run Maven Build
+FROM dspace/dspace-dependencies:dspace-6_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 -P'!dspace-solr,!dspace-jspui,!dspace-xmlui,!dspace-rest,!dspace-xmlui-mirage2,!dspace-rdf,!dspace-sword,!dspace-swordv2' && \
+  mv /app/dspace/target/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM openjdk:8-jdk as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.10.7
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+# Need wget to install ant
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends wget \
+    && apt-get purge -y --auto-remove \
+    && rm -rf /var/lib/apt/lists/*
+# Download and install 'ant'
+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 necessary 'ant' deploy scripts
+RUN ant init_installation update_configs update_code
+
+# Step 3 - Run jdk
+# Create a new jdk image that does not retain the the build directory contents
+FROM openjdk:8-jdk
+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 
+
+# Step 1 - Run Maven Build
+FROM maven:3-jdk-8 as build
+ARG TARGET_DIR=dspace-installer
+WORKDIR /app
+
+# The Mirage2 build cannot run as root.  Setting the user to dspace.
+RUN useradd dspace \
+    && mkdir /home/dspace \
+    && chown -Rv dspace: /home/dspace \
+    && 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
+
+# Trigger the installation of all maven dependencies including the Mirage2 dependencies
+# Clean up the built artifacts in the same step to keep the docker image small
+RUN mvn package -Dmirage2.on=true && mvn clean
+
+# Clear the contents of the /app directory so no artifacts are left when dspace:dspace is built
+USER root
+RUN rm -rf /app/*

Dockerfile.jdk8

@@ -0,0 +1,69 @@
+# This image will be published as dspace/dspace
+# See https://dspace-labs.github.io/DSpace-Docker-Images/ for usage details
+# 
+# This version is JDK8 compatible
+# - tomcat:8-jre8
+# - ANT 1.10.7
+# - maven:3-jdk-8
+# - note: 
+# - default tag for branch: dspace/dspace: dspace/dspace:dspace-6_x-jdk8
+
+# Step 1 - Run Maven Build
+FROM dspace/dspace-dependencies:dspace-6_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 -Dmirage2.on=true && \
+  mv /app/dspace/target/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM tomcat:8-jre8 as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.10.7
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+# Need wget to install ant
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends wget \
+    && apt-get purge -y --auto-remove \
+    && rm -rf /var/lib/apt/lists/*
+# Download and install 'ant'
+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 necessary 'ant' deploy scripts
+RUN ant init_installation update_configs update_code update_webapps update_solr_indexes
+
+# Step 3 - Run tomcat
+# Create a new tomcat image that does not retain the the build directory contents
+FROM tomcat:8-jre8
+ENV DSPACE_INSTALL=/dspace
+COPY --from=ant_build /dspace $DSPACE_INSTALL
+EXPOSE 8080 8009
+
+ENV JAVA_OPTS=-Xmx2000m
+
+RUN ln -s $DSPACE_INSTALL/webapps/solr    /usr/local/tomcat/webapps/solr    && \
+    ln -s $DSPACE_INSTALL/webapps/xmlui   /usr/local/tomcat/webapps/xmlui   && \
+    ln -s $DSPACE_INSTALL/webapps/jspui   /usr/local/tomcat/webapps/jspui   && \
+    ln -s $DSPACE_INSTALL/webapps/rest    /usr/local/tomcat/webapps/rest    && \
+    ln -s $DSPACE_INSTALL/webapps/oai     /usr/local/tomcat/webapps/oai     && \
+    ln -s $DSPACE_INSTALL/webapps/rdf     /usr/local/tomcat/webapps/rdf     && \
+    ln -s $DSPACE_INSTALL/webapps/sword   /usr/local/tomcat/webapps/sword   && \
+    ln -s $DSPACE_INSTALL/webapps/swordv2 /usr/local/tomcat/webapps/swordv2

Dockerfile.jdk8-test

@@ -0,0 +1,75 @@
+# This image will be published as dspace/dspace
+# See https://dspace-labs.github.io/DSpace-Docker-Images/ for usage details
+# 
+# This version is JDK8 compatible
+# - tomcat:8-jre8
+# - ANT 1.10.7
+# - maven:3-jdk-8
+# - note: expose /solr to any host; provide /rest over http
+# - default tag for branch: dspace/dspace: dspace/dspace:dspace-6_x-jdk8
+
+# Step 1 - Run Maven Build
+FROM dspace/dspace-dependencies:dspace-6_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 -Dmirage2.on=true && \
+  mv /app/dspace/target/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM tomcat:8-jre8 as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.10.7
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+# Need wget to install ant
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends wget \
+    && apt-get purge -y --auto-remove \
+    && rm -rf /var/lib/apt/lists/*
+# Download and install 'ant'
+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 necessary 'ant' deploy scripts
+RUN ant init_installation update_configs update_code update_webapps update_solr_indexes
+
+# Step 3 - Run tomcat
+# Create a new tomcat image that does not retain the the build directory contents
+FROM tomcat:8-jre8
+ENV DSPACE_INSTALL=/dspace
+COPY --from=ant_build /dspace $DSPACE_INSTALL
+EXPOSE 8080 8009
+
+ENV JAVA_OPTS=-Xmx2000m
+
+RUN ln -s $DSPACE_INSTALL/webapps/solr    /usr/local/tomcat/webapps/solr    && \
+    ln -s $DSPACE_INSTALL/webapps/xmlui   /usr/local/tomcat/webapps/xmlui   && \
+    ln -s $DSPACE_INSTALL/webapps/jspui   /usr/local/tomcat/webapps/jspui   && \
+    ln -s $DSPACE_INSTALL/webapps/rest    /usr/local/tomcat/webapps/rest    && \
+    ln -s $DSPACE_INSTALL/webapps/oai     /usr/local/tomcat/webapps/oai     && \
+    ln -s $DSPACE_INSTALL/webapps/rdf     /usr/local/tomcat/webapps/rdf     && \
+    ln -s $DSPACE_INSTALL/webapps/sword   /usr/local/tomcat/webapps/sword   && \
+    ln -s $DSPACE_INSTALL/webapps/swordv2 /usr/local/tomcat/webapps/swordv2
+
+COPY dspace/src/main/docker/test/solr_web.xml $DSPACE_INSTALL/webapps/solr/WEB-INF/web.xml
+COPY dspace/src/main/docker/test/rest_web.xml $DSPACE_INSTALL/webapps/rest/WEB-INF/web.xml
+
+RUN sed -i -e "s|\${dspace.dir}|$DSPACE_INSTALL|" $DSPACE_INSTALL/webapps/solr/WEB-INF/web.xml && \
+    sed -i -e "s|\${dspace.dir}|$DSPACE_INSTALL|" $DSPACE_INSTALL/webapps/rest/WEB-INF/web.xml

LICENSE

@@ -1,7 +1,6 @@
-DSpace source code license:
+BSD 3-Clause License
 
-
-Copyright (c) 2002-2016, DuraSpace.  All rights reserved.
+Copyright (c) 2002-2022, LYRASIS.  All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are
@@ -14,13 +13,12 @@ notice, this list of conditions and the following disclaimer.
 notice, this list of conditions and the following disclaimer in the
 documentation and/or other materials provided with the distribution.
 
-- Neither the name DuraSpace nor the name of the DSpace Foundation
-nor the names of its contributors may be used to endorse or promote
-products derived from this software without specific prior written
-permission.
+- Neither the name of the copyright holder nor the names of its
+contributors may be used to endorse or promote products derived from
+this software without specific prior written permission.
 
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
@@ -31,10 +29,3 @@ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
 TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
 USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
 DAMAGE.
-
-
-DSpace uses third-party libraries which may be distributed under
-different licenses to the above. Information about these licenses 
-is detailed in the LICENSES_THIRD_PARTY file at the root of the source 
-tree.  You must agree to the terms of these licenses, in addition to 
-the above DSpace source code license, in order to use this software.

LICENSES_THIRD_PARTY

@@ -15,37 +15,35 @@ PLEASE NOTE: Some dependencies may be listed under multiple licenses if they
 are dual-licensed. This is especially true of anything listed as 
 "GNU General Public Library" below, as DSpace actually does NOT allow for any 
 dependencies that are solely released under GPL terms. For more info see:
-https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
+https://wiki.lyrasis.org/display/DSPACE/Code+Contribution+Guidelines
 ---------------------------------------------------
 
     Apache Software License, Version 2.0:
 
         * Ant-Contrib Tasks (ant-contrib:ant-contrib:1.0b3 - http://ant-contrib.sourceforge.net)
         * Code Generation Library (cglib:cglib:2.2.2 - http://cglib.sourceforge.net/)
+        * reload4j (ch.qos.reload4j:reload4j:1.2.20 - https://reload4j.qos.ch)
         * AWS SDK for Java - Core (com.amazonaws:aws-java-sdk-core:1.10.50 - https://aws.amazon.com/sdkforjava)
         * AWS Java SDK for AWS KMS (com.amazonaws:aws-java-sdk-kms:1.10.50 - https://aws.amazon.com/sdkforjava)
         * AWS Java SDK for Amazon S3 (com.amazonaws:aws-java-sdk-s3:1.10.50 - https://aws.amazon.com/sdkforjava)
         * HPPC Collections (com.carrotsearch:hppc:0.5.2 - http://labs.carrotsearch.com/hppc.html/hppc)
         * metadata-extractor (com.drewnoakes:metadata-extractor:2.6.2 - http://code.google.com/p/metadata-extractor/)
-        * Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.5.4 - http://github.com/FasterXML/jackson)
-        * Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.7.0 - http://github.com/FasterXML/jackson)
-        * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.5.4 - https://github.com/FasterXML/jackson)
-        * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.7.0 - https://github.com/FasterXML/jackson-core)
-        * jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.5.4 - http://github.com/FasterXML/jackson)
-        * jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.7.0 - http://github.com/FasterXML/jackson)
-        * Jackson-JAXRS-base (com.fasterxml.jackson.jaxrs:jackson-jaxrs-base:2.5.4 - http://wiki.fasterxml.com/JacksonHome/jackson-jaxrs-base)
-        * Jackson-JAXRS-JSON (com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.5.4 - http://wiki.fasterxml.com/JacksonHome/jackson-jaxrs-json-provider)
-        * Jackson-module-JAXB-annotations (com.fasterxml.jackson.module:jackson-module-jaxb-annotations:2.5.4 - http://wiki.fasterxml.com/JacksonJAXBAnnotations)
-        * Google APIs Client Library for Java (com.google.api-client:google-api-client:1.21.0 - https://github.com/google/google-api-java-client/google-api-client)
-        * Google Analytics API v3-rev123-1.21.0 (com.google.apis:google-api-services-analytics:v3-rev123-1.21.0 - http://nexus.sonatype.org/oss-repository-hosting.html/google-api-services-analytics)
+        * Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.8.11 - http://github.com/FasterXML/jackson)
+        * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.8.11 - https://github.com/FasterXML/jackson-core)
+        * jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.8.11.1 - http://github.com/FasterXML/jackson)
+        * Jackson-JAXRS-base (com.fasterxml.jackson.jaxrs:jackson-jaxrs-base:2.8.11 - http://github.com/FasterXML/jackson-jaxrs-providers/jackson-jaxrs-base)
+        * Jackson-JAXRS-JSON (com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.8.11 - http://github.com/FasterXML/jackson-jaxrs-providers/jackson-jaxrs-json-provider)
+        * Jackson module: JAXB-annotations (com.fasterxml.jackson.module:jackson-module-jaxb-annotations:2.8.11 - http://github.com/FasterXML/jackson-module-jaxb-annotations)
+        * Google APIs Client Library for Java (com.google.api-client:google-api-client:1.23.0 - https://github.com/google/google-api-java-client/google-api-client)
+        * Google Analytics API v3-rev145-1.23.0 (com.google.apis:google-api-services-analytics:v3-rev145-1.23.0 - http://nexus.sonatype.org/oss-repository-hosting.html/google-api-services-analytics)
         * FindBugs-jsr305 (com.google.code.findbugs:jsr305:3.0.1 - http://findbugs.sourceforge.net/)
         * Gson (com.google.code.gson:gson:2.6.1 - https://github.com/google/gson/gson)
         * Guava: Google Core Libraries for Java (com.google.guava:guava:14.0.1 - http://code.google.com/p/guava-libraries/guava)
         * Guava: Google Core Libraries for Java (com.google.guava:guava:19.0 - https://github.com/google/guava/guava)
         * Guava: Google Core Libraries for Java (JDK5 Backport) (com.google.guava:guava-jdk5:17.0 - http://code.google.com/p/guava-libraries/guava-jdk5)
-        * Google HTTP Client Library for Java (com.google.http-client:google-http-client:1.21.0 - https://github.com/google/google-http-java-client/google-http-client)
-        * Jackson 2 extensions to the Google HTTP Client Library for Java. (com.google.http-client:google-http-client-jackson2:1.21.0 - https://github.com/google/google-http-java-client/google-http-client-jackson2)
-        * Google OAuth Client Library for Java (com.google.oauth-client:google-oauth-client:1.21.0 - https://github.com/google/google-oauth-java-client/google-oauth-client)
+        * Google HTTP Client Library for Java (com.google.http-client:google-http-client:1.23.0 - https://github.com/google/google-http-java-client/google-http-client)
+        * Jackson 2 extensions to the Google HTTP Client Library for Java. (com.google.http-client:google-http-client-jackson2:1.23.0 - https://github.com/google/google-http-java-client/google-http-client-jackson2)
+        * Google OAuth Client Library for Java (com.google.oauth-client:google-oauth-client:1.23.0 - https://github.com/google/google-oauth-java-client/google-oauth-client)
         * ConcurrentLinkedHashMap (com.googlecode.concurrentlinkedhashmap:concurrentlinkedhashmap-lru:1.2 - http://code.google.com/p/concurrentlinkedhashmap)
         * ISO Parser (com.googlecode.mp4parser:isoparser:1.0-RC-1 - http://code.google.com/p/mp4parser/)
         * builder-commons (com.lyncode:builder-commons:1.0.2 - http://nexus.sonatype.org/oss-repository-hosting.html/builder-commons)
@@ -53,14 +51,17 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Jtwig Core Functions (com.lyncode:jtwig-functions:2.0.1 - http://www.lyncode.com/jtwig-functions)
         * Jtwig Spring (com.lyncode:jtwig-spring:2.0.1 - http://www.lyncode.com/jtwig-spring)
         * Test Support (com.lyncode:test-support:1.0.3 - http://nexus.sonatype.org/oss-repository-hosting.html/test-support)
+        * MaxMind DB Reader (com.maxmind.db:maxmind-db:1.2.2 - http://dev.maxmind.com/)
+        * MaxMind GeoIP2 API (com.maxmind.geoip2:geoip2:2.11.0 - http://dev.maxmind.com/geoip/geoip2/web-services)
         * Spatial4J (com.spatial4j:spatial4j:0.4.1 - https://github.com/spatial4j/spatial4j)
+        * fastinfoset (com.sun.xml.fastinfoset:FastInfoset:1.2.15 - http://fi.java.net)
         * Apache Commons BeanUtils (commons-beanutils:commons-beanutils:1.9.2 - http://commons.apache.org/proper/commons-beanutils/)
         * Apache Commons CLI (commons-cli:commons-cli:1.3.1 - http://commons.apache.org/proper/commons-cli/)
         * Apache Commons Codec (commons-codec:commons-codec:1.10 - http://commons.apache.org/proper/commons-codec/)
         * Apache Commons Collections (commons-collections:commons-collections:3.2.2 - http://commons.apache.org/collections/)
         * Apache Commons Configuration (commons-configuration:commons-configuration:1.10 - http://commons.apache.org/configuration/)
         * Commons Digester (commons-digester:commons-digester:1.8.1 - http://commons.apache.org/digester/)
-        * Apache Commons FileUpload (commons-fileupload:commons-fileupload:1.3.1 - http://commons.apache.org/proper/commons-fileupload/)
+        * Apache Commons FileUpload (commons-fileupload:commons-fileupload:1.3.3 - http://commons.apache.org/proper/commons-fileupload/)
         * HttpClient (commons-httpclient:commons-httpclient:3.1 - http://jakarta.apache.org/httpcomponents/httpclient-3.x/)
         * Commons IO (commons-io:commons-io:2.4 - http://commons.apache.org/io/)
         * commons-jexl (commons-jexl:commons-jexl:1.0 - no url defined)
@@ -69,7 +70,6 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Apache Commons Logging (commons-logging:commons-logging:1.2 - http://commons.apache.org/proper/commons-logging/)
         * Apache Commons Validator (commons-validator:commons-validator:1.5.0 - http://commons.apache.org/proper/commons-validator/)
         * Boilerpipe -- Boilerplate Removal and Fulltext Extraction from HTML pages (de.l3s.boilerpipe:boilerpipe:1.1.0 - http://code.google.com/p/boilerpipe/)
-        * The Netty Project (io.netty:netty:3.7.0.Final - http://netty.io/)
         * jakarta-regexp (jakarta-regexp:jakarta-regexp:1.4 - no url defined)
         * javax.inject (javax.inject:javax.inject:1 - http://code.google.com/p/atinject/)
         * Bean Validation API (javax.validation:validation-api:1.1.0.Final - http://beanvalidation.org)
@@ -84,8 +84,8 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Abdera Core (org.apache.abdera:abdera-core:1.1.3 - http://abdera.apache.org/abdera-core)
         * I18N Libraries (org.apache.abdera:abdera-i18n:1.1.3 - http://abdera.apache.org)
         * Abdera Parser (org.apache.abdera:abdera-parser:1.1.3 - http://abdera.apache.org/abdera-parser)
-        * org.apache.tools.ant (org.apache.ant:ant:1.7.0 - http://ant.apache.org/ant/)
-        * ant-launcher (org.apache.ant:ant-launcher:1.7.0 - http://ant.apache.org/ant-launcher/)
+        * Apache Ant Core (org.apache.ant:ant:1.9.1 - http://ant.apache.org/)
+        * Apache Ant Launcher (org.apache.ant:ant-launcher:1.9.1 - http://ant.apache.org/)
         * Avalon Framework API (org.apache.avalon.framework:avalon-framework-api:4.3.1 - http://www.apache.org/excalibur/avalon-framework/avalon-framework-api/)
         * Avalon Framework Implementation (org.apache.avalon.framework:avalon-framework-impl:4.3.1 - http://www.apache.org/excalibur/avalon-framework/avalon-framework-impl/)
         * Cocoon Configuration API (org.apache.cocoon:cocoon-configuration-api:1.0.2 - http://cocoon.apache.org/subprojects/configuration/1.0/configuration-api/1.0/)
@@ -111,11 +111,12 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Cocoon XML Implementation (org.apache.cocoon:cocoon-xml-impl:1.0.0 - http://cocoon.apache.org/2.2/core-modules/xml-impl/1.0/)
         * Cocoon XML Resolver (org.apache.cocoon:cocoon-xml-resolver:1.0.0 - http://cocoon.apache.org/2.2/core-modules/xml-resolver/1.0/)
         * Cocoon XML Utilities (org.apache.cocoon:cocoon-xml-util:1.0.0 - http://cocoon.apache.org/2.2/core-modules/xml-util/1.0/)
+        * Apache Commons Collections (org.apache.commons:commons-collections4:4.1 - http://commons.apache.org/proper/commons-collections/)
         * Apache Commons Compress (org.apache.commons:commons-compress:1.7 - http://commons.apache.org/proper/commons-compress/)
         * Apache Commons CSV (org.apache.commons:commons-csv:1.0 - http://commons.apache.org/proper/commons-csv/)
-        * Apache Commons DBCP (org.apache.commons:commons-dbcp2:2.1.1 - http://commons.apache.org/dbcp/)
+        * Apache Commons DBCP (org.apache.commons:commons-dbcp2:2.8.0 - https://commons.apache.org/dbcp/)
         * Apache Commons Lang (org.apache.commons:commons-lang3:3.3.2 - http://commons.apache.org/proper/commons-lang/)
-        * Apache Commons Pool (org.apache.commons:commons-pool2:2.4.2 - http://commons.apache.org/proper/commons-pool/)
+        * Apache Commons Pool (org.apache.commons:commons-pool2:2.10.0 - https://commons.apache.org/proper/commons-pool/)
         * Excalibur Pool API (org.apache.excalibur.components:excalibur-pool-api:2.2.1 - http://www.apache.org/excalibur/excalibur-components-modules/excalibur-pool-modules/excalibur-pool-api/)
         * Excalibur Sourceresolve (org.apache.excalibur.components:excalibur-sourceresolve:2.2.3 - http://www.apache.org/excalibur/excalibur-sourceresolve/)
         * Excalibur Store (org.apache.excalibur.components:excalibur-store:2.2.1 - http://www.apache.org/excalibur/excalibur-components-modules/excalibur-store/)
@@ -171,14 +172,14 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Lucene Spatial (org.apache.lucene:lucene-spatial:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-spatial)
         * Lucene Suggest (org.apache.lucene:lucene-suggest:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-suggest)
         * Lucene Suggest (org.apache.lucene:lucene-suggest:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-suggest)
-        * Apache FontBox (org.apache.pdfbox:fontbox:2.0.2 - http://pdfbox.apache.org/)
+        * Apache FontBox (org.apache.pdfbox:fontbox:2.0.24 - http://pdfbox.apache.org/)
         * Apache JempBox (org.apache.pdfbox:jempbox:1.8.4 - http://www.apache.org/pdfbox-parent/jempbox/)
-        * Apache PDFBox (org.apache.pdfbox:pdfbox:2.0.2 - http://www.apache.org/pdfbox-parent/pdfbox/)
-        * Apache POI (org.apache.poi:poi:3.13 - http://poi.apache.org/)
-        * Apache POI (org.apache.poi:poi-ooxml:3.13 - http://poi.apache.org/)
+        * Apache PDFBox (org.apache.pdfbox:pdfbox:2.0.24 - https://www.apache.org/pdfbox-parent/pdfbox/)
+        * Apache POI (org.apache.poi:poi:3.17 - http://poi.apache.org/)
+        * Apache POI (org.apache.poi:poi-ooxml:3.17 - http://poi.apache.org/)
         * Apache POI (org.apache.poi:poi-ooxml-schemas:3.10.1 - http://poi.apache.org/)
-        * Apache POI (org.apache.poi:poi-ooxml-schemas:3.13 - http://poi.apache.org/)
-        * Apache POI (org.apache.poi:poi-scratchpad:3.13 - http://poi.apache.org/)
+        * Apache POI (org.apache.poi:poi-ooxml-schemas:3.17 - http://poi.apache.org/)
+        * Apache POI (org.apache.poi:poi-scratchpad:3.17 - http://poi.apache.org/)
         * Apache Solr Search Server (org.apache.solr:solr:4.10.4 - http://lucene.apache.org/solr-parent/solr)
         * Apache Solr Analysis Extras (org.apache.solr:solr-analysis-extras:4.10.4 - http://lucene.apache.org/solr-parent/solr-analysis-extras)
         * Apache Solr Content Extraction Library (org.apache.solr:solr-cell:4.10.4 - http://lucene.apache.org/solr-parent/solr-cell)
@@ -191,6 +192,8 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Axiom API (org.apache.ws.commons.axiom:axiom-api:1.2.14 - http://ws.apache.org/axiom/)
         * Axiom Impl (org.apache.ws.commons.axiom:axiom-impl:1.2.14 - http://ws.apache.org/axiom/)
         * XmlBeans (org.apache.xmlbeans:xmlbeans:2.6.0 - http://xmlbeans.apache.org)
+        * Apache Yetus - Audience Annotations (org.apache.yetus:audience-annotations:0.5.0 - https://yetus.apache.org/audience-annotations)
+        * zookeeper (org.apache.zookeeper:zookeeper:3.4.11 - no url defined)
         * zookeeper (org.apache.zookeeper:zookeeper:3.4.6 - no url defined)
         * Evo Inflector (org.atteo:evo-inflector:1.2.1 - http://atteo.org/static/evo-inflector)
         * TagSoup (org.ccil.cowan.tagsoup:tagsoup:1.2.1 - http://home.ccil.org/~cowan/XML/tagsoup/)
@@ -199,6 +202,8 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Woodstox (org.codehaus.woodstox:woodstox-core-asl:4.1.4 - http://woodstox.codehaus.org)
         * Woodstox (org.codehaus.woodstox:wstx-asl:3.2.0 - http://woodstox.codehaus.org)
         * Woodstox (org.codehaus.woodstox:wstx-asl:3.2.7 - http://woodstox.codehaus.org)
+        * databene ContiPerf (org.databene:contiperf:2.3.4 - http://databene.org/contiperf)
+        * elasticsearch (org.elasticsearch:elasticsearch:1.4.0 - http://nexus.sonatype.org/oss-repository-hosting.html/elasticsearch)
         * flyway-core (org.flywaydb:flyway-core:4.0.3 - https://flywaydb.org/flyway-core)
         * Ogg and Vorbis for Java, Core (org.gagravarr:vorbis-java-core:0.1 - https://github.com/Gagravarr/VorbisJava)
         * Apache Tika plugin for Ogg, Vorbis and FLAC (org.gagravarr:vorbis-java-tika:0.1 - https://github.com/Gagravarr/VorbisJava)
@@ -211,8 +216,8 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Objenesis (org.objenesis:objenesis:2.1 - http://objenesis.org)
         * parboiled-core (org.parboiled:parboiled-core:1.1.6 - http://parboiled.org)
         * parboiled-java (org.parboiled:parboiled-java:1.1.6 - http://parboiled.org)
-        * org.restlet (org.restlet.jee:org.restlet:2.1.1 - no url defined)
-        * org.restlet.ext.servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - no url defined)
+        * Restlet Core - API and Engine (org.restlet.jee:org.restlet:2.1.1 - http://www.restlet.org/org.restlet)
+        * Restlet Extension - Servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - http://www.restlet.org/org.restlet.ext.servlet)
         * rome-modules (org.rometools:rome-modules:1.0 - http://www.rometools.org)
         * Spring AOP (org.springframework:spring-aop:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
         * Spring AOP (org.springframework:spring-aop:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
@@ -249,8 +254,7 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * oai4j (se.kb:oai4j:0.6b1 - http://oai4j-client.sourceforge.net/)
         * StAX API (stax:stax-api:1.0.1 - http://stax.codehaus.org/)
         * standard (taglibs:standard:1.1.2 - no url defined)
-        * Xalan Java Serializer (xalan:serializer:2.7.2 - http://xml.apache.org/xalan-j/)
-        * Xalan Java (xalan:xalan:2.7.2 - http://xml.apache.org/xalan-j/)
+        * xalan (xalan:xalan:2.7.0 - no url defined)
         * Xerces2-j (xerces:xercesImpl:2.11.0 - https://xerces.apache.org/xerces2-j/)
         * xmlParserAPIs (xerces:xmlParserAPIs:2.6.2 - no url defined)
         * XML Commons External Components XML APIs (xml-apis:xml-apis:1.4.01 - http://xml.apache.org/commons/components/external/)
@@ -263,6 +267,7 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * XMP Library for Java (com.adobe.xmp:xmpcore:5.1.2 - http://www.adobe.com/devnet/xmp.html)
         * coverity-escapers (com.coverity.security:coverity-escapers:1.1.1 - http://coverity.com/security)
         * JSONLD Java :: Core (com.github.jsonld-java:jsonld-java:0.5.1 - http://github.com/jsonld-java/jsonld-java/jsonld-java/)
+        * curvesapi (com.github.virtuald:curvesapi:1.04 - https://github.com/virtuald/curvesapi)
         * Protocol Buffer Java API (com.google.protobuf:protobuf-java:2.5.0 - http://code.google.com/p/protobuf)
         * Jena IRI (com.hp.hpl.jena:iri:0.8 - http://jena.sf.net/iri)
         * Jena (com.hp.hpl.jena:jena:2.6.4 - http://www.openjena.org/)
@@ -272,47 +277,53 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Biblio Transformation Engine :: Core (gr.ekt.bte:bte-core:0.9.3.5 - http://github.com/EKT/Biblio-Transformation-Engine/bte-core)
         * Biblio Transformation Engine :: Input/Output (gr.ekt.bte:bte-io:0.9.3.5 - http://github.com/EKT/Biblio-Transformation-Engine/bte-io)
         * jaxen (jaxen:jaxen:1.1.6 - http://jaxen.codehaus.org/)
-        * JLine (jline:jline:0.9.94 - http://jline.sourceforge.net)
         * ANTLR 3 Runtime (org.antlr:antlr-runtime:3.5 - http://www.antlr.org)
         * Morfologik FSA (org.carrot2:morfologik-fsa:1.7.1 - http://morfologik.blogspot.com/morfologik-fsa/)
         * Morfologik Stemming Dictionary for Polish (org.carrot2:morfologik-polish:1.7.1 - http://morfologik.blogspot.com/morfologik-polish/)
         * Morfologik Stemming APIs (org.carrot2:morfologik-stemming:1.7.1 - http://morfologik.blogspot.com/morfologik-stemming/)
         * Stax2 API (org.codehaus.woodstox:stax2-api:3.1.1 - http://woodstox.codehaus.org/StAX2)
-        * DSpace Kernel :: API and Implementation (org.dspace:dspace-api:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-api)
-        * DSpace I18N :: Language Packs (org.dspace:dspace-api-lang:6.0.3 - https://github.com/dspace/dspace-api-lang)
-        * DSpace JSP-UI (org.dspace:dspace-jspui:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-jspui)
-        * DSpace OAI-PMH (org.dspace:dspace-oai:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-oai)
-        * DSpace RDF (org.dspace:dspace-rdf:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-rdf)
-        * DSpace REST :: API and Implementation (org.dspace:dspace-rest:6.0-rc4-SNAPSHOT - http://demo.dspace.org)
-        * DSpace Services Framework :: API and Implementation (org.dspace:dspace-services:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-services)
-        * Apache Solr Webapp (org.dspace:dspace-solr:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-solr)
-        * DSpace SWORD (org.dspace:dspace-sword:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-sword)
-        * DSpace SWORD v2 (org.dspace:dspace-swordv2:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-swordv2)
-        * DSpace XML-UI (Manakin) (org.dspace:dspace-xmlui:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-xmlui)
-        * DSpace XML-UI (Manakin) I18N :: Language Packs (org.dspace:dspace-xmlui-lang:6.0.3 - https://github.com/dspace/dspace-xmlui-lang)
+        * dom4j (org.dom4j:dom4j:2.1.0 - http://dom4j.github.io/)
+        * DSpace Kernel :: API and Implementation (org.dspace:dspace-api:6.4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-api)
+        * DSpace I18N :: Language Packs (org.dspace:dspace-api-lang:6.0.6 - https://github.com/dspace/dspace-api-lang)
+        * DSpace JSP-UI (org.dspace:dspace-jspui:6.4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-jspui)
+        * DSpace OAI-PMH (org.dspace:dspace-oai:6.4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-oai)
+        * DSpace RDF (org.dspace:dspace-rdf:6.4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-rdf)
+        * DSpace REST :: API and Implementation (org.dspace:dspace-rest:6.4-SNAPSHOT - http://demo.dspace.org)
+        * DSpace Services Framework :: API and Implementation (org.dspace:dspace-services:6.4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-services)
+        * Apache Solr Webapp (org.dspace:dspace-solr:6.4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-solr)
+        * DSpace SWORD (org.dspace:dspace-sword:6.4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-sword)
+        * DSpace SWORD v2 (org.dspace:dspace-swordv2:6.4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-swordv2)
+        * DSpace XML-UI (Manakin) (org.dspace:dspace-xmlui:6.4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-xmlui)
+        * DSpace XML-UI (Manakin) I18N :: Language Packs (org.dspace:dspace-xmlui-lang:6.0.7 - https://github.com/dspace/dspace-xmlui-lang)
         * handle (org.dspace:handle:6.2 - no url defined)
         * jargon (org.dspace:jargon:1.4.25 - no url defined)
         * mets (org.dspace:mets:1.5.2 - no url defined)
         * oclc-harvester2 (org.dspace:oclc-harvester2:0.1.12 - no url defined)
-        * XOAI : OAI-PMH Java Toolkit (org.dspace:xoai:3.2.10 - http://nexus.sonatype.org/oss-repository-hosting.html/xoai)
+        * XOAI : OAI-PMH Java Toolkit (org.dspace:xoai:3.3.0 - https://github.com/dspace/xoai)
         * Repackaged Cocoon Servlet Service Implementation (org.dspace.dependencies.cocoon:dspace-cocoon-servlet-service-impl:1.0.3 - http://projects.dspace.org/dspace-pom/dspace-cocoon-servlet-service-impl)
-        * DSpace Kernel :: Additions and Local Customizations (org.dspace.modules:additions:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/modules/additions)
+        * DSpace Kernel :: Additions and Local Customizations (org.dspace.modules:additions:6.4-SNAPSHOT - https://github.com/dspace/DSpace/modules/additions)
         * Hamcrest All (org.hamcrest:hamcrest-all:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-all)
-        * Hamcrest Core (org.hamcrest:hamcrest-all:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-all)
+        * Hamcrest Core (org.hamcrest:hamcrest-core:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-core)
         * JBibTeX (org.jbibtex:jbibtex:1.0.10 - http://www.jbibtex.org)
         * ASM Core (org.ow2.asm:asm:4.1 - http://asm.objectweb.org/asm/)
         * ASM Analysis (org.ow2.asm:asm-analysis:4.1 - http://asm.objectweb.org/asm-analysis/)
         * ASM Commons (org.ow2.asm:asm-commons:4.1 - http://asm.objectweb.org/asm-commons/)
         * ASM Tree (org.ow2.asm:asm-tree:4.1 - http://asm.objectweb.org/asm-tree/)
         * ASM Util (org.ow2.asm:asm-util:4.1 - http://asm.objectweb.org/asm-util/)
+        * PostgreSQL JDBC Driver - JDBC 4.2 (org.postgresql:postgresql:42.2.1 - https://github.com/pgjdbc/pgjdbc)
         * XMLUnit for Java (xmlunit:xmlunit:1.1 - http://xmlunit.sourceforge.net/)
         * XMLUnit for Java (xmlunit:xmlunit:1.3 - http://xmlunit.sourceforge.net/)
 
+    BSD-Style License:
+
+        * JAXB2 Basics - Runtime (org.jvnet.jaxb2_commons:jaxb2-basics-runtime:0.9.5 - https://github.com/highsource/jaxb2-basics/jaxb2-basics-runtime)
+
     Common Development and Distribution License (CDDL):
 
-        * JAXB Reference Implementation (com.sun.xml.bind:jaxb-impl:2.2.5 - http://jaxb.java.net/)
+        * istack common utility code runtime (com.sun.istack:istack-commons-runtime:3.0.7 - http://java.net/istack-commons/istack-commons-runtime/)
         * JHighlight (com.uwyn:jhighlight:1.0 - https://jhighlight.dev.java.net/)
         * JavaBeans(TM) Activation Framework (javax.activation:activation:1.1.1 - http://java.sun.com/javase/technologies/desktop/javabeans/jaf/index.jsp)
+        * JavaBeans Activation Framework API jar (javax.activation:javax.activation-api:1.2.0 - http://java.net/all/javax.activation-api/)
         * javax.annotation API (javax.annotation:javax.annotation-api:1.2 - http://jcp.org/en/jsr/detail?id=250)
         * JavaMail API (compat) (javax.mail:mail:1.4.7 - http://kenai.com/projects/javamail/mail)
         * Java Servlet API (javax.servlet:javax.servlet-api:3.1.0 - http://servlet-spec.java.net)
@@ -320,6 +331,7 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * jstl (javax.servlet:jstl:1.2 - no url defined)
         * servlet-api (javax.servlet:servlet-api:2.5 - no url defined)
         * javax.ws.rs-api (javax.ws.rs:javax.ws.rs-api:2.0.1 - http://jax-rs-spec.java.net)
+        * jaxb-api (javax.xml.bind:jaxb-api:2.3.1 - https://github.com/javaee/jaxb-spec/jaxb-api)
         * Class Model for Hk2 (org.glassfish.hk2:class-model:2.4.0-b31 - https://hk2.java.net/class-model)
         * HK2 config types (org.glassfish.hk2:config-types:2.4.0-b31 - https://hk2.java.net/hk2-configuration/hk2-configuration-persistence/hk2-xml-dom/config-types)
         * HK2 module of HK2 itself (org.glassfish.hk2:hk2:2.4.0-b31 - https://hk2.java.net/hk2)
@@ -335,6 +347,8 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * ASM library repackaged as OSGi bundle (org.glassfish.hk2.external:asm-all-repackaged:2.4.0-b31 - https://hk2.java.net/external/asm-all-repackaged)
         * javax.validation:1.1.0.Final as OSGi bundle (org.glassfish.hk2.external:bean-validator:2.4.0-b31 - https://hk2.java.net/external/bean-validator)
         * javax.inject:1 as OSGi bundle (org.glassfish.hk2.external:javax.inject:2.4.0-b31 - https://hk2.java.net/external/javax.inject)
+        * JAXB Runtime (org.glassfish.jaxb:jaxb-runtime:2.3.1 - http://jaxb.java.net/jaxb-runtime-parent/jaxb-runtime)
+        * TXW2 Runtime (org.glassfish.jaxb:txw2:2.3.1 - http://jaxb.java.net/jaxb-txw-parent/txw2)
         * jersey-repackaged-guava (org.glassfish.jersey.bundles.repackaged:jersey-guava:2.22.1 - https://jersey.java.net/project/project/jersey-guava/)
         * jersey-container-servlet (org.glassfish.jersey.containers:jersey-container-servlet:2.22.1 - https://jersey.java.net/project/jersey-container-servlet/)
         * jersey-container-servlet-core (org.glassfish.jersey.containers:jersey-container-servlet-core:2.22.1 - https://jersey.java.net/project/jersey-container-servlet-core/)
@@ -347,6 +361,9 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * jersey-media-json-jackson (org.glassfish.jersey.media:jersey-media-json-jackson:2.22.1 - https://jersey.java.net/project/jersey-media-json-jackson/)
         * Java Transaction API (org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.1.Final - http://www.jboss.org/jboss-transaction-api_1.1_spec)
         * Type arithmetic library for Java5 (org.jvnet:tiger-types:1.4 - http://java.net/tiger-types/)
+        * Extended StAX API (org.jvnet.staxex:stax-ex:1.8 - http://stax-ex.java.net/)
+        * Restlet Core - API and Engine (org.restlet.jee:org.restlet:2.1.1 - http://www.restlet.org/org.restlet)
+        * Restlet Extension - Servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - http://www.restlet.org/org.restlet.ext.servlet)
 
     Eclipse Public License:
 
@@ -356,6 +373,8 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Jetty Server (org.mortbay.jetty:jetty:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/modules/jetty)
         * Jetty Servlet Tester (org.mortbay.jetty:jetty-servlet-tester:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/jetty-servlet-tester)
         * Jetty Utilities (org.mortbay.jetty:jetty-util:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/jetty-util)
+        * Restlet Core - API and Engine (org.restlet.jee:org.restlet:2.1.1 - http://www.restlet.org/org.restlet)
+        * Restlet Extension - Servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - http://www.restlet.org/org.restlet.ext.servlet)
 
     GNU General Public License, Version 2 with the Classpath Exception:
 
@@ -364,7 +383,6 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
     GNU Lesser General Public License (LGPL):
 
         * 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)
@@ -374,6 +392,8 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Javassist (org.javassist:javassist:3.18.1-GA - http://www.javassist.org/)
         * JBoss Logging 3 (org.jboss.logging:jboss-logging:3.1.0.GA - http://www.jboss.org)
         * org.jdesktop - Swing Worker (org.jdesktop:swing-worker:1.1 - no url defined)
+        * Restlet Core - API and Engine (org.restlet.jee:org.restlet:2.1.1 - http://www.restlet.org/org.restlet)
+        * Restlet Extension - Servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - http://www.restlet.org/org.restlet.ext.servlet)
         * xom (xom:xom:1.1 - http://www.xom.nu)
         * XOM (xom:xom:1.2.5 - http://xom.nu)
 
@@ -389,18 +409,20 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
 
         * Bouncy Castle CMS and S/MIME API (org.bouncycastle:bcmail-jdk15:1.46 - http://www.bouncycastle.org/java.html)
         * Bouncy Castle Provider (org.bouncycastle:bcprov-jdk15:1.46 - http://www.bouncycastle.org/java.html)
+        * ORCID Java API generated via JAXB (org.dspace:orcid-jaxb-api:2.1.0 - https://github.com/DSpace/orcid-jaxb-api)
         * Main (org.jmockit:jmockit:1.21 - http://www.jmockit.org)
         * OpenCloud (org.mcavallo:opencloud:0.3 - http://opencloud.mcavallo.org/)
         * Mockito (org.mockito:mockito-core:1.10.19 - http://www.mockito.org)
         * JCL 1.1.1 implemented over SLF4J (org.slf4j:jcl-over-slf4j:1.7.14 - http://www.slf4j.org)
         * JUL to SLF4J bridge (org.slf4j:jul-to-slf4j:1.7.14 - http://www.slf4j.org)
         * SLF4J API Module (org.slf4j:slf4j-api:1.7.14 - http://www.slf4j.org)
-        * SLF4J LOG4J-12 Binding (org.slf4j:slf4j-log4j12:1.7.14 - http://www.slf4j.org)
+        * SLF4J Reload4j Binding (org.slf4j:slf4j-reload4j:1.7.36 - http://reload4j.qos.ch)
 
     Mozilla Public License:
 
         * juniversalchardet (com.googlecode.juniversalchardet:juniversalchardet:1.0.3 - http://juniversalchardet.googlecode.com/)
         * h2 (com.h2database:h2:1.4.187 - no url defined)
+        * Saxon-HE (net.sf.saxon:Saxon-HE:9.8.0-14 - http://www.saxonica.com/)
         * Javassist (org.javassist:javassist:3.18.1-GA - http://www.javassist.org/)
         * Rhino (rhino:js:1.6R7 - http://www.mozilla.org/rhino/)
 
@@ -415,9 +437,9 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
 
         * JDOM (org.jdom:jdom:1.1.3 - http://www.jdom.org)
 
-    The PostgreSQL License:
+    The JSON License:
 
-        * PostgreSQL JDBC Driver - JDBC 4.2 (org.postgresql:postgresql:9.4.1211 - https://github.com/pgjdbc/pgjdbc)
+        * JSON in Java (org.json:json:20180130 - https://github.com/douglascrockford/JSON-java)
 
     license.txt:
 

NOTICE

@@ -1,11 +1,24 @@
+Licenses of Third-Party Libraries
+=================================
 
-Licensing Notice
+DSpace uses third-party libraries which may be distributed under
+different licenses than specified in our LICENSE file. Information
+about these licenses is detailed in the LICENSES_THIRD_PARTY file at
+the root of the source tree. You must agree to the terms of these
+licenses, in addition to the DSpace source code license, in order to
+use this software.
 
-Fedora Commons joined with the DSpace Foundation and began operating under
+Licensing Notices
+=================
+
+[July 2019] DuraSpace joined with LYRASIS (another 501(c)3 organization) in July 2019.
+LYRASIS holds the copyrights of DuraSpace.
+
+[July 2009] Fedora Commons joined with the DSpace Foundation and began operating under
 the new name DuraSpace in July 2009.  DuraSpace holds the copyrights of
 the DSpace Foundation, Inc.
 
-The DSpace Foundation, Inc. is a 501(c)3 corporation established in July 2007 
+[July 2007] The DSpace Foundation, Inc. is a 501(c)3 corporation established in July 2007
 with a mission to promote and advance the dspace platform enabling management,
 access and preservation of digital works. The Foundation was able to transfer
 the legal copyright from Hewlett-Packard Company (HP) and Massachusetts

README.md

@@ -1,31 +1,17 @@
 
 # DSpace
 
-## NOTE: The rest-tutorial branch has been created to support the [DSpace 7 REST documentation](https://dspace-labs.github.io/DSpace7RestTutorial/walkthrough/intro)
-- This branch provides stable, referencable line numbers in code
+[![Build Status](https://github.com/DSpace/DSpace/workflows/Build/badge.svg?branch=dspace-6_x)](https://github.com/DSpace/DSpace/actions?query=workflow%3ABuild)
 
-[![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.lyrasis.org/display/DSDOC/) |
 [DSpace Releases](https://github.com/DSpace/DSpace/releases) |
-[DSpace Wiki](https://wiki.duraspace.org/display/DSPACE/Home) | 
-[Support](https://wiki.duraspace.org/display/DSPACE/Support)
+[DSpace Wiki](https://wiki.lyrasis.org/display/DSPACE/Home) |
+[Support](https://wiki.lyrasis.org/display/DSPACE/Support)
 
 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.
+1000+ 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.
-     * 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.
-***
-
 ## Downloads
 
 The latest release of DSpace can be downloaded from the [DSpace website](http://www.dspace.org/latest-release/) or from [GitHub](https://github.com/DSpace/DSpace/releases).
@@ -34,29 +20,32 @@ 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.lyrasis.org/display/DSDOC/).
 
 The latest DSpace Installation instructions are available at:
-https://wiki.duraspace.org/display/DSDOC6x/Installing+DSpace
+https://wiki.lyrasis.org/display/DSDOC6x/Installing+DSpace
 
 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 6 in Docker
+See [Running DSpace 6 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,
 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:
-* [How to Contribute to DSpace](https://wiki.duraspace.org/display/DSPACE/How+to+Contribute+to+DSpace): How to contribute in general (via code, documentation, bug reports, expertise, etc)
-* [Code Contribution Guidelines](https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines): How to give back code or contribute features, bug fixes, etc.
-* [DSpace Community Advisory Team (DCAT)](https://wiki.duraspace.org/display/cmtygp/DSpace+Community+Advisory+Team): If you are not a developer, we also have an interest group specifically for repository managers. The DCAT group meets virtually, once a month, and sends open invitations to join their meetings via the [DCAT mailing list](https://groups.google.com/d/forum/DSpaceCommunityAdvisoryTeam).
+* [How to Contribute to DSpace](https://wiki.lyrasis.org/display/DSPACE/How+to+Contribute+to+DSpace): How to contribute in general (via code, documentation, bug reports, expertise, etc)
+* [Code Contribution Guidelines](https://wiki.lyrasis.org/display/DSPACE/Code+Contribution+Guidelines): How to give back code or contribute features, bug fixes, etc.
+* [DSpace Community Advisory Team (DCAT)](https://wiki.lyrasis.org/display/cmtygp/DSpace+Community+Advisory+Team): If you are not a developer, we also have an interest group specifically for repository managers. The DCAT group meets virtually, once a month, and sends open invitations to join their meetings via the [DCAT mailing list](https://groups.google.com/d/forum/DSpaceCommunityAdvisoryTeam).
 
-We also encourage GitHub Pull Requests (PRs) at any time. Please see our [Development with Git](https://wiki.duraspace.org/display/DSPACE/Development+with+Git) guide for more info.
+We also encourage GitHub Pull Requests (PRs) at any time. Please see our [Development with Git](https://wiki.lyrasis.org/display/DSPACE/Development+with+Git) guide for more info.
 
 In addition, a listing of all known contributors to DSpace software can be
-found online at: https://wiki.duraspace.org/display/DSPACE/DSpaceContributors
+found online at: https://wiki.lyrasis.org/display/DSPACE/DSpaceContributors
 
 ## Getting Help
 
@@ -64,12 +53,10 @@ DSpace provides public mailing lists where you can post questions or raise topic
 We welcome everyone to participate in these lists:
 
 * [dspace-community@googlegroups.com](https://groups.google.com/d/forum/dspace-community) : General discussion about DSpace platform, announcements, sharing of best practices
-* [dspace-tech@googlegroups.com](https://groups.google.com/d/forum/dspace-tech) : Technical support mailing list. See also our guide for [How to troubleshoot an error](https://wiki.duraspace.org/display/DSPACE/Troubleshoot+an+error).
+* [dspace-tech@googlegroups.com](https://groups.google.com/d/forum/dspace-tech) : Technical support mailing list. See also our guide for [How to troubleshoot an error](https://wiki.lyrasis.org/display/DSPACE/Troubleshoot+an+error).
 * [dspace-devel@googlegroups.com](https://groups.google.com/d/forum/dspace-devel) : Developers / Development mailing list
 
-Great Q&A is also available under the [DSpace tag on Stackoverflow](http://stackoverflow.com/questions/tagged/dspace)
-
-Additional support options are listed at https://wiki.duraspace.org/display/DSPACE/Support
+Additional support options are listed at https://wiki.lyrasis.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
@@ -77,7 +64,8 @@ install, upgrade, customize or host DSpace, then we recommend getting in touch w
 
 ## Issue Tracker
 
-The DSpace Issue Tracker can be found at: https://jira.duraspace.org/projects/DS/summary
+DSpace uses Github to track issues: 
+https://github.com/DSpace/DSpace/issues
 
 ## License
 

checkstyle-suppressions.xml

@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE suppressions PUBLIC
-        "-//Puppy Crawl//DTD Suppressions 1.2//EN"
-        "http://checkstyle.sourceforge.net/dtds/suppressions_1_2.dtd">
-<suppressions>
-    <!-- Temporarily suppress indentation checks for all Tests -->
-    <!-- TODO: We should have these turned on. But, currently there's a known bug with indentation checks
-         on JMockIt Expectations blocks and similar. See https://github.com/checkstyle/checkstyle/issues/3739 -->
-    <suppress checks="Indentation" files="src[/\\]test[/\\]java"/>
-</suppressions>

checkstyle.xml

@@ -1,144 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE module PUBLIC
-        "-//Puppy Crawl//DTD Check Configuration 1.3//EN"
-        "http://checkstyle.sourceforge.net/dtds/configuration_1_3.dtd">
-<!--
-DSpace CodeStyle Requirements
-
-  1. 4-space indents for Java, and 2-space indents for XML. NO TABS ALLOWED.
-  2. K&R style braces required. Braces required on all blocks.
-  3. Do not use wildcard imports (e.g. import java.util.*). Duplicated or unused imports also not allowed.
-  4. Javadocs should exist for all public classes and methods. (Methods rule is unenforced at this time.) Keep it short and to the point
-  5. Maximum line length is 120 characters (except for long URLs, packages or imports)
-  6. No trailing spaces allowed (except in comments)
-  7. Tokens should be surrounded by whitespace (see http://checkstyle.sourceforge.net/config_whitespace.html#WhitespaceAround)
-  8. Each source file must include our license header (validated separately by license-maven-plugin, see pom.xml)
-
-For more information on CheckStyle configurations below, see: http://checkstyle.sourceforge.net/checks.html
--->
-<module name="Checker">
-    <!-- Configure checker to use UTF-8 encoding -->
-    <property name="charset" value="UTF-8"/>
-    <!-- Configure checker to run on files with these extensions -->
-    <property name="fileExtensions" value="java, properties, cfg, xml"/>
-
-    <!-- Suppression configurations in checkstyle-suppressions.xml in same directory -->
-    <module name="SuppressionFilter">
-        <property name="file" value="${checkstyle.suppressions.file}" default="checkstyle-suppressions.xml"/>
-    </module>
-
-    <!-- No tab characters ('\t') allowed in the source code -->
-    <module name="FileTabCharacter">
-        <property name="eachLine" value="true"/>
-        <property name="fileExtensions" value="java, properties, cfg, css, js, xml"/>
-    </module>
-
-    <!-- No Trailing Whitespace, except on lines that only have an asterisk (e.g. Javadoc comments) -->
-    <module name="RegexpSingleline">
-        <property name="format" value="(?&lt;!\*)\s+$|\*\s\s+$"/>
-        <property name="message" value="Line has trailing whitespace"/>
-        <property name="fileExtensions" value="java, properties, cfg, css, js, xml"/>
-    </module>
-
-    <!-- Allow individual lines of code to be excluded from these rules, if they are annotated
-         with @SuppressWarnings. See also SuppressWarningsHolder below -->
-    <module name="SuppressWarningsFilter" />
-
-    <!-- Check individual Java source files for specific rules -->
-    <module name="TreeWalker">
-        <!-- Maximum line length is 120 characters -->
-        <module name="LineLength">
-            <property name="max" value="120"/>
-            <!-- Only exceptions for packages, imports, URLs, and JavaDoc {@link} tags -->
-            <property name="ignorePattern" value="^package.*|^import.*|http://|https://|@link"/>
-        </module>
-
-        <!-- Highlight any TODO or FIXME comments in info messages -->
-        <module name="TodoComment">
-            <property name="severity" value="info"/>
-            <property name="format" value="(TODO)|(FIXME)"/>
-        </module>
-
-        <!-- Do not report errors on any lines annotated with @SuppressWarnings -->
-        <module name="SuppressWarningsHolder"/>
-
-        <!-- ##### Import statement requirements ##### -->
-        <!-- Star imports (e.g. import java.util.*) are NOT ALLOWED -->
-        <module name="AvoidStarImport"/>
-        <!-- Redundant import statements are NOT ALLOWED -->
-        <module name="RedundantImport"/>
-        <!-- Unused import statements are NOT ALLOWED -->
-        <module name="UnusedImports"/>
-        <!-- Ensure imports appear alphabetically and grouped -->
-        <module name="CustomImportOrder">
-            <property name="sortImportsInGroupAlphabetically" value="true"/>
-            <property name="separateLineBetweenGroups" value="true"/>
-            <property name="customImportOrderRules" value="STATIC###STANDARD_JAVA_PACKAGE###THIRD_PARTY_PACKAGE"/>
-        </module>
-
-        <!-- ##### Javadocs requirements ##### -->
-        <!-- Requirements for Javadocs for classes/interfaces -->
-        <module name="JavadocType">
-            <!-- All public classes/interfaces MUST HAVE Javadocs -->
-            <property name="scope" value="public"/>
-            <!-- Add an exception for anonymous inner classes -->
-            <property name="excludeScope" value="anoninner"/>
-            <!-- Ignore errors related to unknown tags -->
-            <property name="allowUnknownTags" value="true"/>
-            <!-- Allow params tags to be optional -->
-            <property name="allowMissingParamTags" value="false"/>
-        </module>
-        <!-- Requirements for Javadocs for methods -->
-        <module name="JavadocMethod">
-            <!-- All public methods MUST HAVE Javadocs -->
-            <!-- <property name="scope" value="public"/> -->
-            <!-- TODO: Above rule has been disabled because of large amount of missing public method Javadocs -->
-            <property name="scope" value="nothing"/>
-            <!-- Allow RuntimeExceptions to be undeclared -->
-            <property name="allowUndeclaredRTE" value="true"/>
-            <!-- Allow params, throws and return tags to be optional -->
-            <property name="allowMissingParamTags" value="true"/>
-            <property name="allowMissingThrowsTags" value="true"/>
-            <property name="allowMissingReturnTag" value="true"/>
-        </module>
-
-        <!-- ##### Requirements for K&R Style braces ##### -->
-        <!-- Code blocks MUST HAVE braces, even single line statements (if, while, etc) -->
-        <module name="NeedBraces"/>
-        <!-- Left braces should be at the end of current line (default value)-->
-        <module name="LeftCurly"/>
-        <!-- Right braces should be on start of a new line (default value) -->
-        <module name="RightCurly"/>
-
-        <!-- ##### Indentation / Whitespace requirements ##### -->
-        <!-- Require 4-space indentation (default value) -->
-        <module name="Indentation"/>
-        <!-- Whitespace should exist around all major tokens -->
-        <module name="WhitespaceAround">
-            <!-- However, make an exception for empty constructors, methods, types, etc. -->
-            <property name="allowEmptyConstructors" value="true"/>
-            <property name="allowEmptyMethods" value="true"/>
-            <property name="allowEmptyTypes" value="true"/>
-            <property name="allowEmptyLoops" value="true"/>
-        </module>
-        <!-- Validate whitespace around Generics (angle brackets) per typical conventions
-             http://checkstyle.sourceforge.net/config_whitespace.html#GenericWhitespace -->
-        <module name="GenericWhitespace"/>
-
-        <!-- ##### Requirements for "switch" statements ##### -->
-        <!-- "switch" statements MUST have a "default" clause -->
-        <module name="MissingSwitchDefault"/>
-        <!-- "case" clauses in switch statements MUST include break, return, throw or continue -->
-        <module name="FallThrough"/>
-
-        <!-- ##### Other / Miscellaneous requirements ##### -->
-        <!-- Require utility classes do not have a public constructor -->
-        <module name="HideUtilityClassConstructor"/>
-        <!-- Require each variable declaration is its own statement on its own line -->
-        <module name="MultipleVariableDeclarations"/>
-        <!-- Each line of code can only include one statement -->
-        <module name="OneStatementPerLine"/>
-        <!-- Require that "catch" statements are not empty (must at least contain a comment) -->
-        <module name="EmptyCatchBlock"/>
-    </module>
-</module>

docker-compose-cli.yml

@@ -0,0 +1,33 @@
+#
+# 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/
+#
+
+version: "3.7"
+
+services:
+  dspace-cli:
+    image: "dspace/dspace-cli:${DSPACE_VER:-dspace-6_x}"
+    container_name: dspace-cli
+    build:
+      context: .
+      dockerfile: Dockerfile.cli.jdk8
+    #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 +1,53 @@
+#
+# 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/
+#
+
+version: '3.7'
+networks:
+  dspacenet:
+services:
+  dspace:
+    container_name: dspace
+    depends_on:
+    - dspacedb
+    image: "${DOCKER_OWNER:-dspace}/dspace:${DSPACE_VER:-dspace-6_x-jdk8-test}"
+    build:
+      context: .
+      dockerfile: Dockerfile.jdk8-test
+    networks:
+      dspacenet:
+    ports:
+    - published: 8080
+      target: 8080
+    stdin_open: true
+    tty: true
+    volumes:
+    - ./dspace/src/main/docker-compose/local.cfg:/dspace/config/local.cfg
+    - ./dspace/src/main/docker-compose/xmlui.xconf:/dspace/config/xmlui.xconf
+    - assetstore:/dspace/assetstore
+    - solr_authority:/dspace/solr/authority/data
+    - solr_oai:/dspace/solr/oai/data
+    - solr_search:/dspace/solr/search/data
+    - solr_statistics:/dspace/solr/statistics/data
+  dspacedb:
+    container_name: dspacedb
+    environment:
+      PGDATA: /pgdata
+    image: dspace/dspace-postgres-pgcrypto
+    networks:
+      dspacenet:
+    stdin_open: true
+    tty: true
+    volumes:
+    - pgdata:/pgdata
+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>6.4</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -206,8 +205,7 @@
                         <executions>
                             <execution>
                                 <id>setproperty</id>
-                                <phase>generate-test-resources
-                                </phase> <!-- XXX I think this should be 'initialize' - MHW -->
+                                <phase>generate-test-resources</phase> <!-- XXX I think this should be 'initialize' - MHW -->
                                 <goals>
                                     <goal>execute</goal>
                                 </goals>
@@ -268,12 +266,16 @@
                                      <include>**/*.xsl</include>
                                      <include>**/*.xmap</include>
                                  </includes>
+                                 <excludes>
+                                     <exclude>**/node/node_modules/**</exclude>
+                                 </excludes>
                               </validationSet>
                           </validationSets>
                         </configuration>
                     </plugin>
 
 
+
                     <!-- Run Integration Testing! This plugin just kicks off the tests (when enabled). -->
                     <plugin>
                         <artifactId>maven-failsafe-plugin</artifactId>
@@ -292,6 +294,7 @@
         </profile>
     </profiles>
 
+
     <dependencies>
         <dependency>
             <groupId>org.hibernate</groupId>
@@ -307,21 +310,10 @@
         	<groupId>org.hibernate</groupId>
         	<artifactId>hibernate-ehcache</artifactId>
         </dependency>
-        <dependency>
-           <groupId>org.hibernate</groupId>
-           <artifactId>hibernate-validator-cdi</artifactId>
-           <version>${hibernate-validator.version}</version>
-        </dependency>
         <dependency>
             <groupId>org.springframework</groupId>
             <artifactId>spring-orm</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.glassfish</groupId>
-            <artifactId>javax.el</artifactId>
-            <version>3.0.1-b10</version>
-        </dependency>
-
         <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>handle</artifactId>
@@ -344,12 +336,12 @@
             <type>pom</type>
             <exclusions>
                 <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-core</artifactId>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
                 </exclusion>
                 <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-databind</artifactId>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
                 </exclusion>
             </exclusions>
         </dependency>
@@ -365,10 +357,6 @@
             <groupId>commons-collections</groupId>
             <artifactId>commons-collections</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-collections4</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-dbcp2</artifactId>
@@ -418,8 +406,8 @@
             <artifactId>jdom</artifactId>
         </dependency>
         <dependency>
-            <groupId>log4j</groupId>
-            <artifactId>log4j</artifactId>
+            <groupId>ch.qos.reload4j</groupId>
+            <artifactId>reload4j</artifactId>
         </dependency>
         <dependency>
             <groupId>oro</groupId>
@@ -449,6 +437,10 @@
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-scratchpad</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.apache.poi</groupId>
+            <artifactId>poi-ooxml</artifactId>
+        </dependency>
         <dependency>
             <groupId>rome</groupId>
             <artifactId>rome</artifactId>
@@ -511,12 +503,16 @@
             <artifactId>h2</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.databene</groupId>
+            <artifactId>contiperf</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>org.mockito</groupId>
             <artifactId>mockito-core</artifactId>
             <scope>test</scope>
         </dependency>
-
         <dependency>
             <groupId>org.rometools</groupId>
             <artifactId>rome-modules</artifactId>
@@ -532,6 +528,14 @@
                     <groupId>org.mockito</groupId>
                     <artifactId>mockito-core</artifactId>
                 </exclusion>
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
         <dependency>
@@ -549,6 +553,10 @@
                     <groupId>org.mockito</groupId>
                     <artifactId>mockito-core</artifactId>
                 </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
         <dependency>
@@ -572,6 +580,14 @@
                     <groupId>org.slf4j</groupId>
                     <artifactId>slf4j-api</artifactId>
                 </exclusion>
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
 
@@ -595,9 +611,9 @@
         </dependency>
 
         <dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-core</artifactId>
-            <version>4.10.4</version>
+            <groupId>org.elasticsearch</groupId>
+            <artifactId>elasticsearch</artifactId>
+            <version>1.4.0</version>
         </dependency>
 
         <dependency>
@@ -683,6 +699,7 @@
         <dependency>
             <groupId>joda-time</groupId>
             <artifactId>joda-time</artifactId>
+            <version>2.9.2</version>
         </dependency>
         <dependency>
             <groupId>javax.inject</groupId>
@@ -719,20 +736,19 @@
                     <groupId>joda-time</groupId>
                     <artifactId>joda-time</artifactId>
                 </exclusion>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-databind</artifactId>
-                </exclusion>
             </exclusions>
         </dependency>
-        <!-- S3 also wanted jackson... -->
+
+        <!-- For ORCID v2 integration -->
         <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <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>
     </dependencies>
 

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

@@ -19,6 +19,7 @@ package org.apache.solr.handler.extraction;
 
 /**
  * The various Solr Parameters names to use when extracting content.
+ *
  **/
 public interface ExtractingParams {
 
@@ -40,6 +41,8 @@ public interface ExtractingParams {
    * <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.";
 
@@ -52,6 +55,7 @@ public interface ExtractingParams {
    * 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.";
 
@@ -60,6 +64,7 @@ public interface ExtractingParams {
    * <pre>
    *  literal.myField=Foo 
    * </pre>
+   *
    */
   public static final String LITERALS_PREFIX = "literal.";
 
@@ -67,10 +72,10 @@ public interface ExtractingParams {
   /**
    * 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}.
+   * will be passed to the {@link SolrContentHandler}.
    * <p>
    * See Tika's docs for what the extracted document looks like.
-     *
+   * <p>
    * @see #CAPTURE_ELEMENTS
    */
   public static final String XPATH_EXPRESSION = "xpath";
@@ -87,24 +92,20 @@ public interface ExtractingParams {
   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
+   * 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
+   * 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
+   * 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}
+   * The Capture field is based on the localName returned to the {@link SolrContentHandler}
    * by Tika, not to be confused by the mapped field.  The field name can then
    * be mapped into the index schema.
    * <p>
@@ -119,6 +120,7 @@ public interface ExtractingParams {
    * </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";
 

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

@@ -35,7 +35,8 @@ import org.dspace.handle.service.HandleService;
  * @version $Revision$
  */
 
-public class CommunityFiliator {
+public class CommunityFiliator
+{
 
     protected CommunityService communityService;
     protected HandleService handleService;
@@ -46,10 +47,12 @@ public class CommunityFiliator {
     }
 
     /**
-     * @param argv the command line arguments given
+     *
+     * @param argv arguments
      * @throws Exception if error
      */
-    public static void main(String[] argv) throws Exception {
+    public static void main(String[] argv) throws Exception
+    {
         // create an options object and populate it
         CommandLineParser parser = new PosixParser();
 
@@ -70,7 +73,8 @@ public class CommunityFiliator {
         String parentID = null;
         String childID = null;
 
-        if (line.hasOption('h')) {
+        if (line.hasOption('h'))
+        {
             HelpFormatter myhelp = new HelpFormatter();
             myhelp.printHelp("CommunityFiliator\n", options);
             System.out
@@ -81,37 +85,45 @@ public class CommunityFiliator {
             System.exit(0);
         }
 
-        if (line.hasOption('s')) {
+        if (line.hasOption('s'))
+        {
             command = "set";
         }
 
-        if (line.hasOption('r')) {
+        if (line.hasOption('r'))
+        {
             command = "remove";
         }
 
-        if (line.hasOption('p')) { // parent
+        if (line.hasOption('p')) // parent
+        {
             parentID = line.getOptionValue('p');
         }
 
-        if (line.hasOption('c')) { // child
+        if (line.hasOption('c')) // child
+        {
             childID = line.getOptionValue('c');
         }
 
         // now validate
         // must have a command set
-        if (command == null) {
+        if (command == null)
+        {
             System.out
                     .println("Error - must run with either set or remove (run with -h flag for details)");
             System.exit(1);
         }
 
-        if ("set".equals(command) || "remove".equals(command)) {
-            if (parentID == null) {
+        if ("set".equals(command) || "remove".equals(command))
+        {
+            if (parentID == null)
+            {
                 System.out.println("Error - a parentID must be specified (run with -h flag for details)");
                 System.exit(1);
             }
 
-            if (childID == null) {
+            if (childID == null)
+            {
                 System.out.println("Error - a childID must be specified (run with -h flag for details)");
                 System.exit(1);
             }
@@ -123,39 +135,52 @@ public class CommunityFiliator {
         // we are superuser!
         c.turnOffAuthorisationSystem();
 
-        try {
+        try
+        {
             // validate and resolve the parent and child IDs into commmunities
             Community parent = filiator.resolveCommunity(c, parentID);
             Community child = filiator.resolveCommunity(c, childID);
 
-            if (parent == null) {
+            if (parent == null)
+            {
                 System.out.println("Error, parent community cannot be found: "
                         + parentID);
                 System.exit(1);
             }
 
-            if (child == null) {
+            if (child == null)
+            {
                 System.out.println("Error, child community cannot be found: "
                         + childID);
                 System.exit(1);
             }
 
-            if ("set".equals(command)) {
+            if ("set".equals(command))
+            {
                 filiator.filiate(c, parent, child);
-            } else {
+            }
+            else
+            {
                 filiator.defiliate(c, parent, child);
             }
-        } catch (SQLException sqlE) {
+        }
+        catch (SQLException sqlE)
+        {
             System.out.println("Error - SQL exception: " + sqlE.toString());
-        } catch (AuthorizeException authE) {
+        }
+        catch (AuthorizeException authE)
+        {
             System.out.println("Error - Authorize exception: "
                     + authE.toString());
-        } catch (IOException ioE) {
+        }
+        catch (IOException ioE)
+        {
             System.out.println("Error - IO exception: " + ioE.toString());
         }
     }
 
     /**
+     *
      * @param c context
      * @param parent parent Community
      * @param child child community
@@ -164,14 +189,15 @@ public class CommunityFiliator {
      * @throws IOException if IO error
      */
     public void filiate(Context c, Community parent, Community child)
-        throws SQLException, AuthorizeException, IOException {
+            throws SQLException, AuthorizeException, IOException
+    {
         // check that a valid filiation would be established
         // first test - proposed child must currently be an orphan (i.e.
         // top-level)
-        Community childDad = CollectionUtils.isNotEmpty(child.getParentCommunities()) ? child.getParentCommunities()
-                                                                                             .iterator().next() : null;
+        Community childDad = CollectionUtils.isNotEmpty(child.getParentCommunities()) ? child.getParentCommunities().iterator().next() : null;
 
-        if (childDad != null) {
+        if (childDad != null)
+        {
             System.out.println("Error, child community: " + child.getID()
                     + " already a child of: " + childDad.getID());
             System.exit(1);
@@ -180,14 +206,12 @@ 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");
+        if (parentDads.contains(child))
+        {
+            System.out.println(
+                    "Error, circular parentage - child is parent of parent");
             System.exit(1);
         }
-        }
 
         // everthing's OK
         communityService.addSubcommunity(c, parent, child);
@@ -199,6 +223,7 @@ public class CommunityFiliator {
     }
 
     /**
+     *
      * @param c context
      * @param parent parent Community
      * @param child child community
@@ -207,20 +232,12 @@ public class CommunityFiliator {
      * @throws IOException if IO error
      */
     public void defiliate(Context c, Community parent, Community child)
-        throws SQLException, AuthorizeException, IOException {
+            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) {
+        if (!parentKids.contains(child))
+        {
             System.out
                     .println("Error, child community not a child of parent community");
             System.exit(1);
@@ -228,8 +245,8 @@ public class CommunityFiliator {
 
         // 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);
 
@@ -242,27 +259,31 @@ public class CommunityFiliator {
 
     /**
      * Find a community by ID
-     *
      * @param c context
      * @param communityID community ID
      * @return Community object
      * @throws SQLException if database error
      */
     protected Community resolveCommunity(Context c, String communityID)
-        throws SQLException {
+            throws SQLException
+    {
         Community community = null;
 
-        if (communityID.indexOf('/') != -1) {
+        if (communityID.indexOf('/') != -1)
+        {
             // has a / must be a handle
             community = (Community) handleService.resolveToObject(c,
                     communityID);
 
             // ensure it's a community
             if ((community == null)
-                || (community.getType() != Constants.COMMUNITY)) {
+                    || (community.getType() != Constants.COMMUNITY))
+            {
                 community = null;
             }
-        } else {
+        }
+        else
+        {
             community = communityService.find(c, UUID.fromString(communityID));
         }
 

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

@@ -15,6 +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.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
@@ -41,12 +42,12 @@ import org.dspace.eperson.service.GroupService;
  * 
  * @author Robert Tansley
  * @author Richard Jones
+ * 
  * @version $Revision$
  */
-public final class CreateAdministrator {
-    /**
-     * DSpace Context object
-     */
+public final class CreateAdministrator
+{
+	/** DSpace Context object */
 	private final Context context;
 
     protected EPersonService ePersonService;
@@ -56,11 +57,13 @@ public final class CreateAdministrator {
      * For invoking via the command line.  If called with no command line arguments,
      * it will negotiate with the user for the administrator details
      * 
-     * @param argv the command line arguments given
+     * @param argv
+     *            command-line arguments
      * @throws Exception if error
      */
     public static void main(String[] argv)
-        throws Exception {
+    	throws Exception
+    {
     	CommandLineParser parser = new PosixParser();
     	Options options = new Options();
     	
@@ -75,11 +78,14 @@ public final class CreateAdministrator {
     	CommandLine line = parser.parse(options, argv);
     	
     	if (line.hasOption("e") && line.hasOption("f") && line.hasOption("l") &&
-            line.hasOption("c") && line.hasOption("p")) {
+    			line.hasOption("c") && line.hasOption("p"))
+    	{
     		ca.createAdministrator(line.getOptionValue("e"),
     				line.getOptionValue("f"), line.getOptionValue("l"),
     				line.getOptionValue("c"), line.getOptionValue("p"));
-        } else {
+    	}
+    	else
+    	{
     		ca.negotiateAdministratorDetails();
     	}
     }
@@ -90,7 +96,8 @@ public final class CreateAdministrator {
      * @throws Exception if error
      */
     protected CreateAdministrator()
-        throws Exception {
+    	throws Exception
+    {
     	context = new Context();
         groupService = EPersonServiceFactory.getInstance().getGroupService();
         ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
@@ -103,7 +110,8 @@ public final class CreateAdministrator {
      * @throws Exception if error
      */
     protected void negotiateAdministratorDetails()
-        throws Exception {
+    	throws Exception
+    {
         Console console = System.console();
     	
     	System.out.println("Creating an initial administrator account");
@@ -117,14 +125,18 @@ public final class CreateAdministrator {
         char[] password2 = null;
     	String language = I18nUtil.DEFAULTLOCALE.getLanguage();
     	
-        while (!dataOK) {
+    	while (!dataOK)
+    	{
     		System.out.print("E-mail address: ");
     		System.out.flush();
     		
     		email = console.readLine();
-            if (!StringUtils.isBlank(email)) {
+            if (!StringUtils.isBlank(email))
+            {
                 email = email.trim();
-            } else {
+            }
+            else
+            {
                 System.out.println("Please provide an email address.");
                 continue;
             }
@@ -134,7 +146,8 @@ public final class CreateAdministrator {
     		
     		firstName = console.readLine();
 
-            if (firstName != null) {
+            if (firstName != null)
+            {
                 firstName = firstName.trim();
             }
     		
@@ -143,19 +156,21 @@ public final class CreateAdministrator {
     		
     		lastName = console.readLine();
 
-            if (lastName != null) {
+            if (lastName != null)
+            {
                 lastName = lastName.trim();
             }
    		
-            if (ConfigurationManager.getProperty("webui.supported.locales") != null) {
-                System.out.println("Select one of the following languages: " + ConfigurationManager
-                    .getProperty("webui.supported.locales"));
+            if (ConfigurationManager.getProperty("webui.supported.locales") != null)
+            {
+                System.out.println("Select one of the following languages: " + ConfigurationManager.getProperty("webui.supported.locales"));
                 System.out.print("Language: ");
                 System.out.flush();
             
     		    language = console.readLine();
 
-                if (language != null) {
+                if (language != null)
+                {
                     language = language.trim();
                     language = I18nUtil.getSupportedLocale(new Locale(language)).getLanguage();
                 }
@@ -173,20 +188,25 @@ public final class CreateAdministrator {
     		password2 = console.readPassword();
 
             //TODO real password validation
-            if (password1.length > 1 && Arrays.equals(password1, password2)) {
+            if (password1.length > 1 && Arrays.equals(password1, password2))
+    		{
     			// password OK
     			System.out.print("Is the above data correct? (y or n): ");
     			System.out.flush();
     			
     			String s = console.readLine();
 
-                if (s != null) {
+                if (s != null)
+                {
                     s = s.trim();
-                    if (s.toLowerCase().startsWith("y")) {
+                    if (s.toLowerCase().startsWith("y"))
+                    {
                         dataOK = true;
                     }
                 }
-            } else {
+    		}
+    		else
+    		{
     			System.out.println("Passwords don't match");
     		}
     	}
@@ -208,11 +228,13 @@ public final class CreateAdministrator {
      * @param last	user's last name
      * @param language preferred language
      * @param pw	desired password
+     * 
      * @throws Exception if error
      */
     protected void createAdministrator(String email, String first, String last,
     		String language, String pw)
-        throws Exception {
+    	throws Exception
+    {
     	// Of course we aren't an administrator yet so we need to
     	// circumvent authorisation
     	context.turnOffAuthorisationSystem();
@@ -220,7 +242,8 @@ public final class CreateAdministrator {
     	// Find administrator group
     	Group admins = groupService.findByName(context, Group.ADMIN);
     	
-        if (admins == null) {
+    	if (admins == null)
+    	{
     		throw new IllegalStateException("Error, no admin group (group 1) found");
     	}
     	
@@ -229,7 +252,8 @@ public final class CreateAdministrator {
         
         // check if the email belongs to a registered user,
         // if not create a new user with this email
-        if (eperson == null) {
+        if (eperson == null)
+        {
             eperson = ePersonService.create(context);
             eperson.setEmail(email);
             eperson.setCanLogIn(true);

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

@@ -7,19 +7,7 @@
  */
 package org.dspace.administer;
 
-import java.io.BufferedWriter;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
+import org.apache.commons.cli.*;
 import org.apache.xml.serialize.Method;
 import org.apache.xml.serialize.OutputFormat;
 import org.apache.xml.serialize.XMLSerializer;
@@ -31,6 +19,14 @@ import org.dspace.content.service.MetadataSchemaService;
 import org.dspace.core.Context;
 import org.xml.sax.SAXException;
 
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
 
 /**
  * @author Graham Triggs
@@ -48,17 +44,11 @@ import org.xml.sax.SAXException;
  * </metadata-schemas>
  * }
  */
-public class MetadataExporter {
+public class MetadataExporter
+{
 
-    protected static MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance()
-                                                                                        .getMetadataSchemaService();
-    protected static MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance()
-                                                                                      .getMetadataFieldService();
-
-    /**
-     * Default constructor
-     */
-    private MetadataExporter() { }
+    protected static MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance().getMetadataSchemaService();
+    protected static MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance().getMetadataFieldService();
 
     /**
      * @param args commandline arguments
@@ -68,8 +58,8 @@ public class MetadataExporter {
      * @throws SQLException if database error
      * @throws RegistryExportException if export error
      */
-    public static void main(String[] args)
-        throws ParseException, SQLException, IOException, SAXException, RegistryExportException {
+    public static void main(String[] args) throws ParseException, SQLException, IOException, SAXException, RegistryExportException
+    {
         // create an options object and populate it
         CommandLineParser parser = new PosixParser();
         Options options = new Options();
@@ -80,14 +70,18 @@ public class MetadataExporter {
         String file   = null;
         String schema = null;
 
-        if (line.hasOption('f')) {
+        if (line.hasOption('f'))
+        {
             file   = line.getOptionValue('f');
-        } else {
+        }
+        else
+        {
             usage();
             System.exit(0);
         }
         
-        if (line.hasOption('s')) {
+        if (line.hasOption('s'))
+        {
             schema = line.getOptionValue('s');
         }
 
@@ -96,7 +90,6 @@ public class MetadataExporter {
 
     /**
      * Save a registry to a filepath
-     *
      * @param file filepath
      * @param schema schema definition to save
      * @throws SQLException if database error
@@ -104,8 +97,8 @@ public class MetadataExporter {
      * @throws SAXException if XML error
      * @throws RegistryExportException if export error
      */
-    public static void saveRegistry(String file, String schema)
-        throws SQLException, IOException, SAXException, RegistryExportException {
+    public static void saveRegistry(String file, String schema) throws SQLException, IOException, SAXException, RegistryExportException
+    {
         // create a context
         Context context = new Context();
         context.turnOffAuthorisationSystem();
@@ -125,22 +118,27 @@ public class MetadataExporter {
         List<MetadataField> mdFields = null;
 
         // If a single schema has been specified
-        if (schema != null && !"".equals(schema)) {
+        if (schema != null && !"".equals(schema))
+        {
             // Get the id of that schema
             MetadataSchema mdSchema = metadataSchemaService.find(context, schema);
-            if (mdSchema == null) {
+            if (mdSchema == null)
+            {
                 throw new RegistryExportException("no schema to export");
             }
             
             // Get the metadata fields only for the specified schema
             mdFields = metadataFieldService.findAllInSchema(context, mdSchema);
-        } else {
+        }
+        else
+        {
             // Get the metadata fields for all the schemas
             mdFields = metadataFieldService.findAll(context);
         }
         
         // Output the metadata fields
-        for (MetadataField mdField : mdFields) {
+        for (MetadataField mdField : mdFields)
+        {
             saveType(context, xmlSerializer, mdField);
         }
         
@@ -153,7 +151,6 @@ public class MetadataExporter {
     
     /**
      * Serialize the schema registry. If the parameter 'schema' is null or empty, save all schemas
-     *
      * @param context DSpace Context
      * @param xmlSerializer XML serializer
      * @param schema schema (may be null to save all)
@@ -161,18 +158,22 @@ public class MetadataExporter {
      * @throws SAXException if XML error
      * @throws RegistryExportException if export error
      */
-    public static void saveSchema(Context context, XMLSerializer xmlSerializer, String schema)
-        throws SQLException, SAXException, RegistryExportException {
-        if (schema != null && !"".equals(schema)) {
+    public static void saveSchema(Context context, XMLSerializer xmlSerializer, String schema) throws SQLException, SAXException, RegistryExportException
+    {
+        if (schema != null && !"".equals(schema))
+        {
             // Find a single named schema
             MetadataSchema mdSchema = metadataSchemaService.find(context, schema);
             
             saveSchema(xmlSerializer, mdSchema);
-        } else {
+        }
+        else
+        {
             // Find all schemas
             List<MetadataSchema> mdSchemas = metadataSchemaService.findAll(context);
             
-            for (MetadataSchema mdSchema : mdSchemas) {
+            for (MetadataSchema mdSchema : mdSchemas)
+            {
                 saveSchema(xmlSerializer, mdSchema);
             }
         }
@@ -186,22 +187,25 @@ public class MetadataExporter {
      * @throws SAXException if XML error
      * @throws RegistryExportException if export error
      */
-    private static void saveSchema(XMLSerializer xmlSerializer, MetadataSchema mdSchema)
-        throws SAXException, RegistryExportException {
+    private static void saveSchema(XMLSerializer xmlSerializer, MetadataSchema mdSchema) throws SAXException, RegistryExportException
+    {
         // If we haven't got a schema, it's an error
-        if (mdSchema == null) {
+        if (mdSchema == null)
+        {
             throw new RegistryExportException("no schema to export");
         }
         
         String name      = mdSchema.getName();
         String namespace = mdSchema.getNamespace();
         
-        if (name == null || "".equals(name)) {
+        if (name == null || "".equals(name))
+        {
             System.out.println("name is null, skipping");
             return;
         }
 
-        if (namespace == null || "".equals(namespace)) {
+        if (namespace == null || "".equals(namespace))
+        {
             System.out.println("namespace is null, skipping");
             return;
         }
@@ -233,10 +237,11 @@ public class MetadataExporter {
      * @throws SQLException if database error
      * @throws IOException if IO error
      */
-    private static void saveType(Context context, XMLSerializer xmlSerializer, MetadataField mdField)
-        throws SAXException, RegistryExportException, SQLException, IOException {
+    private static void saveType(Context context, XMLSerializer xmlSerializer, MetadataField mdField) throws SAXException, RegistryExportException, SQLException, IOException
+    {
         // If we haven't been given a field, it's an error
-        if (mdField == null) {
+        if (mdField == null)
+        {
             throw new RegistryExportException("no field to export");
         }
         
@@ -247,7 +252,8 @@ public class MetadataExporter {
         String scopeNote = mdField.getScopeNote();
 
         // We must have a schema and element
-        if (schemaName == null || element == null) {
+        if (schemaName == null || element == null)
+        {
             throw new RegistryExportException("incomplete field information");
         }
 
@@ -265,20 +271,26 @@ public class MetadataExporter {
         xmlSerializer.endElement("element");
 
         // Output the qualifier, if present
-        if (qualifier != null) {
+        if (qualifier != null)
+        {
             xmlSerializer.startElement("qualifier", null);
             xmlSerializer.characters(qualifier.toCharArray(), 0, qualifier.length());
             xmlSerializer.endElement("qualifier");
-        } else {
+        }
+        else
+        {
             xmlSerializer.comment("unqualified");
         }
         
         // Output the scope note, if present
-        if (scopeNote != null) {
+        if (scopeNote != null)
+        {
             xmlSerializer.startElement("scope_note", null);
             xmlSerializer.characters(scopeNote.toCharArray(), 0, scopeNote.length());
             xmlSerializer.endElement("scope_note");
-        } else {
+        }
+        else
+        {
             xmlSerializer.comment("no scope note");
         }
         
@@ -286,29 +298,31 @@ public class MetadataExporter {
     }
     
     static Map<Integer, String> schemaMap = new HashMap<Integer, String>();
-
     /**
      * Helper method to retrieve a schema name for the field.
      * Caches the name after looking up the id.
-     *
      * @param context DSpace Context
      * @param mdField DSpace metadata field
      * @return name of schema
      * @throws SQLException if database error
      * @throws RegistryExportException if export error
      */
-    private static String getSchemaName(Context context, MetadataField mdField)
-        throws SQLException, RegistryExportException {
+    private static String getSchemaName(Context context, MetadataField mdField) throws SQLException, RegistryExportException
+    {
         // Get name from cache
         String name = schemaMap.get(mdField.getMetadataSchema().getID());
 
-        if (name == null) {
+        if (name == null)
+        {
             // Name not retrieved before, so get the schema now
             MetadataSchema mdSchema = metadataSchemaService.find(context, mdField.getMetadataSchema().getID());
-            if (mdSchema != null) {
+            if (mdSchema != null)
+            {
                 name = mdSchema.getName();
                 schemaMap.put(mdSchema.getID(), name);
-            } else {
+            }
+            else
+            {
                 // Can't find the schema
                 throw new RegistryExportException("Can't get schema name for field");
             }
@@ -319,7 +333,8 @@ public class MetadataExporter {
     /**
      * Print the usage message to stdout
      */
-    public static void usage() {
+    public static void usage()
+    {
         String usage = "Use this class with the following options:\n" +
                         " -f <xml output file> : specify the output file for the schemas\n" +
                         " -s <schema> : name of the schema to export\n";

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

@@ -9,6 +9,7 @@ package org.dspace.administer;
 
 import java.io.IOException;
 import java.sql.SQLException;
+
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
@@ -17,7 +18,9 @@ import org.apache.commons.cli.CommandLineParser;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.cli.PosixParser;
+
 import org.apache.xpath.XPathAPI;
+
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
@@ -28,9 +31,11 @@ import org.dspace.content.service.MetadataSchemaService;
 import org.dspace.core.Context;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
+
 import org.xml.sax.SAXException;
 
 /**
@@ -56,26 +61,17 @@ import org.xml.sax.SAXException;
  * </dspace-dc-types>
  * }
  */
-public class MetadataImporter {
-    protected static MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance()
-                                                                                        .getMetadataSchemaService();
-    protected static MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance()
-                                                                                      .getMetadataFieldService();
+public class MetadataImporter
+{
+    protected static MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance().getMetadataSchemaService();
+    protected static MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance().getMetadataFieldService();
 
-    /**
-     * logging category
-     */
+    /** logging category */
     private static final Logger log = LoggerFactory.getLogger(MetadataImporter.class);
 
-    /**
-     * Default constructor
-     */
-    private MetadataImporter() { }
-
     /**
      * main method for reading user input from the command line
-     *
-     * @param args the command line arguments given
+     * @param args arguments
      * @throws ParseException if parse error
      * @throws SQLException if database error
      * @throws IOException if IO error
@@ -89,7 +85,8 @@ public class MetadataImporter {
     public static void main(String[] args)
     	throws ParseException, SQLException, IOException, TransformerException,
     			ParserConfigurationException, AuthorizeException, SAXException,
-        NonUniqueMetadataException, RegistryImportException {
+    			NonUniqueMetadataException, RegistryImportException
+    {
         boolean forceUpdate = false;
         
         // create an options object and populate it
@@ -100,9 +97,12 @@ public class MetadataImporter {
         CommandLine line = parser.parse(options, args);
         
         String file = null;
-        if (line.hasOption('f')) {
+        if (line.hasOption('f'))
+        {
             file = line.getOptionValue('f');
-        } else {
+        }
+        else
+        {
             usage();
             System.exit(0);
         }
@@ -127,10 +127,12 @@ public class MetadataImporter {
      */
     public static void loadRegistry(String file, boolean forceUpdate)
     	throws SQLException, IOException, TransformerException, ParserConfigurationException, 
-        AuthorizeException, SAXException, NonUniqueMetadataException, RegistryImportException {
+    		AuthorizeException, SAXException, NonUniqueMetadataException, RegistryImportException
+    {
         Context context = null;
 
-        try {
+        try
+        {
             // create a context
             context = new Context();
             context.turnOffAuthorisationSystem();
@@ -142,7 +144,8 @@ public class MetadataImporter {
             NodeList schemaNodes = XPathAPI.selectNodeList(document, "/dspace-dc-types/dc-schema");
 
             // Add each one as a new format to the registry
-            for (int i = 0; i < schemaNodes.getLength(); i++) {
+            for (int i = 0; i < schemaNodes.getLength(); i++)
+            {
                 Node n = schemaNodes.item(i);
                 loadSchema(context, n, forceUpdate);
             }
@@ -151,18 +154,20 @@ public class MetadataImporter {
             NodeList typeNodes = XPathAPI.selectNodeList(document, "/dspace-dc-types/dc-type");
 
             // Add each one as a new format to the registry
-            for (int i = 0; i < typeNodes.getLength(); i++) {
+            for (int i = 0; i < typeNodes.getLength(); i++)
+            {
                 Node n = typeNodes.item(i);
                 loadType(context, n);
             }
 
             context.restoreAuthSystemState();
             context.complete();
-        } finally {
-            // Clean up our context, if it still exists & it was never completed
-            if (context != null && context.isValid()) {
-                context.abort();
         }
+        finally
+        {
+           // Clean up our context, if it still exists & it was never completed
+            if(context!=null && context.isValid())
+                context.abort();
         }
     }
     
@@ -170,8 +175,10 @@ public class MetadataImporter {
      * Process a node in the metadata registry XML file.  If the
      * schema already exists, it will not be recreated
      * 
-     * @param context DSpace context object
-     * @param node    the node in the DOM tree
+     * @param context
+     *            DSpace context object
+     * @param node
+     *            the node in the DOM tree
      * @throws SQLException if database error
      * @throws IOException if IO error
      * @throws TransformerException if transformer error
@@ -181,43 +188,51 @@ public class MetadataImporter {
      */
     private static void loadSchema(Context context, Node node, boolean updateExisting)
         throws SQLException, IOException, TransformerException,
-        AuthorizeException, NonUniqueMetadataException, RegistryImportException {
+            AuthorizeException, NonUniqueMetadataException, RegistryImportException
+    {
         // Get the values
         String name = RegistryImporter.getElementData(node, "name");
         String namespace = RegistryImporter.getElementData(node, "namespace");
         
-        if (name == null || "".equals(name)) {
+        if (name == null || "".equals(name))
+        {
             throw new RegistryImportException("Name of schema must be supplied");
         }
 
-        if (namespace == null || "".equals(namespace)) {
+        if (namespace == null || "".equals(namespace))
+        {
             throw new RegistryImportException("Namespace of schema must be supplied");
         }
 
         // check to see if the schema already exists
         MetadataSchema s = metadataSchemaService.find(context, name);
         
-        if (s == null) {
+        if (s == null)
+        {
             // Schema does not exist - create
             log.info("Registering Schema " + name + " (" + namespace + ")");
             metadataSchemaService.create(context, name, namespace);
-        } else {
+        }
+        else
+        {
             // Schema exists - if it's the same namespace, allow the type imports to continue
-            if (s.getNamespace().equals(namespace)) {
+            if (s.getNamespace().equals(namespace))
+            {
                 // This schema already exists with this namespace, skipping it
                 return;
             }
             
             // It's a different namespace - have we been told to update?
-            if (updateExisting) {
+            if (updateExisting)
+            {
                 // Update the existing schema namespace and continue to type import
                 log.info("Updating Schema " + name + ": New namespace " + namespace);
                 s.setNamespace(namespace);
                 metadataSchemaService.update(context, s);
-            } else {
-                throw new RegistryImportException(
-                    "Schema " + name + " already registered with different namespace " + namespace + ". Rerun with " +
-                        "'update' option enabled if you wish to update this schema.");
+            }
+            else
+            {
+                throw new RegistryImportException("Schema " + name + " already registered with different namespace " + namespace + ". Rerun with 'update' option enabled if you wish to update this schema.");
             }
         }
         
@@ -228,8 +243,10 @@ public class MetadataImporter {
      * be a "dc-type" node.  If the type already exists, then it
      * will not be reimported
      * 
-     * @param context DSpace context object
-     * @param node    the node in the DOM tree
+     * @param context
+     *            DSpace context object
+     * @param node
+     *            the node in the DOM tree
      * @throws SQLException if database error
      * @throws IOException if IO error
      * @throws TransformerException if transformer error
@@ -239,7 +256,8 @@ public class MetadataImporter {
      */
     private static void loadType(Context context, Node node)
             throws SQLException, IOException, TransformerException,
-        AuthorizeException, NonUniqueMetadataException, RegistryImportException {
+            AuthorizeException, NonUniqueMetadataException, RegistryImportException
+    {
         // Get the values
         String schema = RegistryImporter.getElementData(node, "schema");
         String element = RegistryImporter.getElementData(node, "element");
@@ -247,7 +265,8 @@ public class MetadataImporter {
         String scopeNote = RegistryImporter.getElementData(node, "scope_note");
 
         // If the schema is not provided default to DC
-        if (schema == null) {
+        if (schema == null)
+        {
             schema = MetadataSchema.DC_SCHEMA;
         }
 
@@ -255,21 +274,22 @@ public class MetadataImporter {
         // Find the matching schema object
         MetadataSchema schemaObj = metadataSchemaService.find(context, schema);
         
-        if (schemaObj == null) {
+        if (schemaObj == null)
+        {
             throw new RegistryImportException("Schema '" + schema + "' is not registered and does not exist.");
         }
         
         MetadataField mf = metadataFieldService.findByElement(context, schemaObj, element, qualifier);
-        if (mf != null) {
+        if (mf != null)
+        {
             // Metadata field already exists, skipping it
             return;
         }
         
         // Actually create this metadata field as it doesn't yet exist
         String fieldName = schema + "." + element + "." + qualifier;
-        if (qualifier == null) {
+        if(qualifier==null)
             fieldName = schema + "." + element;
-        }
         log.info("Registering metadata field " + fieldName);
         MetadataField field = metadataFieldService.create(context, schemaObj, element, qualifier, scopeNote);
         metadataFieldService.update(context, field);
@@ -278,7 +298,8 @@ public class MetadataImporter {
     /**
      * Print the usage message to stdout
      */
-    public static void usage() {
+    public static void usage()
+    {
         String usage = "Use this class with the following option:\n" +
         				" -f <xml source file> : specify which xml source file " +
         				"contains the DC fields to import.\n";

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

@@ -12,11 +12,13 @@ package org.dspace.administer;
  *
  * An exception to report any problems with registry exports
  */
-public class RegistryExportException extends Exception {
+public class RegistryExportException extends Exception
+{
     /**
      * Create an empty authorize exception
      */
-    public RegistryExportException() {
+    public RegistryExportException()
+    {
         super();
     }
 
@@ -25,7 +27,8 @@ public class RegistryExportException extends Exception {
      * 
      * @param message exception message
      */
-    public RegistryExportException(String message) {
+    public RegistryExportException(String message)
+    {
         super(message);
     }
     
@@ -35,7 +38,8 @@ public class RegistryExportException extends Exception {
      * @param message exception message
      * @param e reference to Throwable
      */
-    public RegistryExportException(String message, Throwable e) {
+    public RegistryExportException(String message, Throwable e)
+    {
         super(message, e);
     }
     
@@ -44,7 +48,8 @@ public class RegistryExportException extends Exception {
      * 
      * @param e reference to Throwable
      */
-    public RegistryExportException(Throwable e) {
+    public RegistryExportException(Throwable e)
+    {
         super(e);
     }
     

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

@@ -12,11 +12,13 @@ package org.dspace.administer;
  *
  * An exception to report any problems with registry imports
  */
-public class RegistryImportException extends Exception {
+public class RegistryImportException extends Exception
+{
     /**
      * Create an empty authorize exception
      */
-    public RegistryImportException() {
+    public RegistryImportException()
+    {
         super();
     }
 
@@ -25,7 +27,8 @@ public class RegistryImportException extends Exception {
      * 
      * @param message error message
      */
-    public RegistryImportException(String message) {
+    public RegistryImportException(String message)
+    {
         super(message);
     }
     
@@ -35,7 +38,8 @@ public class RegistryImportException extends Exception {
      * @param	message error message
      * @param	e throwable
      */
-    public RegistryImportException(String message, Throwable e) {
+    public RegistryImportException(String message, Throwable e)
+    {
     	super(message, e);
     }
     
@@ -44,7 +48,8 @@ public class RegistryImportException extends Exception {
      * 
      * @param	e throwable
      */
-    public RegistryImportException(Throwable e) {
+    public RegistryImportException(Throwable e)
+    {
     	super(e);
     }
     

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

@@ -9,15 +9,18 @@ package org.dspace.administer;
 
 import java.io.File;
 import java.io.IOException;
+
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
 import org.apache.xpath.XPathAPI;
+
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
+
 import org.xml.sax.SAXException;
 
 /**
@@ -28,24 +31,22 @@ import org.xml.sax.SAXException;
  * I am the author, really I ripped these methods off from other
  * classes
  */
-public class RegistryImporter {
-
-    /**
-     * Default constructor
-     */
-    private RegistryImporter() { }
-
+public class RegistryImporter
+{
     /**
      * Load in the XML from file.
      * 
-     * @param filename the filename to load from
+     * @param filename
+     *            the filename to load from
+     * 
      * @return the DOM representation of the XML file
      * @throws IOException if IO error
      * @throws ParserConfigurationException if configuration parse error
      * @throws SAXException if XML parse error
      */
     public static Document loadXML(String filename) 
-        throws IOException, ParserConfigurationException, SAXException {
+    	throws IOException, ParserConfigurationException, SAXException
+    {
         DocumentBuilder builder = DocumentBuilderFactory.newInstance()
                 .newDocumentBuilder();
 
@@ -66,17 +67,21 @@ public class RegistryImporter {
      * </P>
      * Why this isn't a core part of the XML API I do not know...
      * 
-     * @param parentElement the element, whose child element you want the CDATA from
-     * @param childName     the name of the element you want the CDATA from
-     * @return the CDATA as a <code>String</code>
+     * @param parentElement
+     *            the element, whose child element you want the CDATA from
+     * @param childName
+     *            the name of the element you want the CDATA from
      * @throws TransformerException if error
+     * @return the CDATA as a <code>String</code>
      */
     public static String getElementData(Node parentElement, String childName)
-        throws TransformerException {
+            throws TransformerException
+    {
         // Grab the child node
         Node childNode = XPathAPI.selectSingleNode(parentElement, childName);
 
-        if (childNode == null) {
+        if (childNode == null)
+        {
             // No child node, so no values
             return null;
         }
@@ -84,7 +89,8 @@ public class RegistryImporter {
         // Get the #text
         Node dataNode = childNode.getFirstChild();
 
-        if (dataNode == null) {
+        if (dataNode == null)
+        {
             return null;
         }
 
@@ -109,19 +115,23 @@ public class RegistryImporter {
      * </P>
      * Why this also isn't a core part of the XML API I do not know...
      * 
-     * @param parentElement the element, whose child element you want the CDATA from
-     * @param childName     the name of the element you want the CDATA from
-     * @return the CDATA as a <code>String</code>
+     * @param parentElement
+     *            the element, whose child element you want the CDATA from
+     * @param childName
+     *            the name of the element you want the CDATA from
      * @throws TransformerException if error
+     * @return the CDATA as a <code>String</code>
      */
     public static String[] getRepeatedElementData(Node parentElement,
-                                                  String childName) throws TransformerException {
+            String childName) throws TransformerException
+    {
         // Grab the child node
         NodeList childNodes = XPathAPI.selectNodeList(parentElement, childName);
 
         String[] data = new String[childNodes.getLength()];
 
-        for (int i = 0; i < childNodes.getLength(); i++) {
+        for (int i = 0; i < childNodes.getLength(); i++)
+        {
             // Get the #text node
             Node dataNode = childNodes.item(i).getFirstChild();
 

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

@@ -12,6 +12,7 @@ import java.io.IOException;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Arrays;
+
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
@@ -43,33 +44,29 @@ import org.xml.sax.SAXException;
  * @author Robert Tansley
  * @version $Revision$
  */
-public class RegistryLoader {
-    /**
-     * log4j category
-     */
+public class RegistryLoader
+{
+    /** log4j category */
     private static Logger log = Logger.getLogger(RegistryLoader.class);
 
-    protected static BitstreamFormatService bitstreamFormatService = ContentServiceFactory.getInstance()
-                                                                                          .getBitstreamFormatService();
-
-    /**
-     * Default constructor
-     */
-    private RegistryLoader() { }
+    protected static BitstreamFormatService bitstreamFormatService = ContentServiceFactory.getInstance().getBitstreamFormatService();
 
     /**
      * For invoking via the command line
      * 
-     * @param argv the command line arguments given
+     * @param argv
+     *            command-line arguments
      * @throws Exception if error
      */
-    public static void main(String[] argv) throws Exception {
+    public static void main(String[] argv) throws Exception
+    {
         String usage = "Usage: " + RegistryLoader.class.getName()
                 + " (-bitstream | -metadata) registry-file.xml";
 
         Context context = null;
 
-        try {
+        try
+        {
             context = new Context();
 
             // Can't update registries anonymously, so we need to turn off
@@ -77,12 +74,17 @@ public class RegistryLoader {
             context.turnOffAuthorisationSystem();
 
             // Work out what we're loading
-            if (argv[0].equalsIgnoreCase("-bitstream")) {
+            if (argv[0].equalsIgnoreCase("-bitstream"))
+            {
                 RegistryLoader.loadBitstreamFormats(context, argv[1]);
-            } else if (argv[0].equalsIgnoreCase("-metadata")) {
+            }
+            else if (argv[0].equalsIgnoreCase("-metadata"))
+            {
                 // Call MetadataImporter, as it handles Metadata schema updates
                 MetadataImporter.loadRegistry(argv[1], true);
-            } else {
+            }
+            else
+            {
                 System.err.println(usage);
             }
 
@@ -90,29 +92,36 @@ public class RegistryLoader {
             context.complete();
 
             System.exit(0);
-        } catch (ArrayIndexOutOfBoundsException ae) {
+        }
+        catch (ArrayIndexOutOfBoundsException ae)
+        {
             System.err.println(usage);
 
             System.exit(1);
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             log.fatal(LogManager.getHeader(context, "error_loading_registries",
                     ""), e);
 
             System.err.println("Error: \n - " + e.getMessage());
             System.exit(1);
-        } finally {
-            // Clean up our context, if it still exists & it was never completed
-            if (context != null && context.isValid()) {
-                context.abort();
         }
+        finally
+        {
+            // Clean up our context, if it still exists & it was never completed
+            if(context!=null && context.isValid())
+                context.abort();
         }
     }
 
     /**
      * Load Bitstream Format metadata
      * 
-     * @param context  DSpace context object
-     * @param filename the filename of the XML file to load
+     * @param context
+     *            DSpace context object
+     * @param filename
+     *            the filename of the XML file to load
      * @throws SQLException if database error
      * @throws IOException if IO error
      * @throws TransformerException if transformer error
@@ -122,7 +131,8 @@ public class RegistryLoader {
      */
     public static void loadBitstreamFormats(Context context, String filename)
             throws SQLException, IOException, ParserConfigurationException,
-        SAXException, TransformerException, AuthorizeException {
+            SAXException, TransformerException, AuthorizeException
+    {
         Document document = loadXML(filename);
 
         // Get the nodes corresponding to formats
@@ -130,7 +140,8 @@ public class RegistryLoader {
                 "dspace-bitstream-types/bitstream-type");
 
         // Add each one as a new format to the registry
-        for (int i = 0; i < typeNodes.getLength(); i++) {
+        for (int i = 0; i < typeNodes.getLength(); i++)
+        {
             Node n = typeNodes.item(i);
             loadFormat(context, n);
         }
@@ -143,8 +154,10 @@ public class RegistryLoader {
      * Process a node in the bitstream format registry XML file. The node must
      * be a "bitstream-type" node
      * 
-     * @param context DSpace context object
-     * @param node    the node in the DOM tree
+     * @param context
+     *            DSpace context object
+     * @param node
+     *            the node in the DOM tree
      * @throws SQLException if database error
      * @throws IOException if IO error
      * @throws TransformerException if transformer error
@@ -152,7 +165,8 @@ public class RegistryLoader {
      */
     private static void loadFormat(Context context, Node node)
             throws SQLException, IOException, TransformerException,
-        AuthorizeException {
+            AuthorizeException
+    {
         // Get the values
         String mimeType = getElementData(node, "mimetype");
         String shortDesc = getElementData(node, "short_description");
@@ -170,12 +184,14 @@ public class RegistryLoader {
         BitstreamFormat exists = bitstreamFormatService.findByMIMEType(context, mimeType);
         
         // If not found by mimeType, check by short description (since this must also be unique)
-        if (exists == null) {
+        if(exists==null)
+        {    
             exists = bitstreamFormatService.findByShortDescription(context, shortDesc);
         }
             
         // If it doesn't exist, create it..otherwise skip it.
-        if (exists == null) {
+        if(exists==null)
+        {
             // Create the format object
             BitstreamFormat format = bitstreamFormatService.create(context);
 
@@ -199,14 +215,16 @@ public class RegistryLoader {
     /**
      * Load in the XML from file.
      * 
-     * @param filename the filename to load from
-     * @return the DOM representation of the XML file
+     * @param filename
+     *            the filename to load from
      * @throws IOException if IO error
      * @throws ParserConfigurationException if config error
      * @throws SAXException if parser error
+     * @return the DOM representation of the XML file
      */
     private static Document loadXML(String filename) throws IOException,
-        ParserConfigurationException, SAXException {
+            ParserConfigurationException, SAXException
+    {
         DocumentBuilder builder = DocumentBuilderFactory.newInstance()
                 .newDocumentBuilder();
 
@@ -225,17 +243,21 @@ public class RegistryLoader {
      * </P>
      * Why this isn't a core part of the XML API I do not know...
      * 
-     * @param parentElement the element, whose child element you want the CDATA from
-     * @param childName     the name of the element you want the CDATA from
-     * @return the CDATA as a <code>String</code>
+     * @param parentElement
+     *            the element, whose child element you want the CDATA from
+     * @param childName
+     *            the name of the element you want the CDATA from
      * @throws TransformerException if transformer error
+     * @return the CDATA as a <code>String</code>
      */
     private static String getElementData(Node parentElement, String childName)
-        throws TransformerException {
+            throws TransformerException
+    {
         // Grab the child node
         Node childNode = XPathAPI.selectSingleNode(parentElement, childName);
 
-        if (childNode == null) {
+        if (childNode == null)
+        {
             // No child node, so no values
             return null;
         }
@@ -243,7 +265,8 @@ public class RegistryLoader {
         // Get the #text
         Node dataNode = childNode.getFirstChild();
 
-        if (dataNode == null) {
+        if (dataNode == null)
+        {
             return null;
         }
 
@@ -268,19 +291,23 @@ public class RegistryLoader {
      * </P>
      * Why this also isn't a core part of the XML API I do not know...
      * 
-     * @param parentElement the element, whose child element you want the CDATA from
-     * @param childName     the name of the element you want the CDATA from
-     * @return the CDATA as a <code>String</code>
+     * @param parentElement
+     *            the element, whose child element you want the CDATA from
+     * @param childName
+     *            the name of the element you want the CDATA from
      * @throws TransformerException if transformer error
+     * @return the CDATA as a <code>String</code>
      */
     private static String[] getRepeatedElementData(Node parentElement,
-                                                   String childName) throws TransformerException {
+            String childName) throws TransformerException
+    {
         // Grab the child node
         NodeList childNodes = XPathAPI.selectNodeList(parentElement, childName);
 
         String[] data = new String[childNodes.getLength()];
 
-        for (int i = 0; i < childNodes.getLength(); i++) {
+        for (int i = 0; i < childNodes.getLength(); i++)
+        {
             // Get the #text node
             Node dataNode = childNodes.item(i).getFirstChild();
 

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

@@ -14,6 +14,7 @@ import java.io.IOException;
 import java.sql.SQLException;
 import java.util.HashMap;
 import java.util.Map;
+
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
@@ -21,8 +22,10 @@ import javax.xml.transform.TransformerException;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
+import org.apache.commons.cli.ParseException;
 import org.apache.xpath.XPathAPI;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Collection;
@@ -45,6 +48,7 @@ import org.xml.sax.SAXException;
  * an XML file.
  * 
  * The XML file structure needs to be:
+ * <p>
  * {@code
  * <import_structure>
  *     <community>
@@ -56,39 +60,37 @@ import org.xml.sax.SAXException;
  *     </community>
  * </import_structure>
  * }
- * it can be arbitrarily deep, and supports all the metadata elements
+ * <p>
+ * It can be arbitrarily deep, and supports all the metadata elements
  * that make up the community and collection metadata.  See the system
- * documentation for more details
+ * documentation for more details.
  *
  * @author Richard Jones
+ *
  */
 
 public class StructBuilder {
     /**
-     * the output xml document which will contain updated information about the
-     * imported structure
+     * The output XML document which will contain updated information about the
+     * imported structure.
      */
-    private static org.jdom.Document xmlOutput = new org.jdom.Document(new Element("imported_structure"));
+    private static final org.jdom.Document xmlOutput
+            = new org.jdom.Document(new Element("imported_structure"));
 
     /**
-     * a hashtable to hold metadata for the collection being worked on
+     * A hash table to hold metadata for the collection being worked on.
      */
-    private static Map<String, String> collectionMap = new HashMap<String, String>();
+    private static final Map<String, String> collectionMap = new HashMap<>();
 
     /**
-     * a hashtable to hold metadata for the community being worked on
+     * A hash table to hold metadata for the community being worked on.
      */
-    private static Map<String, String> communityMap = new HashMap<String, String>();
+    private static final Map<String, String> communityMap = new HashMap<>();
 
     protected static CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
     protected static CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
     protected static EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
 
-    /**
-     * Default constructor
-     */
-    private StructBuilder() { }
-
     /**
      * Main method to be run from the command line to import a structure into
      * DSpace
@@ -101,19 +103,34 @@ public class StructBuilder {
      * with the handle for each imported item added as an attribute.
      *
      * @param argv the command line arguments given
-     * @throws Exception if an error occurs
+     * @throws ParserConfigurationException passed through.
+     * @throws SQLException passed through.
      */
     public static void main(String[] argv)
-        throws Exception {
-        CommandLineParser parser = new PosixParser();
+            throws ParserConfigurationException, SQLException {
+        CommandLineParser parser = new DefaultParser();
 
         Options options = new Options();
 
-        options.addOption("f", "file", true, "file");
+        options.addOption("h", "help", false, "help");
+        options.addOption("?", "help");
+        options.addOption("f", "file", true, "input structure document");
         options.addOption("e", "eperson", true, "eperson");
-        options.addOption("o", "output", true, "output");
+        options.addOption("o", "output", true, "output structure document");
 
-        CommandLine line = parser.parse(options, argv);
+        CommandLine line = null;
+        try {
+            line = parser.parse(options, argv);
+        } catch (ParseException ex) {
+            System.err.println(ex.getMessage());
+            usage(options);
+            System.exit(1);
+        }
+
+        if (line.hasOption('h') || line.hasOption('?')) {
+            usage(options);
+            System.exit(0);
+        }
 
         String file = null;
         String eperson = null;
@@ -132,22 +149,41 @@ public class StructBuilder {
         }
 
         if (output == null || eperson == null || file == null) {
-            usage();
-            System.exit(0);
+            usage(options);
+            System.exit(1);
         }
 
         // create a context
         Context context = new Context();
         
         // set the context
+        try {
             context.setCurrentUser(ePersonService.findByEmail(context, eperson));
+        } catch (SQLException ex) {
+            System.err.format("That user could not be found:  %s%n", ex.getMessage());
+            System.exit(1);
+        }
 
         // load the XML
-        Document document = loadXML(file);
+        Document document = null;
+        try {
+            document = loadXML(file);
+        } catch (IOException ex) {
+            System.err.format("The input document could not be read:  %s%n", ex.getMessage());
+            System.exit(1);
+        } catch (SAXException ex) {
+            System.err.format("The input document could not be parsed:  %s%n", ex.getMessage());
+            System.exit(1);
+        }
 
         // run the preliminary validation, to be sure that the the XML document
         // is properly structured
+        try {
             validate(document);
+        } catch (TransformerException ex) {
+            System.err.format("The input document is invalid:  %s%n", ex.getMessage());
+            System.exit(1);
+        }
 
         // load the mappings into the member variable hashmaps
         communityMap.put("name", "name");
@@ -164,71 +200,83 @@ public class StructBuilder {
         collectionMap.put("license", "license");
         collectionMap.put("provenance", "provenance_description");
 
+        Element[] elements = new Element[]{};
+        try {
             // get the top level community list
             NodeList first = XPathAPI.selectNodeList(document, "/import_structure/community");
 
             // run the import starting with the top level communities
-        Element[] elements = handleCommunities(context, first, null);
+            elements = handleCommunities(context, first, null);
+        } catch (TransformerException ex) {
+            System.err.format("Input content not understood:  %s%n", ex.getMessage());
+            System.exit(1);
+        } catch (AuthorizeException ex) {
+            System.err.format("Not authorized:  %s%n", ex.getMessage());
+            System.exit(1);
+        }
 
         // generate the output
         Element root = xmlOutput.getRootElement();
-        for (int i = 0; i < elements.length; i++) {
-            root.addContent(elements[i]);
+        for (Element element : elements) {
+            root.addContent(element);
         }
         
         // finally write the string into the output file
-        try {
-            BufferedWriter out = new BufferedWriter(new FileWriter(output));
+        try (BufferedWriter out = new BufferedWriter(new FileWriter(output));) {
             out.write(new XMLOutputter().outputString(xmlOutput));
-            out.close();
         } catch (IOException e) {
             System.out.println("Unable to write to output file " + output);
-            System.exit(0);
+            System.exit(1);
         }
         
         context.complete();
     }
     
     /**
-     * Output the usage information
+     * Output the usage information.
      */
-    private static void usage() {
-        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 void usage(Options options) {
+        HelpFormatter helper = new HelpFormatter();
+        helper.printHelp("java StructBuilder -f <source XML file> -o <output file> -e <eperson email>",
+                "Load community/collection structure from a file.",
+                options,
+                "Communities will be created from the top level,"
+                        + " and a map of communities to handles will be returned"
+                        + " in the output file.");
     }
     
     /**
-     * Validate the XML document.  This method does not return, but if validation
-     * fails it generates an error and ceases execution
+     * 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);
         }
         
         String errs = validateCommunities(first, 1);
-        if (errs != null) {
+        if (errs != null)
+        {
             err.append(errs);
             trip = true;
         }
         
-        if (trip) {
+        if (trip)
+        {
             System.out.println(err.toString());
             System.exit(0);
         }
@@ -236,27 +284,30 @@ public class StructBuilder {
     
     /**
      * Validate the communities section of the XML document.  This returns a string
-     * containing any errors encountered, or null if there were no errors
+     * containing any errors encountered, or null if there were no errors.
      *
      * @param communities the NodeList of communities to validate
      * @param level the level in the XML document that we are at, for the purposes
      * 			of error reporting
+     * 
      * @return the errors that need to be generated by the calling method, or null if
      * 			no errors.
      */
     private static String validateCommunities(NodeList communities, int level)
             throws TransformerException {
-        StringBuffer err = new StringBuffer();
+        StringBuilder err = new StringBuilder();
         boolean trip = false;
         String errs = null;
         
-        for (int i = 0; i < communities.getLength(); i++) {
+        for (int i = 0; i < communities.getLength(); i++)
+        {
             Node n = communities.item(i);
             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;
             }
 
@@ -277,7 +328,8 @@ public class StructBuilder {
             }
         }
         
-        if (trip) {
+        if (trip)
+        {
             errs = err.toString();
         }
         
@@ -286,30 +338,34 @@ 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
+     * 
      * @return the errors to be generated by the calling method, or null if none
      */
     private static String validateCollections(NodeList collections, int level)
             throws TransformerException {
-        StringBuffer err = new StringBuffer();
+        StringBuilder err = new StringBuilder();
         boolean trip = false;
         String errs = null;
         
-        for (int i = 0; i < collections.getLength(); i++) {
+        for (int i = 0; i < collections.getLength(); i++)
+        {
             Node n = collections.item(i);
             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;
             }
         }
         
-        if (trip) {
+        if (trip)
+        {
             errs = err.toString();
         }
         
@@ -319,11 +375,14 @@ public class StructBuilder {
     /**
      * Load in the XML from file.
      * 
-     * @param filename the filename to load from
+     * @param filename
+     *            the filename to load from
+     * 
      * @return the DOM representation of the XML file
      */
     private static org.w3c.dom.Document loadXML(String filename) 
-        throws IOException, ParserConfigurationException, SAXException {
+    	throws IOException, ParserConfigurationException, SAXException
+    {
         DocumentBuilder builder = DocumentBuilderFactory.newInstance()
                 .newDocumentBuilder();
 
@@ -336,15 +395,19 @@ public class StructBuilder {
      * Return the String value of a Node
      * 
      * @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) {
+    public static String getStringValue(Node node)
+    {
         String value = node.getNodeValue();
 
-        if (node.hasChildNodes()) {
+        if (node.hasChildNodes())
+        {
             Node first = node.getFirstChild();
 
-            if (first.getNodeType() == Node.TEXT_NODE) {
+            if (first.getNodeType() == Node.TEXT_NODE)
+            {
                 return first.getNodeValue().trim();
             }
         }
@@ -359,21 +422,26 @@ public class StructBuilder {
      * @param context the context of the request
      * @param communities a nodelist of communities to create along with their sub-structures
      * @param parent the parent community of the nodelist of communities to create
+     * 
      * @return an element array containing additional information regarding the 
      * 			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++) {
+        for (int i = 0; i < communities.getLength(); i++)
+        {
             Community community;
             Element element = new Element("community");
             
             // create the community or sub community
-            if (parent != null) {
+            if (parent != null)
+            {
                 community = communityService.create(parent, context);
-            } else {
+            }
+            else
+            {
                 community = communityService.create(null, context);
             }
             
@@ -382,20 +450,20 @@ public class StructBuilder {
             
             // now update the metadata
             Node tn = communities.item(i);
-            for (Map.Entry<String, String> entry : communityMap.entrySet()) {
+            for (Map.Entry<String, String> entry : communityMap.entrySet())
+            {
                 NodeList nl = XPathAPI.selectNodeList(tn, entry.getKey());
-                if (nl.getLength() == 1) {
+                if (nl.getLength() == 1)
+                {
                     communityService.setMetadata(context, community, entry.getValue(), getStringValue(nl.item(0)));
                 }
             }
             
             // 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);
@@ -414,25 +482,29 @@ public class StructBuilder {
             nameElement.setText(communityService.getMetadata(community, "name"));
             element.addContent(nameElement);
             
-            if (communityService.getMetadata(community, "short_description") != null) {
+            if (communityService.getMetadata(community, "short_description") != null)
+            {
                 Element descriptionElement = new Element("description");
                 descriptionElement.setText(communityService.getMetadata(community, "short_description"));
                 element.addContent(descriptionElement);
             }
             
-            if (communityService.getMetadata(community, "introductory_text") != null) {
+            if (communityService.getMetadata(community, "introductory_text") != null)
+            {
                 Element introElement = new Element("intro");
                 introElement.setText(communityService.getMetadata(community, "introductory_text"));
                 element.addContent(introElement);
             }
             
-            if (communityService.getMetadata(community, "copyright_text") != null) {
+            if (communityService.getMetadata(community, "copyright_text") != null)
+            {
                 Element copyrightElement = new Element("copyright");
                 copyrightElement.setText(communityService.getMetadata(community, "copyright_text"));
                 element.addContent(copyrightElement);
             }
             
-            if (communityService.getMetadata(community, "side_bar_text") != null) {
+            if (communityService.getMetadata(community, "side_bar_text") != null)
+            {
                 Element sidebarElement = new Element("sidebar");
                 sidebarElement.setText(communityService.getMetadata(community, "side_bar_text"));
                 element.addContent(sidebarElement);
@@ -447,10 +519,12 @@ public class StructBuilder {
             Element[] collectionElements = handleCollections(context, collections, community);
             
             int j;
-            for (j = 0; j < subCommunityElements.length; j++) {
+            for (j = 0; j < subCommunityElements.length; j++)
+            {
                 element.addContent(subCommunityElements[j]);
             }
-            for (j = 0; j < collectionElements.length; j++) {
+            for (j = 0; j < collectionElements.length; j++)
+            {
                 element.addContent(collectionElements[j]);
             }
             
@@ -466,14 +540,16 @@ public class StructBuilder {
      * @param context the context of the request
      * @param collections the node list of collections to be created
      * @param parent the parent community to whom the collections belong
+     * 
      * @return an Element array containing additional information about the
      * 			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++) {
+        for (int i = 0; i < collections.getLength(); i++)
+        {
             Element element = new Element("collection");
             Collection collection = collectionService.create(context, parent);
             
@@ -482,9 +558,11 @@ public class StructBuilder {
             
             // import the rest of the metadata
             Node tn = collections.item(i);
-            for (Map.Entry<String, String> entry : collectionMap.entrySet()) {
+            for (Map.Entry<String, String> entry : collectionMap.entrySet())
+            {
                 NodeList nl = XPathAPI.selectNodeList(tn, entry.getKey());
-                if (nl.getLength() == 1) {
+                if (nl.getLength() == 1)
+                {
                     collectionService.setMetadata(context, collection, entry.getValue(), getStringValue(nl.item(0)));
                 }
             }
@@ -497,37 +575,43 @@ public class StructBuilder {
             nameElement.setText(collectionService.getMetadata(collection, "name"));
             element.addContent(nameElement);
             
-            if (collectionService.getMetadata(collection, "short_description") != null) {
+            if (collectionService.getMetadata(collection, "short_description") != null)
+            {
                 Element descriptionElement = new Element("description");
                 descriptionElement.setText(collectionService.getMetadata(collection, "short_description"));
                 element.addContent(descriptionElement);
             }
             
-            if (collectionService.getMetadata(collection, "introductory_text") != null) {
+            if (collectionService.getMetadata(collection, "introductory_text") != null)
+            {
                 Element introElement = new Element("intro");
                 introElement.setText(collectionService.getMetadata(collection, "introductory_text"));
                 element.addContent(introElement);
             }
             
-            if (collectionService.getMetadata(collection, "copyright_text") != null) {
+            if (collectionService.getMetadata(collection, "copyright_text") != null)
+            {
                 Element copyrightElement = new Element("copyright");
                 copyrightElement.setText(collectionService.getMetadata(collection, "copyright_text"));
                 element.addContent(copyrightElement);
             }
             
-            if (collectionService.getMetadata(collection, "side_bar_text") != null) {
+            if (collectionService.getMetadata(collection, "side_bar_text") != null)
+            {
                 Element sidebarElement = new Element("sidebar");
                 sidebarElement.setText(collectionService.getMetadata(collection, "side_bar_text"));
                 element.addContent(sidebarElement);
             }
             
-            if (collectionService.getMetadata(collection, "license") != null) {
+            if (collectionService.getMetadata(collection, "license") != null)
+            {
                 Element sidebarElement = new Element("license");
                 sidebarElement.setText(collectionService.getMetadata(collection, "license"));
                 element.addContent(sidebarElement);
             }
             
-            if (collectionService.getMetadata(collection, "provenance_description") != null) {
+            if (collectionService.getMetadata(collection, "provenance_description") != null)
+            {
                 Element sidebarElement = new Element("provenance");
                 sidebarElement.setText(collectionService.getMetadata(collection, "provenance_description"));
                 element.addContent(sidebarElement);

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

@@ -7,93 +7,67 @@
  */
 package org.dspace.app.bulkedit;
 
+import org.dspace.content.Item;
+import org.dspace.content.Collection;
+
 import java.util.ArrayList;
 import java.util.List;
 
-import org.dspace.content.Collection;
-import org.dspace.content.Item;
-
 /**
  * Utility class to store changes to item that may occur during a batch edit.
  *
  * @author Stuart Lewis
  */
-public class BulkEditChange {
-    /**
-     * The item these changes relate to
-     */
+public class BulkEditChange
+{
+    /** The item these changes relate to */
     private Item item;
 
-    /**
-     * The List of hashtables with the new elements
-     */
+    /** The List of hashtables with the new elements */
     private List<BulkEditMetadataValue> adds;
 
-    /**
-     * The List of hashtables with the removed elements
-     */
+    /** The List of hashtables with the removed elements */
     private List<BulkEditMetadataValue> removes;
 
-    /**
-     * The List of hashtables with the unchanged elements
-     */
+    /** The List of hashtables with the unchanged elements */
     private List<BulkEditMetadataValue> constant;
 
-    /**
-     * The List of the complete set of new values (constant + adds)
-     */
+    /** The List of the complete set of new values (constant + adds) */
     private List<BulkEditMetadataValue> complete;
 
-    /**
-     * The list of old collections the item used to be mapped to
-     */
+    /** The list of old collections the item used to be mapped to */
     private List<Collection> oldMappedCollections;
 
-    /**
-     * The list of new collections the item has been mapped into
-     */
+    /** The list of new collections the item has been mapped into */
     private List<Collection> newMappedCollections;
 
-    /**
-     * The old owning collection
-     */
+    /** The old owning collection */
     private Collection oldOwningCollection;
 
-    /**
-     * The new owning collection
-     */
+    /** The new owning collection */
     private Collection newOwningCollection;
 
-    /**
-     * Is this a new item
-     */
+    /** Is this a new item */
     private boolean newItem;
 
-    /**
-     * Has this item been deleted?
-     */
+    /** Has this item been deleted? */
     private boolean deleted;
 
-    /**
-     * Has this item been withdrawn?
-     */
+    /** Has this item been withdrawn? */
     private boolean withdrawn;
 
-    /**
-     * Has this item been reinstated?
-     */
+    /** Has this item been reinstated? */
     private boolean reinstated;
 
-    /**
-     * Have any changes actually been made?
-     */
+    /** Have any changes actually been made? */
     private boolean empty;
 
 
     /**
      * Initialise a change holder for a new item 
      */
-    public BulkEditChange() {
+    public BulkEditChange()
+    {
         // Set the item to be null
         item = null;
         newItem = true;
@@ -115,7 +89,8 @@ public class BulkEditChange {
      *
      * @param i The Item to store
      */
-    public BulkEditChange(Item i) {
+    public BulkEditChange(Item i)
+    {
         // Store the item
         item = i;
         newItem = false;
@@ -135,7 +110,8 @@ public class BulkEditChange {
      *
      * @param i The item
      */
-    public void setItem(Item i) {
+    public void setItem(Item i)
+    {
         // Store the item
         item = i;
     }
@@ -145,7 +121,8 @@ public class BulkEditChange {
      *
      * @param dcv The value to add
      */
-    public void registerAdd(BulkEditMetadataValue dcv) {
+    public void registerAdd(BulkEditMetadataValue dcv)
+    {
         // Add the added value
         adds.add(dcv);
         complete.add(dcv);
@@ -157,7 +134,8 @@ public class BulkEditChange {
      *
      * @param dcv The value to remove
      */
-    public void registerRemove(BulkEditMetadataValue dcv) {
+    public void registerRemove(BulkEditMetadataValue dcv)
+    {
         // Add the removed value
         removes.add(dcv);
         empty = false;
@@ -168,7 +146,8 @@ public class BulkEditChange {
      *
      * @param dcv The value to keep unchanged
      */
-    public void registerConstant(BulkEditMetadataValue dcv) {
+    public void registerConstant(BulkEditMetadataValue dcv)
+    {
         // Add the removed value
         constant.add(dcv);
         complete.add(dcv);
@@ -179,7 +158,8 @@ public class BulkEditChange {
      *
      * @param c The new mapped Collection
      */
-    public void registerNewMappedCollection(Collection c) {
+    public void registerNewMappedCollection(Collection c)
+    {
         // Add the new owning Collection
         newMappedCollections.add(c);
         empty = false;
@@ -190,22 +170,27 @@ public class BulkEditChange {
      *
      * @param c The old mapped Collection
      */
-    public void registerOldMappedCollection(Collection c) {
+    public void registerOldMappedCollection(Collection c)
+    {
         // Add the old owning Collection (if it isn't there already, or is an old collection)
         boolean found = false;
 
         if ((this.getOldOwningCollection() != null) &&
-            (this.getOldOwningCollection().getHandle().equals(c.getHandle()))) {
+            (this.getOldOwningCollection().getHandle().equals(c.getHandle())))
+        {
             found = true;
         }
 
-        for (Collection collection : oldMappedCollections) {
-            if (collection.getHandle().equals(c.getHandle())) {
+        for (Collection collection : oldMappedCollections)
+        {
+            if (collection.getHandle().equals(c.getHandle()))
+            {
                 found = true;
             }
         }
 
-        if (!found) {
+        if (!found)
+        {
             oldMappedCollections.add(c);
             empty = false;
         }
@@ -217,7 +202,8 @@ public class BulkEditChange {
      * @param oldC The old owning collection
      * @param newC The new owning collection
      */
-    public void changeOwningCollection(Collection oldC, Collection newC) {
+    public void changeOwningCollection(Collection oldC, Collection newC)
+    {
         // Store the old owning collection
         oldOwningCollection = oldC;
 
@@ -231,7 +217,8 @@ public class BulkEditChange {
      *
      * @param newC The new owning collection
      */
-    public void setOwningCollection(Collection newC) {
+    public void setOwningCollection(Collection newC)
+    {
         // Store the new owning collection
         newOwningCollection = newC;
         //empty = false;
@@ -242,7 +229,8 @@ public class BulkEditChange {
      *
      * @return The item
      */
-    public Item getItem() {
+    public Item getItem()
+    {
         // Return the item
         return item;
     }
@@ -252,7 +240,8 @@ public class BulkEditChange {
      *
      * @return the list of elements and their values that have been added.
      */
-    public List<BulkEditMetadataValue> getAdds() {
+    public List<BulkEditMetadataValue> getAdds()
+    {
         // Return the array
         return adds;
     }
@@ -262,7 +251,8 @@ public class BulkEditChange {
      *
      * @return the list of elements and their values that have been removed.
      */
-    public List<BulkEditMetadataValue> getRemoves() {
+    public List<BulkEditMetadataValue> getRemoves()
+    {
         // Return the array
         return removes;
     }
@@ -272,7 +262,8 @@ public class BulkEditChange {
      *
      * @return the list of unchanged values
      */
-    public List<BulkEditMetadataValue> getConstant() {
+    public List<BulkEditMetadataValue> getConstant()
+    {
         // Return the array
         return constant;
     }
@@ -282,7 +273,8 @@ public class BulkEditChange {
      *
      * @return the list of all values
      */
-    public List<BulkEditMetadataValue> getComplete() {
+    public List<BulkEditMetadataValue> getComplete()
+    {
         // Return the array
         return complete;
     }
@@ -292,7 +284,8 @@ public class BulkEditChange {
      *
      * @return the list of new mapped collections
      */
-    public List<Collection> getNewMappedCollections() {
+    public List<Collection> getNewMappedCollections()
+    {
         // Return the array
         return newMappedCollections;
     }
@@ -302,7 +295,8 @@ public class BulkEditChange {
      *
      * @return the list of old mapped collections
      */
-    public List<Collection> getOldMappedCollections() {
+    public List<Collection> getOldMappedCollections()
+    {
         // Return the array
         return oldMappedCollections;
     }
@@ -312,7 +306,8 @@ public class BulkEditChange {
      *
      * @return the old owning collection
      */
-    public Collection getOldOwningCollection() {
+    public Collection getOldOwningCollection()
+    {
         // Return the old owning collection
         return oldOwningCollection;
     }
@@ -322,7 +317,8 @@ public class BulkEditChange {
      *
      * @return the new owning collection
      */
-    public Collection getNewOwningCollection() {
+    public Collection getNewOwningCollection()
+    {
         // Return the new owning collection
         return newOwningCollection;
     }
@@ -332,7 +328,8 @@ public class BulkEditChange {
      *
      * @return Whether or not this is for a new item
      */
-    public boolean isNewItem() {
+    public boolean isNewItem()
+    {
         // Return the new item status
         return newItem;
     }
@@ -342,7 +339,8 @@ public class BulkEditChange {
      *
      * @return Whether or not this is for a deleted item
      */
-    public boolean isDeleted() {
+    public boolean isDeleted()
+    {
         // Return the new item status
         return deleted;
     }
@@ -361,7 +359,8 @@ public class BulkEditChange {
      *
      * @return Whether or not this is for a withdrawn item
      */
-    public boolean isWithdrawn() {
+    public boolean isWithdrawn()
+    {
         // Return the new item status
         return withdrawn;
     }
@@ -380,7 +379,8 @@ public class BulkEditChange {
      *
      * @return Whether or not this is for a reinstated item
      */
-    public boolean isReinstated() {
+    public boolean isReinstated()
+    {
         // Return the new item status
         return reinstated;
     }
@@ -399,7 +399,8 @@ public class BulkEditChange {
      *
      * @return Whether or not changes have been made
      */
-    public boolean hasChanges() {
+    public boolean hasChanges()
+    {
         return !empty;
     }
 }

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

@@ -7,26 +7,7 @@
  */
 package org.dspace.app.bulkedit;
 
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-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;
@@ -35,14 +16,19 @@ import org.dspace.content.Item;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
 import org.dspace.content.MetadataValue;
-import org.dspace.content.authority.Choices;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
 import org.dspace.content.service.MetadataFieldService;
 import org.dspace.content.service.MetadataSchemaService;
+import org.dspace.content.authority.Choices;
 import org.dspace.core.Context;
 import org.dspace.services.factory.DSpaceServicesFactory;
 
+import java.util.*;
+import java.util.regex.Pattern;
+import java.util.regex.Matcher;
+import java.io.*;
+
 /**
  * Utility class to read and write CSV files
  *
@@ -57,69 +43,45 @@ import org.dspace.services.factory.DSpaceServicesFactory;
  *
  * @author Stuart Lewis
  */
-public class DSpaceCSV implements Serializable {
-    /**
-     * The headings of the CSV file
-     */
+public class DSpaceCSV implements Serializable
+{
+    /** The headings of the CSV file */
     protected List<String> headings;
 
-    /**
-     * An array list of CSV lines
-     */
+    /** An array list of CSV lines */
     protected List<DSpaceCSVLine> lines;
 
-    /**
-     * A counter of how many CSV lines this object holds
-     */
+    /** A counter of how many CSV lines this object holds */
     protected int counter;
 
-    /**
-     * The value separator (defaults to double pipe '||')
-     */
+    /** The value separator (defaults to double pipe '||') */
     protected String valueSeparator;
 
-    /**
-     * The value separator in an escaped form for using in regexes
-     */
+    /** The value separator in an escaped form for using in regexes */
     protected String escapedValueSeparator;
 
-    /**
-     * The field separator (defaults to comma)
-     */
+    /** The field separator (defaults to comma) */
     protected String fieldSeparator;
 
-    /**
-     * The field separator in an escaped form for using in regexes
-     */
+    /** The field separator in an escaped form for using in regexes */
     protected String escapedFieldSeparator;
 
-    /**
-     * The authority separator (defaults to double colon '::')
-     */
+    /** The authority separator (defaults to double colon '::') */
     protected String authoritySeparator;
 
-    /**
-     * The authority separator in an escaped form for using in regexes
-     */
+    /** The authority separator in an escaped form for using in regexes */
     protected String escapedAuthoritySeparator;
 
     protected transient final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-    protected transient final MetadataSchemaService metadataSchemaService =
-        ContentServiceFactory.getInstance().getMetadataSchemaService();
-    protected transient final MetadataFieldService metadataFieldService =
-        ContentServiceFactory.getInstance().getMetadataFieldService();
-    protected transient final AuthorityValueService authorityValueService =
-        AuthorityServiceFactory.getInstance().getAuthorityValueService();
+    protected transient final MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance().getMetadataSchemaService();
+    protected transient final MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance().getMetadataFieldService();
+    protected transient final AuthorityValueService authorityValueService = AuthorityServiceFactory.getInstance().getAuthorityValueService();
 
 
-    /**
-     * Whether to export all metadata such as handles and provenance information
-     */
+    /** Whether to export all metadata such as handles and provenance information */
     protected boolean exportAll;
 
-    /**
-     * A list of metadata elements to ignore
-     */
+    /** A list of metadata elements to ignore */
     protected Map<String, String> ignore;
 
 
@@ -128,7 +90,8 @@ public class DSpaceCSV implements Serializable {
      *
      * @param exportAll Whether to export all metadata such as handles and provenance information
      */
-    public DSpaceCSV(boolean exportAll) {
+    public DSpaceCSV(boolean exportAll)
+    {
         // Initialise the class
         init();
 
@@ -141,37 +104,48 @@ public class DSpaceCSV implements Serializable {
      *
      * @param f The file to read from
      * @param c The DSpace Context
+     *
      * @throws Exception thrown if there is an error reading or processing the file
      */
-    public DSpaceCSV(File f, Context c) throws Exception {
+    public DSpaceCSV(File f, Context c) throws Exception
+    {
         // Initialise the class
         init();
 
         // Open the CSV file
         BufferedReader input = null;
-        try {
+        try
+        {
             input = new BufferedReader(new InputStreamReader(new FileInputStream(f),"UTF-8"));
 
             // Read the heading line
             String head = input.readLine();
             String[] headingElements = head.split(escapedFieldSeparator);
             int columnCounter = 0;
-            for (String element : headingElements) {
+            for (String element : headingElements)
+            {
                 columnCounter++;
 
                 // Remove surrounding quotes if there are any
-                if ((element.startsWith("\"")) && (element.endsWith("\""))) {
+                if ((element.startsWith("\"")) && (element.endsWith("\"")))
+                {
                     element = element.substring(1, element.length() - 1);
                 }
 
                 // Store the heading
-                if ("collection".equals(element)) {
+                if ("collection".equals(element))
+                {
                     // Store the heading
                     headings.add(element);
-                } else if ("action".equals(element)) { // Store the action
+                }
+                // Store the action
+                else if ("action".equals(element))
+                {
                     // Store the heading
                     headings.add(element);
-                } else if (!"id".equals(element)) {
+                }
+                else if (!"id".equals(element))
+                {
                     String authorityPrefix = "";
                     AuthorityValue authorityValueType = authorityValueService.getAuthorityValueType(element);
                     if (authorityValueType != null) {
@@ -206,8 +180,7 @@ public class DSpaceCSV implements Serializable {
                     }
 
                     // Check that the metadata element exists in the schema
-                    MetadataField foundField = metadataFieldService
-                        .findByElement(c, foundSchema, metadataElement, metadataQualifier);
+                    MetadataField foundField = metadataFieldService.findByElement(c, foundSchema, metadataElement, metadataQualifier);
                     if (foundField == null) {
                         throw new MetadataImportInvalidHeadingException(clean[0],
                                                                         MetadataImportInvalidHeadingException.ELEMENT,
@@ -223,7 +196,8 @@ public class DSpaceCSV implements Serializable {
             StringBuilder lineBuilder = new StringBuilder();
             String lineRead;
 
-            while ((lineRead = input.readLine()) != null) {
+            while ((lineRead = input.readLine()) != null)
+            {
                 if (lineBuilder.length() > 0) {
                     // Already have a previously read value - add this line
                     lineBuilder.append("\n").append(lineRead);
@@ -262,8 +236,11 @@ public class DSpaceCSV implements Serializable {
                     addItem(lineRead);
                 }
             }
-        } finally {
-            if (input != null) {
+        }
+        finally
+        {
+            if (input != null)
+            {
                 input.close();
             }
         }
@@ -272,7 +249,8 @@ public class DSpaceCSV implements Serializable {
     /**
      * Initialise this class with values from dspace.cfg
      */
-    protected void init() {
+    protected void init()
+    {
         // Set the value separator
         setValueSeparator();
 
@@ -295,16 +273,13 @@ public class DSpaceCSV implements Serializable {
         ignore = new HashMap<>();
 
         // Specify default values
-        String[] defaultValues =
-            new String[] {
-                "dc.date.accessioned, dc.date.available, dc.date.updated, dc.description.provenance"
-            };
-        String[] toIgnoreArray =
-            DSpaceServicesFactory.getInstance()
-                                 .getConfigurationService()
-                                 .getArrayProperty("bulkedit.ignore-on-export", defaultValues);
-        for (String toIgnoreString : toIgnoreArray) {
-            if (!"".equals(toIgnoreString.trim())) {
+        String[] defaultValues = new String[]{"dc.date.accessioned", "dc.date.available", 
+                                              "dc.date.updated", "dc.description.provenance"};
+        String[] toIgnoreArray = DSpaceServicesFactory.getInstance().getConfigurationService().getArrayProperty("bulkedit.ignore-on-export", defaultValues);
+        for (String toIgnoreString : toIgnoreArray)
+        {
+            if (!"".equals(toIgnoreString.trim()))
+            {
                 ignore.put(toIgnoreString.trim(), toIgnoreString.trim());
             }
         }
@@ -332,13 +307,16 @@ public class DSpaceCSV implements Serializable {
      *
      * If not set, defaults to double pipe '||'
      */
-    private void setValueSeparator() {
+    private void setValueSeparator()
+    {
         // Get the value separator
-        valueSeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
-                                              .getProperty("bulkedit.valueseparator");
-        if ((valueSeparator != null) && (!"".equals(valueSeparator.trim()))) {
+        valueSeparator = DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("bulkedit.valueseparator");
+        if ((valueSeparator != null) && (!"".equals(valueSeparator.trim())))
+        {
             valueSeparator = valueSeparator.trim();
-        } else {
+        }
+        else
+        {
             valueSeparator = "||";
         }
 
@@ -358,22 +336,32 @@ public class DSpaceCSV implements Serializable {
      * Special values are 'tab', 'hash' and 'semicolon' which will
      * get substituted from the text to the value.
      */
-    private void setFieldSeparator() {
+    private void setFieldSeparator()
+    {
         // Get the value separator
-        fieldSeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
-                                              .getProperty("bulkedit.fieldseparator");
-        if ((fieldSeparator != null) && (!"".equals(fieldSeparator.trim()))) {
+        fieldSeparator =DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("bulkedit.fieldseparator");
+        if ((fieldSeparator != null) && (!"".equals(fieldSeparator.trim())))
+        {
             fieldSeparator = fieldSeparator.trim();
-            if ("tab".equals(fieldSeparator)) {
+            if ("tab".equals(fieldSeparator))
+            {
                 fieldSeparator = "\t";
-            } else if ("semicolon".equals(fieldSeparator)) {
+            }
+            else if ("semicolon".equals(fieldSeparator))
+            {
                 fieldSeparator = ";";
-            } else if ("hash".equals(fieldSeparator)) {
+            }
+            else if ("hash".equals(fieldSeparator))
+            {
                 fieldSeparator = "#";
-            } else {
+            }
+            else
+            {
                 fieldSeparator = fieldSeparator.trim();
             }
-        } else {
+        }
+        else
+        {
             fieldSeparator = ",";
         }
 
@@ -390,13 +378,16 @@ public class DSpaceCSV implements Serializable {
      *
      * If not set, defaults to double colon '::'
      */
-    private void setAuthoritySeparator() {
+    private void setAuthoritySeparator()
+    {
         // Get the value separator
-        authoritySeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
-                                                  .getProperty("bulkedit.authorityseparator");
-        if ((authoritySeparator != null) && (!"".equals(authoritySeparator.trim()))) {
+        authoritySeparator = DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("bulkedit.authorityseparator");
+        if ((authoritySeparator != null) && (!"".equals(authoritySeparator.trim())))
+        {
             authoritySeparator = authoritySeparator.trim();
-        } else {
+        }
+        else
+        {
             authoritySeparator = "::";
         }
 
@@ -410,9 +401,11 @@ public class DSpaceCSV implements Serializable {
      * Add a DSpace item to the CSV file
      *
      * @param i The DSpace item
+     *
      * @throws Exception if something goes wrong with adding the Item
      */
-    public final void addItem(Item i) throws Exception {
+    public final void addItem(Item i) throws Exception
+    {
         // If the item does not have an "owningCollection" the the below "getHandle()" call will fail
         // This should not happen but is here for safety.
         if (i.getOwningCollection() == null) {
@@ -428,42 +421,49 @@ public class DSpaceCSV implements Serializable {
 
         // Add in any mapped collections
         List<Collection> collections = i.getCollections();
-        for (Collection c : collections) {
+        for (Collection c : collections)
+        {
             // Only add if it is not the owning collection
-            if (!c.getHandle().equals(owningCollectionHandle)) {
+            if (!c.getHandle().equals(owningCollectionHandle))
+            {
                 line.add("collection", c.getHandle());
             }
         }
 
         // Populate it
         List<MetadataValue> md = itemService.getMetadata(i, Item.ANY, Item.ANY, Item.ANY, Item.ANY);
-        for (MetadataValue value : md) {
+        for (MetadataValue value : md)
+        {
             MetadataField metadataField = value.getMetadataField();
             MetadataSchema metadataSchema = metadataField.getMetadataSchema();
             // Get the key (schema.element)
             String key = metadataSchema.getName() + "." + metadataField.getElement();
 
             // Add the qualifier if there is one (schema.element.qualifier)
-            if (metadataField.getQualifier() != null) {
+            if (metadataField.getQualifier() != null)
+            {
                 key = key + "." + metadataField.getQualifier();
             }
 
             // Add the language if there is one (schema.element.qualifier[langauge])
             //if ((value.language != null) && (!"".equals(value.language)))
-            if (value.getLanguage() != null) {
+            if (value.getLanguage() != null)
+            {
                 key = key + "[" + value.getLanguage() + "]";
             }
 
             // Store the item
-            if (exportAll || okToExport(metadataField)) {
+            if (exportAll || okToExport(metadataField))
+            {
                 // Add authority and confidence if authority is not null
                 String mdValue = value.getValue();
-                if (value.getAuthority() != null && !"".equals(value.getAuthority())) {
-                    mdValue += authoritySeparator + value.getAuthority() + authoritySeparator + (value
-                        .getConfidence() != -1 ? value.getConfidence() : Choices.CF_ACCEPTED);
+                if (value.getAuthority() != null && !"".equals(value.getAuthority()))
+                {
+                    mdValue += authoritySeparator + value.getAuthority() + authoritySeparator + (value.getConfidence() != -1 ? value.getConfidence() : Choices.CF_ACCEPTED);
                 }
                 line.add(key, mdValue);
-                if (!headings.contains(key)) {
+                if (!headings.contains(key))
+                {
                     headings.add(key);
                 }
             }
@@ -478,10 +478,12 @@ public class DSpaceCSV implements Serializable {
      * @param line The line of elements
      * @throws Exception Thrown if an error occurs when adding the item
      */
-    public final void addItem(String line) throws Exception {
+    public final void addItem(String line) throws Exception
+    {
         // Check to see if the last character is a field separator, which hides the last empty column
         boolean last = false;
-        if (line.endsWith(fieldSeparator)) {
+        if (line.endsWith(fieldSeparator))
+        {
             // Add a space to the end, then remove it later
             last = true;
             line += " ";
@@ -494,12 +496,15 @@ public class DSpaceCSV implements Serializable {
 
         // Merge parts with embedded separators
         boolean alldone = false;
-        while (!alldone) {
+        while (!alldone)
+        {
             boolean found = false;
             int i = 0;
-            for (String part : bits) {
+            for (String part : bits)
+            {
                 int bitcounter = part.length() - part.replaceAll("\"", "").length();
-                if ((part.startsWith("\"")) && ((!part.endsWith("\"")) || ((bitcounter & 1) == 1))) {
+                if ((part.startsWith("\"")) && ((!part.endsWith("\"")) || ((bitcounter & 1) == 1)))
+                {
                     found = true;
                     String add = bits.get(i) + fieldSeparator + bits.get(i + 1);
                     bits.remove(i);
@@ -514,8 +519,10 @@ public class DSpaceCSV implements Serializable {
 
         // Deal with quotes around the elements
         int i = 0;
-        for (String part : bits) {
-            if ((part.startsWith("\"")) && (part.endsWith("\""))) {
+        for (String part : bits)
+        {
+            if ((part.startsWith("\"")) && (part.endsWith("\"")))
+            {
                 part = part.substring(1, part.length() - 1);
                 bits.set(i, part);
             }
@@ -524,8 +531,10 @@ public class DSpaceCSV implements Serializable {
 
         // Remove embedded quotes
         i = 0;
-        for (String part : bits) {
-            if (part.contains("\"\"")) {
+        for (String part : bits)
+        {
+            if (part.contains("\"\""))
+            {
                 part = part.replaceAll("\"\"", "\"");
                 bits.set(i, part);
             }
@@ -537,12 +546,18 @@ public class DSpaceCSV implements Serializable {
         DSpaceCSVLine csvLine;
 
         // Is this an existing item, or a new item (where id = '+')
-        if ("+".equals(id)) {
+        if ("+".equals(id))
+        {
             csvLine = new DSpaceCSVLine();
-        } else {
-            try {
+        }
+        else
+        {
+            try
+            {
                 csvLine = new DSpaceCSVLine(UUID.fromString(id));
-            } catch (NumberFormatException nfe) {
+            }
+            catch (NumberFormatException nfe)
+            {
                 System.err.println("Invalid item identifier: " + id);
                 System.err.println("Please check your CSV file for information. " +
                                    "Item id must be numeric, or a '+' to add a new item");
@@ -552,10 +567,13 @@ public class DSpaceCSV implements Serializable {
 
         // Add the rest of the parts
         i = 0;
-        for (String part : bits) {
-            if (i > 0) {
+        for (String part : bits)
+        {
+            if (i > 0)
+            {
                 // Is this a last empty item?
-                if ((last) && (i == headings.size())) {
+                if ((last) && (i == headings.size()))
+                {
                     part = "";
                 }
 
@@ -567,8 +585,10 @@ public class DSpaceCSV implements Serializable {
                 }
                 csvLine.add(headings.get(i - 1), null);
                 String[] elements = part.split(escapedValueSeparator);
-                for (String element : elements) {
-                    if ((element != null) && (!"".equals(element))) {
+                for (String element : elements)
+                {
+                    if ((element != null) && (!"".equals(element)))
+                    {
                         csvLine.add(headings.get(i - 1), element);
                     }
                 }
@@ -584,7 +604,8 @@ public class DSpaceCSV implements Serializable {
      *
      * @return The lines
      */
-    public final List<DSpaceCSVLine> getCSVLines() {
+    public final List<DSpaceCSVLine> getCSVLines()
+    {
         // Return the lines
         return lines;
     }
@@ -594,19 +615,22 @@ public class DSpaceCSV implements Serializable {
      *
      * @return the array of CSV formatted Strings
      */
-    public final String[] getCSVLinesAsStringArray() {
+    public final String[] getCSVLinesAsStringArray()
+    {
         // Create the headings line
         String[] csvLines = new String[counter + 1];
         csvLines[0] = "id" + fieldSeparator + "collection";
         List<String> headingsCopy = new ArrayList<>(headings);
         Collections.sort(headingsCopy);
-        for (String value : headingsCopy) {
+        for (String value : headingsCopy)
+        {
             csvLines[0] = csvLines[0] + fieldSeparator + value;
         }
 
         Iterator<DSpaceCSVLine> i = lines.iterator();
         int c = 1;
-        while (i.hasNext()) {
+        while (i.hasNext())
+        {
             csvLines[c++] = i.next().toCSV(headingsCopy, fieldSeparator, valueSeparator);
         }
 
@@ -617,9 +641,11 @@ public class DSpaceCSV implements Serializable {
      * Save the CSV file to the given filename
      *
      * @param filename The filename to save the CSV file to
+     *
      * @throws IOException Thrown if an error occurs when writing the file
      */
-    public final void save(String filename) throws IOException {
+    public final void save(String filename) throws IOException
+    {
         // Save the file
         BufferedWriter out = new BufferedWriter(
                              new OutputStreamWriter(
@@ -640,10 +666,12 @@ public class DSpaceCSV implements Serializable {
      * @param md The Metadatum to examine
      * @return Whether or not it is OK to export this element
      */
-    protected boolean okToExport(MetadataField md) {
+    protected boolean okToExport(MetadataField md)
+    {
         // Now compare with the list to ignore
         String key = md.getMetadataSchema().getName() + "." + md.getElement();
-        if (md.getQualifier() != null) {
+        if (md.getQualifier() != null)
+        {
             key += "." + md.getQualifier();
         }
         if (ignore.get(key) != null) {
@@ -659,7 +687,8 @@ public class DSpaceCSV implements Serializable {
      *
      * @return The headings
      */
-    public List<String> getHeadings() {
+    public List<String> getHeadings()
+    {
         return headings;
     }
 
@@ -669,11 +698,13 @@ public class DSpaceCSV implements Serializable {
      * @return The formatted String as a csv
      */
     @Override
-    public final String toString() {
+    public final String toString()
+    {
         // Return the csv as one long string
         StringBuilder csvLines = new StringBuilder();
         String[] lines = this.getCSVLinesAsStringArray();
-        for (String line : lines) {
+        for (String line : lines)
+        {
             csvLines.append(line).append("\n");
         }
         return csvLines.toString();

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

@@ -7,41 +7,30 @@
  */
 package org.dspace.app.bulkedit;
 
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-import java.util.UUID;
-
 import org.dspace.authority.AuthorityValue;
 import org.dspace.authority.factory.AuthorityServiceFactory;
 import org.dspace.authority.service.AuthorityValueService;
 
+import java.io.Serializable;
+import java.util.*;
+
 /**
  * Utility class to store a line from a CSV file
  *
  * @author Stuart Lewis
  */
-public class DSpaceCSVLine implements Serializable {
-    /**
-     * The item id of the item represented by this line. -1 is for a new item
-     */
+public class DSpaceCSVLine implements Serializable
+{
+    /** The item id of the item represented by this line. -1 is for a new item */
     private final UUID id;
 
-    /**
-     * The elements in this line in a hashtable, keyed by the metadata type
-     */
+    /** The elements in this line in a hashtable, keyed by the metadata type */
     private final Map<String, ArrayList> items;
 
     protected transient final AuthorityValueService authorityValueService
             = AuthorityServiceFactory.getInstance().getAuthorityValueService();
 
-    /**
-     * ensuring that the order-sensible columns of the csv are processed in the correct order
-     */
+    /** ensuring that the order-sensible columns of the csv are processed in the correct order */
     private transient final Comparator<? super String> headerComparator = new Comparator<String>() {
         @Override
         public int compare(String md1, String md2) {
@@ -52,7 +41,8 @@ public class DSpaceCSVLine implements Serializable {
             int compare;
             if (source1 == null && source2 != null) {
                 compare = -1;
-            } else if (source1 != null && source2 == null) {
+            }
+            else if (source1 != null && source2 == null) {
                 compare = 1;
             } else {
                 // the order of the rest does not matter
@@ -67,7 +57,8 @@ public class DSpaceCSVLine implements Serializable {
      *
      * @param itemId The item ID of the line
      */
-    public DSpaceCSVLine(UUID itemId) {
+    public DSpaceCSVLine(UUID itemId)
+    {
         // Store the ID + separator, and initialise the hashtable
         this.id = itemId;
         items = new TreeMap<>(headerComparator);
@@ -77,7 +68,8 @@ public class DSpaceCSVLine implements Serializable {
     /**
      * Create a new CSV line for a new item
      */
-    public DSpaceCSVLine() {
+    public DSpaceCSVLine()
+    {
         // Set the ID to be null, and initialise the hashtable
         this.id = null;
         this.items = new TreeMap<>(headerComparator);
@@ -88,7 +80,8 @@ public class DSpaceCSVLine implements Serializable {
      *
      * @return The item ID
      */
-    public UUID getID() {
+    public UUID getID()
+    {
         // Return the ID
         return id;
     }
@@ -99,14 +92,17 @@ public class DSpaceCSVLine implements Serializable {
      * @param key The metadata key (e.g. dc.contributor.author)
      * @param value The metadata value
      */
-    public void add(String key, String value) {
+    public void add(String key, String value)
+    {
         // Create the array list if we need to
-        if (items.get(key) == null) {
+        if (items.get(key) == null)
+        {
             items.put(key, new ArrayList<String>());
         }
 
         // Store the item if it is not null
-        if (value != null) {
+        if (value != null)
+        {
             items.get(key).add(value);
         }
     }
@@ -117,7 +113,8 @@ public class DSpaceCSVLine implements Serializable {
      * @param key The metadata key
      * @return All the elements that match
      */
-    public List<String> get(String key) {
+    public List<String> get(String key)
+    {
         // Return any relevant values
         return items.get(key);
     }
@@ -127,7 +124,8 @@ public class DSpaceCSVLine implements Serializable {
      *
      * @return The action (may be blank, 'withdraw', 'reinstate' or 'delete')
      */
-    public String getAction() {
+    public String getAction()
+    {
         if (items.containsKey("action")) {
             ArrayList actions = items.get("action");
             if (actions.size() > 0) {
@@ -142,7 +140,8 @@ public class DSpaceCSVLine implements Serializable {
      *
      * @return An enumeration of all the keys
      */
-    public Set<String> keys() {
+    public Set<String> keys()
+    {
         // Return the keys
         return items.keySet();
     }
@@ -155,7 +154,8 @@ public class DSpaceCSVLine implements Serializable {
      * @param valueSeparator separator between metadata values (within a field)
      * @return The CSV formatted String
      */
-    protected String toCSV(List<String> headings, String fieldSeparator, String valueSeparator) {
+    protected String toCSV(List<String> headings, String fieldSeparator, String valueSeparator)
+    {
         StringBuilder bits = new StringBuilder();
 
         // Add the id
@@ -163,10 +163,12 @@ public class DSpaceCSVLine implements Serializable {
         bits.append(valueToCSV(items.get("collection"),valueSeparator));
 
         // Add the rest of the elements
-        for (String heading : headings) {
+        for (String heading : headings)
+        {
             bits.append(fieldSeparator);
             List<String> values = items.get(heading);
-            if (values != null && !"collection".equals(heading)) {
+            if (values != null && !"collection".equals(heading))
+            {
                 bits.append(valueToCSV(values, valueSeparator));
             }
         }
@@ -181,22 +183,29 @@ public class DSpaceCSVLine implements Serializable {
      * @param valueSeparator value separator
      * @return The line as a CSV formatted String
      */
-    protected String valueToCSV(List<String> values, String valueSeparator) {
+    protected String valueToCSV(List<String> values, String valueSeparator)
+    {
         // Check there is some content
-        if (values == null) {
+        if (values == null)
+        {
             return "";
         }
 
         // Get on with the work
         String s;
-        if (values.size() == 1) {
+        if (values.size() == 1)
+        {
             s = values.get(0);
-        } else {
+        }
+        else
+        {
             // Concatenate any fields together
             StringBuilder str = new StringBuilder();
 
-            for (String value : values) {
-                if (str.length() > 0) {
+            for (String value : values)
+            {
+                if (str.length() > 0)
+                {
                     str.append(valueSeparator);
                 }
 

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

@@ -7,46 +7,37 @@
  */
 package org.dspace.app.bulkedit;
 
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
+import org.apache.commons.cli.*;
 
-import com.google.common.collect.Iterators;
-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.dspace.content.Collection;
-import org.dspace.content.Community;
-import org.dspace.content.DSpaceObject;
-import org.dspace.content.Item;
+import org.dspace.content.*;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.handle.factory.HandleServiceFactory;
 
+import java.util.ArrayList;
+import java.sql.SQLException;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
 /**
  * Metadata exporter to allow the batch export of metadata into a file
  *
  * @author Stuart Lewis
  */
-public class MetadataExport {
-    /**
-     * The items to export
-     */
+public class MetadataExport
+{
+    /** The items to export */
     protected Iterator<Item> toExport;
 
     protected ItemService itemService;
 
     protected Context context;
 
-    /**
-     * Whether to export all metadata, or just normally edited metadata
-     */
+    /** Whether to export all metadata, or just normally edited metadata */
     protected boolean exportAll;
 
     protected MetadataExport() {
@@ -60,7 +51,8 @@ public class MetadataExport {
      * @param toExport The ItemIterator of items to export
      * @param exportAll whether to export all metadata or not (include handle, provenance etc)
      */
-    public MetadataExport(Context c, Iterator<Item> toExport, boolean exportAll) {
+    public MetadataExport(Context c, Iterator<Item> toExport, boolean exportAll)
+    {
         itemService = ContentServiceFactory.getInstance().getItemService();
 
         // Store the export settings
@@ -76,15 +68,19 @@ public class MetadataExport {
      * @param toExport The Community to export
      * @param exportAll whether to export all metadata or not (include handle, provenance etc)
      */
-    public MetadataExport(Context c, Community toExport, boolean exportAll) {
+    public MetadataExport(Context c, Community toExport, boolean exportAll)
+    {
         itemService = ContentServiceFactory.getInstance().getItemService();
 
-        try {
+        try
+        {
             // Try to export the community
             this.toExport = buildFromCommunity(c, toExport, 0);
             this.exportAll = exportAll;
             this.context = c;
-        } catch (SQLException sqle) {
+        }
+        catch (SQLException sqle)
+        {
             // Something went wrong...
             System.err.println("Error running exporter:");
             sqle.printStackTrace(System.err);
@@ -98,23 +94,26 @@ public class MetadataExport {
      * @param context DSpace context
      * @param community The community to build from
      * @param indent How many spaces to use when writing out the names of items added
-     * @return The list of item ids
+     * @return Iterator over the Collection of item ids
      * @throws SQLException if database error
      */
     protected Iterator<Item> buildFromCommunity(Context context, Community community, int indent)
             throws SQLException {
+        Set<Item> result = new HashSet<>();
+
         // Add all the collections
         List<Collection> collections = community.getCollections();
-        Iterator<Item> result = null;
         for (Collection collection : collections) {
             for (int i = 0; i < indent; i++) {
                 System.out.print(" ");
             }
 
             Iterator<Item> items = itemService.findByCollection(context, collection);
-            result = addItemsToResult(result, items);
-
+            while (items.hasNext()) {
+                result.add(items.next());
             }
+        }
+
         // Add all the sub-communities
         List<Community> communities = community.getSubcommunities();
         for (Community subCommunity : communities) {
@@ -122,20 +121,12 @@ public class MetadataExport {
                 System.out.print(" ");
             }
             Iterator<Item> items = buildFromCommunity(context, subCommunity, indent + 1);
-            result = addItemsToResult(result, items);
+            while (items.hasNext()) {
+                result.add(items.next());
+            }
         }
 
-        return result;
-    }
-
-    private Iterator<Item> addItemsToResult(Iterator<Item> result, Iterator<Item> items) {
-        if (result == null) {
-            result = items;
-        } else {
-            result = Iterators.concat(result, items);
-        }
-
-        return result;
+        return result.iterator();
     }
 
     /**
@@ -143,14 +134,17 @@ public class MetadataExport {
      *
      * @return the exported CSV lines
      */
-    public DSpaceCSV export() {
-        try {
+    public DSpaceCSV export()
+    {
+        try
+        {
             Context.Mode originalMode = context.getCurrentMode();
             context.setMode(Context.Mode.READ_ONLY);
 
             // Process each item
             DSpaceCSV csv = new DSpaceCSV(exportAll);
-            while (toExport.hasNext()) {
+            while (toExport.hasNext())
+            {
                 Item item = toExport.next();
                 csv.addItem(item);
                 context.uncacheEntity(item);
@@ -159,7 +153,9 @@ public class MetadataExport {
             context.setMode(originalMode);
             // Return the results
             return csv;
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             // Something went wrong...
             System.err.println("Error exporting to CSV:");
             e.printStackTrace();
@@ -173,7 +169,8 @@ public class MetadataExport {
      * @param options The command line options the user gave
      * @param exitCode the system exit code to use
      */
-    private static void printHelp(Options options, int exitCode) {
+    private static void printHelp(Options options, int exitCode)
+    {
         // print the help message
         HelpFormatter myhelp = new HelpFormatter();
         myhelp.printHelp("MetadataExport\n", options);
@@ -188,7 +185,8 @@ public class MetadataExport {
 	 * @param argv the command line arguments given
          * @throws Exception if error occurs
 	 */
-    public static void main(String[] argv) throws Exception {
+    public static void main(String[] argv) throws Exception
+    {
         // Create an options object and populate it
         CommandLineParser parser = new PosixParser();
 
@@ -196,26 +194,30 @@ public class MetadataExport {
 
         options.addOption("i", "id", true, "ID or handle of thing to export (item, collection, or community)");
         options.addOption("f", "file", true, "destination where you want file written");
-        options.addOption("a", "all", false,
-                          "include all metadata fields that are not normally changed (e.g. provenance)");
+        options.addOption("a", "all", false, "include all metadata fields that are not normally changed (e.g. provenance)");
         options.addOption("h", "help", false, "help");
 
         CommandLine line = null;
 
-        try {
+        try
+        {
             line = parser.parse(options, argv);
-        } catch (ParseException pe) {
+        }
+        catch (ParseException pe)
+        {
             System.err.println("Error with commands.");
             printHelp(options, 1);
             System.exit(0);
         }
 
-        if (line.hasOption('h')) {
+        if (line.hasOption('h'))
+        {
             printHelp(options, 0);
         }
 
         // Check a filename is given
-        if (!line.hasOption('f')) {
+        if (!line.hasOption('f'))
+        {
             System.err.println("Required parameter -f missing!");
             printHelp(options, 1);
         }
@@ -235,31 +237,42 @@ public class MetadataExport {
         ContentServiceFactory contentServiceFactory = ContentServiceFactory.getInstance();
         // Check we have an item OK
         ItemService itemService = contentServiceFactory.getItemService();
-        if (!line.hasOption('i')) {
+        if (!line.hasOption('i'))
+        {
             System.out.println("Exporting whole repository WARNING: May take some time!");
             exporter = new MetadataExport(c, itemService.findAll(c), exportAll);
-        } else {
+        }
+        else
+        {
             String handle = line.getOptionValue('i');
             DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(c, handle);
-            if (dso == null) {
+            if (dso == null)
+            {
                 System.err.println("Item '" + handle + "' does not resolve to an item in your repository!");
                 printHelp(options, 1);
             }
 
-            if (dso.getType() == Constants.ITEM) {
+            if (dso.getType() == Constants.ITEM)
+            {
                 System.out.println("Exporting item '" + dso.getName() + "' (" + handle + ")");
                 List<Item> item = new ArrayList<>();
                 item.add((Item) dso);
                 exporter = new MetadataExport(c, item.iterator(), exportAll);
-            } else if (dso.getType() == Constants.COLLECTION) {
+            }
+            else if (dso.getType() == Constants.COLLECTION)
+            {
                 System.out.println("Exporting collection '" + dso.getName() + "' (" + handle + ")");
                 Collection collection = (Collection)dso;
                 toExport = itemService.findByCollection(c, collection);
                 exporter = new MetadataExport(c, toExport, exportAll);
-            } else if (dso.getType() == Constants.COMMUNITY) {
+            }
+            else if (dso.getType() == Constants.COMMUNITY)
+            {
                 System.out.println("Exporting community '" + dso.getName() + "' (" + handle + ")");
                 exporter = new MetadataExport(c, (Community)dso, exportAll);
-            } else {
+            }
+            else
+            {
                 System.err.println("Error identifying '" + handle + "'");
                 System.exit(1);
             }

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

@@ -12,13 +12,15 @@ package org.dspace.app.bulkedit;
  *
  * @author Stuart Lewis
  */
-public class MetadataImportException extends Exception {
+public class MetadataImportException extends Exception
+{
     /**
      * Instantiate a new MetadataImportException
      *
      * @param message the error message
      */
-    public MetadataImportException(String message) {
+    public MetadataImportException(String message)
+    {
        super(message);
     }
 
@@ -28,7 +30,8 @@ public class MetadataImportException extends Exception {
      * @param message the error message
      * @param exception the root cause
      */
-    public MetadataImportException(String message, Exception exception) {
+    public MetadataImportException(String message, Exception exception)
+    {
        super(message, exception);
     }
 }

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

@@ -12,40 +12,27 @@ package org.dspace.app.bulkedit;
  *
  * @author Stuart Lewis
  */
-public class MetadataImportInvalidHeadingException extends Exception {
-    /**
-     * The type of error (schema or element)
-     */
+public class MetadataImportInvalidHeadingException extends Exception
+{
+    /** The type of error (schema or element) */
     private int type;
 
-    /**
-     * The bad heading
-     */
+    /** The bad heading */
     private String badHeading;
 
-    /**
-     * The column number
-     */
+    /** The column number */
     private int column;
 
-    /**
-     * Error with the schema
-     */
+    /** Error with the schema */
     public static final int SCHEMA = 0;
 
-    /**
-     * Error with the element
-     */
+    /** Error with the element */
     public static final int ELEMENT = 1;
 
-    /**
-     * Error with a missing header
-     */
+    /** Error with a missing header */
     public static final int MISSING = 98;
 
-    /**
-     * Error with the whole entry
-     */
+    /** Error with the whole entry */
     public static final int ENTRY = 99;
 
 
@@ -56,7 +43,8 @@ public class MetadataImportInvalidHeadingException extends Exception {
      * @param theType the type of the error
      * @param theColumn column number
      */
-    public MetadataImportInvalidHeadingException(String message, int theType, int theColumn) {
+    public MetadataImportInvalidHeadingException(String message, int theType, int theColumn)
+    {
         super(message);
         badHeading = message;
         type = theType;
@@ -68,7 +56,8 @@ public class MetadataImportInvalidHeadingException extends Exception {
      *
      *  @return the type of the exception
      */
-    public String getType() {
+    public String getType()
+    {
         return "" + type;
     }
 
@@ -77,7 +66,8 @@ public class MetadataImportInvalidHeadingException extends Exception {
      *
      * @return the invalid heading
      */
-    public String getBadHeader() {
+    public String getBadHeader()
+    {
         return badHeading;
     }
 
@@ -86,7 +76,8 @@ public class MetadataImportInvalidHeadingException extends Exception {
      *
      * @return the invalid column number
      */
-    public int getColumn() {
+    public int getColumn()
+    {
         return column;
     }
 
@@ -96,14 +87,19 @@ public class MetadataImportInvalidHeadingException extends Exception {
      * @return The exception message
      */
     @Override
-    public String getMessage() {
-        if (type == SCHEMA) {
+    public String getMessage()
+    {
+        if (type == SCHEMA)
+        {
             return "Unknown metadata schema in column " + column + ": " + badHeading;
-        } else if (type == ELEMENT) {
+        } else if (type == ELEMENT)
+        {
             return "Unknown metadata element in column " + column + ": " + badHeading;
-        } else if (type == MISSING) {
+        } else if (type == MISSING)
+        {
             return "Row with missing header: column " + column;
-        } else {
+        } else
+        {
             return "Bad metadata declaration in column" + column + ": " + badHeading;
         }
     }

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

@@ -9,11 +9,7 @@ package org.dspace.app.checker;
 
 import java.io.FileNotFoundException;
 import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.List;
-import java.util.UUID;
+import java.util.*;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
@@ -24,15 +20,7 @@ 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.dspace.checker.BitstreamDispatcher;
-import org.dspace.checker.CheckerCommand;
-import org.dspace.checker.HandleDispatcher;
-import org.dspace.checker.IteratorDispatcher;
-import org.dspace.checker.LimitedCountDispatcher;
-import org.dspace.checker.LimitedDurationDispatcher;
-import org.dspace.checker.ResultsLogger;
-import org.dspace.checker.ResultsPruner;
-import org.dspace.checker.SimpleDispatcher;
+import org.dspace.checker.*;
 import org.dspace.content.Bitstream;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.BitstreamService;
@@ -47,7 +35,8 @@ import org.dspace.core.Utils;
  * @author Grace Carpenter
  * @author Nathan Sarr
  */
-public final class ChecksumChecker {
+public final class ChecksumChecker
+{
     private static final Logger LOG = Logger.getLogger(ChecksumChecker.class);
 
     private static final BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();
@@ -55,13 +44,16 @@ public final class ChecksumChecker {
     /**
      * Blanked off constructor, this class should be used as a command line
      * tool.
+     * 
      */
-    private ChecksumChecker() {
+    private ChecksumChecker()
+    {
     }
 
     /**
      * Command line access to the checksum package.
      * 
+     * @param args
      *            <dl>
      *            <dt>-h</dt>
      *            <dd>Print help on command line options</dd>
@@ -80,8 +72,6 @@ public final class ChecksumChecker {
      *            <dt>-p</dt>
      *            <dd>Don't prune results before running checker</dd>
      *            </dl>
-     *
-     * @param args the command line arguments given
      * @throws SQLException if error
      */
     public static void main(String[] args) throws SQLException {
@@ -108,22 +98,27 @@ public final class ChecksumChecker {
         options.addOption(useBitstreamIds);
 
         options.addOption("p", "prune", false, "Prune configuration file");
-        options.addOption(OptionBuilder
+        options
+                .addOption(OptionBuilder
                         .withArgName("prune")
                         .hasOptionalArgs(1)
                         .withDescription(
                                 "Prune old results (optionally using specified properties file for configuration)")
                         .create('p'));
 
-        try {
+        try
+        {
             line = parser.parse(options, args);
-        } catch (ParseException e) {
+        }
+        catch (ParseException e)
+        {
             LOG.fatal(e);
             System.exit(1);
         }
 
         // user asks for help
-        if (line.hasOption('h')) {
+        if (line.hasOption('h'))
+        {
             printHelp(options);
         }
         Context context = null;
@@ -132,13 +127,17 @@ public final class ChecksumChecker {
 
 
             // Prune stage
-            if (line.hasOption('p')) {
+            if (line.hasOption('p'))
+            {
                 ResultsPruner rp = null;
-                try {
+                try
+                {
                     rp = (line.getOptionValue('p') != null) ? ResultsPruner
                             .getPruner(context, line.getOptionValue('p')) : ResultsPruner
                             .getDefaultPruner(context);
-                } catch (FileNotFoundException e) {
+                }
+                catch (FileNotFoundException e)
+                {
                     LOG.error("File not found", e);
                     System.exit(1);
                 }
@@ -153,47 +152,68 @@ public final class ChecksumChecker {
 
             // process should loop infinitely through
             // most_recent_checksum table
-            if (line.hasOption('l')) {
+            if (line.hasOption('l'))
+            {
                 dispatcher = new SimpleDispatcher(context, processStart, false);
-            } else if (line.hasOption('L')) {
+            }
+            else if (line.hasOption('L'))
+            {
                 dispatcher = new SimpleDispatcher(context, processStart, true);
-            } else if (line.hasOption('b')) {
+            }
+            else if (line.hasOption('b'))
+            {
                 // check only specified bitstream(s)
                 String[] ids = line.getOptionValues('b');
                 List<Bitstream> bitstreams = new ArrayList<>(ids.length);
 
-                for (int i = 0; i < ids.length; i++) {
-                    try {
+                for (int i = 0; i < ids.length; i++)
+                {
+                    try
+                    {
                         bitstreams.add(bitstreamService.find(context, UUID.fromString(ids[i])));
-                    } catch (NumberFormatException nfe) {
+                    }
+                    catch (NumberFormatException nfe)
+                    {
                         System.err.println("The following argument: " + ids[i]
                                 + " is not an integer");
                         System.exit(0);
                     }
                 }
                 dispatcher = new IteratorDispatcher(bitstreams.iterator());
-            } else if (line.hasOption('a')) {
+            }
+
+            else if (line.hasOption('a'))
+            {
                 dispatcher = new HandleDispatcher(context, line.getOptionValue('a'));
-            } else if (line.hasOption('d')) {
+            }
+            else if (line.hasOption('d'))
+            {
                 // run checker process for specified duration
-                try {
+                try
+                {
                     dispatcher = new LimitedDurationDispatcher(
                             new SimpleDispatcher(context, processStart, true), new Date(
                                     System.currentTimeMillis()
                                             + Utils.parseDuration(line
                                                     .getOptionValue('d'))));
-                } catch (Exception e) {
+                }
+                catch (Exception e)
+                {
                     LOG.fatal("Couldn't parse " + line.getOptionValue('d')
                             + " as a duration: ", e);
                     System.exit(0);
                 }
-            } else if (line.hasOption('c')) {
+            }
+            else if (line.hasOption('c'))
+            {
                 int count = Integer.valueOf(line.getOptionValue('c'));
 
                 // run checker process for specified number of bitstreams
                 dispatcher = new LimitedCountDispatcher(new SimpleDispatcher(
                         context, processStart, false), count);
-            } else {
+            }
+            else
+            {
                 dispatcher = new LimitedCountDispatcher(new SimpleDispatcher(
                         context, processStart, false), 1);
             }
@@ -201,7 +221,8 @@ public final class ChecksumChecker {
             ResultsLogger logger = new ResultsLogger(processStart);
             CheckerCommand checker = new CheckerCommand(context);
             // verbose reporting
-            if (line.hasOption('v')) {
+            if (line.hasOption('v'))
+            {
                 checker.setReportVerbose(true);
             }
 
@@ -223,19 +244,24 @@ public final class ChecksumChecker {
      * 
      * @param options that are available for the user
      */
-    private static void printHelp(Options options) {
+    private static void printHelp(Options options)
+    {
         HelpFormatter myhelp = new HelpFormatter();
 
         myhelp.printHelp("Checksum Checker\n", options);
-        System.out.println("\nSpecify a duration for checker process, using s(seconds),"
+        System.out
+                .println("\nSpecify a duration for checker process, using s(seconds),"
                         + "m(minutes), or h(hours): ChecksumChecker -d 30s"
                         + " OR ChecksumChecker -d 30m"
                         + " OR ChecksumChecker -d 2h");
-        System.out.println("\nSpecify bitstream IDs: ChecksumChecker -b 13 15 17 20");
+        System.out
+                .println("\nSpecify bitstream IDs: ChecksumChecker -b 13 15 17 20");
         System.out.println("\nLoop once through all bitstreams: "
                 + "ChecksumChecker -l");
-        System.out.println("\nLoop continuously through all bitstreams: ChecksumChecker -L");
-        System.out.println("\nCheck a defined number of bitstreams: ChecksumChecker -c 10");
+        System.out
+                .println("\nLoop continuously through all bitstreams: ChecksumChecker -L");
+        System.out
+                .println("\nCheck a defined number of bitstreams: ChecksumChecker -c 10");
         System.out.println("\nReport all processing (verbose)(default reports only errors): ChecksumChecker -v");
         System.out.println("\nDefault (no arguments) is equivalent to '-c 1'");
         System.exit(0);

dspace-api/src/main/java/org/dspace/app/configuration/APISpringLoader.java

@@ -7,12 +7,12 @@
  */
 package org.dspace.app.configuration;
 
-import java.io.File;
-import java.net.MalformedURLException;
-
 import org.dspace.kernel.config.SpringLoader;
 import org.dspace.services.ConfigurationService;
 
+import java.io.File;
+import java.net.MalformedURLException;
+
 /**
  * @author Kevin Van de Velde (kevin at atmire dot com)
  */

dspace-api/src/main/java/org/dspace/app/harvest/Harvest.java

@@ -7,17 +7,7 @@
  */
 package org.dspace.app.harvest;
 
-import java.io.IOException;
-import java.sql.SQLException;
-import java.util.Iterator;
-import java.util.List;
-import java.util.UUID;
-
-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.PosixParser;
+import org.apache.commons.cli.*;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Collection;
 import org.dspace.content.DSpaceObject;
@@ -37,21 +27,27 @@ import org.dspace.harvest.OAIHarvester;
 import org.dspace.harvest.factory.HarvestServiceFactory;
 import org.dspace.harvest.service.HarvestedCollectionService;
 
+import java.io.IOException;
+import java.sql.SQLException;
+import java.util.Iterator;
+import java.util.List;
+import java.util.UUID;
+
 /**
  *  Test class for harvested collections.
  *
  * @author Alexey Maslov
  */
-public class Harvest {
+public class Harvest
+{
     private static Context context;
 
-    private static final HarvestedCollectionService harvestedCollectionService =
-        HarvestServiceFactory.getInstance().getHarvestedCollectionService();
+    private static final HarvestedCollectionService harvestedCollectionService = HarvestServiceFactory.getInstance().getHarvestedCollectionService();
     private static final EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
-    private static final CollectionService collectionService =
-        ContentServiceFactory.getInstance().getCollectionService();
+    private static final CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
 
-    public static void main(String[] argv) throws Exception {
+    public static void main(String[] argv) throws Exception
+    {
         // create an options object and populate it
         CommandLineParser parser = new PosixParser();
 
@@ -60,26 +56,18 @@ public class Harvest {
         options.addOption("p", "purge", false, "delete all items in the collection");
         options.addOption("r", "run", false, "run the standard harvest procedure");
         options.addOption("g", "ping", false, "test the OAI server and set");
-        options.addOption("o", "once", false, "run the harvest procedure with specified parameters");
         options.addOption("s", "setup", false, "Set the collection up for harvesting");
         options.addOption("S", "start", false, "start the harvest loop");
         options.addOption("R", "reset", false, "reset harvest status on all collections");
-        options.addOption("P", "purge", false, "purge all harvestable collections");
+        options.addOption("P", "purgeAll", false, "purge all harvestable collections");
         
 
-        options.addOption("e", "eperson", true,
-                          "eperson");
-        options.addOption("c", "collection", true,
-                          "harvesting collection (handle or id)");
-        options.addOption("t", "type", true,
-                          "type of harvesting (0 for none)");
-        options.addOption("a", "address", true,
-                          "address of the OAI-PMH server");
-        options.addOption("i", "oai_set_id", true,
-                          "id of the PMH set representing the harvested collection");
-        options.addOption("m", "metadata_format", true,
-                          "the name of the desired metadata format for harvesting, resolved to namespace and " +
-                              "crosswalk in dspace.cfg");
+        options.addOption("e", "eperson", true, "eperson");
+        options.addOption("c", "collection", true, "harvesting collection (handle or id)");
+        options.addOption("t", "type", true, "type of harvesting (0 for none)");
+        options.addOption("a", "address", true, "address of the OAI-PMH server");
+        options.addOption("i", "oai_set_id", true, "id of the PMH set representing the harvested collection");
+        options.addOption("m", "metadata_format", true, "the name of the desired metadata format for harvesting, resolved to namespace and crosswalk in dspace.cfg");
 
         options.addOption("h", "help", false, "help");
 
@@ -93,21 +81,25 @@ public class Harvest {
         String metadataKey = null;
         int harvestType = 0;
         
-        if (line.hasOption('h')) {
+        if (line.hasOption('h'))
+        {
             HelpFormatter myhelp = new HelpFormatter();
             myhelp.printHelp("Harvest\n", options);
-            System.out.println("\nPING OAI server: Harvest -g -a oai_source -i oai_set_id");
-            System.out.println(
-                "RUNONCE harvest with arbitrary options: Harvest -o -e eperson -c collection -t harvest_type -a " +
-                    "oai_source -i oai_set_id -m metadata_format");
-            System.out.println(
-                "SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i " +
-                    "oai_set_id -m metadata_format");
-            System.out.println("RUN harvest once: Harvest -r -e eperson -c collection");
-            System.out.println("START harvest scheduler: Harvest -S");
-            System.out.println("RESET all harvest status: Harvest -R");
-            System.out.println("PURGE a collection of items and settings: Harvest -p -e eperson -c collection");
-            System.out.println("PURGE all harvestable collections: Harvest -P -e eperson");
+            System.out
+    				.println("\nPING OAI server: Harvest -g -a oai_source -i oai_set_id");
+            System.out
+                    .println("SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i oai_set_id -m metadata_format");
+            System.out
+            		.println("RUN harvest once: Harvest -r -e eperson -c collection");
+            System.out
+    				.println("START harvest scheduler: Harvest -S");
+            System.out
+					.println("RESET all harvest status: Harvest -R");
+            System.out
+                    .println("PURGE a collection of items and settings: Harvest -p -e eperson -c collection");
+            System.out
+					.println("PURGE all harvestable collections: Harvest -P -e eperson");
+            
             
 
             System.exit(0);
@@ -125,9 +117,6 @@ public class Harvest {
         if (line.hasOption('g')) {
             command = "ping";
         }
-        if (line.hasOption('o')) {
-            command = "runOnce";
-        }
         if (line.hasOption('S')) {
             command = "start";
         }
@@ -167,13 +156,17 @@ public class Harvest {
         
         
         // Check our options
-        if (command == null) {
+        if (command == null)
+        {
             System.out
                     .println("Error - no parameters specified (run with -h flag for details)");
             System.exit(1);
-        } else if ("run".equals(command)) {
+        }
         // Run a single harvest cycle on a collection using saved settings.
-            if (collection == null || eperson == null) {
+        else if ("run".equals(command))
+        {
+            if (collection == null || eperson == null)
+            {
                 System.out
                         .println("Error - a target collection and eperson must be provided");
                 System.out.println(" (run with -h flag for details)");
@@ -181,33 +174,43 @@ public class Harvest {
             }
             
             harvester.runHarvest(collection, eperson);
-        } else if ("start".equals(command)) {
+        }
         // start the harvest loop
+        else if ("start".equals(command))
+        {
         	startHarvester();
-        } else if ("reset".equals(command)) {
+        }
         // reset harvesting status
+        else if ("reset".equals(command))
+        {
         	resetHarvesting();
-        } else if ("purgeAll".equals(command)) {
+        }
         // purge all collections that are set up for harvesting (obviously for testing purposes only)
-            if (eperson == null) {
+        else if ("purgeAll".equals(command))
+        {
+        	if (eperson == null)
+            {
                 System.out
                         .println("Error - an eperson must be provided");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
             }
             
+            System.out.println("Starting to purge all harvesting collections");
+        	
         	List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context);
-            for (HarvestedCollection harvestedCollection : harvestedCollections) {
-                System.out.println(
-                    "Purging the following collections (deleting items and resetting harvest status): " +
-                        harvestedCollection
-                            .getCollection().getID().toString());
+	    	for (HarvestedCollection harvestedCollection : harvestedCollections)
+	    	{
+                System.out.println("Purging the following collections (deleting items and resetting harvest status): " + harvestedCollection.getCollection().getID().toString());
                 harvester.purgeCollection(harvestedCollection.getCollection().getID().toString(), eperson);
 	    	}
 	    	context.complete();
-        } else if ("purge".equals(command)) {
+        }
         // Delete all items in a collection. Useful for testing fresh harvests.
-            if (collection == null || eperson == null) {
+        else if ("purge".equals(command))
+        {
+            if (collection == null || eperson == null)
+            {
                 System.out
                         .println("Error - a target collection and eperson must be provided");
                 System.out.println(" (run with -h flag for details)");
@@ -218,34 +221,45 @@ public class Harvest {
             context.complete();
             
             //TODO: implement this... remove all items and remember to unset "last-harvested" settings
-        } else if ("config".equals(command)) {
+        }
         // Configure a collection with the three main settings 
-            if (collection == null) {
+        else if ("config".equals(command))
+        {
+            if (collection == null)
+            {
                 System.out.println("Error -  a target collection must be provided");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
             }
-            if (oaiSource == null || oaiSetID == null) {
+            if (oaiSource == null || oaiSetID == null)
+            {
                 System.out.println("Error - both the OAI server address and OAI set id must be specified");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
             }
-            if (metadataKey == null) {
-                System.out
-                    .println("Error - a metadata key (commonly the prefix) must be specified for this collection");
+            if (metadataKey == null)
+            {
+            	System.out.println("Error - a metadata key (commonly the prefix) must be specified for this collection");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);            	
             }
             
             harvester.configureCollection(collection, harvestType, oaiSource, oaiSetID, metadataKey);
-        } else if ("ping".equals(command)) {
-            if (oaiSource == null || oaiSetID == null) {
+        }
+        else if ("ping".equals(command))
+        {
+            if (oaiSource == null || oaiSetID == null)
+            {
                 System.out.println("Error - both the OAI server address and OAI set id must be specified");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
             }
 
             pingResponder(oaiSource, oaiSetID, metadataKey);
+        } else {
+            System.out.println("Error - your command '" + command + "' was not recoginzed properly");
+            System.out.println(" (run with -h flag for details)");
+            System.exit(1);
         }
     }
     
@@ -260,30 +274,40 @@ public class Harvest {
     	
     	try {
 	    	// is the ID a handle?
-            if (collectionID != null) {
-                if (collectionID.indexOf('/') != -1) {
+	        if (collectionID != null)
+            {
+                if (collectionID.indexOf('/') != -1)
+                {
                     // string has a / so it must be a handle - try and resolve it
                     dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(context, collectionID);
 
                     // resolved, now make sure it's a collection
-                    if (dso == null || dso.getType() != Constants.COLLECTION) {
+                    if (dso == null || dso.getType() != Constants.COLLECTION)
+                    {
                         targetCollection = null;
-                    } else {
+                    }
+                    else
+                    {
                         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 integer collection
+                // database ID
+                else
+                {
+                    // 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));
                 }
             }
             // was the collection valid?
-            if (targetCollection == null) {
+            if (targetCollection == null)
+            {
                 System.out.println("Cannot resolve " + collectionID + " to collection");
                 System.exit(1);
             }
-        } catch (SQLException se) {
+    	}
+    	catch (SQLException se) {
     		se.printStackTrace();
     	}
     	
@@ -291,8 +315,7 @@ public class Harvest {
     }
     
     
-    private void configureCollection(String collectionID, int type, String oaiSource, String oaiSetId,
-                                     String mdConfigId) {
+    private void configureCollection(String collectionID, int type, String oaiSource, String oaiSetId, String mdConfigId) {
     	System.out.println("Running: configure collection");
    	
     	Collection collection = resolveCollection(collectionID);
@@ -310,12 +333,15 @@ public class Harvest {
             harvestedCollectionService.update(context, hc);
     		context.restoreAuthSystemState();
     		context.complete();
-        } catch (Exception e) {
+    	} 
+    	catch (Exception e) {
     		System.out.println("Changes could not be committed");
     		e.printStackTrace();
     		System.exit(1);
-        } finally {
-            if (context != null) {
+    	}
+    	finally {
+            if (context != null)
+            {
     		    context.restoreAuthSystemState();
             }
     	}
@@ -329,11 +355,11 @@ public class Harvest {
      * @param email
      */
     private void purgeCollection(String collectionID, String email) {
-        System.out.println(
-            "Purging collection of all items and resetting last_harvested and harvest_message: " + collectionID);
+    	System.out.println("Purging collection of all items and resetting last_harvested and harvest_message: " + collectionID);
     	Collection collection = resolveCollection(collectionID);
    	
-        try {
+    	try 
+    	{
     		EPerson eperson = ePersonService.findByEmail(context, email);
         	context.setCurrentUser(eperson);
     		context.turnOffAuthorisationSystem();
@@ -346,7 +372,9 @@ public class Harvest {
     			Item item = it.next();
     			System.out.println("Deleting: " + item.getHandle());
                 collectionService.removeItem(context, collection, item);
-                context.uncacheEntity(item);// Dispatch events every 50 items
+                context.uncacheEntity(item);
+                
+    			// Dispatch events every 50 items
     			if (i%50 == 0) {
     				context.dispatchEvents();
     				i=0;
@@ -363,11 +391,13 @@ public class Harvest {
     		}
     		context.restoreAuthSystemState();
             context.dispatchEvents();
-        } catch (Exception e) {
+    	}
+    	catch (Exception e) {
     		System.out.println("Changes could not be committed");
     		e.printStackTrace();
     		System.exit(1);
-        } finally {
+    	}
+    	finally {
     		context.restoreAuthSystemState();
     	}
     }
@@ -386,7 +416,8 @@ public class Harvest {
         	HarvestedCollection hc = harvestedCollectionService.find(context, collection);
     		harvester = new OAIHarvester(context, collection, hc);
     		System.out.println("success. ");
-        } catch (HarvestingException hex) {
+    	}
+    	catch (HarvestingException hex) {
     		System.out.print("failed. ");
     		System.out.println(hex.getMessage());
     		throw new IllegalStateException("Unable to harvest", hex);
@@ -403,11 +434,14 @@ public class Harvest {
         	context.setCurrentUser(eperson);
     		harvester.runHarvest();
     		context.complete();
-        } catch (SQLException e) {
+    	}
+        catch (SQLException e) {
             throw new IllegalStateException("Failed to run harvester", e);
-        } catch (AuthorizeException e) {
+        }
+        catch (AuthorizeException e) {
             throw new IllegalStateException("Failed to run harvester", e);
-        } catch (IOException e) {
+        }
+        catch (IOException e) {
             throw new IllegalStateException("Failed to run harvester", e);
         }
 
@@ -415,22 +449,24 @@ public class Harvest {
     }
 
     /**
-     * Resets harvest_status and harvest_start_time flags for all collections that have a row in the
-     * harvested_collections table
+     * Resets harvest_status and harvest_start_time flags for all collections that have a row in the harvested_collections table 
      */
     private static void resetHarvesting() {
     	System.out.print("Resetting harvest status flag on all collections... ");
 
-        try {
+    	try
+    	{
             List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context);
-            for (HarvestedCollection harvestedCollection : harvestedCollections) {
+            for (HarvestedCollection harvestedCollection : harvestedCollections)
+            {
                 //hc.setHarvestResult(null,"");
                 harvestedCollection.setHarvestStartTime(null);
                 harvestedCollection.setHarvestStatus(HarvestedCollection.STATUS_READY);
                 harvestedCollectionService.update(context, harvestedCollection);
             }
             System.out.println("success. ");
-        } catch (Exception ex) {
+    	}
+    	catch (Exception ex) {
             System.out.println("failed. ");
             ex.printStackTrace();
     	}    	
@@ -439,12 +475,15 @@ public class Harvest {
     /**
      * Starts up the harvest scheduler. Terminating this process will stop the scheduler.
      */
-    private static void startHarvester() {
-        try {
+    private static void startHarvester()
+    {
+        try
+        {
             System.out.print("Starting harvest loop... ");
             HarvestServiceFactory.getInstance().getHarvestSchedulingService().startNewScheduler();
             System.out.println("running. ");
-        } catch (Exception ex) {
+    	}
+    	catch (Exception ex) {
             ex.printStackTrace();
     	}
     }
@@ -456,29 +495,30 @@ public class Harvest {
      * @param set name of an item set.
      * @param metadataFormat local prefix name, or null for "dc".
      */
-    private static void pingResponder(String server, String set, String metadataFormat) {
+    private static void pingResponder(String server, String set, String metadataFormat)
+    {
         List<String> errors;
 
         System.out.print("Testing basic PMH access:  ");
         errors = OAIHarvester.verifyOAIharvester(server, set,
                 (null != metadataFormat) ? metadataFormat : "dc", false);
-        if (errors.isEmpty()) {
+        if (errors.isEmpty())
             System.out.println("OK");
-        } else {
-            for (String error : errors) {
+        else
+        {
+            for (String error : errors)
                 System.err.println(error);
         }
-        }
 
         System.out.print("Testing ORE support:  ");
         errors = OAIHarvester.verifyOAIharvester(server, set,
                 (null != metadataFormat) ? metadataFormat : "dc", true);
-        if (errors.isEmpty()) {
+        if (errors.isEmpty())
             System.out.println("OK");
-        } else {
-            for (String error : errors) {
+        else
+        {
+            for (String error : errors)
                 System.err.println(error);
         }
     }
 }
-}

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

@@ -7,17 +7,7 @@
  */
 package org.dspace.app.itemexport;
 
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-import java.util.UUID;
-
-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.PosixParser;
+import org.apache.commons.cli.*;
 import org.dspace.app.itemexport.factory.ItemExportServiceFactory;
 import org.dspace.app.itemexport.service.ItemExportService;
 import org.dspace.content.Collection;
@@ -30,6 +20,8 @@ import org.dspace.core.Context;
 import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.handle.service.HandleService;
 
+import java.util.*;
+
 /**
  * Item exporter to create simple AIPs for DSpace content. Currently exports
  * individual items, or entire collections. For instructions on use, see
@@ -53,21 +45,17 @@ import org.dspace.handle.service.HandleService;
  */
 public class ItemExportCLITool {
 
-    protected static ItemExportService itemExportService = ItemExportServiceFactory.getInstance()
-                                                                                   .getItemExportService();
+    protected static ItemExportService itemExportService = ItemExportServiceFactory.getInstance().getItemExportService();
     protected static HandleService handleService = HandleServiceFactory.getInstance().getHandleService();
     protected static ItemService itemService = ContentServiceFactory.getInstance().getItemService();
     protected static CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
 
-    /**
-     * Default constructor
-     */
-    private ItemExportCLITool() { }
 
     /*
      *
      */
-    public static void main(String[] argv) throws Exception {
+    public static void main(String[] argv) throws Exception
+    {
         // create an options object and populate it
         CommandLineParser parser = new PosixParser();
 
@@ -77,8 +65,7 @@ public class ItemExportCLITool {
         options.addOption("i", "id", true, "ID or handle of thing to export");
         options.addOption("d", "dest", true,
                 "destination where you want items to go");
-        options.addOption("m", "migrate", false,
-                          "export for migration (remove handle and metadata that will be re-created in new system)");
+        options.addOption("m", "migrate", false, "export for migration (remove handle and metadata that will be re-created in new system)");
         options.addOption("n", "number", true,
                 "sequence number to begin exporting items with");
         options.addOption("z", "zip", true, "export as zip file (specify filename e.g. export.zip)");
@@ -99,7 +86,8 @@ public class ItemExportCLITool {
         Item myItem = null;
         Collection mycollection = null;
 
-        if (line.hasOption('h')) {
+        if (line.hasOption('h'))
+        {
             HelpFormatter myhelp = new HelpFormatter();
             myhelp.printHelp("ItemExport\n", options);
             System.out
@@ -110,65 +98,79 @@ public class ItemExportCLITool {
             System.exit(0);
         }
 
-        if (line.hasOption('t')) { // type
+        if (line.hasOption('t')) // type
+        {
             typeString = line.getOptionValue('t');
 
-            if ("ITEM".equals(typeString)) {
+            if ("ITEM".equals(typeString))
+            {
                 myType = Constants.ITEM;
-            } else if ("COLLECTION".equals(typeString)) {
+            }
+            else if ("COLLECTION".equals(typeString))
+            {
                 myType = Constants.COLLECTION;
             }
         }
 
-        if (line.hasOption('i')) { // id
+        if (line.hasOption('i')) // id
+        {
             myIDString = line.getOptionValue('i');
         }
 
-        if (line.hasOption('d')) { // dest
+        if (line.hasOption('d')) // dest
+        {
             destDirName = line.getOptionValue('d');
         }
 
-        if (line.hasOption('n')) { // number
+        if (line.hasOption('n')) // number
+        {
             seqStart = Integer.parseInt(line.getOptionValue('n'));
         }
 
         boolean migrate = false;
-        if (line.hasOption('m')) { // number
+        if (line.hasOption('m')) // number
+        {
             migrate = true;
         }
 
         boolean zip = false;
         String zipFileName = "";
-        if (line.hasOption('z')) {
+        if (line.hasOption('z'))
+        {
             zip = true;
             zipFileName = line.getOptionValue('z');
         }
 
         boolean excludeBitstreams = false;
-        if (line.hasOption('x')) {
+        if (line.hasOption('x'))
+        {
         	excludeBitstreams = true;
         }
 
         // now validate the args
-        if (myType == -1) {
+        if (myType == -1)
+        {
             System.out
                     .println("type must be either COLLECTION or ITEM (-h for help)");
             System.exit(1);
         }
 
-        if (destDirName == null) {
+        if (destDirName == null)
+        {
             System.out
                     .println("destination directory must be set (-h for help)");
             System.exit(1);
         }
 
-        if (seqStart == -1) {
+        if (seqStart == -1)
+        {
             System.out
                     .println("sequence start number must be set (-h for help)");
             System.exit(1);
         }
 
-        if (myIDString == null) {
+        if (myIDString == null)
+        {
             System.out
                     .println("ID must be set to either a database ID or a handle (-h for help)");
             System.exit(1);
@@ -177,62 +179,82 @@ public class ItemExportCLITool {
         Context c = new Context(Context.Mode.READ_ONLY);
         c.turnOffAuthorisationSystem();
 
-        if (myType == Constants.ITEM) {
+        if (myType == Constants.ITEM)
+        {
             // first, is myIDString a handle?
-            if (myIDString.indexOf('/') != -1) {
+            if (myIDString.indexOf('/') != -1)
+            {
                 myItem = (Item) handleService.resolveToObject(c, myIDString);
 
-                if ((myItem == null) || (myItem.getType() != Constants.ITEM)) {
+                if ((myItem == null) || (myItem.getType() != Constants.ITEM))
+                {
                     myItem = null;
                 }
-            } else {
+            }
+            else
+            {
                 myItem = itemService.find(c, UUID.fromString(myIDString));
             }
 
-            if (myItem == null) {
+            if (myItem == null)
+            {
                 System.out
                         .println("Error, item cannot be found: " + myIDString);
             }
-        } else {
-            if (myIDString.indexOf('/') != -1) {
+        }
+        else
+        {
+            if (myIDString.indexOf('/') != -1)
+            {
                 // has a / must be a handle
                 mycollection = (Collection) handleService.resolveToObject(c,
                         myIDString);
 
                 // ensure it's a collection
                 if ((mycollection == null)
-                    || (mycollection.getType() != Constants.COLLECTION)) {
+                        || (mycollection.getType() != Constants.COLLECTION))
+                {
                     mycollection = null;
                 }
-            } else if (myIDString != null) {
+            }
+            else if (myIDString != null)
+            {
                 mycollection = collectionService.find(c, UUID.fromString(myIDString));
             }
 
-            if (mycollection == null) {
+            if (mycollection == null)
+            {
                 System.out.println("Error, collection cannot be found: "
                         + myIDString);
                 System.exit(1);
             }
         }
 
-        if (zip) {
+        if (zip)
+        {
             Iterator<Item> items;
-            if (myItem != null) {
+            if (myItem != null)
+            {
                 List<Item> myItems = new ArrayList<>();
                 myItems.add(myItem);
                 items = myItems.iterator();
-            } else {
+            }
+            else
+            {
                 System.out.println("Exporting from collection: " + myIDString);
                 items = itemService.findByCollection(c, mycollection);
             }
             itemExportService.exportAsZip(c, items, destDirName, zipFileName, seqStart, migrate, excludeBitstreams);
-        } else {
-            if (myItem != null) {
+        }
+        else
+        {
+            if (myItem != null)
+            {
                 // it's only a single item
-                itemExportService
-                    .exportItem(c, Collections.singletonList(myItem).iterator(), destDirName, seqStart, migrate,
-                                excludeBitstreams);
-            } else {
+                itemExportService.exportItem(c, Collections.singletonList(myItem).iterator(), destDirName, seqStart, migrate, excludeBitstreams);
+            }
+            else
+            {
                 System.out.println("Exporting from collection: " + myIDString);
 
                 // it's a collection, so do a bunch of items

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

@@ -10,17 +10,20 @@ package org.dspace.app.itemexport;
 /**
  * An exception that can be thrown when error occur during item export
  */
-public class ItemExportException extends Exception {
+public class ItemExportException extends Exception
+{
     public static final int EXPORT_TOO_LARGE = 0;
 
     private int reason;
 
-    public ItemExportException(int r, String message) {
+    public ItemExportException(int r, String message)
+    {
         super(message);
         reason = r;
     }
 
-    public int getReason() {
+    public int getReason()
+    {
         return reason;
     }
 }

dspace-api/src/main/java/org/dspace/app/itemexport/factory/ItemExportServiceFactory.java

@@ -11,8 +11,7 @@ import org.dspace.app.itemexport.service.ItemExportService;
 import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
- * Abstract factory to get services for the itemexport package, use ItemExportServiceFactory.getInstance() to
- * retrieve an implementation
+ * Abstract factory to get services for the itemexport package, use ItemExportServiceFactory.getInstance() to retrieve an implementation
  *
  * @author kevinvandevelde at atmire.com
  */
@@ -21,7 +20,6 @@ public abstract class ItemExportServiceFactory {
     public abstract ItemExportService getItemExportService();
 
     public static ItemExportServiceFactory getInstance(){
-        return DSpaceServicesFactory.getInstance().getServiceManager()
-                                    .getServiceByName("itemExportServiceFactory", ItemExportServiceFactory.class);
+        return DSpaceServicesFactory.getInstance().getServiceManager().getServiceByName("itemExportServiceFactory", ItemExportServiceFactory.class);
     }
 }

dspace-api/src/main/java/org/dspace/app/itemexport/factory/ItemExportServiceFactoryImpl.java

@@ -11,8 +11,7 @@ import org.dspace.app.itemexport.service.ItemExportService;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
- * Factory implementation to get services for the itemexport package, use ItemExportServiceFactory.getInstance() to
- * retrieve an implementation
+ * Factory implementation to get services for the itemexport package, use ItemExportServiceFactory.getInstance() to retrieve an implementation
  *
  * @author kevinvandevelde at atmire.com
  */

dspace-api/src/main/java/org/dspace/app/itemexport/service/ItemExportService.java

@@ -7,17 +7,17 @@
  */
 package org.dspace.app.itemexport.service;
 
-import java.io.InputStream;
-import java.util.Date;
-import java.util.Iterator;
-import java.util.List;
-import javax.mail.MessagingException;
-
 import org.dspace.content.DSpaceObject;
 import org.dspace.content.Item;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;
 
+import javax.mail.MessagingException;
+import java.io.InputStream;
+import java.util.Date;
+import java.util.Iterator;
+import java.util.List;
+
 /**
  * Item exporter to create simple AIPs for DSpace content. Currently exports
  * individual items, or entire collections. For instructions on use, see
@@ -71,8 +71,10 @@ public interface ItemExportService {
      * Convenience methot to create export a single Community, Collection, or
      * Item
      *
-     * @param dso     - the dspace object to export
-     * @param context - the dspace context
+     * @param dso
+     *            - the dspace object to export
+     * @param context
+     *            - the dspace context
      * @param migrate Whether to use the migrate option or not
      * @throws Exception if error
      */
@@ -83,8 +85,10 @@ public interface ItemExportService {
      * Convenience method to export a List of dspace objects (Community,
      * Collection or Item)
      *
-     * @param dsObjects - List containing dspace objects
-     * @param context   - the dspace context
+     * @param dsObjects
+     *            - List containing dspace objects
+     * @param context
+     *            - the dspace context
      * @param migrate Whether to use the migrate option or not
      * @throws Exception if error
      */
@@ -95,9 +99,12 @@ public interface ItemExportService {
      * Convenience methot to create export a single Community, Collection, or
      * Item
      *
-     * @param dso             - the dspace object to export
-     * @param context         - the dspace context
-     * @param additionalEmail - cc email to use
+     * @param dso
+     *            - the dspace object to export
+     * @param context
+     *            - the dspace context
+     * @param additionalEmail
+     *            - cc email to use
      * @param migrate Whether to use the migrate option or not
      * @throws Exception if error
      */
@@ -108,9 +115,12 @@ public interface ItemExportService {
      * Convenience method to export a List of dspace objects (Community,
      * Collection or Item)
      *
-     * @param dsObjects       - List containing dspace objects
-     * @param context         - the dspace context
-     * @param additionalEmail - cc email to use
+     * @param dsObjects
+     *            - List containing dspace objects
+     * @param context
+     *            - the dspace context
+     * @param additionalEmail
+     *            - cc email to use
      * @param migrate Whether to use the migrate option or not
      * @throws Exception if error
      */
@@ -122,8 +132,10 @@ public interface ItemExportService {
      * Create a file name based on the date and eperson
      *
      * @param type Type of object (as string)
-     * @param eperson - eperson who requested export and will be able to download it
-     * @param date    - the date the export process was created
+     * @param eperson
+     *            - eperson who requested export and will be able to download it
+     * @param date
+     *            - the date the export process was created
      * @return String representing the file name in the form of
      *         'export_yyy_MMM_dd_count_epersonID'
      * @throws Exception if error
@@ -136,7 +148,8 @@ public interface ItemExportService {
      * Use config file entry for org.dspace.app.itemexport.download.dir and id
      * of the eperson to create a download directory name
      *
-     * @param ePerson - the eperson who requested export archive
+     * @param ePerson
+     *            - the eperson who requested export archive
      * @return String representing a directory in the form of
      *         org.dspace.app.itemexport.download.dir/epersonID
      * @throws Exception if error
@@ -157,8 +170,10 @@ public interface ItemExportService {
     /**
      * Used to read the export archived. Inteded for download.
      *
-     * @param fileName the name of the file to download
-     * @param eperson  the eperson requesting the download
+     * @param fileName
+     *            the name of the file to download
+     * @param eperson
+     *            the eperson requesting the download
      * @return an input stream of the file to be downloaded
      * @throws Exception if error
      */
@@ -169,9 +184,10 @@ public interface ItemExportService {
      * Get the file size of the export archive represented by the file name.
      *
      * @param context DSpace context
-     * @param fileName name of the file to get the size.
-     * @return size as long
+     * @param fileName
+     *            name of the file to get the size.
      * @throws Exception if error
+     * @return size as long
      */
     public long getExportFileSize(Context context, String fileName) throws Exception;
 
@@ -179,10 +195,11 @@ public interface ItemExportService {
      * Get the last modified date of the export archive represented by the file name.
      *
      * @param context DSpace context
-     * @param fileName name of the file to get the size.
+     * @param fileName
+     *            name of the file to get the size.
      * @return date as long
-     * @throws Exception if error
      * @see java.io.File#lastModified() 
+     * @throws Exception if error
      */
     public long getExportFileLastModified(Context context, String fileName)
             throws Exception;
@@ -192,8 +209,10 @@ public interface ItemExportService {
      * who created it When requested for download this method can check if the
      * person requesting it is the same one that created it
      *
-     * @param context  dspace context
-     * @param fileName the file name to check auths for
+     * @param context
+     *            dspace context
+     * @param fileName
+     *            the file name to check auths for
      * @return true if it is the same person false otherwise
      */
     public boolean canDownload(Context context, String fileName);
@@ -215,7 +234,8 @@ public interface ItemExportService {
      * uses the config file entry 'org.dspace.app.itemexport.life.span.hours' to
      * determine if the current exports are too old and need pruging
      *
-     * @param eperson - the eperson to clean up
+     * @param eperson
+     *            - the eperson to clean up
      * @throws Exception if error
      */
     public void deleteOldExportArchives(EPerson eperson) throws Exception;
@@ -236,9 +256,12 @@ public interface ItemExportService {
      * communication with email instead. Send a success email once the export
      * archive is complete and ready for download
      *
-     * @param context  - the current Context
-     * @param eperson  - eperson to send the email to
-     * @param fileName - the file name to be downloaded. It is added to the url in
+     * @param context
+     *            - the current Context
+     * @param eperson
+     *            - eperson to send the email to
+     * @param fileName
+     *            - the file name to be downloaded. It is added to the url in
      *            the email
      * @throws MessagingException if error
      */
@@ -251,8 +274,10 @@ public interface ItemExportService {
      * communication with email instead. Send an error email if the export
      * archive fails
      *
-     * @param eperson - EPerson to send the error message to
-     * @param error   - the error message
+     * @param eperson
+     *            - EPerson to send the error message to
+     * @param error
+     *            - the error message
      * @throws MessagingException if error
      */
     public void emailErrorMessage(EPerson eperson, String error)
@@ -260,7 +285,6 @@ public interface ItemExportService {
 
     /**
      * Zip source to target
-     *
      * @param strSource source file
      * @param target target file
      * @throws Exception if error

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

@@ -7,20 +7,23 @@
  */
 package org.dspace.app.itemimport;
 
+import gr.ekt.bte.core.DataLoader;
+import gr.ekt.bte.core.TransformationEngine;
+import gr.ekt.bte.dataloader.FileDataLoader;
+
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import gr.ekt.bte.core.DataLoader;
-import gr.ekt.bte.core.TransformationEngine;
-import gr.ekt.bte.dataloader.FileDataLoader;
+
 
 
 /**
  * This class acts as a Service in the procedure to batch import using the Biblio-Transformation-Engine
  */
-public class BTEBatchImportService {
+public class BTEBatchImportService
+{
 
 	TransformationEngine transformationEngine;
     Map<String, DataLoader> dataLoaders = new HashMap<String, DataLoader>();
@@ -29,31 +32,31 @@ public class BTEBatchImportService {
     /**
      * Default constructor
      */
-    public BTEBatchImportService() {
+    public BTEBatchImportService()
+    {
         super();
     }
 
     /**
      * Setter method for dataLoaders parameter
-     *
      * @param dataLoaders map of data loaders
      */
-    public void setDataLoaders(Map<String, DataLoader> dataLoaders) {
+    public void setDataLoaders(Map<String, DataLoader> dataLoaders)
+    {
         this.dataLoaders = dataLoaders;
     }
 
     /**
      * Get data loaders
-     *
      * @return the map of DataLoaders
      */
-    public Map<String, DataLoader> getDataLoaders() {
+    public Map<String, DataLoader> getDataLoaders()
+    {
         return dataLoaders;
     }
 
     /**
      * Get output map
-     *
      * @return the outputMapping
      */
 	public Map<String, String> getOutputMap() {
@@ -62,7 +65,6 @@ public class BTEBatchImportService {
 
 	/**
 	 * Setter method for the outputMapping
-     *
 	 * @param outputMap the output mapping
 	 */
 	public void setOutputMap(Map<String, String> outputMap) {
@@ -71,7 +73,6 @@ public class BTEBatchImportService {
 
         /**
          * Get transformation engine
-     *
          * @return transformation engine
          */
 	public TransformationEngine getTransformationEngine() {
@@ -80,7 +81,6 @@ public class BTEBatchImportService {
 
         /**
          * set transformation engine
-     *
          * @param transformationEngine transformation engine
          */
 	public void setTransformationEngine(TransformationEngine transformationEngine) {
@@ -89,7 +89,6 @@ public class BTEBatchImportService {
 	
         /**
          * Getter of file data loaders
-     *
          * @return List of file data loaders
          */
 	public List<String> getFileDataLoaders(){

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

@@ -20,6 +20,7 @@ import java.util.List;
 
 /**
  * @author kstamatis
+ *
  */
 public class BatchUpload {
 
@@ -34,7 +35,6 @@ public class BatchUpload {
 	
 	/**
          * Initialize with directory
-     *
 	 * @param dirPath directory path
 	 */
 	public BatchUpload(String dirPath) {
@@ -45,7 +45,6 @@ public class BatchUpload {
 
         /**
          * Initialize with directory
-     *
          * @param dir directory path
          */
 	public BatchUpload(File dir) {
@@ -56,7 +55,6 @@ public class BatchUpload {
 
         /**
          * Initialize with directory
-     *
          * @param dir directory path
          */
 	private void initializeWithFile(File dir){
@@ -98,7 +96,6 @@ public class BatchUpload {
 	
         /**
          * Count lines in file
-     *
          * @param filename file name
          * @return lines in file
          * @throws IOException if IO error
@@ -109,12 +106,11 @@ public class BatchUpload {
 	    String lineRead = "";
 	    while ((lineRead = reader.readLine()) != null) {
 	    	String[] parts = lineRead.split(" ");
-            if (parts.length > 1) {
+	    	if (parts.length > 1)
 	    		handlesImported.add(parts[1].trim());
-            } else {
+	    	else 
 	    		handlesImported.add(lineRead);
 	    }
-        }
 
 	    cnt = reader.getLineNumber(); 
 	    reader.close();
@@ -123,7 +119,6 @@ public class BatchUpload {
 	
         /**
          * Read a file
-     *
          * @param filename file name
          * @throws IOException if IO error
          */
@@ -135,9 +130,11 @@ public class BatchUpload {
 	    	
 	    	if (lineRead.startsWith("\tat ")){
 	    		this.errorMsgHTML += "<span class=\"batchimport-error-tab\">" + lineRead + "</span><br/>";
-            } else if (lineRead.startsWith("Caused by")) {
+	    	}
+	    	else if (lineRead.startsWith("Caused by")){
 	    		this.errorMsgHTML += "<span class=\"batchimport-error-caused\">" + lineRead + "</span><br/>";
-            } else {
+	    	}
+	    	else {
 	    		this.errorMsgHTML += lineRead + "<br/>";
 	    	}
 	    }
@@ -146,7 +143,6 @@ public class BatchUpload {
 
         /**
          * Get date
-     *
          * @return Date
          */
 	public Date getDate() {
@@ -155,7 +151,6 @@ public class BatchUpload {
 
         /**
          * Get path to directory
-     *
          * @return directory
          */
 	public File getDir() {
@@ -164,7 +159,6 @@ public class BatchUpload {
 
         /**
          * Whether successulf
-     *
          * @return true or false
          */
 	public boolean isSuccessful() {
@@ -173,7 +167,6 @@ public class BatchUpload {
 
         /**
          * Get items imported
-     *
          * @return number of items
          */
 	public int getItemsImported() {
@@ -182,7 +175,6 @@ public class BatchUpload {
 
         /**
          * Get total items
-     *
          * @return total
          */
 	public int getTotalItems() {
@@ -191,7 +183,6 @@ public class BatchUpload {
 	
         /**
          * Get formatted date (DD/MM/YY)
-     *
          * @return date as string
          */
 	public String getDateFormatted(){
@@ -202,7 +193,6 @@ public class BatchUpload {
 
         /**
          * Get handles of imported files
-     *
          * @return list of handles
          */
 	public List<String> getHandlesImported() {
@@ -211,7 +201,6 @@ public class BatchUpload {
 
         /**
          * Get error message
-     *
          * @return error message
          */
 	public String getErrorMsg() {
@@ -220,7 +209,6 @@ public class BatchUpload {
 
         /**
          * Get error message as HTML
-     *
          * @return error message string as HTML
          */
 	public String getErrorMsgHTML() {

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

@@ -7,17 +7,7 @@
  */
 package org.dspace.app.itemimport;
 
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.UUID;
-
-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.PosixParser;
+import org.apache.commons.cli.*;
 import org.dspace.app.itemimport.factory.ItemImportServiceFactory;
 import org.dspace.app.itemimport.service.ItemImportService;
 import org.dspace.content.Collection;
@@ -31,6 +21,12 @@ import org.dspace.eperson.service.EPersonService;
 import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.handle.service.HandleService;
 
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.UUID;
+
 /**
  * Import items into DSpace. The conventional use is upload files by copying
  * them. DSpace writes the item's bitstreams into its assetstore. Metadata is
@@ -51,17 +47,12 @@ public class ItemImportCLITool {
 
     private static boolean template = false;
 
-    private static final CollectionService collectionService = ContentServiceFactory.getInstance()
-                                                                                    .getCollectionService();
+    private static final CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
     private static final EPersonService epersonService = EPersonServiceFactory.getInstance().getEPersonService();
     private static final HandleService handleService = HandleServiceFactory.getInstance().getHandleService();
 
-    /**
-     * Default constructor
-     */
-    private ItemImportCLITool() { }
-
-    public static void main(String[] argv) throws Exception {
+    public static void main(String[] argv) throws Exception
+    {
         Date startTime = new Date();
         int status = 0;
 
@@ -117,17 +108,13 @@ public class ItemImportCLITool {
                 System.out
                         .println("\nadding items:    ItemImport -a -e eperson -c collection -s sourcedir -m mapfile");
                 System.out
-                    .println(
-                        "\nadding items from zip file:    ItemImport -a -e eperson -c collection -s sourcedir -z " +
-                            "filename.zip -m mapfile");
+                        .println("\nadding items from zip file:    ItemImport -a -e eperson -c collection -s sourcedir -z filename.zip -m mapfile");
                 System.out
                         .println("replacing items: ItemImport -r -e eperson -c collection -s sourcedir -m mapfile");
                 System.out
                         .println("deleting items:  ItemImport -d -e eperson -m mapfile");
                 System.out
-                    .println(
-                        "If multiple collections are specified, the first collection will be the one that owns the " +
-                            "item.");
+                        .println("If multiple collections are specified, the first collection will be the one that owns the item.");
 
                 System.exit(0);
             }
@@ -168,19 +155,23 @@ public class ItemImportCLITool {
                 template = true;
             }
 
-            if (line.hasOption('s')) { // source
+            if (line.hasOption('s')) // source
+            {
                 sourcedir = line.getOptionValue('s');
             }
 
-            if (line.hasOption('m')) { // mapfile
+            if (line.hasOption('m')) // mapfile
+            {
                 mapfile = line.getOptionValue('m');
             }
 
-            if (line.hasOption('e')) { // eperson
+            if (line.hasOption('e')) // eperson
+            {
                 eperson = line.getOptionValue('e');
             }
 
-            if (line.hasOption('c')) { // collections
+            if (line.hasOption('c')) // collections
+            {
                 collections = line.getOptionValues('c');
             }
 
@@ -236,8 +227,7 @@ public class ItemImportCLITool {
                     commandLineCollections = false;
                 }
             } else if ("add-bte".equals(command)) {
-                //Source dir can be null, the user can specify the parameters for his loader in the Spring XML
-                // configuration file
+                //Source dir can be null, the user can specify the parameters for his loader in the Spring XML configuration file
 
                 if (mapfile == null) {
                     System.out
@@ -260,9 +250,7 @@ public class ItemImportCLITool {
 
                 if (bteInputType == null) {
                     System.out
-                        .println(
-                            "Error - an input type (tsv, csv, ris, endnote, bibtex or any other type you have " +
-                                "specified in BTE Spring XML configuration file) must be specified");
+                            .println("Error - an input type (tsv, csv, ris, endnote, bibtex or any other type you have specified in BTE Spring XML configuration file) must be specified");
                     System.out.println(" (run with -h flag for details)");
                     System.exit(1);
                 }
@@ -349,8 +337,10 @@ public class ItemImportCLITool {
                                 || (mycollections.get(i).getType() != Constants.COLLECTION)) {
                             mycollections.set(i, null);
                         }
-                    } else if (collections[i] != null) {
-                        // not a handle, try and treat it as an integer collection database ID
+                    }
+                    // not a handle, try and treat it as an integer collection
+                    // database ID
+                    else if (collections[i] != null) {
                         mycollections.set(i, collectionService.find(c, UUID.fromString(collections[i])));
                     }
 
@@ -404,13 +394,11 @@ public class ItemImportCLITool {
             try {
                 if (zip) {
                     System.gc();
-                    System.out.println(
-                        "Deleting temporary zip directory: " + myloader.getTempWorkDirFile().getAbsolutePath());
+                    System.out.println("Deleting temporary zip directory: " + myloader.getTempWorkDirFile().getAbsolutePath());
                     myloader.cleanupZipTemp();
                 }
             } catch (Exception ex) {
-                System.out.println("Unable to delete temporary zip archive location: " + myloader.getTempWorkDirFile()
-                                                                                                 .getAbsolutePath());
+                System.out.println("Unable to delete temporary zip archive location: " + myloader.getTempWorkDirFile().getAbsolutePath());
             }
 
 
@@ -421,9 +409,7 @@ public class ItemImportCLITool {
             Date endTime = new Date();
             System.out.println("Started: " + startTime.getTime());
             System.out.println("Ended: " + endTime.getTime());
-            System.out.println(
-                "Elapsed time: " + ((endTime.getTime() - startTime.getTime()) / 1000) + " secs (" + (endTime
-                    .getTime() - startTime.getTime()) + " msecs)");
+            System.out.println("Elapsed time: " + ((endTime.getTime() - startTime.getTime()) / 1000) + " secs (" + (endTime.getTime() - startTime.getTime()) + " msecs)");
         }
 
         System.exit(status);

dspace-api/src/main/java/org/dspace/app/itemimport/factory/ItemImportServiceFactory.java

@@ -11,8 +11,7 @@ import org.dspace.app.itemimport.service.ItemImportService;
 import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
- * Abstract factory to get services for the itemimport package, use ItemImportService.getInstance() to retrieve an
- * implementation
+ * Abstract factory to get services for the itemimport package, use ItemImportService.getInstance() to retrieve an implementation
  *
  * @author kevinvandevelde at atmire.com
  */
@@ -21,7 +20,6 @@ public abstract class ItemImportServiceFactory {
     public abstract ItemImportService getItemImportService();
 
     public static ItemImportServiceFactory getInstance(){
-        return DSpaceServicesFactory.getInstance().getServiceManager()
-                                    .getServiceByName("itemImportServiceFactory", ItemImportServiceFactory.class);
+        return DSpaceServicesFactory.getInstance().getServiceManager().getServiceByName("itemImportServiceFactory", ItemImportServiceFactory.class);
     }
 }

dspace-api/src/main/java/org/dspace/app/itemimport/factory/ItemImportServiceFactoryImpl.java

@@ -11,8 +11,7 @@ import org.dspace.app.itemimport.service.ItemImportService;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
- * Factory implementation to get services for the itemimport package, use ItemImportService.getInstance() to retrieve
- * an implementation
+ * Factory implementation to get services for the itemimport package, use ItemImportService.getInstance() to retrieve an implementation
  *
  * @author kevinvandevelde at atmire.com
  */

dspace-api/src/main/java/org/dspace/app/itemimport/service/ItemImportService.java

@@ -7,16 +7,16 @@
  */
 package org.dspace.app.itemimport.service;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.List;
-import javax.mail.MessagingException;
-
 import org.dspace.app.itemimport.BatchUpload;
 import org.dspace.content.Collection;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;
 
+import javax.mail.MessagingException;
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+
 /**
  * Import items into DSpace. The conventional use is upload files by copying
  * them. DSpace writes the item's bitstreams into its assetstore. Metadata is
@@ -37,6 +37,7 @@ public interface ItemImportService {
 
 
     /**
+     * 
      * @param c DSpace Context
      * @param mycollections List of Collections
      * @param sourceDir source location
@@ -44,12 +45,10 @@ public interface ItemImportService {
      * @param template whether to use template item
      * @throws Exception if error 
      */
-    public void addItemsAtomic(Context c, List<Collection> mycollections, String sourceDir, String mapFile,
-                               boolean template) throws Exception;
+    public void addItemsAtomic(Context c, List<Collection> mycollections, String sourceDir, String mapFile, boolean template) throws Exception;
 
     /**
      * Add items
-     *
      * @param c DSpace Context
      * @param mycollections List of Collections
      * @param sourceDir source location
@@ -62,7 +61,6 @@ public interface ItemImportService {
 
     /**
      * Unzip a file
-     *
      * @param zipfile file
      * @return unzip location
      * @throws IOException if error
@@ -71,7 +69,6 @@ public interface ItemImportService {
 
     /**
      * Unzip a file to a destination
-     *
      * @param zipfile file
      * @param destDir destination directory
      * @return unzip location
@@ -81,7 +78,6 @@ public interface ItemImportService {
 
     /**
      * Unzip a file in a specific source directory
-     *
      * @param sourcedir source directory
      * @param zipfilename file name
      * @return unzip location
@@ -90,8 +86,8 @@ public interface ItemImportService {
     public String unzip(String sourcedir, String zipfilename) throws IOException;
 
     /**
-     * Given a public URL to a zip file that has the Simple Archive Format, this method imports the contents to DSpace
      *
+     * Given a public URL to a zip file that has the Simple Archive Format, this method imports the contents to DSpace
      * @param url The public URL of the zip file
      * @param owningCollection The owning collection the items will belong to
      * @param collections The collections the created items will be inserted to, apart from the owning one
@@ -101,8 +97,7 @@ public interface ItemImportService {
      * @param template whether to use template item
      * @throws Exception if error
      */
-    public void processUIImport(String url, Collection owningCollection, String[] collections, String resumeDir,
-                                String inputType, Context context, boolean template) throws Exception;
+    public void processUIImport(String url, Collection owningCollection, String[] collections, String resumeDir, String inputType, Context context, boolean template) throws Exception;
 
     /**
      * Since the BTE batch import is done in a new thread we are unable to communicate
@@ -110,9 +105,12 @@ public interface ItemImportService {
      * communication with email instead. Send a success email once the batch
      * import is complete
      *
-     * @param context  - the current Context
-     * @param eperson  - eperson to send the email to
-     * @param fileName - the filepath to the mapfile created by the batch import
+     * @param context
+     *            - the current Context
+     * @param eperson
+     *            - eperson to send the email to
+     * @param fileName
+     *            - the filepath to the mapfile created by the batch import
      * @throws MessagingException if error
      */
     public void emailSuccessMessage(Context context, EPerson eperson,
@@ -124,8 +122,10 @@ public interface ItemImportService {
      * communication with email instead. Send an error email if the batch
      * import fails
      *
-     * @param eperson - EPerson to send the error message to
-     * @param error   - the error message
+     * @param eperson
+     *            - EPerson to send the error message to
+     * @param error
+     *            - the error message
      * @throws MessagingException if error
      */
     public void emailErrorMessage(EPerson eperson, String error)
@@ -134,7 +134,6 @@ public interface ItemImportService {
 
     /**
      * Get imports available for a person
-     *
      * @param eperson EPerson object
      * @return List of batch uploads
      * @throws Exception if error
@@ -144,7 +143,6 @@ public interface ItemImportService {
 
     /**
      * Get import upload directory
-     *
      * @param ePerson EPerson object
      * @return directory
      * @throws Exception if error 
@@ -154,7 +152,6 @@ public interface ItemImportService {
 
     /**
      * Delete a batch by ID
-     *
      * @param c DSpace Context
      * @param uploadId identifier
      * @throws Exception if error
@@ -163,7 +160,6 @@ public interface ItemImportService {
 
     /**
      * Replace items
-     *
      * @param c DSpace Context
      * @param mycollections List of Collections
      * @param sourcedir source directory
@@ -171,12 +167,10 @@ public interface ItemImportService {
      * @param template whether to use template item
      * @throws Exception if error
      */
-    public void replaceItems(Context c, List<Collection> mycollections, String sourcedir, String mapfile,
-                             boolean template) throws Exception;
+    public void replaceItems(Context c, List<Collection> mycollections, String sourcedir, String mapfile, boolean template) throws Exception;
 
     /**
      * Delete items via mapfile
-     *
      * @param c DSpace Context
      * @param mapfile map file
      * @throws Exception if error
@@ -185,7 +179,6 @@ public interface ItemImportService {
 
     /**
      * Add items
-     *
      * @param c DSpace Context
      * @param mycollections List of Collections
      * @param sourcedir source directory
@@ -195,23 +188,19 @@ public interface ItemImportService {
      * @param workingDir working directory
      * @throws Exception if error
      */
-    public void addBTEItems(Context c, List<Collection> mycollections, String sourcedir, String mapfile,
-                            boolean template, String bteInputType, String workingDir) throws Exception;
+    public void addBTEItems(Context c, List<Collection> mycollections, String sourcedir, String mapfile, boolean template, String bteInputType, String workingDir) throws Exception;
 
     /**
      * Get temporary work directory
-     *
      * @return directory as string
      */
     public String getTempWorkDir();
 
     /**
      * Get temporary work directory (as File)
-     *
      * @return directory as File
-     * @throws java.io.IOException if the directory cannot be created.
      */
-    public File getTempWorkDirFile() throws IOException;
+    public File getTempWorkDirFile();
 
     /**
      * Cleanup
@@ -220,21 +209,18 @@ public interface ItemImportService {
 
     /**
      * Set test flag
-     *
      * @param isTest true or false 
      */
     public void setTest(boolean isTest);
 
     /**
      * Set resume flag
-     *
      * @param isResume true or false 
      */
     public void setResume(boolean isResume);
 
     /**
      * Set use workflow
-     *
      * @param useWorkflow whether to enable workflow
      */
     public void setUseWorkflow(boolean useWorkflow);
@@ -246,7 +232,6 @@ public interface ItemImportService {
 
     /**
      * Set quiet flag
-     *
      * @param isQuiet true or false
      */
     public void setQuiet(boolean isQuiet);

dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingAvailabilityBitstreamStrategy.java

@@ -25,6 +25,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  * based on the existence of bitstreams within the ORIGINAL bundle.
  * 
  * @author Kostas Stamatis
+ * 
  */
 public class ItemMarkingAvailabilityBitstreamStrategy implements ItemMarkingExtractor {
 
@@ -48,14 +49,16 @@ public class ItemMarkingAvailabilityBitstreamStrategy implements ItemMarkingExtr
 			markInfo.setImageName(nonAvailableImageName);	
 			
 			return markInfo;
-        } else {
+		}
+		else {
 			Bundle originalBundle = bundles.iterator().next();
 			if (originalBundle.getBitstreams().size() == 0){
 				ItemMarkingInfo markInfo = new ItemMarkingInfo();
 				markInfo.setImageName(nonAvailableImageName);
 				
 				return markInfo;
-            } else {
+			}
+			else {
                 Bitstream bitstream = originalBundle.getBitstreams().get(0);
 
                 ItemMarkingInfo signInfo = new ItemMarkingInfo();
@@ -63,6 +66,7 @@ public class ItemMarkingAvailabilityBitstreamStrategy implements ItemMarkingExtr
                 signInfo.setTooltip(bitstream.getName());
 				
 				
+				
 				String bsLink = "";
 
                 bsLink = bsLink + "bitstream/"

dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingCollectionStrategy.java

@@ -20,6 +20,7 @@ import org.dspace.core.Context;
  * based on the collection the items belong to
  * 
  * @author Kostas Stamatis
+ * 
  */
 public class ItemMarkingCollectionStrategy implements ItemMarkingExtractor {
 

dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingExtractor.java

@@ -16,6 +16,7 @@ import org.dspace.core.Context;
  * Interface to abstract the strategy for item signing
  * 
  * @author Kostas Stamatis
+ * 
  */
 public interface ItemMarkingExtractor {
 	public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)

dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingInfo.java

@@ -11,6 +11,7 @@ package org.dspace.app.itemmarking;
  * Simple DTO to transfer data about the marking info for an item
  * 
  * @author Kostas Stamatis
+ * 
  */
 public class ItemMarkingInfo {
 	private String imageName;

dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingMetadataStrategy.java

@@ -24,6 +24,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  * metadata field
  * 
  * @author Kostas Stamatis
+ * 
  */
 public class ItemMarkingMetadataStrategy implements ItemMarkingExtractor {
 
@@ -40,9 +41,11 @@ public class ItemMarkingMetadataStrategy implements ItemMarkingExtractor {
 	public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
 			throws SQLException {
 		
-        if (metadataField != null && mapping != null) {
+		if (metadataField != null && mapping!=null)
+		{
 			List<MetadataValue> vals = itemService.getMetadataByMetadataString(item, metadataField);
-            if (vals.size() > 0) {
+			if (vals.size() > 0)
+			{
 				for (MetadataValue value : vals){
 					String type = value.getValue();
 					if (mapping.containsKey(type)){

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

@@ -16,6 +16,8 @@ import java.util.Map;
  *    Order of actions is very import for correct processing.  This implementation
  *     supports an iterator that returns the actions in the order in which they are
  *     put in.  Adding the same action a second time has no effect on this order.
+ * 
+ *
  */
 public class ActionManager implements Iterable<UpdateAction> {
 	
@@ -24,17 +26,18 @@ public class ActionManager implements Iterable<UpdateAction> {
 	
         /**
          * Get update action
-     *
          * @param actionClass UpdateAction class
          * @return instantiation of UpdateAction class
          * @throws InstantiationException if instantiation error
          * @throws IllegalAccessException if illegal access error
          */
 	public UpdateAction getUpdateAction(Class<? extends UpdateAction> actionClass) 
-        throws InstantiationException, IllegalAccessException {
+	throws InstantiationException, IllegalAccessException
+	{
 		UpdateAction action =  registry.get(actionClass);
 		
-        if (action == null) {
+		if (action == null)
+		{
 			action = actionClass.newInstance();
 			registry.put(actionClass, action);
 		}
@@ -43,9 +46,11 @@ public class ActionManager implements Iterable<UpdateAction> {
 	}
 	
 	/**
+	 * 
 	 * @return whether any actions have been registered with this manager
 	 */
-    public boolean hasActions() {
+	public boolean hasActions()
+	{
 		return !registry.isEmpty();
 	}
 	
@@ -56,23 +61,28 @@ public class ActionManager implements Iterable<UpdateAction> {
 	 * @return iterator for UpdateActions
 	 */
 	@Override
-    public Iterator<UpdateAction> iterator() {
-        return new Iterator<UpdateAction>() {
+    public Iterator<UpdateAction> iterator()
+	{
+		return new Iterator<UpdateAction>() 
+		{ 			
 			private Iterator<Class<? extends UpdateAction>> itr = registry.keySet().iterator();
 			
 			@Override
-            public boolean hasNext() {
+            public boolean hasNext()
+			{
 				return itr.hasNext();
 			}
 			
 			@Override
-            public UpdateAction next() {
+            public UpdateAction next()
+			{
 				return registry.get(itr.next());
 			}
 			
 			//not supported
 			@Override
-            public void remove() {
+            public void remove()
+			{
 				throw new UnsupportedOperationException();
 			}
 		};

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

@@ -19,11 +19,7 @@ import java.util.List;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.authorize.factory.AuthorizeServiceFactory;
 import org.dspace.authorize.service.AuthorizeService;
-import org.dspace.content.Bitstream;
-import org.dspace.content.BitstreamFormat;
-import org.dspace.content.Bundle;
-import org.dspace.content.DCDate;
-import org.dspace.content.Item;
+import org.dspace.content.*;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.BitstreamFormatService;
 import org.dspace.content.service.InstallItemService;
@@ -34,16 +30,18 @@ import org.dspace.eperson.service.GroupService;
 
 /**
  * 	 Action to add bitstreams listed in item contents file to the item in DSpace	
+ *   
+ *
  */
 public class AddBitstreamsAction extends UpdateBitstreamsAction {
 
     protected AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
-    protected BitstreamFormatService bitstreamFormatService = ContentServiceFactory.getInstance()
-                                                                                   .getBitstreamFormatService();
+    protected BitstreamFormatService bitstreamFormatService = ContentServiceFactory.getInstance().getBitstreamFormatService();
     protected GroupService groupService = EPersonServiceFactory.getInstance().getGroupService();
     protected InstallItemService installItemService = ContentServiceFactory.getInstance().getInstallItemService();
 
-    public AddBitstreamsAction() {
+	public AddBitstreamsAction()
+	{
 		//empty	
 	}
 	
@@ -63,13 +61,15 @@ public class AddBitstreamsAction extends UpdateBitstreamsAction {
 	@Override
     public void execute(Context context, ItemArchive itarch, boolean isTest,
             boolean suppressUndo) throws IllegalArgumentException,
-        ParseException, IOException, AuthorizeException, SQLException {
+            ParseException, IOException, AuthorizeException, SQLException 
+	{
 		Item item = itarch.getItem();
 		File dir = itarch.getDirectory();
 		
 		List<ContentsEntry> contents = MetadataUtilities.readContentsFile(new File(dir, ItemUpdate.CONTENTS_FILE));
 		
-        if (contents.isEmpty()) {
+		if (contents.isEmpty())
+		{
 			ItemUpdate.pr("Contents is empty - no bitstreams to add");
 			return;
 		}
@@ -78,30 +78,36 @@ public class AddBitstreamsAction extends UpdateBitstreamsAction {
 		
 		String[] files = dir.list(ItemUpdate.fileFilter);
 		List<String> fileList = new ArrayList<String>();
-        for (String filename : files) {
+		for (String filename : files)
+		{
 			fileList.add(filename);
 			ItemUpdate.pr("file: " + filename);
 		}
 		
-        for (ContentsEntry ce : contents) {
+		for (ContentsEntry ce : contents)
+		{
 			//validate match to existing file in archive
-            if (!fileList.contains(ce.filename)) {
+			if (!fileList.contains(ce.filename))
+			{
 				throw new IllegalArgumentException("File listed in contents is missing: " + ce.filename);
 			}
 		}
 		int bitstream_bundles_updated = 0;
 		
 		//now okay to add
-        for (ContentsEntry ce : contents) {
+		for (ContentsEntry ce : contents)
+		{        				
 			String targetBundleName = addBitstream(context, itarch, item, dir, ce, suppressUndo, isTest);
 			if (!targetBundleName.equals("")
 			    && !targetBundleName.equals("THUMBNAIL")
-                && !targetBundleName.equals("TEXT")) {
+			    && !targetBundleName.equals("TEXT"))
+			{
 				bitstream_bundles_updated++;
 			}
 		}
 
-        if (alterProvenance && bitstream_bundles_updated > 0) {
+	        if (alterProvenance && bitstream_bundles_updated > 0)
+	        {
 	        	DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
 	        
 	        	String append = ". Added " + Integer.toString(bitstream_bundles_updated)
@@ -113,7 +119,6 @@ public class AddBitstreamsAction extends UpdateBitstreamsAction {
 		
         /**
          * Add bitstream
-     *
          * @param context DSpace Context
          * @param itarch Item Archive
          * @param item DSpace Item
@@ -130,7 +135,8 @@ public class AddBitstreamsAction extends UpdateBitstreamsAction {
          */
 	protected String addBitstream(Context context, ItemArchive itarch, Item item, File dir,
 			                  ContentsEntry ce, boolean suppressUndo, boolean isTest)
-        throws IOException, IllegalArgumentException, SQLException, AuthorizeException, ParseException {
+	throws IOException, IllegalArgumentException, SQLException, AuthorizeException, ParseException
+	{
 		ItemUpdate.pr("contents entry for bitstream: " + ce.toString());
     	File f = new File(dir, ce.filename);
     	
@@ -140,29 +146,40 @@ public class AddBitstreamsAction extends UpdateBitstreamsAction {
         Bitstream bs = null;
         String newBundleName = ce.bundlename;
 
-        if (ce.bundlename == null) { // should be required but default convention established
-            if (ce.filename.equals("license.txt")) {
+        if (ce.bundlename == null)  // should be required but default convention established
+        {
+            if (ce.filename.equals("license.txt"))
+            {
                 newBundleName = "LICENSE";
-            } else {
+            }
+            else  
+            {
                 newBundleName = "ORIGINAL";
             }
         }
         ItemUpdate.pr("  Bitstream " + ce.filename + " to be added to bundle: " + newBundleName);
         
-        if (!isTest) {
+        if (!isTest)
+        {
 	        // find the bundle
 	        List<Bundle> bundles = itemService.getBundles(item, newBundleName);
 	        Bundle targetBundle = null;
 	
-            if (bundles.size() < 1) {
+	        if (bundles.size() < 1)
+	        {
 	            // not found, create a new one
 	            targetBundle = bundleService.create(context, item, newBundleName);
-            } else {
+	        }
+	        else
+	        {
 	    		//verify bundle + name are not duplicates
-                for (Bundle b : bundles) {
+	        	for (Bundle b : bundles)
+	        	{
 	        		List<Bitstream> bitstreams = b.getBitstreams();
-                    for (Bitstream bsm : bitstreams) {
-                        if (bsm.getName().equals(ce.filename)) {
+	        		for (Bitstream bsm : bitstreams)
+	        		{
+                        if (bsm.getName().equals(ce.filename))
+	        			{
 	        				throw new IllegalArgumentException("Duplicate bundle + filename cannot be added: " 
 	        						+ b.getName() + " + " + bsm.getName());
 	        			}
@@ -181,14 +198,17 @@ public class AddBitstreamsAction extends UpdateBitstreamsAction {
 	        BitstreamFormat fmt = bitstreamFormatService.guessFormat(context, bs);
 	    	bitstreamService.setFormat(context, bs, fmt);
 
-            if (ce.description != null) {
+	        if (ce.description != null)
+	        {
 	        	bs.setDescription(context, ce.description);
 	        }
 	        	        
-            if ((ce.permissionsActionId != -1) && (ce.permissionsGroupName != null)) {
+	        if ((ce.permissionsActionId != -1) && (ce.permissionsGroupName != null))
+	        {
 				Group group = groupService.findByName(context, ce.permissionsGroupName);
 				
-                if (group != null) {
+				if (group != null)
+				{
                     authorizeService.removeAllPolicies(context, bs);  // remove the default policy
                     authorizeService.createResourcePolicy(context, bs, group, null, ce.permissionsActionId, null);
 				}
@@ -197,7 +217,8 @@ public class AddBitstreamsAction extends UpdateBitstreamsAction {
 	        //update after all changes are applied
             bitstreamService.update(context, bs);
         
-            if (!suppressUndo) {
+	        if (!suppressUndo)
+	        {
 	        	itarch.addUndoDeleteContents(bs.getID());
 	        }
 		return targetBundle.getName();

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

@@ -11,10 +11,11 @@ import java.sql.SQLException;
 import java.util.List;
 
 import org.dspace.authorize.AuthorizeException;
+import org.dspace.content.MetadataValue;
 import org.dspace.content.Item;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
-import org.dspace.content.MetadataValue;
+
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.MetadataFieldService;
 import org.dspace.content.service.MetadataSchemaService;
@@ -22,11 +23,11 @@ import org.dspace.core.Context;
 
 /**
  *   Action to add metadata to item
+ *
  */
 public class AddMetadataAction extends UpdateMetadataAction {
 
-    protected MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance()
-                                                                                 .getMetadataSchemaService();
+    protected MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance().getMetadataSchemaService();
     protected MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance().getMetadataFieldService();
 
 	/**
@@ -41,68 +42,79 @@ public class AddMetadataAction extends UpdateMetadataAction {
 	 */
 	@Override
     public void execute(Context context, ItemArchive itarch, boolean isTest,
-                        boolean suppressUndo) throws AuthorizeException, SQLException {
+            boolean suppressUndo) throws AuthorizeException, SQLException
+	{
 		Item item = itarch.getItem();
 		String dirname = itarch.getDirectoryName();
 	    	
-        for (DtoMetadata dtom : itarch.getMetadataFields()) {
-            for (String f : targetFields) {
-                if (dtom.matches(f, false)) {
+		for (DtoMetadata dtom : itarch.getMetadataFields())
+		{
+			for (String f : targetFields)
+			{
+				if (dtom.matches(f, false))
+				{
 					// match against metadata for this field/value in repository
 					// qualifier must be strictly matched, possibly null					
 					List<MetadataValue> ardcv = null;
 					ardcv = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
 					
 					boolean found = false;
-                    for (MetadataValue dcv : ardcv) {
-                        if (dcv.getValue().equals(dtom.value)) {
+					for (MetadataValue dcv : ardcv)
+					{
+						if (dcv.getValue().equals(dtom.value))
+						{
 							found = true;
 							break;
 						}
 					}
 					
-                    if (found) {
+					if (found)
+					{
 						ItemUpdate.pr("Warning:  No new metadata found to add to item " + dirname 
 								+ " for element " + f);						
-                    } else {
-                        if (isTest) {
+					}
+					else
+					{
+						if (isTest)
+						{
 							ItemUpdate.pr("Metadata to add: " + dtom.toString());
 							   //validity tests that would occur in actual processing
 	        	            // If we're just test the import, let's check that the actual metadata field exists.
 	        	        	MetadataSchema foundSchema = metadataSchemaService.find(context, dtom.schema);
 	        	        	
-                            if (foundSchema == null) {
+	        	        	if (foundSchema == null)
+	        	        	{
 	        	        		ItemUpdate.pr("ERROR: schema '" 
-                                                  + dtom.schema + "' was not found in the registry; found on item " +
-                                                  dirname);
-                            } else {
-                                MetadataField foundField = metadataFieldService
-                                    .findByElement(context, foundSchema, dtom.element, dtom.qualifier);
+	        	        			+ dtom.schema + "' was not found in the registry; found on item " + dirname);
+	        	        	}
+	        	        	else
+	        	        	{
+		        	        	MetadataField foundField = metadataFieldService.findByElement(context, foundSchema, dtom.element, dtom.qualifier);
 		        	        	
-                                if (foundField == null) {
+		        	        	if (foundField == null)
+		        	        	{
 		        	        		ItemUpdate.pr("ERROR: Metadata field: '" + dtom.schema + "." + dtom.element + "." 
-                                                      + dtom.qualifier + "' not found in registry; found on item " +
-                                                      dirname);
+		        	        				+ dtom.qualifier + "' not found in registry; found on item " + dirname);
 		        	            }		
 	        				}						
-                        } else {
-                            itemService
-                                .addMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language,
-                                             dtom.value);
+						}
+						else
+						{
+							itemService.addMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language, dtom.value);
 							ItemUpdate.pr("Metadata added: " + dtom.toString());
 	
-                            if (!suppressUndo) {
+							if (!suppressUndo)
+							{
 								//itarch.addUndoDtom(dtom);
 								//ItemUpdate.pr("Undo metadata: " + dtom);
 								
 								// add all as a replace record to be preceded by delete
-                                for (MetadataValue dcval : ardcv) {
+								for (MetadataValue dcval : ardcv)
+								{
                                     MetadataField metadataField = dcval.getMetadataField();
                                     MetadataSchema metadataSchema = metadataField.getMetadataSchema();
-                                    itarch.addUndoMetadataField(
-                                        DtoMetadata.create(metadataSchema.getName(), metadataField.getElement(),
-                                                           metadataField.getQualifier(), dcval.getLanguage(),
-                                                           dcval.getValue()));
+                                    itarch.addUndoMetadataField(DtoMetadata.create(metadataSchema.getName(), metadataField.getElement(),
+                                            metadataField.getQualifier(), dcval.getLanguage(), dcval.getValue()));
 								}
 								
 							}

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

@@ -7,17 +7,17 @@
  */
 package org.dspace.app.itemupdate;
 
-import java.io.FileInputStream;
 import java.io.IOException;
-import java.io.InputStream;
 import java.util.Properties;
-
+import java.io.InputStream;
+import java.io.FileInputStream;
 import org.dspace.content.Bitstream;
 
 /**
  *   Filter interface to be used by ItemUpdate 
  *   to determine which bitstreams in an Item
  *   acceptable for removal.
+ *
  */
 public abstract class BitstreamFilter {
 
@@ -33,20 +33,26 @@ public abstract class BitstreamFilter {
 	public abstract boolean accept(Bitstream bitstream) throws BitstreamFilterException;
 	
 	/**
+	 * 
 	 * @param filepath - The complete path for the properties file
 	 * @throws IOException if IO error
 	 */
 	public void initProperties(String filepath)
-        throws IOException {
+	throws IOException
+	{
 		props = new Properties();
 		
 		InputStream in = null;
 
-        try {
+        try
+        {
             in = new FileInputStream(filepath);
             props.load(in);
-        } finally {
-            if (in != null) {
+        }
+        finally
+        {
+            if (in != null)
+            {
                 in.close();
             }
         }

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

@@ -15,12 +15,14 @@ import org.dspace.content.Bundle;
 
 /**
  *   BitstreamFilter implementation to filter by bundle name
+ *
  */
 public class BitstreamFilterByBundleName extends BitstreamFilter {
 
 	protected String bundleName;
 	
-    public BitstreamFilterByBundleName() {
+	public BitstreamFilterByBundleName()
+	{
 		//empty
 	}
 
@@ -28,27 +30,36 @@ public class BitstreamFilterByBundleName extends BitstreamFilter {
 	 *    Filter bitstream based on bundle name found in properties file
 	 *    
 	 *    @param bitstream Bitstream
-     * @return whether bitstream is in bundle
 	 *    @throws BitstreamFilterException if filter error
+	 *    @return whether bitstream is in bundle
+	 *    
 	 */
 	@Override
 	public boolean accept(Bitstream bitstream)
-        throws BitstreamFilterException {
-        if (bundleName == null) {
+	throws BitstreamFilterException
+	{
+		if (bundleName == null)
+		{
 			bundleName = props.getProperty("bundle");
-            if (bundleName == null) {
+			if (bundleName == null)
+			{
 				throw new BitstreamFilterException("Property 'bundle' not found.");
 			}			
 		}
 		
-        try {
+		try
+		{
 			List<Bundle> bundles = bitstream.getBundles();
-            for (Bundle b : bundles) {
-                if (b.getName().equals(bundleName)) {
+			for (Bundle b : bundles)
+			{
+                if (b.getName().equals(bundleName))
+				{
 					return true;
 				}
 			}		
-        } catch (SQLException e) {
+		}
+		catch(SQLException e)
+		{
 			throw new BitstreamFilterException(e);
 		}
 		return false;

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

@@ -7,20 +7,21 @@
  */
 package org.dspace.app.itemupdate;
 
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
+import java.util.regex.*;
 
 import org.dspace.content.Bitstream;
 
 /**
  * BitstreamFilter implementation to filter by filename pattern
+ *
  */
 public class BitstreamFilterByFilename extends BitstreamFilter {
 	
 	protected Pattern pattern;
     protected String filenameRegex;
 	
-    public BitstreamFilterByFilename() {
+	public BitstreamFilterByFilename()
+	{
 		//empty
 	}
 
@@ -30,13 +31,16 @@ public class BitstreamFilterByFilename extends BitstreamFilter {
 	 * 
          * @param bitstream Bitstream
 	 * @return whether bitstream name matches the regular expression
-     * @throws BitstreamFilterException if filter error
+         * @exception BitstreamFilterException if filter error
 	 */
 	@Override
-    public boolean accept(Bitstream bitstream) throws BitstreamFilterException {
-        if (filenameRegex == null) {
+    public boolean accept(Bitstream bitstream) throws BitstreamFilterException
+	{		
+		if (filenameRegex == null)
+		{
 			filenameRegex = props.getProperty("filename");
-            if (filenameRegex == null) {
+			if (filenameRegex == null)
+			{
 				throw new BitstreamFilterException("BitstreamFilter property 'filename' not found.");
 			}
 			pattern = Pattern.compile(filenameRegex);

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

@@ -9,25 +9,28 @@ package org.dspace.app.itemupdate;
 
 /**
  *    Exception class for BitstreamFilters
+ *
  */
-public class BitstreamFilterException extends Exception {
+public class BitstreamFilterException extends Exception 
+{
 	
 	private static final long serialVersionUID = 1L;
 	
-    public BitstreamFilterException() {
-    }
-
+	public BitstreamFilterException() {}
         /**
+         * 
          * @param msg exception message
          */
-    public BitstreamFilterException(String msg) {
+	public BitstreamFilterException(String msg)
+	{
 		super(msg);
 	}
-
         /**
+         * 
          * @param e exception
          */
-    public BitstreamFilterException(Exception e) {
+	public BitstreamFilterException(Exception e)
+	{
 		super(e);
 	}
 	

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

@@ -8,8 +8,7 @@
 package org.dspace.app.itemupdate;
 
 import java.text.ParseException;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
+import java.util.regex.*;
 
 import org.dspace.core.Constants;
 
@@ -27,8 +26,11 @@ import org.dspace.core.Constants;
  *      permissions: -[r|w] ['group name']
  *      description: <the description of the file>
  *      }
+ * 
+ *
  */
-public class ContentsEntry {
+public class ContentsEntry 
+{
 	public static final String HDR_BUNDLE = "bundle:";
 	public static final String HDR_PERMISSIONS = "permissions:";
 	public static final String HDR_DESCRIPTION = "description:";
@@ -45,7 +47,8 @@ public class ContentsEntry {
 			             String bundlename,
 			             int permissionsActionId,
 			             String permissionsGroupName,
-                            String description) {
+			             String description)
+	{
 		this.filename = filename;
 		this.bundlename = bundlename;
 		this.permissionsActionId = permissionsActionId;
@@ -61,7 +64,8 @@ public class ContentsEntry {
 	 * @throws ParseException if parse error
 	 */
 	public static ContentsEntry parse(String line)
-        throws ParseException {
+	throws ParseException
+	{
 		String[] ar = line.split("\t");
 		ItemUpdate.pr("ce line split: " + ar.length);
 		
@@ -71,33 +75,46 @@ public class ContentsEntry {
 		String groupName = null;
 		int actionId = -1;
 
-        if (ar.length > 1) {
-            for (int i = 1; i < ar.length; i++) {
+		if (ar.length > 1)
+		{
+			for (int i=1; i < ar.length; i++)
+			{
 				ItemUpdate.pr("ce " + i + " : " + ar[i]);
-                if (ar[i].startsWith(HDR_BUNDLE)) {
+				if (ar[i].startsWith(HDR_BUNDLE))
+				{
 					arp[1] = ar[i].substring(HDR_BUNDLE.length()).trim();
 					
-                } else if (ar[i].startsWith(HDR_PERMISSIONS)) {
+				}
+				else if (ar[i].startsWith(HDR_PERMISSIONS))
+				{
 					arp[2] = ar[i].substring(HDR_PERMISSIONS.length()).trim();
 					
 					// parse into actionId and group name
 					
 					Matcher m = permissionsPattern.matcher(arp[2]);
-                    if (m.matches()) {
+					if (m.matches())
+					{
 						String action = m.group(1); //
-                        if (action.equals("r")) {
+						if (action.equals("r"))
+						{
 							 actionId = Constants.READ;
-                        } else if (action.equals("w")) {
+						}
+						else if (action.equals("w"))
+						{
 							 actionId = Constants.WRITE;
 						}
 						
 						groupName = m.group(2).trim();
 					}
 					
-                } else if (ar[i].startsWith(HDR_DESCRIPTION)) {
+				}
+				else if (ar[i].startsWith(HDR_DESCRIPTION))
+				{
 					arp[3] = ar[i].substring(HDR_DESCRIPTION.length()).trim();
 					
-                } else {
+				}
+				else
+				{
 					throw new ParseException("Unknown text in contents file: " + ar[i], 0);				
 				}			
 			}
@@ -105,23 +122,30 @@ public class ContentsEntry {
 		return new ContentsEntry(arp[0], arp[1], actionId, groupName, arp[3]);
 	}
 	
-    public String toString() {
+	public String toString()
+	{
 		StringBuilder sb = new StringBuilder(filename);
-        if (bundlename != null) {
+		if (bundlename != null)
+		{
 			sb.append(HDR_BUNDLE).append(" ").append(bundlename);
 		}
 		
-        if (permissionsGroupName != null) {
+		if (permissionsGroupName != null)
+		{
 			sb.append(HDR_PERMISSIONS);
-            if (permissionsActionId == Constants.READ) {
+			if (permissionsActionId == Constants.READ)
+			{
 				sb.append(" -r ");
-            } else if (permissionsActionId == Constants.WRITE) {
+			}
+			else if (permissionsActionId == Constants.WRITE)
+			{
 				sb.append(" -w ");
 			}
 			sb.append(permissionsGroupName);
 		}
 		
-        if (description != null) {
+		if (description != null)
+		{
 			sb.append(HDR_DESCRIPTION).append(" ").append(description);
 		}		
 		

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

@@ -14,10 +14,7 @@ import java.text.ParseException;
 import java.util.List;
 
 import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-import org.dspace.content.DCDate;
-import org.dspace.content.Item;
+import org.dspace.content.*;
 import org.dspace.core.Context;
 
 /**
@@ -26,8 +23,10 @@ import org.dspace.core.Context;
  * 	  Undo not supported for this UpdateAction
  * 
  *    Derivatives of the bitstream to be deleted are not also deleted 
+ *
  */
-public class DeleteBitstreamsAction extends UpdateBitstreamsAction {
+public class DeleteBitstreamsAction extends UpdateBitstreamsAction 
+{
 	/**
 	 *   Delete bitstream from item
 	 * 
@@ -44,46 +43,65 @@ public class DeleteBitstreamsAction extends UpdateBitstreamsAction {
 	@Override
     public void execute(Context context, ItemArchive itarch, boolean isTest,
             boolean suppressUndo) throws IllegalArgumentException, IOException,
-        SQLException, AuthorizeException, ParseException {
+            SQLException, AuthorizeException, ParseException 
+	{
 		File f = new File(itarch.getDirectory(), ItemUpdate.DELETE_CONTENTS_FILE);
-        if (!f.exists()) {
+		if (!f.exists())
+		{
 			ItemUpdate.pr("Warning: Delete_contents file for item " + itarch.getDirectoryName() + " not found.");
-        } else {
+		}
+		else
+		{
 			List<String> list = MetadataUtilities.readDeleteContentsFile(f);
-            if (list.isEmpty()) {
+			if (list.isEmpty())
+			{
 				ItemUpdate.pr("Warning: empty delete_contents file for item " + itarch.getDirectoryName() );
-            } else {
-                for (String id : list) {
-                    try {
+			}
+			else
+			{
+				for (String id : list)
+				{
+					try
+					{
 			    		Bitstream bs = bitstreamService.findByIdOrLegacyId(context, id);
-                        if (bs == null) {
+			    		if (bs == null)
+			    		{
 			    			ItemUpdate.pr("Bitstream not found by id: " + id);
-                        } else {
+			    		}
+			    		else
+			    		{
 				    		List<Bundle> bundles = bs.getBundles();
-                            for (Bundle b : bundles) {
-                                if (isTest) {
+				    		for (Bundle b : bundles)
+				    		{
+                                if (isTest)
+				    			{
 					    			ItemUpdate.pr("Delete bitstream with id = " + id);
-                                } else {
+				    			}
+				    			else
+				    			{
 				    				bundleService.removeBitstream(context, b, bs);
 					    			ItemUpdate.pr("Deleted bitstream with id = " + id);
 					    			
 				    			}
 				    		}	
 			    		
-                            if (alterProvenance) {
+				            if (alterProvenance)
+				            {
 				            	DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
 				            	
-                                String append = "Bitstream " + bs.getName() + " deleted on " + DCDate
-                                    .getCurrent() + "; ";
+				            	String append = "Bitstream " + bs.getName() + " deleted on " + DCDate.getCurrent() + "; ";
 				            	Item item = bundles.iterator().next().getItems().iterator().next();
 					    		ItemUpdate.pr("Append provenance with: " + append);
 					    		
-                                if (!isTest) {
+					    		if (!isTest)
+					    		{
 					    			MetadataUtilities.appendMetadata(context, item, dtom, false, append);
 					    		}
 				            }
 			    		}	
-                    } catch (SQLException e) {
+					}
+					catch(SQLException e)
+					{
 						ItemUpdate.pr("Error finding bitstream from id: " + id + " : " + e.toString());
 					}
 				}

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

@@ -14,10 +14,7 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-import org.dspace.content.DCDate;
-import org.dspace.content.Item;
+import org.dspace.content.*;
 import org.dspace.core.Context;
 
 /**
@@ -28,6 +25,8 @@ import org.dspace.core.Context;
  *      
  *      Note:  Multiple filters are impractical if trying to manage multiple properties files
  *      in a commandline environment
+ * 
+ *
  */
 public class DeleteBitstreamsByFilterAction extends UpdateBitstreamsAction {
 
@@ -38,16 +37,17 @@ public class DeleteBitstreamsByFilterAction extends UpdateBitstreamsAction {
 	 *   
 	 * @param filter BitstreamFilter
 	 */
-    public void setBitstreamFilter(BitstreamFilter filter) {
+	public void setBitstreamFilter(BitstreamFilter filter)
+	{
 		this.filter = filter;
 	}
 	
 	/**
 	 *   Get filter
-     *
 	 * @return filter 
 	 */
-    public BitstreamFilter getBitstreamFilter() {
+	public BitstreamFilter getBitstreamFilter()
+	{
 		return filter;
 	}
 	
@@ -67,25 +67,33 @@ public class DeleteBitstreamsByFilterAction extends UpdateBitstreamsAction {
 	@Override
     public void execute(Context context, ItemArchive itarch, boolean isTest,
             boolean suppressUndo) throws AuthorizeException,
-        BitstreamFilterException, IOException, ParseException, SQLException {
+            BitstreamFilterException, IOException, ParseException, SQLException 
+	{
 		
 		List<String> deleted = new ArrayList<String>();
 		
 		Item item = itarch.getItem();
 		List<Bundle> bundles = item.getBundles();
 		
-        for (Bundle b : bundles) {
+		for (Bundle b : bundles)    
+		{
 			List<Bitstream> bitstreams = b.getBitstreams();
 			String bundleName = b.getName();
 
-            for (Bitstream bs : bitstreams) {
-                if (filter.accept(bs)) {
-                    if (isTest) {
+			for (Bitstream bs : bitstreams)
+			{
+                if (filter.accept(bs))
+				{
+	    			if (isTest)
+	    			{
 		    			ItemUpdate.pr("Delete from bundle " + bundleName + " bitstream " + bs.getName() 
 		    					+ " with id = " + bs.getID());
-                    } else {
+	    			}
+	    			else
+	    			{	    					    				
 	    				//provenance is not maintained for derivative bitstreams
-                        if (!bundleName.equals("THUMBNAIL") && !bundleName.equals("TEXT")) {
+	    				if (!bundleName.equals("THUMBNAIL") && !bundleName.equals("TEXT"))
+	    				{
 	    					deleted.add(bs.getName());
 	    				}
 	    				bundleService.removeBitstream(context, b, bs);
@@ -96,11 +104,13 @@ public class DeleteBitstreamsByFilterAction extends UpdateBitstreamsAction {
 			}			
 		}
 		
-        if (alterProvenance && !deleted.isEmpty()) {
+        if (alterProvenance && !deleted.isEmpty())
+        {     	
     		StringBuilder sb = new StringBuilder("  Bitstreams deleted on "); 	
     		sb.append(DCDate.getCurrent()).append(": ");
     		
-            for (String s : deleted) {
+    		for (String s : deleted)
+    		{
             	sb.append(s).append(", ");
     		}
     		        	
@@ -108,7 +118,8 @@ public class DeleteBitstreamsByFilterAction extends UpdateBitstreamsAction {
         	
     		ItemUpdate.pr("Append provenance with: " + sb.toString());
     		
-            if (!isTest) {
+    		if (!isTest)
+    		{
     			MetadataUtilities.appendMetadata(context, item, dtom, false, sb.toString());
     		}
         }

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

@@ -12,14 +12,16 @@ import java.text.ParseException;
 import java.util.List;
 
 import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.Item;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
 import org.dspace.content.MetadataValue;
+import org.dspace.content.Item;
 import org.dspace.core.Context;
 
 /**
  *    Action to delete metadata 
+ * 
+ *
  */
 public class DeleteMetadataAction extends UpdateMetadataAction {
 
@@ -38,22 +40,26 @@ public class DeleteMetadataAction extends UpdateMetadataAction {
     public void execute(Context context, ItemArchive itarch, boolean isTest,
             boolean suppressUndo) throws AuthorizeException, ParseException, SQLException {
 		Item item = itarch.getItem();
-        for (String f : targetFields) {
+		for (String f : targetFields)
+		{
 			DtoMetadata dummy = DtoMetadata.create(f, Item.ANY, "");
 			List<MetadataValue> ardcv = itemService.getMetadataByMetadataString(item, f);
 
 			ItemUpdate.pr("Metadata to be deleted: ");
-            for (MetadataValue dcv : ardcv) {
+			for (MetadataValue dcv : ardcv)
+			{
 				ItemUpdate.pr("  " + MetadataUtilities.getDCValueString(dcv));
 			}
 
-            if (!isTest) {
-                if (!suppressUndo) {
-                    for (MetadataValue dcv : ardcv) {
+			if (!isTest)
+			{
+				if (!suppressUndo)
+				{
+					for (MetadataValue dcv : ardcv)
+					{
                         MetadataField metadataField = dcv.getMetadataField();
                         MetadataSchema metadataSchema = metadataField.getMetadataSchema();
-                        itarch.addUndoMetadataField(
-                            DtoMetadata.create(metadataSchema.getName(), metadataField.getElement(),
+                        itarch.addUndoMetadataField(DtoMetadata.create(metadataSchema.getName(), metadataField.getElement(),
                                 metadataField.getQualifier(), dcv.getLanguage(), dcv.getValue()));
 					}
 				}

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

@@ -11,10 +11,12 @@ import java.util.Properties;
 
 /**
  *   Bitstream filter to delete from TEXT bundle
+ *
  */
 public class DerivativeTextBitstreamFilter extends BitstreamFilterByBundleName {
 	
-    public DerivativeTextBitstreamFilter() {
+	public DerivativeTextBitstreamFilter()
+	{
 		props = new Properties();
 		props.setProperty("bundle", "TEXT");
 	}

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

@@ -8,7 +8,6 @@
 package org.dspace.app.itemupdate;
 
 import java.text.ParseException;
-
 import org.dspace.content.Item;
 
 /**
@@ -17,19 +16,22 @@ import org.dspace.content.Item;
  *   
  *   Adds some utility methods
  *   
- * Really not at all general enough but supports Dublin Core and the compound form notation {@code <schema>
- * .<element>[.<qualifier>]}
+ *   Really not at all general enough but supports Dublin Core and the compound form notation {@code <schema>.<element>[.<qualifier>]}
  *   
  *   Does not support wildcard for qualifier
+ * 
+ *
  */
-class DtoMetadata {
+class DtoMetadata 
+{
 	final String schema;   
 	final String element;
 	final String qualifier;
 	final String language;
 	final String value;
 	
-    protected DtoMetadata(String schema, String element, String qualifier, String language, String value) {
+	protected DtoMetadata(String schema, String element, String qualifier, String language, String value)
+	{
 		this.schema = schema;
 		this.element = element;
 		this.qualifier = qualifier;
@@ -40,6 +42,7 @@ class DtoMetadata {
 	/**
 	 *  Factory method
 	 *  
+	 *  
 	 * @param schema     not null, not empty -  'dc' is the standard case
 	 * @param element    not null, not empty
 	 * @param qualifier  null; don't allow empty string or * indicating 'any'
@@ -53,8 +56,10 @@ class DtoMetadata {
 			    String qualifier,
 			    String language,
 			    String value)
-        throws IllegalArgumentException {
-        if ((qualifier != null) && (qualifier.equals(Item.ANY) || qualifier.equals(""))) {
+	throws IllegalArgumentException
+    {
+		if ((qualifier != null) &&  (qualifier.equals(Item.ANY) || qualifier.equals("")))
+		{
 			throw new IllegalArgumentException("Invalid qualifier: " + qualifier);
 		}
 		return new DtoMetadata(schema, element, qualifier, language, value);
@@ -63,6 +68,7 @@ class DtoMetadata {
 	/**
 	 *   Factory method to create metadata object
 	 *   
+	 * 
 	 * @param compoundForm   of the form <schema>.<element>[.<qualifier>]
 	 * @param language   null or empty
 	 * @param value      value
@@ -70,11 +76,13 @@ class DtoMetadata {
          * @throws IllegalArgumentException if arg error
 	 */
 	public static DtoMetadata create(String compoundForm, String language, String value)
-        throws ParseException, IllegalArgumentException {
+	throws ParseException, IllegalArgumentException  
+    {
 		String[] ar = MetadataUtilities.parseCompoundForm(compoundForm);
 		
 		String qual = null;
-        if (ar.length > 2) {
+		if (ar.length > 2)
+		{
     		qual = ar[2];
 		}
 		
@@ -85,44 +93,56 @@ class DtoMetadata {
 	 *   Determine if this metadata field matches the specified type:
 	 *    schema.element or schema.element.qualifier
 	 *    
+	 * 
 	 * @param compoundForm   of the form <schema>.<element>[.<qualifier>|.*]
 	 * @param wildcard       allow wildcards in compoundForm param
 	 * @return whether matches
 	 */
-    public boolean matches(String compoundForm, boolean wildcard) {
+	public boolean matches(String compoundForm, boolean wildcard)
+	{
 		String[] ar = compoundForm.split("\\s*\\.\\s*"); //MetadataUtilities.parseCompoundForm(compoundForm);
 		
-        if ((ar.length < 2) || (ar.length > 3)) {
+		if ((ar.length < 2) || (ar.length > 3))
+		{
 			return false;
 		}
 		
-        if (!this.schema.equals(ar[0]) || !this.element.equals(ar[1])) {
+		if (!this.schema.equals(ar[0]) || !this.element.equals(ar[1]))
+		{
 			return false;
 		}
 		
-        if (ar.length == 2) {
-            if (this.qualifier != null) {
+		if (ar.length == 2)
+		{
+			if (this.qualifier != null)
+			{
 				return false;
 			}
 		}
 		
-        if (ar.length == 3) {
-            if (this.qualifier == null) {
+		if (ar.length == 3)	
+		{
+			if (this.qualifier == null)
+			{
 				return false;
 			}
-            if (wildcard && ar[2].equals(Item.ANY)) {
+			if (wildcard && ar[2].equals(Item.ANY))
+			{
 				return true;
 			}
-            if (!this.qualifier.equals(ar[2])) {
+			if (!this.qualifier.equals(ar[2]))
+			{
 				return false;
 			}
 		}
 		return true;		
 	}
 	
-    public String toString() {
+	public String toString()
+	{
 		String s =  "\tSchema: " + schema + " Element: " + element;
-        if (qualifier != null) {
+		if (qualifier != null)
+		{
 			s+= " Qualifier: " + qualifier;
 		}
 		s+= " Language: " + ((language == null) ? "[null]" : language);
@@ -131,7 +151,8 @@ class DtoMetadata {
         return s;
 	}
 	
-    public String getValue() {
+	public String getValue()
+	{
 		return value;
 	}
 		

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

@@ -10,11 +10,12 @@ package org.dspace.app.itemupdate;
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.FileWriter;
+import java.io.FilenameFilter;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
-import java.io.FileWriter;
-import java.io.IOException;
 import java.io.InputStream;
+import java.io.IOException;
 import java.io.OutputStream;
 import java.io.PrintWriter;
 import java.sql.SQLException;
@@ -22,13 +23,14 @@ import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 import java.util.UUID;
+
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerConfigurationException;
 import javax.xml.transform.TransformerException;
 import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.TransformerConfigurationException;
 
 import org.apache.log4j.Logger;
 import org.dspace.app.util.LocalSchemaFilenameFilter;
@@ -38,6 +40,7 @@ import org.dspace.content.Item;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
 import org.dspace.core.Context;
+
 import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.handle.service.HandleService;
 import org.w3c.dom.Document;
@@ -45,6 +48,7 @@ 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); 
@@ -67,13 +71,13 @@ public class ItemArchive {
     protected ItemService itemService;
 
 //constructors
-    protected ItemArchive() {
+    protected ItemArchive()
+	{
         handleService = HandleServiceFactory.getInstance().getHandleService();
         itemService = ContentServiceFactory.getInstance().getItemService();
 	}
 	
-    /**
-     * factory method
+/** factory method
  * 
  * 	Minimal requirements for dublin_core.xml for this application
  *  is the presence of dc.identifier.uri
@@ -85,38 +89,48 @@ public class ItemArchive {
  *                     if null, the default is the handle in the dc.identifier.uri field
  *  @return ItemArchive object
  *  @throws Exception if error
+ * 
  */
 	public static ItemArchive create(Context context, File dir, String itemField)
-        throws Exception {
+	throws Exception
+	{
 		ItemArchive itarch = new ItemArchive(); 
 		itarch.dir = dir;
 		itarch.dirname = dir.getName();
         InputStream is = null;
-        try {
+        try
+        {
             is = new FileInputStream(new File(dir, DUBLIN_CORE_XML));
             itarch.dtomList = MetadataUtilities.loadDublinCore(getDocumentBuilder(), is);
             
-            //The code to search for local schema files was copied from org.dspace.app.itemimport
-            // .ItemImportServiceImpl.java
+            //The code to search for local schema files was copied from org.dspace.app.itemimport.ItemImportServiceImpl.java
             File file[] = dir.listFiles(new LocalSchemaFilenameFilter());
-            for (int i = 0; i < file.length; i++) {
+            for (int i = 0; i < file.length; i++)
+            {
                 is = new FileInputStream(file[i]);
                 itarch.dtomList.addAll(MetadataUtilities.loadDublinCore(getDocumentBuilder(), is));
             }
-        } finally {
-            if (is != null) {
+        }
+        finally
+        {
+            if (is != null)
+            {
                 is.close();
             }
         }
 		ItemUpdate.pr("Loaded metadata with " + itarch.dtomList.size() + " fields");
 		
-        if (itemField == null) {
+		if (itemField == null)
+		{
 			itarch.item = itarch.itemFromHandleInput(context);  // sets the item instance var and seeds the undo list
-        } else {
+		}
+		else
+		{
 			itarch.item = itarch.itemFromMetadataField(context, itemField);  			
 		}
 		
-        if (itarch.item == null) {
+		if (itarch.item == null)
+		{
 			throw new Exception("Item not instantiated: " + itarch.dirname);
 		}
 		
@@ -126,8 +140,10 @@ public class ItemArchive {
 	}
 		
 	protected static DocumentBuilder getDocumentBuilder()
-        throws ParserConfigurationException {
-        if (builder == null) {
+	throws ParserConfigurationException
+	{
+		if (builder == null)
+		{
 		    builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
 		}
 		return builder;
@@ -135,13 +151,14 @@ public class ItemArchive {
 
     /**
      * Getter for Transformer
-     *
      * @return Transformer
      * @throws TransformerConfigurationException if config error
      */
     protected Transformer getTransformer()
-        throws TransformerConfigurationException {
-        if (transformer == null) {
+	throws TransformerConfigurationException
+	{
+		if (transformer == null)
+		{
 		    transformer = TransformerFactory.newInstance().newTransformer();
 		}
 		return transformer;
@@ -149,55 +166,55 @@ public class ItemArchive {
 
 	/**
 	 *   Getter for the DSpace item referenced in the archive
-     *
 	 * @return DSpace item 
 	 */
-    public Item getItem() {
+	public Item getItem()
+	{
 		return item;
 	}
 	
 	/**
 	 *   Getter for directory in archive on disk
-     *
 	 * @return directory in archive
 	 */
-    public File getDirectory() {
+	public File getDirectory()
+	{
 		return dir;
 	}
 	
 	/**
 	 *   Getter for directory name in archive
-     *
 	 * @return directory name in archive
 	 */
-    public String getDirectoryName() {
+	public String getDirectoryName()
+	{
 		return dirname;
 	}
 	
 	/**
 	 *   Add metadata field to undo list
-     *
 	 * @param dtom DtoMetadata (represents metadata field)
 	 */
-    public void addUndoMetadataField(DtoMetadata dtom) {
+	public void addUndoMetadataField(DtoMetadata dtom)
+	{
 		this.undoDtomList.add(dtom);
 	}
 	
 	/**
 	 *    Getter for list of metadata fields 
-     *
 	 * @return list of metadata fields
 	 */
-    public List<DtoMetadata> getMetadataFields() {
+	public List<DtoMetadata> getMetadataFields()
+	{
 		return dtomList;
 	}
 	
 	/**
 	 *   Add bitstream id to delete contents file
-     *
 	 * @param bitstreamId bitstream ID
 	 */
-    public void addUndoDeleteContents(UUID bitstreamId) {
+	public void addUndoDeleteContents(UUID bitstreamId)
+	{
 		this.undoAddContents.add(bitstreamId);
 	}
 	
@@ -207,15 +224,16 @@ public class ItemArchive {
      *   This is the default implementation
      *   that uses the dc.identifier.uri metadatafield 
      *   that contains the item handle as its value  
-     *
      *   @param context DSpace Context
      *   @throws SQLException if database error
      *   @throws Exception if error
      */
     private Item itemFromHandleInput(Context context)
-        throws SQLException, Exception {
+    throws SQLException, Exception
+    {
     	DtoMetadata dtom = getMetadataField("dc.identifier.uri");
-        if (dtom == null) {
+    	if (dtom == null)
+    	{
     		throw new Exception("No dc.identier.uri field found for handle"); 
     	}
     	
@@ -223,7 +241,8 @@ public class ItemArchive {
     	
 		String uri = dtom.value;
 		
-        if (!uri.startsWith(ItemUpdate.HANDLE_PREFIX)) {
+    	if (!uri.startsWith(ItemUpdate.HANDLE_PREFIX))
+    	{
     		throw new Exception("dc.identifier.uri for item " + uri 
     				+ " does not begin with prefix: " + ItemUpdate.HANDLE_PREFIX);
     	}
@@ -231,9 +250,12 @@ public class ItemArchive {
     	String handle = uri.substring(ItemUpdate.HANDLE_PREFIX.length());
     		
 		DSpaceObject dso = handleService.resolveToObject(context, handle);
-        if (dso instanceof Item) {
+		if (dso instanceof Item)
+		{
 			item =  (Item) dso;
-        } else {
+		}
+		else
+		{
 			ItemUpdate.pr("Warning: item not instantiated");
 			throw new IllegalArgumentException("Item " + handle + " not instantiated.");
 		}	
@@ -244,50 +266,55 @@ public class ItemArchive {
      * 	 Find and instantiate Item from the dublin_core.xml based
      *   on the specified itemField for the item identifier,
      *   
+     * 
      * @param context   - the DSpace context
      * @param itemField - the compound form of the metadata element <schema>.<element>.<qualifier>
      * @throws SQLException if database error
      * @throws Exception if error
      */
     private Item itemFromMetadataField(Context context, String itemField)
-        throws SQLException, AuthorizeException, Exception {
+    throws SQLException, AuthorizeException, Exception
+    {
     	DtoMetadata dtom = getMetadataField(itemField);
     	
     	Item item = null;
     	
-        if (dtom == null) {
+    	if (dtom == null)
+    	{
     		throw new IllegalArgumentException("No field found for item identifier field: " + itemField);
     	}  
     	ItemUpdate.prv("Metadata field to match for item: " + dtom.toString());
 
     	this.addUndoMetadataField(dtom);  //seed the undo list with the identifier field
     	
-        Iterator<Item> itr = itemService
-            .findByMetadataField(context, dtom.schema, dtom.element, dtom.qualifier, dtom.value);
+	    Iterator<Item> itr = itemService.findByMetadataField(context, dtom.schema, dtom.element, dtom.qualifier, dtom.value);
 		int count = 0;
-        while (itr.hasNext()) {
+		while (itr.hasNext())
+		{
 			item = itr.next();
 			count++;
 		}
 
 		ItemUpdate.prv("items matching = " + count );
 		
-        if (count != 1) {
+		if (count != 1)
+		{
 			throw new Exception ("" + count + " items matching item identifier: " + dtom.value);
 		}
         
     	return item;    	
     }  
-
     /**
      * Get DtoMetadata field
-     *
      * @param compoundForm compound form
      * @return DtoMetadata field
      */
-    private DtoMetadata getMetadataField(String compoundForm) {
-        for (DtoMetadata dtom : dtomList) {
-            if (dtom.matches(compoundForm, false)) {
+    private DtoMetadata  getMetadataField(String compoundForm)
+    {
+    	for (DtoMetadata dtom : dtomList)
+    	{
+			if (dtom.matches(compoundForm, false))
+			{
 				return dtom;
 			}
     	}
@@ -306,35 +333,46 @@ public class ItemArchive {
      */
 	public void writeUndo(File undoDir)
 	throws IOException, ParserConfigurationException, TransformerConfigurationException, 
-        TransformerException, FileNotFoundException {
+	       TransformerException, FileNotFoundException
+	{
 		// create directory for item
 		File dir = new File(undoDir, dirname);
-        if (!dir.exists() && !dir.mkdir()) {
+		if (!dir.exists() && !dir.mkdir())
+        {
             log.error("Unable to create undo directory");
         }
 		
 		OutputStream out = null;
 
-        try {
+        try
+        {
             out = new FileOutputStream(new File(dir, "dublin_core.xml"));
             Document doc = MetadataUtilities.writeDublinCore(getDocumentBuilder(), undoDtomList);
             MetadataUtilities.writeDocument(doc, getTransformer(), out);
 
             // if undo has delete bitstream
-            if (undoAddContents.size() > 0) {
+            if (undoAddContents.size() > 0)
+            {
                 PrintWriter pw = null;
-                try {
+                try
+                {
                     File f = new File(dir, ItemUpdate.DELETE_CONTENTS_FILE);
                     pw = new PrintWriter(new BufferedWriter(new FileWriter(f)));
-                    for (UUID i : undoAddContents) {
+                    for (UUID i : undoAddContents)
+                    {
                         pw.println(i);
                     }
-                } finally {
+                }
+                finally
+                {
                     pw.close();
                 }
             }
-        } finally {
-            if (out != null) {
+        }
+        finally
+        {
+            if (out != null)
+            {
                 out.close();
             }
         }

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

@@ -28,6 +28,7 @@ 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.lang.StringUtils;
 import org.dspace.content.Item;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
@@ -36,8 +37,11 @@ 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:
  *   	Metadata fields - Add, Delete
  *      Bitstreams - Add, Delete
@@ -62,7 +66,9 @@ import org.dspace.eperson.service.EPersonService;
  *      Some of this has been placed into the MetadataUtilities class
  *      for possible reuse elsewhere. 
  *   
+ * 
  * @author W. Hays based on a conceptual design by R. Rodgers
+ *
  */
 public class ItemUpdate {
 	
@@ -78,28 +84,33 @@ 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 {
+	static
+	{
 		filterAliases.put("ORIGINAL", "org.dspace.app.itemupdate.OriginalBitstreamFilter");
-        filterAliases
-            .put("ORIGINAL_AND_DERIVATIVES", "org.dspace.app.itemupdate.OriginalWithDerivativesBitstreamFilter");
+		filterAliases.put("ORIGINAL_AND_DERIVATIVES", "org.dspace.app.itemupdate.OriginalWithDerivativesBitstreamFilter");
 		filterAliases.put("TEXT", "org.dspace.app.itemupdate.DerivativeTextBitstreamFilter");		
 		filterAliases.put("THUMBNAIL", "org.dspace.app.itemupdate.ThumbnailBitstreamFilter");		
 	}
 	          	                
     // File listing filter to check for folders
-    static FilenameFilter directoryFilter = new FilenameFilter() {
+    static FilenameFilter directoryFilter = new FilenameFilter()
+    {
         @Override
-        public boolean accept(File dir, String n) {
+		public boolean accept(File dir, String n)
+        {
             File f = new File(dir.getAbsolutePath() + File.separatorChar + n);
             return f.isDirectory();
         }
     };
  
     // File listing filter to check for files (not directories)
-    static FilenameFilter fileFilter = new FilenameFilter() {
+    static FilenameFilter fileFilter = new FilenameFilter()
+    {
         @Override
-        public boolean accept(File dir, String n) {
+		public boolean accept(File dir, String n)
+        {
             File f = new File(dir.getAbsolutePath() + File.separatorChar + n);
             return (f.isFile());
         }
@@ -111,9 +122,11 @@ public class ItemUpdate {
     protected String eperson;
    
     /**
-     * @param argv the command line arguments given
+     * 
+     * @param argv commandline args
      */
-    public static void main(String[] argv) {
+    public static void main(String[] argv)
+    {
         // create an options object and populate it
         CommandLineParser parser = new PosixParser();
 
@@ -124,23 +137,20 @@ public class ItemUpdate {
         options.addOption("s", "source", true, "root directory of source dspace archive ");
       
     //actions  on items     
-        options.addOption("a", "addmetadata", true,
-                          "add metadata specified for each item; multiples separated by semicolon ';'");
+        options.addOption("a", "addmetadata", true, "add metadata specified for each item; multiples separated by semicolon ';'");
         options.addOption("d", "deletemetadata", true, "delete metadata specified for each item");
         
         options.addOption("A", "addbitstreams", false, "add bitstreams as specified for each item");
         
         // extra work to get optional argument
-        Option delBitstreamOption = new Option("D", "deletebitstreams", true,
-                                               "delete bitstreams as specified for each item");
+        Option delBitstreamOption = new Option("D", "deletebitstreams", true, "delete bitstreams as specified for each item");
         delBitstreamOption.setOptionalArg(true);
         delBitstreamOption.setArgName("BitstreamFilter");
         options.addOption(delBitstreamOption);
                                
 //other params        
         options.addOption("e", "eperson", true, "email of eperson doing the update");
-        options.addOption("i", "itemfield", true,
-                          "optional metadata field that containing item identifier; default is dc.identifier.uri");
+        options.addOption("i", "itemfield", true, "optional metadata field that containing item identifier; default is dc.identifier.uri");
         options.addOption("F", "filter-properties", true, "filter class name; only for deleting bitstream");  
         options.addOption("v", "verbose", false, "verbose logging");
       
@@ -158,10 +168,12 @@ public class ItemUpdate {
         Context context = null;
         ItemUpdate iu = new ItemUpdate();	
 
-        try {
+        try
+        {       
 	        CommandLine line = parser.parse(options, argv);
 	
-            if (line.hasOption('h')) {
+	        if (line.hasOption('h'))
+	        {
 	            HelpFormatter myhelp = new HelpFormatter();
 	            myhelp.printHelp("ItemUpdate", options);
 	            pr("");
@@ -175,79 +187,91 @@ public class ItemUpdate {
 	            System.exit(0);
 	        }
 	        
-            if (line.hasOption('v')) {
+	        if (line.hasOption('v'))
+	        {
 	        	verbose = true;
 	        }
 
  
-            if (line.hasOption('P')) {
+	        if (line.hasOption('P'))
+	        {
 	        	alterProvenance = false;
 	        	pr("Suppressing changes to Provenance field option");
 	        }
 
 	        iu.eperson = line.getOptionValue('e'); // db ID or email
 	        
-            if (!line.hasOption('s')) { // item specific changes from archive dir
+	        if (!line.hasOption('s')) // item specific changes from archive dir
+	        {
 	        	pr("Missing source archive option");
 	        	System.exit(1);
 	        }
 	        String sourcedir = line.getOptionValue('s');
 	        
-            if (line.hasOption('t')) { //test
+        	if (line.hasOption('t'))  //test
+        	{
         		isTest = true;
 	            pr("**Test Run** - not actually updating items.");
        		       	
 	        }
         	
-            if (line.hasOption('i')) {
+        	if (line.hasOption('i'))
+        	{
         		itemField = line.getOptionValue('i');      		
         	}
 
-            if (line.hasOption('d')) {
+	        if (line.hasOption('d'))
+	        {
 	        	String[] targetFields = line.getOptionValues('d'); 
 	        	
-                DeleteMetadataAction delMetadataAction = (DeleteMetadataAction) iu.actionMgr
-                    .getUpdateAction(DeleteMetadataAction.class);
+	        	DeleteMetadataAction delMetadataAction = (DeleteMetadataAction) iu.actionMgr.getUpdateAction(DeleteMetadataAction.class);
 	        	delMetadataAction.addTargetFields(targetFields);
 	        	
 	        	//undo is an add 
-                for (String field : targetFields) {
+	        	for (String field : targetFields)
+	        	{
 	        		iu.undoActionList.add(" -a " + field + " ");
 	        	}
 	        	
 	        	pr("Delete metadata for fields: ");
-                for (String s : targetFields) {
+	        	for (String s : targetFields)
+	        	{
 	        		pr("    " + s);
 	        	}
 	        }
 	        
-            if (line.hasOption('a')) {
+    		if (line.hasOption('a'))
+    		{
     			String[] targetFields = line.getOptionValues('a'); 
         	
-                AddMetadataAction addMetadataAction = (AddMetadataAction) iu.actionMgr
-                    .getUpdateAction(AddMetadataAction.class);
+    			AddMetadataAction addMetadataAction = (AddMetadataAction) iu.actionMgr.getUpdateAction(AddMetadataAction.class); 
     			addMetadataAction.addTargetFields(targetFields);
         		
         		//undo is a delete followed by an add of a replace record for target fields
-                for (String field : targetFields) {
+	        	for (String field : targetFields)
+	        	{
 	        		iu.undoActionList.add(" -d " + field + " ");
 	        	}
     			
-                for (String field : targetFields) {
+	        	for (String field : targetFields)
+	        	{
 	        		iu.undoActionList.add(" -a " + field + " ");
 	        	}
     			
 	        	pr("Add metadata for fields: ");
-                for (String s : targetFields) {
+	        	for (String s : targetFields)
+	        	{
 	        		pr("    " + s);
 	        	}
         	}
     		
-            if (line.hasOption('D')) { // undo not supported
+	        if (line.hasOption('D'))  // undo not supported 
+	        {
 	        	pr("Delete bitstreams ");
 	        	
 	        	String[] filterNames = line.getOptionValues('D');
-                if ((filterNames != null) && (filterNames.length > 1)) {
+	        	if ((filterNames != null) && (filterNames.length > 1))
+	        	{
 	        		pr("Error: Only one filter can be a used at a time.");
 	        		System.exit(1);
 	        	}
@@ -255,71 +279,84 @@ public class ItemUpdate {
 	        	String filterName = line.getOptionValue('D');
 	        	pr("Filter argument: " + filterName);
 	        	
-                if (filterName == null) { // indicates using delete_contents files
-                    DeleteBitstreamsAction delAction = (DeleteBitstreamsAction) iu.actionMgr
-                        .getUpdateAction(DeleteBitstreamsAction.class);
+	        	if (filterName == null)  // indicates using delete_contents files
+	        	{
+	        		DeleteBitstreamsAction delAction = (DeleteBitstreamsAction) iu.actionMgr.getUpdateAction(DeleteBitstreamsAction.class);
 		        	delAction.setAlterProvenance(alterProvenance);
-                } else {
+	        	}
+	        	else
+	        	{
 	        	    // check if param is on ALIAS list
 	        		String filterClassname = filterAliases.get(filterName);
 	        		
-                    if (filterClassname == null) {
+	        		if (filterClassname == null)
+	        		{
 	        			filterClassname = filterName;
 	        		}
 	        			        		
 	        	    BitstreamFilter filter = null; 
 
-                    try {
+	        	    try
+	        	    {
 		    			Class<?> cfilter = Class.forName(filterClassname);
 		    			pr("BitstreamFilter class to instantiate: " + cfilter.toString());
 		    			
 		    			filter =  (BitstreamFilter) cfilter.newInstance();  //unfortunate cast, an erasure consequence
-                    } catch (Exception e) {
+	        	    }
+	        	    catch(Exception e)
+	        	    {
 	        	    	pr("Error:  Failure instantiating bitstream filter class: " + filterClassname);
 	        	    	System.exit(1);
 	        	    }
 	        	    
 	        	    String filterPropertiesName = line.getOptionValue('F');
-                    if (filterPropertiesName != null) { //not always required
-                        try {
+	        	    if (filterPropertiesName != null)  //not always required
+	        	    {
+	        	    	try
+	        	    	{
 	        	    		// TODO try multiple relative locations, e.g. source dir
-                            if (!filterPropertiesName.startsWith("/")) {
+	        	    		if (!filterPropertiesName.startsWith("/"))
+	        	    		{
 	        	    			filterPropertiesName = sourcedir + File.separator + filterPropertiesName;
 	        	    		}
 	        	    		
 	        	    		filter.initProperties(filterPropertiesName);
-                        } catch (Exception e) {
-                            pr("Error:  Failure finding properties file for bitstream filter class: " +
-                                   filterPropertiesName);
+	        	    	}
+	        	    	catch(Exception e)
+	        	    	{
+		        	    	pr("Error:  Failure finding properties file for bitstream filter class: " + filterPropertiesName);
 		        	    	System.exit(1);
 	        	    	}
 	        	    }
 	        	    
 	        		DeleteBitstreamsByFilterAction delAction = 
-                        (DeleteBitstreamsByFilterAction) iu.actionMgr
-                            .getUpdateAction(DeleteBitstreamsByFilterAction.class);
+	        			(DeleteBitstreamsByFilterAction) iu.actionMgr.getUpdateAction(DeleteBitstreamsByFilterAction.class);
 		        	delAction.setAlterProvenance(alterProvenance);
 		        	delAction.setBitstreamFilter(filter);
 	        	    //undo not supported
 	        	}        	
 	        }
 
-            if (line.hasOption('A')) {
+	        if (line.hasOption('A'))
+	        {
 	        	pr("Add bitstreams ");    	        	
-                AddBitstreamsAction addAction = (AddBitstreamsAction) iu.actionMgr
-                    .getUpdateAction(AddBitstreamsAction.class);
+        		AddBitstreamsAction addAction = (AddBitstreamsAction) iu.actionMgr.getUpdateAction(AddBitstreamsAction.class);
 	        	addAction.setAlterProvenance(alterProvenance);
 	        	
 	        	iu.undoActionList.add(" -D ");  // delete_contents file will be written, no arg required	        	
 	        }    	        
 	        	        
-            if (!iu.actionMgr.hasActions()) {
+	        if (!iu.actionMgr.hasActions())
+	        {
                 pr("Error - an action must be specified");
                 System.exit(1);
-            } else {
+	        }
+	        else  
+	        {
 	        	pr("Actions to be performed: ");
 	        	
-                for (UpdateAction ua : iu.actionMgr) {
+	        	for (UpdateAction ua : iu.actionMgr)
+	        	{
 	        		pr("    " + ua.getClass().getName());
 	        	}
 	        }
@@ -330,28 +367,32 @@ 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);		        	            
 
 	        context.complete();  // complete all transactions
-        } catch (Exception e) {
-            if (context != null && context.isValid()) {
+        }
+        catch (Exception e)
+        {
+            if (context != null && context.isValid())
+            {
                 context.abort();
             }
             e.printStackTrace();
             pr(e.toString());
             status = 1;
-        } finally {
+        }
+        finally {
         	context.restoreAuthSystemState();
         }
 
-        if (isTest) {
+        if (isTest)
+        {
             pr("***End of Test Run***");
-        } else {
+        }
+        else
+        {
         	pr("End.");
         	
         }
@@ -360,7 +401,6 @@ public class ItemUpdate {
 
     /**
      * process an archive
-     *
      * @param context DSpace Context
      * @param sourceDirPath source path
      * @param itemField item field
@@ -371,11 +411,13 @@ public class ItemUpdate {
      */
     protected void processArchive(Context context, String sourceDirPath, String itemField,
     		String metadataIndexName, boolean alterProvenance, boolean isTest)
-        throws Exception {
+    throws Exception
+    {
         // open and process the source directory
         File sourceDir = new File(sourceDirPath);
 
-        if ((sourceDir == null) || !sourceDir.exists() || !sourceDir.isDirectory()) {
+        if ((sourceDir == null) || !sourceDir.exists() || !sourceDir.isDirectory())
+        {
             pr("Error, cannot open archive source directory " + sourceDirPath);
             throw new Exception("error with archive source directory " + sourceDirPath);
         }
@@ -386,73 +428,90 @@ public class ItemUpdate {
         //Undo is suppressed to prevent undo of undo
         boolean suppressUndo = false;
         File fSuppressUndo = new File(sourceDir, SUPPRESS_UNDO_FILENAME);
-        if (fSuppressUndo.exists()) {
+        if (fSuppressUndo.exists())
+        {
         	suppressUndo = true;
         }
 
         File undoDir = null;  //sibling directory of source archive
         
-        if (!suppressUndo && !isTest) {
+    	if (!suppressUndo && !isTest) 
+    	{
     		undoDir = initUndoArchive(sourceDir);	
     	}
         
     	int itemCount = 0;
     	int successItemCount = 0;
     	
-        for (String dirname : dircontents) {
+        for (String dirname : dircontents)
+        {
         	itemCount++;
     		pr("");
     		pr("processing item " + dirname);
     		
-            try {
+    		try
+    		{
 	    		ItemArchive itarch = ItemArchive.create(context, new File(sourceDir, dirname), itemField);
 	    		
-                for (UpdateAction action : actionMgr) {
+	    		for (UpdateAction action : actionMgr)
+	    		{
 	    			pr("action: " + action.getClass().getName());
 	    			action.execute(context, itarch, isTest, suppressUndo);
-                    if (!isTest && !suppressUndo) {
+	    			if (!isTest && !suppressUndo)
+                    {
                         itarch.writeUndo(undoDir);
                     }
 	    		}
-                if (!isTest) {
+	    		if (!isTest)
+	    		{
     				Item item = itarch.getItem();
                     itemService.update(context, item);  //need to update before commit
 					context.uncacheEntity(item);
 	    		}
     			ItemUpdate.pr("Item " + dirname + " completed");
     			successItemCount++;
-            } catch (Exception e) {
+    		}
+    		catch(Exception e)
+    		{
     			pr("Exception processing item " + dirname + ": " + e.toString());
                 e.printStackTrace();
     		}
         }  
         
-        if (!suppressUndo && !isTest) {
+        if (!suppressUndo && !isTest)
+        {        	     	
         	StringBuilder sb = new StringBuilder("dsrun org.dspace.app.itemupdate.ItemUpdate ");
         	sb.append(" -e ").append(this.eperson);
         	sb.append(" -s ").append(undoDir);
         	
-            if (itemField != null) {
+        	if (itemField != null)
+        	{
         		sb.append(" -i ").append(itemField);
         	}
         	
-            if (!alterProvenance) {
+         	if (!alterProvenance)
+        	{
         		sb.append(" -P ");
         	}
-            if (isTest) {
+        	if (isTest)
+        	{
         		sb.append(" -t ");
         	}
         	
-            for (String actionOption : undoActionList) {
+        	for (String actionOption : undoActionList)
+        	{
         		sb.append(actionOption);
         	}   
         	
         	PrintWriter pw = null;
-            try {
+        	try
+        	{
                	File cmdFile = new File (undoDir.getParent(), undoDir.getName() + "_command.sh");
 	        	pw = new PrintWriter(new BufferedWriter(new FileWriter(cmdFile)));
 	        	pw.println(sb.toString());
-            } finally {
+        	}
+        	finally
+        	{
         		pw.close();
         	}
         }
@@ -464,6 +523,7 @@ public class ItemUpdate {
            
     
     /**
+     * 
      * to avoid overwriting the undo source tree on repeated processing
      * sequence numbers are added and checked 
      * 
@@ -473,33 +533,38 @@ public class ItemUpdate {
      * @throws IOException if IO error
      */
     protected File initUndoArchive(File sourceDir)
-        throws FileNotFoundException, IOException {
+	throws FileNotFoundException, IOException
+	{				
 		File parentDir = sourceDir.getCanonicalFile().getParentFile();
-        if (parentDir == null) {
-            throw new FileNotFoundException(
-                "Parent directory of archive directory not found; unable to write UndoArchive; no processing " +
-                    "performed");
+		if (parentDir == null)
+		{
+			throw new FileNotFoundException("Parent directory of archive directory not found; unable to write UndoArchive; no processing performed");    			
 		}
 		
 		String sourceDirName = sourceDir.getName();
 		int seqNo = 1;
 		
 		File undoDir = new File(parentDir, "undo_" + sourceDirName + "_" + seqNo);
-        while (undoDir.exists()) {
+		while (undoDir.exists())
+		{
     		undoDir = new File(parentDir, "undo_" + sourceDirName+ "_" + ++seqNo); //increment
 		}
 		
 		// create root directory
-        if (!undoDir.mkdir()) {
+		if (!undoDir.mkdir())
+		{
 			pr("ERROR creating  Undo Archive directory " + undoDir.getCanonicalPath());
 			throw new IOException("ERROR creating  Undo Archive directory " + undoDir.getCanonicalPath());
 		}
 		
         //Undo is suppressed to prevent undo of undo
         File fSuppressUndo = new File(undoDir, ItemUpdate.SUPPRESS_UNDO_FILENAME);
-        try {
+        try
+        {
         	fSuppressUndo.createNewFile();
-        } catch (IOException e) {
+        }
+        catch(IOException e)
+        {
         	pr("ERROR creating Suppress Undo File " + e.toString());
         	throw e;
         }
@@ -510,29 +575,33 @@ public class ItemUpdate {
 
     /**
      * Set EPerson doing import
-     *
      * @param context DSpace Context
      * @param eperson EPerson obj
      * @throws Exception if error
      */
     protected void setEPerson(Context context, String eperson)
-        throws Exception {
-        if (eperson == null) {
+    throws Exception
+    {
+        if (eperson == null)
+        {
             pr("Error - an eperson to do the importing must be specified");
             pr(" (run with -h flag for details)");
-            throw new Exception("EPerson not specified.");
-        }
+            throw new Exception("EPerson not specified.");        }
 
         EPerson myEPerson = null;
 
-        if (eperson.indexOf('@') != -1) {
+        if (eperson.indexOf('@') != -1)
+        {
             // @ sign, must be an email
             myEPerson = epersonService.findByEmail(context, eperson);
-        } else {
+        }
+        else
+        {
             myEPerson = epersonService.find(context, UUID.fromString(eperson));
         }
 
-        if (myEPerson == null) {
+        if (myEPerson == null)
+        {
             pr("Error, eperson cannot be found: " + eperson);
             throw new Exception("Invalid EPerson");
         }
@@ -544,20 +613,21 @@ public class ItemUpdate {
      *   poor man's logging
 	 *   As with ItemImport, API logging goes through log4j to the DSpace.log files
 	 *   whereas the batch logging goes to the console to be captured there.
-     *
      * @param s String
      */
-    static void pr(String s) {
+    static void pr(String s)
+    {
     	System.out.println(s);
     }
     
     /**
      *  print if verbose flag is set
-     *
      * @param s String
      */
-    static void prv(String s) {
-        if (verbose) {
+    static void prv(String s)
+    {
+    	if (verbose) 
+    	{
         	System.out.println(s);
     	}
     }

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

@@ -11,13 +11,14 @@ import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
-import java.io.IOException;
 import java.io.InputStream;
+import java.io.IOException;
 import java.io.OutputStream;
 import java.sql.SQLException;
 import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.List;
+
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.Result;
@@ -30,14 +31,10 @@ import javax.xml.transform.stream.StreamResult;
 
 import org.apache.commons.lang.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.MetadataValue;
+
+import org.dspace.content.*;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -46,6 +43,9 @@ import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 import org.xml.sax.SAXException;
 
+import org.dspace.authorize.AuthorizeException;
+import org.dspace.core.ConfigurationManager;
+
 
 /**
  * 	Miscellaneous methods for metadata handling that build on the API
@@ -53,37 +53,37 @@ import org.xml.sax.SAXException;
  *      in context in ItemUpdate.
  *      
  *      The XML methods were based on those in ItemImport
+ * 
+ *
  */
 public class MetadataUtilities {
 
     protected static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
 
     /**      
-     * Default constructor
-     */
-    private MetadataUtilities() { }
-
-    /**
+     * 
      *  Working around Item API to delete a value-specific Metadatum
-     * For a given element/qualifier/lang:
-     * get all DCValues
-     * clear (i.e. delete) all of these DCValues
+  For a given element/qualifier/lang:
+      get all DCValues
+      clear (i.e. delete) all of these DCValues
      *      add them back, minus the one to actually delete
      *  
      * @param context DSpace Context
      * @param item Item Object
      * @param dtom metadata field
      * @param isLanguageStrict whether strict or not
-     * @return true if metadata field is found with matching value and was deleted
      * @throws SQLException if database error
+     * @return true if metadata field is found with matching value and was deleted
      */
-    public static boolean deleteMetadataByValue(Context context, Item item, DtoMetadata dtom, boolean isLanguageStrict)
-        throws SQLException {
+    public static boolean deleteMetadataByValue(Context context, Item item, DtoMetadata dtom, boolean isLanguageStrict) throws SQLException {
     	List<MetadataValue> ar = null;
     	
-        if (isLanguageStrict) {   // get all for given type
+    	if (isLanguageStrict)
+    	{   // get all for given type
     		ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-        } else {
+    	}
+    	else
+    	{
     		ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
     	}
     	
@@ -91,18 +91,26 @@ public class MetadataUtilities {
     	
     	//build new set minus the one to delete
     	List<String> vals = new ArrayList<String>();
-        for (MetadataValue dcv : ar) {
-            if (dcv.getValue().equals(dtom.value)) {
+    	for (MetadataValue dcv : ar)
+    	{
+    		if (dcv.getValue().equals(dtom.value))
+    		{
     			found = true;
-            } else {
+    		}
+    		else
+    		{
     			vals.add(dcv.getValue());
     		}
     	}
     	
-        if (found) {  //remove all for given type  ??synchronize this block??
-            if (isLanguageStrict) {
+    	if (found)  //remove all for given type  ??synchronize this block??
+    	{   
+        	if (isLanguageStrict)
+        	{           		
                 itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-            } else {
+        	}
+        	else
+        	{
                 itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
         	}
     	
@@ -128,34 +136,46 @@ public class MetadataUtilities {
     	List<MetadataValue> ar = null;
     	
     	// get all values for given element/qualifier
-        if (isLanguageStrict) {  // get all for given element/qualifier
+    	if (isLanguageStrict)  // get all for given element/qualifier
+    	{   
     		ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-        } else {
+    	}
+    	else
+    	{
     		ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
     	}
     	
-        if (ar.size() == 0) {
+    	if (ar.size() == 0)
+    	{
     		throw new IllegalArgumentException("Metadata to append to not found");
     	}
     	
     	int idx = 0;  //index of field to change
-        if (ar.size() > 1) { //need to pick one, can't be sure it's the last one
+    	if (ar.size() > 1)  //need to pick one, can't be sure it's the last one
+    	{
     		// TODO maybe get highest id ?
     	}
     	
     	//build new set minus the one to delete
     	List<String> vals = new ArrayList<String>();
-        for (int i = 0; i < ar.size(); i++) {
-            if (i == idx) {
+    	for (int i=0; i < ar.size(); i++)
+    	{
+    		if (i == idx)
+    		{
     			vals.add(ar.get(i).getValue() + textToAppend);
-            } else {
+    		}
+    		else
+    		{
     			vals.add(ar.get(i).getValue());
     		}
     	}
 
-        if (isLanguageStrict) {
+    	if (isLanguageStrict)
+    	{           		
             itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-        } else {
+    	}
+    	else
+    	{
             itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
     	}
 	
@@ -178,7 +198,8 @@ public class MetadataUtilities {
      */
     public static List<DtoMetadata> loadDublinCore(DocumentBuilder docBuilder, InputStream is)
     throws SQLException, IOException, ParserConfigurationException,
-        SAXException, TransformerException, AuthorizeException {
+           SAXException, TransformerException, AuthorizeException
+	{    	
 		Document document = docBuilder.parse(is);
 		
 		List<DtoMetadata> dtomList = new ArrayList<DtoMetadata>();
@@ -188,43 +209,55 @@ public class MetadataUtilities {
 		String schema = null;
 		NodeList metadata = XPathAPI.selectNodeList(document, "/dublin_core");		
 		Node schemaAttr = metadata.item(0).getAttributes().getNamedItem("schema");
-        if (schemaAttr == null) {
+		if (schemaAttr == null)
+		{
 		    schema = MetadataSchema.DC_SCHEMA;
-        } else {
+		}
+		else
+		{
 		    schema = schemaAttr.getNodeValue();
 		}
 
 		// Get the nodes corresponding to formats
 		NodeList dcNodes = XPathAPI.selectNodeList(document, "/dublin_core/dcvalue");
 		
-        for (int i = 0; i < dcNodes.getLength(); i++) {
+		for (int i = 0; i < dcNodes.getLength(); i++)
+		{
 		    Node n = dcNodes.item(i);		    
 	        String value = getStringValue(n).trim(); 
 	        // compensate for empty value getting read as "null", which won't display
-            if (value == null) {
+	        if (value == null)
+	        {
 	            value = "";
 	        }
 	        String element = getAttributeValue(n, "element");
-            if (element != null) {
+	        if (element != null)
+	        {
 	        	element = element.trim();
 	        }
 	        String qualifier = getAttributeValue(n, "qualifier"); 
-            if (qualifier != null) {
+	        if (qualifier != null)
+	        {
 	        	qualifier = qualifier.trim();
 	        }
 	        String language = getAttributeValue(n, "language");
-            if (language != null) {
+	        if (language != null)
+	        {
 	        	language = language.trim();
 	        }
 
-            if ("none".equals(qualifier) || "".equals(qualifier)) {
+	        if ("none".equals(qualifier) || "".equals(qualifier))
+	        {
 	            qualifier = null;
 	        }
 	        
 	        // a goofy default, but consistent with DSpace treatment elsewhere  
-            if (language == null) {
+	        if (language == null)
+	        {
 	            language = "en";
-            } else if ("".equals(language)) {
+	        }
+	        else if ("".equals(language))
+	        {
 	            language = ConfigurationManager.getProperty("default.language");
 	        }
 	        
@@ -246,23 +279,31 @@ public class MetadataUtilities {
      * @throws TransformerException if transformer error
      */
 	public static Document writeDublinCore(DocumentBuilder docBuilder, List<DtoMetadata> dtomList)
-        throws ParserConfigurationException, TransformerConfigurationException, TransformerException {
+	throws ParserConfigurationException, TransformerConfigurationException, TransformerException
+	{		
         Document doc = docBuilder.newDocument();
         Element root = doc.createElement("dublin_core");
         doc.appendChild(root);
     
-        for (DtoMetadata dtom : dtomList) {
+        for (DtoMetadata dtom : dtomList)
+        {
         	Element mel = doc.createElement("dcvalue");
         	mel.setAttribute("element", dtom.element);
-            if (dtom.qualifier == null) {
+        	if (dtom.qualifier == null)
+        	{
         		mel.setAttribute("qualifier", "none");
-            } else {
+        	}
+        	else
+        	{
         		mel.setAttribute("qualifier", dtom.qualifier);
         	}
  
-            if (StringUtils.isEmpty(dtom.language)) {
+        	if (StringUtils.isEmpty(dtom.language))
+        	{
         		mel.setAttribute("language", "en");
-            } else {
+        	}
+        	else
+        	{
         		mel.setAttribute("language", dtom.language);
         	}
         	mel.setTextContent(dtom.value);
@@ -274,7 +315,6 @@ public class MetadataUtilities {
 	
     /**
      *   write xml document to output stream
-     *
      * @param doc XML Document
      * @param transformer XML Transformer
      * @param out OutputStream
@@ -282,29 +322,32 @@ public class MetadataUtilities {
      * @throws TransformerException if Transformer error
      */
 	public static void writeDocument(Document doc, Transformer transformer, OutputStream out)
-        throws IOException, TransformerException {
+	throws IOException, TransformerException
+	{
         Source src = new DOMSource(doc); 
         Result dest = new StreamResult(out); 
         transformer.transform(src, dest); 
 	}
     
     
-    // XML utility methods
     
+    // XML utility methods
     /**
      * Lookup an attribute from a DOM node.
-     *
      * @param n Node
      * @param name name
      * @return attribute value
      */
-    private static String getAttributeValue(Node n, String name) {
+    private static String getAttributeValue(Node n, String name)
+    {
         NamedNodeMap nm = n.getAttributes();
 
-        for (int i = 0; i < nm.getLength(); i++) {
+        for (int i = 0; i < nm.getLength(); i++)
+        {
             Node node = nm.item(i);
 
-            if (name.equals(node.getNodeName())) {
+            if (name.equals(node.getNodeName()))
+            {
                 return node.getNodeValue();
             }
         }
@@ -314,17 +357,19 @@ public class MetadataUtilities {
     
     /**
      * Return the String value of a Node.
-     *
      * @param node node
      * @return string value
      */
-    private static String getStringValue(Node node) {
+    private static String getStringValue(Node node)
+    {
         String value = node.getNodeValue();
 
-        if (node.hasChildNodes()) {
+        if (node.hasChildNodes())
+        {
             Node first = node.getFirstChild();
 
-            if (first.getNodeType() == Node.TEXT_NODE) {
+            if (first.getNodeType() == Node.TEXT_NODE)
+            {
                 return first.getNodeValue();
             }
         }
@@ -343,27 +388,36 @@ public class MetadataUtilities {
      * @throws ParseException if parse error
      */
     public static List<ContentsEntry> readContentsFile(File f)
-        throws FileNotFoundException, IOException, ParseException {
+    throws FileNotFoundException, IOException, ParseException
+    {
     	List<ContentsEntry> list = new ArrayList<ContentsEntry>();
     	
     	BufferedReader in = null;
     	
-        try {
+    	try
+    	{
 	    	in = new BufferedReader(new FileReader(f));
 	    	String line = null;
 	    	
-            while ((line = in.readLine()) != null) {
+	    	while ((line = in.readLine()) != null)
+	    	{
 	    		line = line.trim();
-                if ("".equals(line)) {
+	            if ("".equals(line))
+	            {
 	                continue;
 	            }
 	            ItemUpdate.pr("Contents entry: " + line);	            
 	    		list.add(ContentsEntry.parse(line));	 
 	    	}
-        } finally {
-            try {
+    	}
+    	finally
+    	{
+    		try
+    		{
     			in.close();
-            } catch (IOException e) {
+    		}
+    		catch(IOException e)
+    		{
     			//skip
     		}
     	}
@@ -372,33 +426,43 @@ public class MetadataUtilities {
     }
 
     /**
+     * 
      * @param f file
      * @return list of lines as strings
      * @throws FileNotFoundException if file doesn't exist
      * @throws IOException if IO Error
      */
     public static List<String> readDeleteContentsFile(File f)
-        throws FileNotFoundException, IOException {
+    throws FileNotFoundException, IOException
+    {
     	List<String> list = new ArrayList<>();
     	
     	BufferedReader in = null;
     	
-        try {
+    	try
+    	{
 	    	in = new BufferedReader(new FileReader(f));
 	    	String line = null;
 	    	
-            while ((line = in.readLine()) != null) {
+	    	while ((line = in.readLine()) != null)
+	    	{
 	    		line = line.trim();
-                if ("".equals(line)) {
+	            if ("".equals(line))
+	            {
 	                continue;
 	            }
 	            
                 list.add(line);
 	    	}
-        } finally {
-            try {
+    	}
+    	finally
+    	{
+    		try
+    		{
     			in.close();
-            } catch (IOException e) {
+    		}
+    		catch(IOException e)
+    		{
     			//skip
     		}
     	}
@@ -412,28 +476,29 @@ public class MetadataUtilities {
      * @param dcv MetadataValue
      * @return string displaying elements of the Metadatum
      */
-    public static String getDCValueString(MetadataValue dcv) {
+    public static String getDCValueString(MetadataValue dcv)
+    {
         MetadataField metadataField = dcv.getMetadataField();
         MetadataSchema metadataSchema = metadataField.getMetadataSchema();
-        return "schema: " + metadataSchema.getName() + "; element: " + metadataField
-            .getElement() + "; qualifier: " + metadataField.getQualifier() +
+        return "schema: " + metadataSchema.getName() + "; element: " + metadataField.getElement() + "; qualifier: " + metadataField.getQualifier() +
     	       "; language: " + dcv.getLanguage() + "; value: " + dcv.getValue();
     }
 
 	/**
          * Return compound form of a metadata field (i.e. schema.element.qualifier)
-     *
 	 * @param schema schema
          * @param element element
          * @param qualifier qualifier
 	 * @return a String representation of the two- or three-part form of a metadata element
 	 *         e.g. dc.identifier.uri
 	 */
-    public static String getCompoundForm(String schema, String element, String qualifier) {
+	public static  String getCompoundForm(String schema, String element, String qualifier)
+	{
 		StringBuilder sb = new StringBuilder();
 		sb.append(schema).append(".").append(element);
 		
-        if (qualifier != null) {
+		if (qualifier != null)
+		{
 			sb.append(".").append(qualifier);
 		}
 		return sb.toString();
@@ -446,16 +511,20 @@ public class MetadataUtilities {
          *    @param compoundForm compound form of metadata field
 	 *    @return String Array
 	 *    @throws ParseException if validity checks fail
+	 *    
 	 */
 	public static String[] parseCompoundForm(String compoundForm)
-        throws ParseException {
+	throws ParseException
+	{
 		String[] ar = compoundForm.split("\\s*\\.\\s*");  //trim ends
 				
-        if ("".equals(ar[0])) {
+		if ("".equals(ar[0]))
+		{
 			throw new ParseException("schema is empty string: " + compoundForm, 0);
 		}
 		
-        if ((ar.length < 2) || (ar.length > 3) || "".equals(ar[1])) {
+		if ((ar.length < 2) || (ar.length > 3) || "".equals(ar[1]))
+		{
 			throw new ParseException("element is malformed or empty string: " + compoundForm, 0);
 		}
 		

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

@@ -18,29 +18,37 @@ import org.dspace.content.Bundle;
  *      Also delete all derivative bitstreams, i.e.
  *      all bitstreams in the TEXT and THUMBNAIL bundles
  */
-public class OriginalBitstreamFilter extends BitstreamFilterByBundleName {
-    public OriginalBitstreamFilter() {
+public class OriginalBitstreamFilter extends BitstreamFilterByBundleName 
+{	
+	public OriginalBitstreamFilter()
+	{
 		//empty
 	}
 	
 	/**
 	 *   Tests bitstreams for containment in an ORIGINAL bundle
-     *
 	 *  @param bitstream Bitstream
 	 *  @return true if the bitstream is in the ORIGINAL bundle
+	 *  
 	 *  @throws BitstreamFilterException if filter error
 	 */
 	@Override
     public boolean accept(Bitstream bitstream)
-        throws BitstreamFilterException {
-        try {
+	throws BitstreamFilterException
+	{		
+		try
+		{
 			List<Bundle> bundles = bitstream.getBundles();
-            for (Bundle bundle : bundles) {
-                if (bundle.getName().equals("ORIGINAL")) {
+			for (Bundle bundle : bundles)
+			{
+                if (bundle.getName().equals("ORIGINAL"))
+				{
 					return true;
 				}
 			}		
-        } catch (SQLException e) {
+		}
+		catch(SQLException e)
+		{
 			throw new BitstreamFilterException(e);
 		}
 		return false;

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

@@ -18,10 +18,12 @@ import org.dspace.content.Bundle;
  *      Also delete all derivative bitstreams, i.e.
  *      all bitstreams in the TEXT and THUMBNAIL bundles
  */
-public class OriginalWithDerivativesBitstreamFilter extends BitstreamFilter {
+public class OriginalWithDerivativesBitstreamFilter extends BitstreamFilter 
+{
     protected String[] bundlesToEmpty = { "ORIGINAL", "TEXT", "THUMBNAIL" };
 	
-    public OriginalWithDerivativesBitstreamFilter() {
+	public OriginalWithDerivativesBitstreamFilter()
+	{
 		//empty
 	}
 	
@@ -29,22 +31,29 @@ public class OriginalWithDerivativesBitstreamFilter extends BitstreamFilter {
 	 * 	Tests bitstream for membership in specified bundles (ORIGINAL, TEXT, THUMBNAIL)
 	 * 
 	 * @param bitstream Bitstream
-     * @return true if bitstream is in specified bundles
 	 * @throws BitstreamFilterException if error
+	 * @return true if bitstream is in specified bundles
 	 */
 	@Override
     public boolean accept(Bitstream bitstream)
-        throws BitstreamFilterException {
-        try {
+	throws BitstreamFilterException
+	{		
+		try
+		{
 			List<Bundle> bundles = bitstream.getBundles();
-            for (Bundle b : bundles) {
-                for (String bn : bundlesToEmpty) {
-                    if (b.getName().equals(bn)) {
+			for (Bundle b : bundles)
+			{
+                for (String bn : bundlesToEmpty)
+				{
+					if (b.getName().equals(bn))
+					{
 						return true;
 					}
 				}
 			}		
-        } catch (SQLException e) {
+		}
+		catch(SQLException e)
+		{
 			throw new BitstreamFilterException(e);
 		}
 		return false;

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

@@ -11,10 +11,12 @@ import java.util.Properties;
 
 /**
  *    Bitstream filter targetting the THUMBNAIL bundle
+ *
  */
 public class ThumbnailBitstreamFilter extends BitstreamFilterByBundleName {
 	
-    public ThumbnailBitstreamFilter() {
+	public ThumbnailBitstreamFilter()
+	{
 		props = new Properties();
 		props.setProperty("bundle", "THUMBNAIL");
 	}

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

@@ -13,8 +13,10 @@ import org.dspace.core.Context;
 
 /**
  *    Interface for actions to update an item
+ *
  */
-public interface UpdateAction {
+public interface UpdateAction 
+{
     public ItemService itemService = ContentServiceFactory.getInstance().getItemService();
 
 

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

@@ -13,6 +13,8 @@ import org.dspace.content.service.BundleService;
 
 /**
  * 	  Base class for Bitstream actions
+ * 
+ *
  */
 public abstract class UpdateBitstreamsAction implements UpdateAction {
 
@@ -25,18 +27,20 @@ public abstract class UpdateBitstreamsAction implements UpdateAction {
 	/**
 	 *        Set variable to indicate that the dc.description.provenance field may 
 	 *        be changed as a result of Bitstream changes by ItemUpdate
-     *
 	 * @param alterProvenance whether to alter provenance
 	 */
-    public void setAlterProvenance(boolean alterProvenance) {
+	public void setAlterProvenance(boolean alterProvenance)
+	{
 		this.alterProvenance = alterProvenance;
 	}
 	
 	/**
+	 * 
 	 * @return boolean value to indicate whether the dc.description.provenance field may 
 	 *        be changed as a result of Bitstream changes by ItemUpdate
 	 */
-    public boolean getAlterProvenance() {
+	public boolean getAlterProvenance()
+	{
 		return alterProvenance;
 	}
 

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

@@ -17,6 +17,8 @@ import java.util.Set;
  *   on which to apply the action when the method execute is called.
  * 
  *   Implemented as a Set to avoid problems with duplicates
+ * 
+ *
  */
 public abstract class UpdateMetadataAction implements UpdateAction {
 
@@ -37,7 +39,8 @@ public abstract class UpdateMetadataAction implements UpdateAction {
 	 * @param targetFields Set of target fields to update
 	 */
 	public void addTargetFields(Set<String> targetFields) {
-        for (String tf : targetFields) {
+		for (String tf : targetFields)
+		{
 			this.targetFields.add(tf);
 		}
 		
@@ -45,11 +48,11 @@ public abstract class UpdateMetadataAction implements UpdateAction {
 
 	/**
 	 *    Add array of target fields to update
-     *
 	 * @param targetFields array of target fields to update
 	 */
 	public void addTargetFields(String[] targetFields) {
-        for (String tf : targetFields) {
+		for (String tf : targetFields)
+		{
 			this.targetFields.add(tf);
 		}
 		

dspace-api/src/main/java/org/dspace/app/launcher/CommandRunner.java

@@ -15,29 +15,29 @@ import java.io.Reader;
 import java.io.StreamTokenizer;
 import java.util.ArrayList;
 import java.util.List;
-
 import org.jdom.Document;
 
 /**
+ *
  * @author mwood
  */
-public class CommandRunner {
-
+public class CommandRunner
+{
     /**
-     * Default constructor
-     */
-    private CommandRunner() { }
-
-    /**
-     * @param args the command line arguments given
+     * 
+     * @param args commandline args
      * @throws IOException if IO error
      * @throws FileNotFoundException if file doesn't exist
      */
     public static void main(String[] args)
-        throws FileNotFoundException, IOException {
-        if (args.length > 0) {
+            throws FileNotFoundException, IOException
+    {
+        if (args.length > 0)
+        {
             runManyCommands(args[0]);
-        } else {
+        }
+        else
+        {
             runManyCommands("-");
         }
         // There is no sensible way to use the status returned by runManyCommands().
@@ -58,11 +58,15 @@ public class CommandRunner {
      * @throws FileNotFoundException if file doesn't exist
      */
     static int runManyCommands(String script)
-        throws FileNotFoundException, IOException {
+            throws FileNotFoundException, IOException
+    {
         Reader input;
-        if ("-".equals(script)) {
+        if ("-".equals(script))
+        {
             input = new InputStreamReader(System.in);
-        } else {
+        }
+        else
+        {
             input = new FileReader(script);
         }
 
@@ -85,16 +89,22 @@ public class CommandRunner {
         int status = 0;
         List<String> tokens = new ArrayList<String>();
         Document commandConfigs = ScriptLauncher.getConfig();
-        while (StreamTokenizer.TT_EOF != tokenizer.nextToken()) {
-            if (StreamTokenizer.TT_EOL == tokenizer.ttype) {
-                if (tokens.size() > 0) {
+        while (StreamTokenizer.TT_EOF != tokenizer.nextToken())
+        {
+            if (StreamTokenizer.TT_EOL == tokenizer.ttype)
+            {
+                if (tokens.size() > 0)
+                {
                     status = ScriptLauncher.runOneCommand(commandConfigs, tokens.toArray(new String[tokens.size()]));
-                    if (status > 0) {
+                    if (status > 0)
+                    {
                         break;
                     }
                     tokens.clear();
                 }
-            } else {
+            }
+            else
+            {
                 tokens.add(tokenizer.sval);
             }
         }

dspace-api/src/main/java/org/dspace/app/launcher/ScriptLauncher.java

@@ -12,7 +12,6 @@ import java.io.IOException;
 import java.lang.reflect.Method;
 import java.util.List;
 import java.util.TreeMap;
-
 import org.dspace.servicemanager.DSpaceKernelImpl;
 import org.dspace.servicemanager.DSpaceKernelInit;
 import org.dspace.services.RequestService;
@@ -26,17 +25,11 @@ import org.jdom.input.SAXBuilder;
  * @author Stuart Lewis
  * @author Mark Diggory
  */
-public class ScriptLauncher {
-    /**
-     * The service manager kernel
-     */
+public class ScriptLauncher
+{
+    /** The service manager kernel */
     private static transient DSpaceKernelImpl kernelImpl;
 
-    /**
-     * Default constructor
-     */
-    private ScriptLauncher() { }
-
     /**
      * Execute the DSpace script launcher
      *
@@ -45,18 +38,25 @@ public class ScriptLauncher {
      * @throws FileNotFoundException if file doesn't exist
      */
     public static void main(String[] args)
-        throws FileNotFoundException, IOException {
+            throws FileNotFoundException, IOException
+    {
         // Initialise the service manager kernel
-        try {
+        try
+        {
             kernelImpl = DSpaceKernelInit.getKernel(null);
-            if (!kernelImpl.isRunning()) {
+            if (!kernelImpl.isRunning())
+            {
                 kernelImpl.start();
             }
-        } catch (Exception e) {
+        } catch (Exception e)
+        {
             // Failed to start so destroy it and log and throw an exception
-            try {
+            try
+            {
                 kernelImpl.destroy();
-            } catch (Exception e1) {
+            }
+            catch (Exception e1)
+            {
                 // Nothing to do
             }
             String message = "Failure during kernel init: " + e.getMessage();
@@ -69,7 +69,8 @@ public class ScriptLauncher {
         Document commandConfigs = getConfig();
 
         // Check that there is at least one argument (if not display command options)
-        if (args.length < 1) {
+        if (args.length < 1)
+        {
             System.err.println("You must provide at least one command argument");
             display(commandConfigs);
             System.exit(1);
@@ -80,7 +81,8 @@ public class ScriptLauncher {
         status = runOneCommand(commandConfigs, args);
 
         // Destroy the service kernel if it is still alive
-        if (kernelImpl != null) {
+        if (kernelImpl != null)
+        {
             kernelImpl.destroy();
             kernelImpl = null;
         }
@@ -88,29 +90,28 @@ public class ScriptLauncher {
         System.exit(status);
     }
 
-    protected static int runOneCommand(Document commandConfigs, String[] args) {
-        return runOneCommand(commandConfigs, args, kernelImpl);
-    }
-
     /**
      * Recognize and execute a single command.
-     *
-     * @param commandConfigs  Document
-     * @param args the command line arguments given
+     * @param doc Document
+     * @param args arguments
      */
-    public static int runOneCommand(Document commandConfigs, String[] args, DSpaceKernelImpl kernelImpl) {
+    static int runOneCommand(Document commandConfigs, String[] args)
+    {
         String request = args[0];
         Element root = commandConfigs.getRootElement();
         List<Element> commands = root.getChildren("command");
         Element command = null;
-        for (Element candidate : commands) {
-            if (request.equalsIgnoreCase(candidate.getChild("name").getValue())) {
+        for (Element candidate : commands)
+        {
+            if (request.equalsIgnoreCase(candidate.getChild("name").getValue()))
+            {
                 command = candidate;
                 break;
             }
         }
 
-        if (null == command) {
+        if (null == command)
+        {
             // The command wasn't found
             System.err.println("Command not found: " + args[0]);
             display(commandConfigs);
@@ -119,26 +120,33 @@ public class ScriptLauncher {
 
         // Run each step
         List<Element> steps = command.getChildren("step");
-        for (Element step : steps) {
+        for (Element step : steps)
+        {
             // Instantiate the class
             Class target = null;
 
             // Is it the special case 'dsrun' where the user provides the class name?
             String className;
-            if ("dsrun".equals(request)) {
-                if (args.length < 2) {
+            if ("dsrun".equals(request))
+            {
+                if (args.length < 2)
+                {
                     System.err.println("Error in launcher.xml: Missing class name");
                     return 1;
                 }
                 className = args[1];
-            } else {
+            }
+            else {
                 className = step.getChild("class").getValue();
             }
-            try {
+            try
+            {
                 target = Class.forName(className,
                                        true,
                                        Thread.currentThread().getContextClassLoader());
-            } catch (ClassNotFoundException e) {
+            }
+            catch (ClassNotFoundException e)
+            {
                 System.err.println("Error in launcher.xml: Invalid class name: " + className);
                 return 1;
             }
@@ -149,20 +157,26 @@ public class ScriptLauncher {
             Class[] argTypes = {useargs.getClass()};
             boolean passargs = true;
             if ((step.getAttribute("passuserargs") != null) &&
-                ("false".equalsIgnoreCase(step.getAttribute("passuserargs").getValue()))) {
+                ("false".equalsIgnoreCase(step.getAttribute("passuserargs").getValue())))
+            {
                 passargs = false;
             }
-            if ((args.length == 1) || (("dsrun".equals(request)) && (args.length == 2)) || (!passargs)) {
+            if ((args.length == 1) || (("dsrun".equals(request)) && (args.length == 2)) || (!passargs))
+            {
                 useargs = new String[0];
-            } else {
+            }
+            else
+            {
                 // The number of arguments to ignore
                 // If dsrun is the command, ignore the next, as it is the class name not an arg
                 int x = 1;
-                if ("dsrun".equals(request)) {
+                if ("dsrun".equals(request))
+                {
                     x = 2;
                 }
                 String[] argsnew = new String[useargs.length - x];
-                for (int i = x; i < useargs.length; i++) {
+                for (int i = x; i < useargs.length; i++)
+                {
                     argsnew[i - x] = useargs[i];
                 }
                 useargs = argsnew;
@@ -170,13 +184,16 @@ public class ScriptLauncher {
 
             // Add any extra properties
             List<Element> bits = step.getChildren("argument");
-            if (step.getChild("argument") != null) {
+            if (step.getChild("argument") != null)
+            {
                 String[] argsnew = new String[useargs.length + bits.size()];
                 int i = 0;
-                for (Element arg : bits) {
+                for (Element arg : bits)
+                {
                     argsnew[i++] = arg.getValue();
                 }
-                for (; i < bits.size() + useargs.length; i++) {
+                for (; i < bits.size() + useargs.length; i++)
+                {
                     argsnew[i] = useargs[i - bits.size()];
                 }
                 useargs = argsnew;
@@ -185,7 +202,8 @@ public class ScriptLauncher {
             // Establish the request service startup
             RequestService requestService = kernelImpl.getServiceManager().getServiceByName(
                     RequestService.class.getName(), RequestService.class);
-            if (requestService == null) {
+            if (requestService == null)
+            {
                 throw new IllegalStateException(
                         "Could not get the DSpace RequestService to start the request transaction");
             }
@@ -195,7 +213,8 @@ public class ScriptLauncher {
             requestService.startRequest();
 
             // Run the main() method
-            try {
+            try
+            {
                 Object[] arguments = {useargs};
 
                 // Useful for debugging, so left in the code...
@@ -211,7 +230,9 @@ public class ScriptLauncher {
 
                 // ensure we close out the request (happy request)
                 requestService.endRequest(null);
-            } catch (Exception e) {
+            }
+            catch (Exception e)
+            {
                 // Failure occurred in the request so we destroy it
                 requestService.endRequest(e);
 
@@ -232,20 +253,20 @@ public class ScriptLauncher {
      *
      * @return The XML configuration file Document
      */
-    protected static Document getConfig() {
-        return getConfig(kernelImpl);
-    }
-
-    public static Document getConfig(DSpaceKernelImpl kernelImpl) {
+    protected static Document getConfig()
+    {
         // Load the launcher configuration file
         String config = kernelImpl.getConfigurationService().getProperty("dspace.dir") +
                         System.getProperty("file.separator") + "config" +
                         System.getProperty("file.separator") + "launcher.xml";
         SAXBuilder saxBuilder = new SAXBuilder();
         Document doc = null;
-        try {
+        try
+        {
             doc = saxBuilder.build(config);
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             System.err.println("Unable to load the launcher configuration file: [dspace]/config/launcher.xml");
             System.err.println(e.getMessage());
             e.printStackTrace();
@@ -256,10 +277,10 @@ public class ScriptLauncher {
 
     /**
      * Display the commands that the current launcher config file knows about
-     *
      * @param commandConfigs configs as Document
      */
-    private static void display(Document commandConfigs) {
+    private static void display(Document commandConfigs)
+    {
         // List all command elements
         List<Element> commands = commandConfigs.getRootElement().getChildren("command");
 
@@ -267,13 +288,15 @@ public class ScriptLauncher {
         // We cannot just use commands.sort() because it tries to remove and
         // reinsert Elements within other Elements, and that doesn't work.
         TreeMap<String, Element> sortedCommands = new TreeMap<>();
-        for (Element command : commands) {
+        for (Element command : commands)
+        {
             sortedCommands.put(command.getChild("name").getValue(), command);
         }
 
         // Display the sorted list
         System.out.println("Usage: dspace [command-name] {parameters}");
-        for (Element command : sortedCommands.values()) {
+        for (Element command : sortedCommands.values())
+        {
             System.out.println(" - " + command.getChild("name").getValue() +
                                ": " + command.getChild("description").getValue());
         }

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

@@ -7,12 +7,12 @@
  */
 package org.dspace.app.mediafilter;
 
+import java.awt.image.BufferedImage;
 import java.awt.Color;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics2D;
 import java.awt.Rectangle;
-import java.awt.image.BufferedImage;
 
 /**
  * Class to attach a footer to an image using ImageMagick.
@@ -20,7 +20,8 @@ import java.awt.image.BufferedImage;
  * This version of the code is basically Ninh's but reorganised a little. Used with permission.
  */
 
-public class Brand {
+public class Brand
+{
 	private int brandWidth;
 	private int brandHeight;
 	private Font font;
@@ -33,11 +34,13 @@ public class Brand {
 	 * @param brandHeight height of the footer in pixels
 	 * @param font font to use for text on the footer
 	 * @param xOffset number of pixels text should be indented from left-hand side of footer
+	 *
 	 */
 	public Brand(int brandWidth,
 		      int brandHeight,
 		      Font font,
-                 int xOffset) {
+		      int xOffset)
+	{
 		this.brandWidth = brandWidth;
 		this.brandHeight = brandHeight;
 		this.font = font;
@@ -52,34 +55,46 @@ public class Brand {
 	 *	the image is resized such that brandLeftText will not fit. <code>null</code> if not
 	 *	required
 	 * @param brandRightText text that should appear in the bottom right of the image
+	 *
 	 * @return BufferedImage a BufferedImage object describing the brand image file
 	 */
 	public BufferedImage create(String brandLeftText,
 			   String shortLeftText,
-                                String brandRightText) {
+			   String brandRightText)
+	{
 		BrandText[] allBrandText = null;
 
 		BufferedImage brandImage =
 			new BufferedImage(brandWidth, brandHeight, BufferedImage.TYPE_INT_RGB);
 
-        if (brandWidth >= 350) {
-            allBrandText = new BrandText[] {
+		if (brandWidth >= 350)
+		{
+			allBrandText = new BrandText[]
+			{
 				new BrandText(BrandText.BL, brandLeftText),
 				new BrandText(BrandText.BR, brandRightText)
 			};
-        } else if (brandWidth >= 190) {
-            allBrandText = new BrandText[] {
+		} 
+		else if (brandWidth >= 190)
+		{
+			allBrandText = new BrandText[]
+			{
 				new BrandText(BrandText.BL, shortLeftText),
 				new BrandText(BrandText.BR, brandRightText)
 			};
-        } else {
-            allBrandText = new BrandText[] {
+		}
+		else
+		{
+			allBrandText = new BrandText[]
+			{
 				new BrandText(BrandText.BR, brandRightText)
 			};
 		}
 
-        if (allBrandText != null && allBrandText.length > 0) {
-            for (int i = 0; i < allBrandText.length; ++i) {
+		if (allBrandText != null && allBrandText.length > 0)
+		{
+      		for (int i = 0; i < allBrandText.length; ++i)
+			{
         		drawImage(brandImage, allBrandText[i]);
       		}
     	}
@@ -96,37 +111,48 @@ public class Brand {
 	 *	position within the brand
 	 */
 	private void drawImage(BufferedImage brandImage,
-                           BrandText brandText) {
+			BrandText brandText)
+	{
 		int imgWidth = brandImage.getWidth();
 		int imgHeight = brandImage.getHeight();
 
+		int bx, by, tx, ty, bWidth, bHeight;
+
 		Graphics2D g2 = brandImage.createGraphics();
 		g2.setFont(font);
 		FontMetrics fm = g2.getFontMetrics();
 
-        int bWidth = fm.stringWidth(brandText.getText()) + xOffset * 2 + 1;
-        int bHeight = fm.getHeight();
 
-        int bx = 0;
-        int by = 0;
+		bWidth = fm.stringWidth(brandText.getText()) + xOffset * 2 + 1;
+		bHeight = fm.getHeight();
 
-        if (brandText.getLocation().equals(BrandText.TL)) {
 		bx = 0;
         by = 0;
-        } else if (brandText.getLocation().equals(BrandText.TR)) {
+
+		if (brandText.getLocation().equals(BrandText.TL))
+		{
+			bx = 0;
+			by = 0;
+		}
+		else if (brandText.getLocation().equals(BrandText.TR))
+		{
 			bx = imgWidth - bWidth;
 			by = 0;
-        } else if (brandText.getLocation().equals(BrandText.BL)) {
+		}
+		else if (brandText.getLocation().equals(BrandText.BL))
+		{
 			bx = 0;
 			by = imgHeight - bHeight;
-        } else if (brandText.getLocation().equals(BrandText.BR)) {
+		}
+		else if (brandText.getLocation().equals(BrandText.BR))
+		{
 			bx = imgWidth - bWidth;
 			by = imgHeight - bHeight;
 		}
 
 		Rectangle box = new Rectangle(bx, by, bWidth, bHeight);
-        int tx = bx + xOffset;
-        int ty = by + fm.getAscent();
+		tx = bx + xOffset;
+		ty = by + fm.getAscent();
 
     	g2.setColor(Color.black);
 		g2.fill(box);

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

@@ -13,22 +13,15 @@ package org.dspace.app.mediafilter;
  * This is a copy of Picture Australia's PiObj class re-organised with methods.
  * Thanks to Ninh Nguyen at the National Library for providing the original source.
  */
-class BrandText {
-    /**
-     * Bottom Left
-     */
+class BrandText
+{
+	/** Bottom Left */
 	public static final String BL = "bl";
-    /**
-     * Bottom Right
-     */
+	/** Bottom Right */
 	public static final String BR = "br";
-    /**
-     * Top Left
-     */
+	/** Top Left */
 	public static final String TL = "tl";
-    /**
-     * Top Right
-     */
+	/** Top Right */
 	public static final String TR = "tr";
 
 	private String location;
@@ -41,7 +34,8 @@ class BrandText {
 	 * @param location one of the class location constants e.g. <code>Identifier.BL</code>
 	 * @param the text associated with the location
 	 */
-    public BrandText(String location, String text) {
+	public BrandText(String location, String text)
+	{
 		this.location = location;
 		this.text = text;
 	}
@@ -51,7 +45,8 @@ class BrandText {
 	 *
 	 * @return String one the class location constants e.g. <code>Identifier.BL</code>
 	 */
-    public String getLocation() {
+	public String getLocation()
+	{
 		return location;
 	}
 
@@ -61,7 +56,8 @@ class BrandText {
 	 *
 	 * @return String the text associated with the Identifier object
 	 */
-    public String getText() {
+	public String getText()
+	{
 		return text;
 	}
 
@@ -71,7 +67,8 @@ class BrandText {
 	 *
 	 * @param location one of the class location constants
 	 */
-    public void setLocation(String location) {
+	public void setLocation(String location)
+	{
 		this.location = location;
 	}
 
@@ -81,7 +78,8 @@ class BrandText {
 	 *
 	 * @param text any text string (typically a branding or identifier)
 	 */
-    public void setText(String text) {
+	public void setText(String text)
+	{
 		this.text = text;
 	}
 }

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

@@ -7,13 +7,16 @@
  */
 package org.dspace.app.mediafilter;
 
-import java.awt.image.BufferedImage;
+import java.awt.image.*;
 import java.io.InputStream;
+
 import javax.imageio.ImageIO;
 
 import org.dspace.content.Item;
 import org.dspace.core.ConfigurationManager;
 
+import org.dspace.app.mediafilter.JPEGFilter;
+
 /**
  * Filter image bitstreams, scaling the image to be within the bounds of
  * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
@@ -21,17 +24,21 @@ import org.dspace.core.ConfigurationManager;
  *
  * @author Jason Sherman jsherman@usao.edu
  */
-public class BrandedPreviewJPEGFilter extends MediaFilter {
+public class BrandedPreviewJPEGFilter extends MediaFilter
+{
     @Override
-    public String getFilteredName(String oldFilename) {
+    public String getFilteredName(String oldFilename)
+    {
         return oldFilename + ".preview.jpg";
     }
 
     /**
      * @return String bundle name
+     *  
      */
     @Override
-    public String getBundleName() {
+    public String getBundleName()
+    {
         return "BRANDED_PREVIEW";
     }
 
@@ -39,7 +46,8 @@ public class BrandedPreviewJPEGFilter extends MediaFilter {
      * @return String bitstreamformat
      */
     @Override
-    public String getFormatString() {
+    public String getFormatString()
+    {
         return "JPEG";
     }
 
@@ -47,21 +55,25 @@ public class BrandedPreviewJPEGFilter extends MediaFilter {
      * @return String description
      */
     @Override
-    public String getDescription() {
+    public String getDescription()
+    {
         return "Generated Branded Preview";
     }
 
    
     /**
      * @param currentItem item
-     * @param source      source input stream
+     * @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 {
+            throws Exception
+    {
         // read in bitstream's image
         BufferedImage buf = ImageIO.read(source);
 
@@ -79,8 +91,6 @@ public class BrandedPreviewJPEGFilter extends MediaFilter {
         int brandFontPoint = ConfigurationManager.getIntProperty("webui.preview.brand.fontpoint");
         
         JPEGFilter jpegFilter = new JPEGFilter();
-        return jpegFilter
-            .getThumbDim(currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, brandHeight, brandFontPoint,
-                         brandFont);
+        return jpegFilter.getThumbDim(currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, brandHeight, brandFontPoint, brandFont);
     }
 }

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

@@ -11,11 +11,12 @@ import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
 import org.apache.poi.POITextExtractor;
 import org.apache.poi.extractor.ExtractorFactory;
 import org.apache.poi.hssf.extractor.ExcelExtractor;
 import org.apache.poi.xssf.extractor.XSSFExcelExtractor;
+
+import org.apache.log4j.Logger;
 import org.dspace.content.Item;
 
 /*
@@ -34,32 +35,40 @@ import org.dspace.content.Item;
  * filter.org.dspace.app.mediafilter.ExcelFilter.inputFormats = Microsoft Excel, Microsoft Excel XML
  *
  */
-public class ExcelFilter extends MediaFilter {
+public class ExcelFilter extends MediaFilter
+{
 
     private static Logger log = Logger.getLogger(ExcelFilter.class);
 
-    public String getFilteredName(String oldFilename) {
+    public String getFilteredName(String oldFilename)
+    {
         return oldFilename + ".txt";
     }
 
     /**
      * @return String bundle name
+     * 
      */
-    public String getBundleName() {
+    public String getBundleName()
+    {
         return "TEXT";
     }
 
     /**
      * @return String bitstream format
+     * 
+     *
      */
-    public String getFormatString() {
+    public String getFormatString()
+    {
         return "Text";
     }
 
     /**
      * @return String description
      */
-    public String getDescription() {
+    public String getDescription()
+    {
         return "Extracted text";
     }
 
@@ -67,29 +76,38 @@ public class ExcelFilter extends MediaFilter {
      * @param item 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 item, InputStream source, boolean verbose)
-        throws Exception {
+            throws Exception
+    {
         String extractedText = null;
 
-        try {
+        try
+        {
             POITextExtractor theExtractor = ExtractorFactory.createExtractor(source);
-            if (theExtractor instanceof ExcelExtractor) {
+            if (theExtractor instanceof ExcelExtractor)
+            {
                 // for xls file
                 extractedText = (theExtractor).getText();
-            } else if (theExtractor instanceof XSSFExcelExtractor) {
+            }
+            else if (theExtractor instanceof XSSFExcelExtractor)
+            {
                 // for xlsx file
                 extractedText = (theExtractor).getText();
             }
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             log.error("Error filtering bitstream: " + e.getMessage(), e);
             throw e;
         }
 
-        if (extractedText != null) {
+        if (extractedText != null)
+        {
             // generate an input stream with the extracted text
             return IOUtils.toInputStream(extractedText, StandardCharsets.UTF_8);
         }

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

@@ -18,11 +18,13 @@ import org.dspace.core.Context;
  * from one format to another.  This interface should be implemented by any class
  * which defines a "filter" to be run by the MediaFilterManager.
  */
-public interface FormatFilter {
+public interface FormatFilter
+{
     /**
      * Get a filename for a newly created filtered bitstream
      * 
-     * @param sourceName name of source bitstream
+     * @param sourceName
+     *            name of source bitstream
      * @return filename generated by the filter - for example, document.pdf
      *         becomes document.pdf.txt
      */
@@ -51,8 +53,10 @@ public interface FormatFilter {
      * Read the source stream and produce the filtered content.
      *
      * @param item Item
-     * @param source  input stream
+     * @param source
+     *            input stream
      * @param verbose verbosity flag
+     * 
      * @return result of filter's transformation as a byte stream.
      * @throws Exception if error
      */
@@ -67,10 +71,12 @@ public interface FormatFilter {
      * is necessary).  Return false if bitstream should be skipped
      * for any reason.
      * 
+     * 
      * @param c context
      * @param item item containing bitstream to process
      * @param source source bitstream to be processed
      * @param verbose verbose mode
+     * 
      * @return true if bitstream processing should continue, 
      * 			false if this bitstream should be skipped
      * @throws Exception if error
@@ -86,9 +92,13 @@ public interface FormatFilter {
      * is necessary).  Return false if bitstream should be skipped
      * for some reason.
      * 
-     * @param c                  context
-     * @param item               item containing bitstream to process
-     * @param generatedBitstream the bitstream which was generated by
+     * 
+     * @param c
+     *            context
+     * @param item
+     *            item containing bitstream to process
+     * @param generatedBitstream
+     *            the bitstream which was generated by
      *            this filter.
      * @throws Exception if error
      */

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

@@ -7,31 +7,36 @@
  */
 package org.dspace.app.mediafilter;
 
+import org.dspace.content.Item;
+
 import java.io.ByteArrayInputStream;
 import java.io.InputStream;
+
 import javax.swing.text.Document;
 import javax.swing.text.html.HTMLEditorKit;
 
-import org.dspace.content.Item;
-
 /*
  * 
  * to do: helpful error messages - can't find mediafilter.cfg - can't
  * instantiate filter - bitstream format doesn't exist
  *  
  */
-public class HTMLFilter extends MediaFilter {
+public class HTMLFilter extends MediaFilter
+{
 
     @Override
-    public String getFilteredName(String oldFilename) {
+    public String getFilteredName(String oldFilename)
+    {
         return oldFilename + ".txt";
     }
 
     /**
      * @return String bundle name
+     *  
      */
     @Override
-    public String getBundleName() {
+    public String getBundleName()
+    {
         return "TEXT";
     }
 
@@ -39,7 +44,8 @@ public class HTMLFilter extends MediaFilter {
      * @return String bitstreamformat
      */
     @Override
-    public String getFormatString() {
+    public String getFormatString()
+    {
         return "Text";
     }
 
@@ -47,7 +53,8 @@ public class HTMLFilter extends MediaFilter {
      * @return String description
      */
     @Override
-    public String getDescription() {
+    public String getDescription()
+    {
         return "Extracted text";
     }
 
@@ -55,12 +62,14 @@ public class HTMLFilter extends MediaFilter {
      * @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 {
+            throws Exception
+    {
         // try and read the document - set to ignore character set directive,
         // assuming that the input stream is already set properly (I hope)
         HTMLEditorKit kit = new HTMLEditorKit();

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

@@ -7,41 +7,48 @@
  */
 package org.dspace.app.mediafilter;
 
+import org.dspace.content.Item;
+
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.InputStream;
 import java.nio.file.Files;
 
-import org.dspace.content.Item;
-
 
 /**
  * Filter image bitstreams, scaling the image to be within the bounds of
  * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
  * no bigger than. Creates only JPEGs.
  */
-public class ImageMagickImageThumbnailFilter extends ImageMagickThumbnailFilter {
+public class ImageMagickImageThumbnailFilter extends ImageMagickThumbnailFilter 
+{
 
     /**
      * @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 {
+            throws Exception
+    {
 		File f = inputStreamToTempFile(source, "imthumb", ".tmp");
     	File f2 = null;
-        try {
+	    try
+	    {
 		    f2 = getThumbnailFile(f, verbose);
 		    byte[] bytes = Files.readAllBytes(f2.toPath());
 		    return new ByteArrayInputStream(bytes);
-        } finally {
+	    }
+	    finally
+	    {
 		    //noinspection ResultOfMethodCallIgnored
 		    f.delete();
-            if (f2 != null) {
+		    if (f2 != null)
+		    {
 			    //noinspection ResultOfMethodCallIgnored
 			    f2.delete();
 		    }

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

@@ -7,33 +7,39 @@
  */
 package org.dspace.app.mediafilter;
 
+import org.dspace.content.Item;
+
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.InputStream;
 import java.nio.file.Files;
 
-import org.dspace.content.Item;
-
 public class ImageMagickPdfThumbnailFilter extends ImageMagickThumbnailFilter {
    @Override
    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
-        throws Exception {
+        throws Exception
+    {
 		File f = inputStreamToTempFile(source, "impdfthumb", ".pdf");
 		File f2 = null;
 	    File f3 = null;
-        try {
+	    try
+	    {
 		    f2 = getImageFile(f, 0, verbose);
 		    f3 = getThumbnailFile(f2, verbose);
 		    byte[] bytes = Files.readAllBytes(f3.toPath());
 		    return new ByteArrayInputStream(bytes);
-        } finally {
+	    }
+		finally
+	    {
 		    //noinspection ResultOfMethodCallIgnored
 		    f.delete();
-            if (f2 != null) {
+		    if (f2 != null)
+		    {
 			    //noinspection ResultOfMethodCallIgnored
 			    f2.delete();
 		    }
-            if (f3 != null) {
+		    if (f3 != null)
+		    {
 			    //noinspection ResultOfMethodCallIgnored
 			    f3.delete();
 		    }

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

@@ -14,19 +14,22 @@ import java.io.InputStream;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
 
+import javax.imageio.ImageIO;
+
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
 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.im4java.core.ConvertCmd;
+import org.im4java.core.Info;
 import org.im4java.core.IM4JavaException;
 import org.im4java.core.IMOperation;
-import org.im4java.core.Info;
 import org.im4java.process.ProcessStarter;
 
+import org.dspace.core.ConfigurationManager;
+
 /**
  * Filter image bitstreams, scaling the image to be within the bounds of
  * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
@@ -75,6 +78,7 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter {
 
         /**
          * @return String bundle name
+         * 
          */
         @Override
         public String getBundleName() {
@@ -143,7 +147,7 @@ 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);
@@ -166,11 +170,10 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter {
                                 String n = bit.getName();
                                 if (n != null) {
                                         if (nsrc != null) {
-                        if (!n.startsWith(nsrc)) {
+                                                if (!n.startsWith(nsrc))
                                                         continue;
                                         }
                                 }
-                }
                                 String description = bit.getDescription();
                                 // If anything other than a generated thumbnail
                                 // is found, halt processing

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

@@ -7,18 +7,16 @@
  */
 package org.dspace.app.mediafilter;
 
-import java.awt.Color;
-import java.awt.Font;
 import java.awt.Graphics2D;
+import java.awt.Color;
+import java.awt.image.*;
 import java.awt.RenderingHints;
 import java.awt.Transparency;
-import java.awt.image.BufferedImage;
-import java.awt.image.BufferedImageOp;
-import java.awt.image.ConvolveOp;
-import java.awt.image.Kernel;
+import java.awt.Font;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.InputStream;
+
 import javax.imageio.ImageIO;
 
 import org.dspace.content.Item;
@@ -31,17 +29,21 @@ import org.dspace.core.ConfigurationManager;
  *
  * @author Jason Sherman jsherman@usao.edu
  */
-public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats {
+public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
+{
     @Override
-    public String getFilteredName(String oldFilename) {
+    public String getFilteredName(String oldFilename)
+    {
         return oldFilename + ".jpg";
     }
 
     /**
      * @return String bundle name
+     *  
      */
     @Override
-    public String getBundleName() {
+    public String getBundleName()
+    {
         return "THUMBNAIL";
     }
 
@@ -49,7 +51,8 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
      * @return String bitstreamformat
      */
     @Override
-    public String getFormatString() {
+    public String getFormatString()
+    {
         return "JPEG";
     }
 
@@ -57,7 +60,8 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
      * @return String description
      */
     @Override
-    public String getDescription() {
+    public String getDescription()
+    {
         return "Generated Thumbnail";
     }
 
@@ -65,12 +69,14 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
      * @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 {
+            throws Exception
+    {
         // read in bitstream's image
         BufferedImage buf = ImageIO.read(source);
 
@@ -78,7 +84,8 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
     }
 
     public InputStream getThumb(Item currentItem, BufferedImage buf, boolean verbose)
-        throws Exception {
+            throws Exception
+    {
         // get config params
         float xmax = (float) ConfigurationManager
                 .getIntProperty("thumbnail.maxwidth");
@@ -92,28 +99,30 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
         return getThumbDim(currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, 0, 0, null);
     }
 
-    public InputStream getThumbDim(Item currentItem, BufferedImage buf, boolean verbose, float xmax, float ymax,
-                                   boolean blurring, boolean hqscaling, int brandHeight, int brandFontPoint,
-                                   String brandFont)
-        throws Exception {
+    public InputStream getThumbDim(Item currentItem, BufferedImage buf, boolean verbose, float xmax, float ymax, boolean blurring, boolean hqscaling, int brandHeight, int brandFontPoint, String brandFont)
+            throws Exception
+    {
         // now get the image dimensions
         float xsize = (float) buf.getWidth(null);
         float ysize = (float) buf.getHeight(null);
 
         // if verbose flag is set, print out dimensions
         // to STDOUT
-        if (verbose) {
+        if (verbose)
+        {
             System.out.println("original size: " + xsize + "," + ysize);
         }
 
         // scale by x first if needed
-        if (xsize > xmax) {
+        if (xsize > xmax)
+        {
             // calculate scaling factor so that xsize * scale = new size (max)
             float scale_factor = xmax / xsize;
 
             // if verbose flag is set, print out extracted text
             // to STDOUT
-            if (verbose) {
+            if (verbose)
+            {
                 System.out.println("x scale factor: " + scale_factor);
             }
 
@@ -124,13 +133,15 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
 
             // if verbose flag is set, print out extracted text
             // to STDOUT
-            if (verbose) {
+            if (verbose)
+            {
                 System.out.println("size after fitting to maximum width: " + xsize + "," + ysize);
             }
         }
 
         // scale by y if needed
-        if (ysize > ymax) {
+        if (ysize > ymax)
+        {
             float scale_factor = ymax / ysize;
 
             // now reduce x size
@@ -140,7 +151,8 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
         }
 
         // if verbose flag is set, print details to STDOUT
-        if (verbose) {
+        if (verbose)
+        {
             System.out.println("size after fitting to maximum height: " + xsize + ", "
                     + ysize);
         }
@@ -151,14 +163,16 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
 
         // Use blurring if selected in config.
         // a little blur before scaling does wonders for keeping moire in check.
-        if (blurring) {
+        if (blurring)
+        {
                 // send the buffered image off to get blurred.
                 buf = getBlurredInstance((BufferedImage) buf);
         }
 
         // Use high quality scaling method if selected in config.
         // this has a definite performance penalty.
-        if (hqscaling) {
+        if (hqscaling)
+        {
                 // send the buffered image off to get an HQ downscale.
                 buf = getScaledInstance((BufferedImage) buf, (int) xsize, (int) ysize,
                         (Object) RenderingHints.VALUE_INTERPOLATION_BICUBIC, (boolean) true);
@@ -190,27 +204,32 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
 
 
     @Override
-    public String[] getInputMIMETypes() {
+    public String[] getInputMIMETypes()
+    {
         return ImageIO.getReaderMIMETypes();
     }
 
     @Override
-    public String[] getInputDescriptions() {
+    public String[] getInputDescriptions()
+    {
         return null;
     }
 
     @Override
-    public String[] getInputExtensions() {
+    public String[] getInputExtensions()
+    {
         // Temporarily disabled as JDK 1.6 only
         // return ImageIO.getReaderFileSuffixes();
         return null;
     }
 
-    public BufferedImage getNormalizedInstance(BufferedImage buf) {
+    public BufferedImage getNormalizedInstance(BufferedImage buf)
+    {
      int type = (buf.getTransparency() == Transparency.OPAQUE) ?
             BufferedImage.TYPE_INT_RGB : BufferedImage.TYPE_INT_ARGB_PRE;
-        int w = buf.getWidth();
-        int h = buf.getHeight();
+     int w, h;
+     w = buf.getWidth();
+     h = buf.getHeight();
      BufferedImage normal = new BufferedImage(w, h, type);
      Graphics2D g2d = normal.createGraphics();
      g2d.drawImage(buf, 0, 0, w, h, Color.WHITE, null);
@@ -225,7 +244,8 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
      * @param buf buffered image
      * @return updated BufferedImage
      */
-    public BufferedImage getBlurredInstance(BufferedImage buf) {
+    public BufferedImage getBlurredInstance(BufferedImage buf)
+    {
      buf = getNormalizedInstance(buf);
 
      // kernel for blur op
@@ -267,12 +287,12 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
                                            int targetWidth,
                                            int targetHeight,
                                            Object hint,
-                                           boolean higherQuality) {
+                                           boolean higherQuality)
+    {
         int type = (buf.getTransparency() == Transparency.OPAQUE) ?
             BufferedImage.TYPE_INT_RGB : BufferedImage.TYPE_INT_ARGB;
         BufferedImage scalebuf = (BufferedImage)buf;
-        int w;
-        int h;
+        int w, h;
         if (higherQuality) {
             // Use multi-step technique: start with original size, then
             // scale down in multiple passes with drawImage()

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

@@ -18,7 +18,8 @@ import org.dspace.core.Context;
  * by the MediaFilterManager.  More complex filters should likely implement the FormatFilter
  * interface directly, so that they can define their own pre/postProcessing methods.
  */
-public abstract class MediaFilter implements FormatFilter {
+public abstract class MediaFilter implements FormatFilter
+{
 	/**
      * Perform any pre-processing of the source bitstream *before* the actual 
      * filtering takes place in MediaFilterManager.processBitstream().
@@ -27,17 +28,20 @@ public abstract class MediaFilter implements FormatFilter {
      * is necessary).  Return false if bitstream should be skipped
      * for any reason.
      * 
+     * 
      * @param c context
      * @param item item containing bitstream to process
      * @param source source bitstream to be processed
      * @param verbose verbose mode
+     * 
      * @return true if bitstream processing should continue, 
      *          false if this bitstream should be skipped
      * @throws Exception if error
      */
     @Override
     public boolean preProcessBitstream(Context c, Item item, Bitstream source, boolean verbose)
-        throws Exception {
+            throws Exception
+    {
         return true;  //default to no pre-processing
     }
      
@@ -49,15 +53,20 @@ public abstract class MediaFilter implements FormatFilter {
      * is necessary).  Return false if bitstream should be skipped
      * for some reason.
      * 
-     * @param c                  context
-     * @param item               item containing bitstream to process
-     * @param generatedBitstream the bitstream which was generated by
+     * 
+     * @param c
+     *            context
+     * @param item
+     *            item containing bitstream to process
+     * @param generatedBitstream
+     *            the bitstream which was generated by
      *            this filter.
-     * @throws Exception if error
+     * @throws java.lang.Exception
      */
     @Override
     public void postProcessBitstream(Context c, Item item, Bitstream generatedBitstream)
-        throws Exception {
+            throws Exception
+    {
         //default to no post-processing necessary
     }
 }

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

@@ -7,22 +7,7 @@
  */
 package org.dspace.app.mediafilter;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.MissingArgumentException;
-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.cli.*;
 import org.dspace.app.mediafilter.factory.MediaFilterServiceFactory;
 import org.dspace.app.mediafilter.service.MediaFilterService;
 import org.dspace.content.Collection;
@@ -34,6 +19,9 @@ import org.dspace.core.Context;
 import org.dspace.core.SelfNamedPlugin;
 import org.dspace.core.factory.CoreServiceFactory;
 import org.dspace.handle.factory.HandleServiceFactory;
+
+import java.util.*;
+import org.apache.commons.lang.ArrayUtils;
 import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
@@ -56,12 +44,8 @@ public class MediaFilterCLITool {
     //suffix (in dspace.cfg) for input formats supported by each filter
     private static final String INPUT_FORMATS_SUFFIX = "inputFormats";
 
-    /**
-     * Default constructor
-     */
-    private MediaFilterCLITool() { }
-
-    public static void main(String[] argv) throws Exception {
+    public static void main(String[] argv) throws Exception
+    {
         // set headless for non-gui workstations
         System.setProperty("java.awt.headless", "true");
 
@@ -115,39 +99,48 @@ public class MediaFilterCLITool {
         Map<String, List<String>> filterFormats = new HashMap<>();
 
         CommandLine line = null;
-        try {
+        try
+        {
             line = parser.parse(options, argv);
-        } catch (MissingArgumentException e) {
+        }
+        catch(MissingArgumentException e)
+        {
             System.out.println("ERROR: " + e.getMessage());
             HelpFormatter myhelp = new HelpFormatter();
             myhelp.printHelp("MediaFilterManager\n", options);
             System.exit(1);
         }
 
-        if (line.hasOption('h')) {
+        if (line.hasOption('h'))
+        {
             HelpFormatter myhelp = new HelpFormatter();
             myhelp.printHelp("MediaFilterManager\n", options);
 
             System.exit(0);
         }
 
-        if (line.hasOption('v')) {
+        if (line.hasOption('v'))
+        {
             isVerbose = true;
         }
 
         isQuiet = line.hasOption('q');
 
-        if (line.hasOption('f')) {
+        if (line.hasOption('f'))
+        {
             isForce = true;
         }
 
-        if (line.hasOption('i')) {
+        if (line.hasOption('i'))
+        {
             identifier = line.getOptionValue('i');
         }
 
-        if (line.hasOption('m')) {
+        if (line.hasOption('m'))
+        {
             max2Process = Integer.parseInt(line.getOptionValue('m'));
-            if (max2Process <= 1) {
+            if (max2Process <= 1)
+            {
                 System.out.println("Invalid maximum value '" +
                         line.getOptionValue('m') + "' - ignoring");
                 max2Process = Integer.MAX_VALUE;
@@ -155,21 +148,24 @@ public class MediaFilterCLITool {
         }
 
         String filterNames[] = null;
-        if (line.hasOption('p')) {
+        if(line.hasOption('p'))
+        {
             //specified which media filter plugins we are using
             filterNames = line.getOptionValues('p');
 
-            if (filterNames == null || filterNames.length == 0) {   //display error, since no plugins specified
+            if(filterNames==null || filterNames.length==0)
+            {   //display error, since no plugins specified
                 System.err.println("\nERROR: -p (-plugin) option requires at least one plugin to be specified.\n" +
                         "(e.g. MediaFilterManager -p \"Word Text Extractor\",\"PDF Text Extractor\")\n");
                 HelpFormatter myhelp = new HelpFormatter();
                 myhelp.printHelp("MediaFilterManager\n", options);
                 System.exit(1);
             }
-        } else {
+        }
+        else
+        {
             //retrieve list of all enabled media filter plugins!
-            filterNames = DSpaceServicesFactory.getInstance().getConfigurationService()
-                                               .getArrayProperty(MEDIA_FILTER_PLUGINS_KEY);
+            filterNames = DSpaceServicesFactory.getInstance().getConfigurationService().getArrayProperty(MEDIA_FILTER_PLUGINS_KEY);
         }
 
         MediaFilterService mediaFilterService = MediaFilterServiceFactory.getInstance().getMediaFilterService();
@@ -182,16 +178,17 @@ public class MediaFilterCLITool {
         List<FormatFilter> filterList = new ArrayList<FormatFilter>();
 
         //set up each filter
-        for (int i = 0; i < filterNames.length; i++) {
+        for(int i=0; i< filterNames.length; i++)
+        {
             //get filter of this name & add to list of filters
-            FormatFilter filter = (FormatFilter) CoreServiceFactory.getInstance().getPluginService()
-                                                                   .getNamedPlugin(FormatFilter.class, filterNames[i]);
-            if (filter == null) {
-                System.err.println(
-                    "\nERROR: Unknown MediaFilter specified (either from command-line or in dspace.cfg): '" +
-                        filterNames[i] + "'");
+            FormatFilter filter = (FormatFilter) CoreServiceFactory.getInstance().getPluginService().getNamedPlugin(FormatFilter.class, filterNames[i]);
+            if(filter==null)
+            {
+                System.err.println("\nERROR: Unknown MediaFilter specified (either from command-line or in dspace.cfg): '" + filterNames[i] + "'");
                 System.exit(1);
-            } else {
+            }
+            else
+            {
                 filterList.add(filter);
 
                 String filterClassName = filter.getClass().getName();
@@ -203,7 +200,8 @@ public class MediaFilterCLITool {
                 //each "named" plugin that it defines.
                 //So, we have to look for every key that fits the
                 //following format: filter.<class-name>.<plugin-name>.inputFormats
-                if (SelfNamedPlugin.class.isAssignableFrom(filter.getClass())) {
+                if( SelfNamedPlugin.class.isAssignableFrom(filter.getClass()) )
+                {
                     //Get the plugin instance name for this class
                     pluginName = ((SelfNamedPlugin) filter).getPluginInstanceName();
                 }
@@ -221,28 +219,31 @@ public class MediaFilterCLITool {
                         "." + INPUT_FORMATS_SUFFIX);
 
                 //add to internal map of filters to supported formats
-                if (ArrayUtils.isNotEmpty(formats)) {
+                if (ArrayUtils.isNotEmpty(formats))
+                {
                     //For SelfNamedPlugins, map key is:
                     //  <class-name><separator><plugin-name>
                     //For other MediaFilters, map key is just:
                     //  <class-name>
                     filterFormats.put(filterClassName +
-                                          (pluginName != null ? MediaFilterService.FILTER_PLUGIN_SEPARATOR +
-                                              pluginName : ""),
+                                    (pluginName!=null ? MediaFilterService.FILTER_PLUGIN_SEPARATOR + pluginName : ""),
                             Arrays.asList(formats));
                 }
             }//end if filter!=null
         }//end for
 
         //If verbose, print out loaded mediafilter info
-        if (isVerbose) {
+        if(isVerbose)
+        {
             System.out.println("The following MediaFilters are enabled: ");
             Iterator<String> i = filterFormats.keySet().iterator();
-            while (i.hasNext()) {
+            while(i.hasNext())
+            {
                 String filterName = i.next();
                 System.out.println("Full Filter Name: " + filterName);
                 String pluginName = null;
-                if (filterName.contains(MediaFilterService.FILTER_PLUGIN_SEPARATOR)) {
+                if(filterName.contains(MediaFilterService.FILTER_PLUGIN_SEPARATOR))
+                {
                     String[] fields = filterName.split(MediaFilterService.FILTER_PLUGIN_SEPARATOR);
                     filterName=fields[0];
                     pluginName=fields[1];
@@ -260,11 +261,13 @@ public class MediaFilterCLITool {
 
         //Retrieve list of identifiers to skip (if any)
         String skipIds[] = null;
-        if (line.hasOption('s')) {
+        if(line.hasOption('s'))
+        {
             //specified which identifiers to skip when processing
             skipIds = line.getOptionValues('s');
 
-            if (skipIds == null || skipIds.length == 0) {   //display error, since no identifiers specified to skip
+            if(skipIds==null || skipIds.length==0)
+            {   //display error, since no identifiers specified to skip
                 System.err.println("\nERROR: -s (-skip) option requires at least one identifier to SKIP.\n" +
                         "Make sure to separate multiple identifiers with a comma!\n" +
                         "(e.g. MediaFilterManager -s 123456789/34,123456789/323)\n");
@@ -279,24 +282,29 @@ public class MediaFilterCLITool {
 
         Context c = null;
 
-        try {
+        try
+        {
             c = new Context();
 
             // have to be super-user to do the filtering
             c.turnOffAuthorisationSystem();
 
             // now apply the filters
-            if (identifier == null) {
+            if (identifier == null)
+            {
                 mediaFilterService.applyFiltersAllItems(c);
-            } else {
-                // restrict application scope to identifier
+            }
+            else  // restrict application scope to identifier
+            {
                 DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(c, identifier);
-                if (dso == null) {
+                if (dso == null)
+                {
                     throw new IllegalArgumentException("Cannot resolve "
                             + identifier + " to a DSpace object");
                 }
 
-                switch (dso.getType()) {
+                switch (dso.getType())
+                {
                     case Constants.COMMUNITY:
                         mediaFilterService.applyFiltersCommunity(c, (Community) dso);
                         break;
@@ -306,17 +314,20 @@ public class MediaFilterCLITool {
                     case Constants.ITEM:
                         mediaFilterService.applyFiltersItem(c, (Item) dso);
                         break;
-                    default:
-                        break;
                 }
             }
 
             c.complete();
             c = null;
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             status = 1;
-        } finally {
-            if (c != null) {
+        }
+        finally
+        {
+            if (c != null)
+            {
                 c.abort();
             }
         }

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

@@ -7,28 +7,11 @@
  */
 package org.dspace.app.mediafilter;
 
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
 import org.dspace.app.mediafilter.service.MediaFilterService;
 import org.dspace.authorize.service.AuthorizeService;
-import org.dspace.content.Bitstream;
-import org.dspace.content.BitstreamFormat;
-import org.dspace.content.Bundle;
+import org.dspace.content.*;
 import org.dspace.content.Collection;
-import org.dspace.content.Community;
-import org.dspace.content.DCDate;
-import org.dspace.content.Item;
-import org.dspace.content.service.BitstreamFormatService;
-import org.dspace.content.service.BitstreamService;
-import org.dspace.content.service.BundleService;
-import org.dspace.content.service.CollectionService;
-import org.dspace.content.service.CommunityService;
-import org.dspace.content.service.ItemService;
+import org.dspace.content.service.*;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.SelfNamedPlugin;
@@ -38,6 +21,10 @@ import org.dspace.services.ConfigurationService;
 import org.springframework.beans.factory.InitializingBean;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.*;
+
 /**
  * MediaFilterManager is the class that invokes the media/format filters over the
  * repository's content. A few command line flags affect the operation of the
@@ -47,7 +34,8 @@ import org.springframework.beans.factory.annotation.Autowired;
  * scope to a community, collection or item; and -m [max] limits processing to a
  * maximum number of items.
  */
-public class MediaFilterServiceImpl implements MediaFilterService, InitializingBean {
+public class MediaFilterServiceImpl implements MediaFilterService, InitializingBean
+{
     @Autowired(required = true)
     protected AuthorizeService authorizeService;
     @Autowired(required = true)
@@ -85,14 +73,14 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
     protected boolean isQuiet = false;
     protected boolean isForce = false; // default to not forced
 
-    protected MediaFilterServiceImpl() {
+    protected MediaFilterServiceImpl()
+    {
 
     }
 
     @Override
     public void afterPropertiesSet() throws Exception {
-        String[] publicPermissionFilters = configurationService
-            .getArrayProperty("filter.org.dspace.app.mediafilter.publicPermission");
+        String[] publicPermissionFilters = configurationService.getArrayProperty("filter.org.dspace.app.mediafilter.publicPermission");
 
         if(publicPermissionFilters != null) {
             for(String filter : publicPermissionFilters) {
@@ -102,8 +90,10 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
     }
 
     @Override
-    public void applyFiltersAllItems(Context context) throws Exception {
-        if (skipList != null) {
+    public void applyFiltersAllItems(Context context) throws Exception
+    {
+        if(skipList!=null)
+        {    
             //if a skip-list exists, we need to filter community-by-community
             //so we can respect what is in the skip-list
             List<Community> topLevelCommunities = communityService.findAllTop(context);
@@ -111,10 +101,13 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
             for (Community topLevelCommunity : topLevelCommunities) {
                 applyFiltersCommunity(context, topLevelCommunity);
             }
-        } else {
+        }
+        else 
+        {
             //otherwise, just find every item and process
             Iterator<Item> itemIterator = itemService.findAll(context);
-            while (itemIterator.hasNext() && processed < max2Process) {
+            while (itemIterator.hasNext() && processed < max2Process)
+            {
                 applyFiltersItem(context, itemIterator.next());
             }
         }
@@ -122,8 +115,10 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
 
     @Override
     public void applyFiltersCommunity(Context context, Community community)
-        throws Exception {   //only apply filters if community not in skip-list
-        if (!inSkipList(community.getHandle())) {
+                                             throws Exception
+    {   //only apply filters if community not in skip-list
+        if(!inSkipList(community.getHandle()))
+        {    
            	List<Community> subcommunities = community.getSubcommunities();
             for (Community subcommunity : subcommunities) {
                 applyFiltersCommunity(context, subcommunity);
@@ -138,25 +133,31 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
 
     @Override
     public void applyFiltersCollection(Context context, Collection collection)
-        throws Exception {
+                                              throws Exception
+    {
         //only apply filters if collection not in skip-list
-        if (!inSkipList(collection.getHandle())) {
+        if(!inSkipList(collection.getHandle()))
+        {
             Iterator<Item> itemIterator = itemService.findAllByCollection(context, collection);
-            while (itemIterator.hasNext() && processed < max2Process) {
+            while (itemIterator.hasNext() && processed < max2Process)
+            {
                 applyFiltersItem(context, itemIterator.next());
             }
         }
     }
        
     @Override
-    public void applyFiltersItem(Context c, Item item) throws Exception {
+    public void applyFiltersItem(Context c, Item item) throws Exception
+    {
         //only apply filters if item not in skip-list
-        if (!inSkipList(item.getHandle())) {
+        if(!inSkipList(item.getHandle()))
+        {
     	  //cache this item in MediaFilterManager
     	  //so it can be accessed by MediaFilters as necessary
     	  currentItem = item;
     	
-            if (filterItem(c, item)) {
+          if (filterItem(c, item))
+          {
               // increment processed count
               ++processed;
           }
@@ -167,7 +168,8 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
     }
 
     @Override
-    public boolean filterItem(Context context, Item myItem) throws Exception {
+    public boolean filterItem(Context context, Item myItem) throws Exception
+    {
         // get 'original' bundles
         List<Bundle> myBundles = itemService.getBundles(myItem, "ORIGINAL");
         boolean done = false;
@@ -184,7 +186,8 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
 
     @Override
     public boolean filterBitstream(Context context, Item myItem,
-                                   Bitstream myBitstream) throws Exception {
+            Bitstream myBitstream) throws Exception
+    {
     	boolean filtered = false;
     	
     	// iterate through filter classes. A single format may be actioned
@@ -220,7 +223,7 @@ 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();
 
@@ -299,9 +302,11 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
     
     @Override
     public boolean processBitstream(Context context, Item item, Bitstream source, FormatFilter formatFilter)
-        throws Exception {
+            throws Exception
+    {
         //do pre-processing of this bitstream, and if it fails, skip this bitstream!
-        if (!formatFilter.preProcessBitstream(context, item, source, isVerbose)) {
+    	if(!formatFilter.preProcessBitstream(context, item, source, isVerbose))
+        {
             return false;
         }
         	
@@ -310,29 +315,29 @@ 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
-
-        List<Bundle> bundles = itemService.getBundles(item, formatFilter.getBundleName());
-
         // check if destination bitstream exists
-        if (bundles.size() > 0) {
+        Bundle existingBundle = null;
+        Bitstream existingBitstream = null;
+        List<Bundle> bundles = itemService.getBundles(item, formatFilter.getBundleName());
+        if (bundles.size() > 0)
+        {
             // only finds the last match (FIXME?)
             for (Bundle bundle : bundles) {
                 List<Bitstream> bitstreams = bundle.getBitstreams();
 
                 for (Bitstream bitstream : bitstreams) {
                     if (bitstream.getName().trim().equals(newName.trim())) {
-                        targetBundle = bundle;
+                        existingBundle = bundle;
                         existingBitstream = bitstream;
                     }
                 }
             }
         }
-
         // if exists and overwrite = false, exit
-        if (!overWrite && (existingBitstream != null)) {
-            if (!isQuiet) {
+        if (!overWrite && (existingBitstream != null))
+        {
+            if (!isQuiet)
+            {
                 System.out.println("SKIPPED: bitstream " + source.getID()
                         + " (item: " + item.getHandle() + ") because '" + newName + "' already exists");
             }
@@ -345,40 +350,44 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
                 + " (item: " + item.getHandle() + ")");
         }
 
-        InputStream destStream;
-        try {
         System.out.println("File: " + newName);
-            destStream = formatFilter.getDestinationStream(item, bitstreamService.retrieve(context, source), isVerbose);
+
+        // start filtering of the bitstream, using try with resource to close all InputStreams properly
+        try (
+                // get the source stream
+                InputStream srcStream = bitstreamService.retrieve(context, source);
+                // filter the source stream to produce the destination stream
+                // this is the hard work, check for OutOfMemoryErrors at the end of the try clause.
+                InputStream destStream = formatFilter.getDestinationStream(item, srcStream, isVerbose);
+        ) {
             if (destStream == null) {
                 if (!isQuiet) {
                     System.out.println("SKIPPED: bitstream " + source.getID()
                             + " (item: " + item.getHandle() + ") because filtering was unsuccessful");
                 }
-
-                return false;
-            }
-        } catch (OutOfMemoryError oome) {
-            System.out.println("!!! OutOfMemoryError !!!");
                 return false;
             }
 
+            Bundle targetBundle; // bundle we're modifying
+            if (bundles.size() < 1)
+            {
                 // create new bundle if needed
-        if (bundles.size() < 1) {
                 targetBundle = bundleService.create(context, item, formatFilter.getBundleName());
-        } else {
-            // take the first match
+            }
+            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);
-
-        // Now set the format and name of the bitstream
+            // 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());
-
-        // Find the proper format
+            // Set the format of the bitstream
             BitstreamFormat bf = bitstreamFormatService.findByShortDescription(context,
                     formatFilter.getFormatString());
             bitstreamService.setFormat(context, b, bf);
@@ -398,36 +407,49 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
                 authorizeService.inheritPolicies(context, source, b);
             }
 
-        // fixme - set date?
-        // we are overwriting, so remove old bitstream
-        if (existingBitstream != null) {
-            bundleService.removeBitstream(context, targetBundle, existingBitstream);
+            //do post-processing of the generated bitstream
+            formatFilter.postProcessBitstream(context, item, b);
+
+
+        } catch (OutOfMemoryError oome) {
+            System.out.println("!!! OutOfMemoryError !!!");
         }
 
-        if (!isQuiet) {
+        // fixme - set date?
+        // we are overwriting, so remove old bitstream
+        if (existingBitstream != null)
+        {
+            bundleService.removeBitstream(context, existingBundle, existingBitstream);
+        }
+
+        if (!isQuiet)
+        {
             System.out.println("FILTERED: bitstream " + source.getID()
                     + " (item: " + item.getHandle() + ") and created '" + newName + "'");
         }
 
-        //do post-processing of the generated bitstream
-        formatFilter.postProcessBitstream(context, item, b);
-
         return true;
     }
     
     @Override
-    public Item getCurrentItem() {
+    public Item getCurrentItem()
+    {
         return currentItem;
     }
     
     @Override
-    public boolean inSkipList(String identifier) {
-        if (skipList != null && skipList.contains(identifier)) {
-            if (!isQuiet) {
+    public boolean inSkipList(String identifier)
+    {
+        if(skipList!=null && skipList.contains(identifier))
+        {
+            if (!isQuiet)
+            {
                 System.out.println("SKIP-LIST: skipped bitstreams within identifier " + identifier);
             }
             return true;
-        } else {
+        }    
+        else
+        {
             return false;
         }
     }

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

@@ -7,10 +7,8 @@
  */
 package org.dspace.app.mediafilter;
 
-import java.awt.image.BufferedImage;
+import java.awt.image.*;
 import java.io.InputStream;
-import javax.imageio.ImageIO;
-
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.rendering.PDFRenderer;
 import org.dspace.content.Item;
@@ -25,17 +23,21 @@ import org.dspace.content.Item;
  * @author Ivan Masár helix84@centrum.sk
  * @author Jason Sherman jsherman@usao.edu
  */
-public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFormats {
+public class PDFBoxThumbnail extends MediaFilter
+{
     @Override
-    public String getFilteredName(String oldFilename) {
+    public String getFilteredName(String oldFilename)
+    {
         return oldFilename + ".jpg";
     }
 
     /**
      * @return String bundle name
+     *  
      */
     @Override
-    public String getBundleName() {
+    public String getBundleName()
+    {
         return "THUMBNAIL";
     }
 
@@ -43,7 +45,8 @@ public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFor
      * @return String bitstreamformat
      */
     @Override
-    public String getFormatString() {
+    public String getFormatString()
+    {
         return "JPEG";
     }
 
@@ -51,7 +54,8 @@ public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFor
      * @return String description
      */
     @Override
-    public String getDescription() {
+    public String getDescription()
+    {
         return "Generated Thumbnail";
     }
 
@@ -59,12 +63,14 @@ public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFor
      * @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 {
+            throws Exception
+    {
         PDDocument doc = PDDocument.load(source);
         PDFRenderer renderer = new PDFRenderer(doc);
         BufferedImage buf = renderer.renderImage(0);
@@ -74,21 +80,4 @@ public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFor
         JPEGFilter jpegFilter = new JPEGFilter();
         return jpegFilter.getThumb(currentItem, buf, verbose);
     }
-
-    @Override
-    public String[] getInputMIMETypes() {
-        return ImageIO.getReaderMIMETypes();
-    }
-
-    @Override
-    public String[] getInputDescriptions() {
-        return null;
-    }
-
-    @Override
-    public String[] getInputExtensions() {
-        // Temporarily disabled as JDK 1.6 only
-        // return ImageIO.getReaderFileSuffixes();
-        return null;
-    }
 }

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

@@ -28,20 +28,24 @@ import org.dspace.core.ConfigurationManager;
  * instantiate filter - bitstream format doesn't exist
  *
  */
-public class PDFFilter extends MediaFilter {
+public class PDFFilter extends MediaFilter
+{
 
     private static Logger log = Logger.getLogger(PDFFilter.class);
 
     @Override
-    public String getFilteredName(String oldFilename) {
+    public String getFilteredName(String oldFilename)
+    {
         return oldFilename + ".txt";
     }
 
     /**
      * @return String bundle name
+     *
      */
     @Override
-    public String getBundleName() {
+    public String getBundleName()
+    {
         return "TEXT";
     }
 
@@ -49,7 +53,8 @@ public class PDFFilter extends MediaFilter {
      * @return String bitstreamformat
      */
     @Override
-    public String getFormatString() {
+    public String getFormatString()
+    {
         return "Text";
     }
 
@@ -57,7 +62,8 @@ public class PDFFilter extends MediaFilter {
      * @return String description
      */
     @Override
-    public String getDescription() {
+    public String getDescription()
+    {
         return "Extracted text";
     }
 
@@ -65,13 +71,16 @@ public class PDFFilter extends MediaFilter {
      * @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 {
-        try {
+            throws Exception
+    {
+        try
+        {
             boolean useTemporaryFile = ConfigurationManager.getBooleanProperty("pdffilter.largepdfs", false);
 
             // get input stream from bitstream
@@ -83,43 +92,62 @@ public class PDFFilter extends MediaFilter {
             File tempTextFile = null;
             ByteArrayOutputStream byteStream = null;
 
-            if (useTemporaryFile) {
+            if (useTemporaryFile)
+            {
                 tempTextFile = File.createTempFile("dspacepdfextract" + source.hashCode(), ".txt");
                 tempTextFile.deleteOnExit();
                 writer = new OutputStreamWriter(new FileOutputStream(tempTextFile));
-            } else {
+            }
+            else
+            {
                 byteStream = new ByteArrayOutputStream();
                 writer = new OutputStreamWriter(byteStream);
             }
             
-            try {
+            try
+            {
                 pdfDoc = PDDocument.load(source);
                 pts.writeText(pdfDoc, writer);
-            } finally {
-                try {
-                    if (pdfDoc != null) {
+            }
+            finally
+            {
+                try
+                {
+                    if (pdfDoc != null)
+                    {
                         pdfDoc.close();
                     }
-                } catch (Exception e) {
+                }
+                catch(Exception e)
+                {
                    log.error("Error closing PDF file: " + e.getMessage(), e);
                 }
 
-                try {
+                try
+                {
                     writer.close();
-                } catch (Exception e) {
+                }
+                catch(Exception e)
+                {
                    log.error("Error closing temporary extract file: " + e.getMessage(), e);
                 }
             }
 
-            if (useTemporaryFile) {
+            if (useTemporaryFile)
+            {
                 return new FileInputStream(tempTextFile);
-            } else {
+            }
+            else
+            {
                 byte[] bytes = byteStream.toByteArray();
                 return new ByteArrayInputStream(bytes);
             }
-        } catch (OutOfMemoryError oome) {
+        }
+        catch (OutOfMemoryError oome)
+        {
             log.error("Error parsing PDF document " + oome.getMessage(), oome);
-            if (!ConfigurationManager.getBooleanProperty("pdffilter.skiponmemoryexception", false)) {
+            if (!ConfigurationManager.getBooleanProperty("pdffilter.skiponmemoryexception", false))
+            {
                 throw oome;
             }
         }

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

@@ -8,8 +8,8 @@
 package org.dspace.app.mediafilter;
 
 import java.io.ByteArrayInputStream;
-import java.io.IOException;
 import java.io.InputStream;
+import java.io.IOException;
 
 import org.apache.poi.POITextExtractor;
 import org.apache.poi.extractor.ExtractorFactory;
@@ -23,45 +23,55 @@ import org.slf4j.LoggerFactory;
  * Extract flat text from Microsoft Word documents (.doc, .docx).
  */
 public class PoiWordFilter
-    extends MediaFilter {
+        extends MediaFilter
+{
     private static final Logger LOG = LoggerFactory.getLogger(PoiWordFilter.class);
 
     @Override
-    public String getFilteredName(String oldFilename) {
+    public String getFilteredName(String oldFilename)
+    {
         return oldFilename + ".txt";
     }
 
     @Override
-    public String getBundleName() {
+    public String getBundleName()
+    {
         return "TEXT";
     }
 
     @Override
-    public String getFormatString() {
+    public String getFormatString()
+    {
         return "Text";
     }
 
     @Override
-    public String getDescription() {
+    public String getDescription()
+    {
         return "Extracted text";
     }
 
     @Override
     public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
-        throws Exception {
+            throws Exception
+    {
         String text;
-        try {
+        try  
+        {
             // get input stream from bitstream, pass to filter, get string back
             POITextExtractor extractor = ExtractorFactory.createExtractor(source);
             text = extractor.getText();
-        } catch (IOException | OpenXML4JException | XmlException e) {
+        }
+        catch (IOException | OpenXML4JException | XmlException e)
+        {
             System.err.format("Invalid File Format:  %s%n", e.getMessage());
             LOG.error("Unable to parse the bitstream:  ", e);
             throw e;
         }
 
         // if verbose flag is set, print out extracted text to STDOUT
-        if (verbose) {
+        if (verbose)
+        {
             System.out.println(text);
         }
 

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

@@ -10,31 +10,36 @@ package org.dspace.app.mediafilter;
 import java.io.ByteArrayInputStream;
 import java.io.InputStream;
 
-import org.apache.log4j.Logger;
-import org.apache.poi.POITextExtractor;
 import org.apache.poi.extractor.ExtractorFactory;
-import org.apache.poi.hslf.extractor.PowerPointExtractor;
 import org.apache.poi.xslf.extractor.XSLFPowerPointExtractor;
+import org.apache.poi.hslf.extractor.PowerPointExtractor;
+import org.apache.poi.POITextExtractor;
+
+import org.apache.log4j.Logger;
 import org.dspace.content.Item;
 
 /*
  * TODO: Allow user to configure extraction of only text or only notes
  * 
  */
-public class PowerPointFilter extends MediaFilter {
+public class PowerPointFilter extends MediaFilter
+{
 
     private static Logger log = Logger.getLogger(PowerPointFilter.class);
 
     @Override
-    public String getFilteredName(String oldFilename) {
+    public String getFilteredName(String oldFilename)
+    {
         return oldFilename + ".txt";
     }
 
     /**
      * @return String bundle name
+     * 
      */
     @Override
-    public String getBundleName() {
+    public String getBundleName()
+    {
         return "TEXT";
     }
 
@@ -44,7 +49,8 @@ public class PowerPointFilter extends MediaFilter {
      *         TODO: Check that this is correct
      */
     @Override
-    public String getFormatString() {
+    public String getFormatString()
+    {
         return "Text";
     }
 
@@ -52,7 +58,8 @@ public class PowerPointFilter extends MediaFilter {
      * @return String description
      */
     @Override
-    public String getDescription() {
+    public String getDescription()
+    {
         return "Extracted text";
     }
 
@@ -60,14 +67,17 @@ public class PowerPointFilter extends MediaFilter {
      * @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 {
+            throws Exception
+    {
 
-        try {
+        try
+        {
 
             String extractedText = null;
             new ExtractorFactory();
@@ -78,22 +88,29 @@ public class PowerPointFilter extends MediaFilter {
             // require different classes and APIs for text extraction
 
             // If this is a PowerPoint XML file, extract accordingly
-            if (pptExtractor instanceof XSLFPowerPointExtractor) {
+            if (pptExtractor instanceof XSLFPowerPointExtractor)
+            {
 
                 // The true method arguments indicate that text from
                 // the slides and the notes is desired
                 extractedText = ((XSLFPowerPointExtractor) pptExtractor)
                         .getText(true, true);
-            } else if (pptExtractor instanceof PowerPointExtractor) { // Legacy PowerPoint files
+            }
+
+            // Legacy PowerPoint files
+            else if (pptExtractor instanceof PowerPointExtractor)
+            {
 
                 extractedText = ((PowerPointExtractor) pptExtractor).getText()
                         + " " + ((PowerPointExtractor) pptExtractor).getNotes();
 
             }
-            if (extractedText != null) {
+            if (extractedText != null)
+            {
                 // if verbose flag is set, print out extracted text
                 // to STDOUT
-                if (verbose) {
+                if (verbose)
+                {
                     System.out.println(extractedText);
                 }
 
@@ -103,7 +120,9 @@ public class PowerPointFilter extends MediaFilter {
 
                 return bais;
             }
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             log.error("Error filtering bitstream: " + e.getMessage(), e);
             throw e;
         }

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

@@ -11,7 +11,8 @@ package org.dspace.app.mediafilter;
  * Interface to allow filters to register the input formats they handle
  * (useful for exposing underlying capabilities of libraries used)
  */
-public interface SelfRegisterInputFormats {
+public interface SelfRegisterInputFormats
+{
     public String[] getInputMIMETypes();
 
     public String[] getInputDescriptions();

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

@@ -8,10 +8,11 @@
 package org.dspace.app.mediafilter;
 
 import java.io.ByteArrayInputStream;
-import java.io.IOException;
 import java.io.InputStream;
+import java.io.IOException;
 
 import org.apache.log4j.Logger;
+
 import org.dspace.content.Item;
 import org.textmining.extraction.TextExtractor;
 import org.textmining.extraction.word.WordTextExtractorFactory;
@@ -22,20 +23,24 @@ import org.textmining.extraction.word.WordTextExtractorFactory;
  * instantiate filter - bitstream format doesn't exist.
  *  
  */
-public class WordFilter extends MediaFilter {
+public class WordFilter extends MediaFilter
+{
 
     private static Logger log = Logger.getLogger(WordFilter.class);
 
     @Override
-    public String getFilteredName(String oldFilename) {
+    public String getFilteredName(String oldFilename)
+    {
         return oldFilename + ".txt";
     }
 
     /**
      * @return String bundle name
+     *  
      */
     @Override
-    public String getBundleName() {
+    public String getBundleName()
+    {
         return "TEXT";
     }
 
@@ -43,7 +48,8 @@ public class WordFilter extends MediaFilter {
      * @return String bitstreamformat
      */
     @Override
-    public String getFormatString() {
+    public String getFormatString()
+    {
         return "Text";
     }
 
@@ -51,7 +57,8 @@ public class WordFilter extends MediaFilter {
      * @return String description
      */
     @Override
-    public String getDescription() {
+    public String getDescription()
+    {
         return "Extracted text";
     }
 
@@ -59,22 +66,26 @@ public class WordFilter extends MediaFilter {
      * @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 {
+            throws Exception
+    {
         // get input stream from bitstream
         // pass to filter, get string back
-        try {
+        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) {
+            if (verbose)
+            {
                 System.out.println(extractedText);
             }
 
@@ -83,7 +94,9 @@ public class WordFilter extends MediaFilter {
             ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
 
             return bais; // will this work? or will the byte array be out of scope?
-        } catch (IOException ioe) {
+        } 
+        catch (IOException ioe)
+        {
             System.out.println("Invalid Word Format");
             log.error("Error detected - Word File format not recognized: "
                     + ioe.getMessage(), ioe);

dspace-api/src/main/java/org/dspace/app/mediafilter/factory/MediaFilterServiceFactory.java

@@ -11,8 +11,7 @@ import org.dspace.app.mediafilter.service.MediaFilterService;
 import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
- * Abstract factory to get services for the mediafilter package, use MediaFilterServiceFactory.getInstance() to
- * retrieve an implementation
+ * Abstract factory to get services for the mediafilter package, use MediaFilterServiceFactory.getInstance() to retrieve an implementation
  *
  * @author kevinvandevelde at atmire.com
  */
@@ -21,7 +20,6 @@ public abstract class MediaFilterServiceFactory {
     public abstract MediaFilterService getMediaFilterService();
 
     public static MediaFilterServiceFactory getInstance(){
-        return DSpaceServicesFactory.getInstance().getServiceManager()
-                                    .getServiceByName("mediaFilterServiceFactory", MediaFilterServiceFactory.class);
+        return DSpaceServicesFactory.getInstance().getServiceManager().getServiceByName("mediaFilterServiceFactory", MediaFilterServiceFactory.class);
     }
 }

dspace-api/src/main/java/org/dspace/app/mediafilter/factory/MediaFilterServiceFactoryImpl.java

@@ -11,8 +11,7 @@ import org.dspace.app.mediafilter.service.MediaFilterService;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
- * Factory implementation to get services for the mediafilter package, use MediaFilterServiceFactory.getInstance() to
- * retrieve an implementation
+ * Factory implementation to get services for the mediafilter package, use MediaFilterServiceFactory.getInstance() to retrieve an implementation
  *
  * @author kevinvandevelde at atmire.com
  */