Update README.md

Merge pull request #2066 from 4Science/DS-3915
DS-3915 RestResourceController hides not existing endpoints under other errors
2025-10-07 10:04:21 +00:00 · 2018-06-22 14:33:35 -07:00 · 2018-05-28 08:36:26 +02:00 · 2018-05-28 08:29:51 +02:00 · 2018-05-20 21:13:20 +02:00 · 2018-05-20 19:16:46 +02:00
3584 changed files with 268221 additions and 367426 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -1,16 +1,22 @@
 ## Ignore the MVN compiled output directories from version tracking
 target/

+## Ignore tags index files created by Exuberant Ctags
+tags
+
 ## Ignore project files created by Eclipse
 .settings/
+/bin/
 .project
 .classpath
+.checkstyle

 ## Ignore project files created by IntelliJ IDEA
 *.iml
 *.ipr
 *.iws
 .idea/
+overlays/

 ## Ignore project files created by NetBeans
 nbproject/private/
@@ -20,8 +26,19 @@ dist/
 nbdist/
 nbactions.xml
 nb-configuration.xml
-META-INF/

-## Ignore all *.properties file, EXCEPT build.properties (the default)
-*.properties
-!build.properties
+## 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)
+/*.properties
+!/build.properties
+
+# Ignore a local.cfg file in root folder, if it exists
+/local.cfg
+# Also ignore it under dspace/config
+/dspace/config/local.cfg
+
+##Mac noise
+.DS_Store
+
+##Ignore JRebel project configuration
+rebel.xml
--- a/.travis.yml
+++ b/.travis.yml
@@ -0,0 +1,44 @@
+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+  # Remove outdated settings.xml from Travis builds.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"
--- a/2
+++ b/2
@@ -1,7 +1,7 @@
 DSpace source code license:


-Copyright (c) 2002-2012, DuraSpace.  All rights reserved.
+Copyright (c) 2002-2016, DuraSpace.  All rights reserved.

 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are
--- a/490
+++ b/490
@@ -1,112 +1,424 @@
+
 DSpace uses third-party libraries which may be distributed under different
-licenses. We have attempted to list all of these third party libraries and 
-their licenses below (however the most up-to-date information can be found
-via Maven, see NOTE #2 at bottom of this page). 
+licenses. We have listed all of these third party libraries and their licenses
+below. This file can be regenerated at any time by simply running:
+
+    mvn clean verify -Dthird.party.licenses=true

 You must agree to the terms of these licenses, in addition to the DSpace
 source code license, in order to use this software.

--------------------------------------------------
-Third party Java libraries listed by License type
-[Format: Name (Maven Project) - URL]
--------------------------------------------------
+---------------------------------------------------
+Third party Java libraries listed by License type.

-Apache Software License, Version 2.0 (http://opensource.org/licenses/apache2.0)
-  * Ant-Contrib Tasks (ant-contrib:*) - http://ant-contrib.sourceforge.net/
-  * Apache Abdera (org.apache.abdera::*) - http://projects.apache.org/projects/abdera.html
-  * Apache Ant (org.apache.ant:*) - http://ant.apache.org/
-  * Apache Axis (axis:*) - http://axis.apache.org/axis/
-  * Apache Cocoon (org.apache.cocoon:*) - http://cocoon.apache.org/2.2/license.html
-  * Apache Commons CLI (commons-cli:*) - http://commons.apache.org/cli/license.html
-  * Apache Commons Codec (commons-codec:*) - http://commons.apache.org/codec/license.html
-  * Apache Commons Collections (commons-collections:*) - http://commons.apache.org/collections/license.html
-  * Apache Commons DBCP (commons-dbcp:*) - http://commons.apache.org/dbcp/license.html
-  * Apache Commons Discovery (commons-discovery:*) - http://commons.apache.org/discovery/license.html
-  * Apache Commons FileUpload (commons-fileupload:*) - http://commons.apache.org/fileupload/license.html
-  * Apache Commons HTTP Client (commons-httpclient:*) - http://commons.apache.org/httpclient/license.html
-  * Apache Commons IO (commons-io:*) - http://commons.apache.org/io/license.html
-  * Apache Commons JXPath (commons-jxpath:*) - http://commons.apache.org/jxpath/license.html
-  * Apache Commons Lang (commons-lang:*) - http://commons.apache.org/lang/license.html
-  * Apache Commons Logging (commons-logging:*) - http://commons.apache.org/logging/license.html
-  * Apache Commons Pool (commons-pool:*) - http://commons.apache.org/pool/license.html
-  * Apache Commons Validator (commons-validator:*) - http://commons.apache.org/validator/license.html
-  * Apache Jakarta ORO (oro:*) - http://svn.apache.org/repos/asf/jakarta/oro/trunk/LICENSE
-  * Apache log4j (log4j:*) : http://logging.apache.org/log4j/
-  * Apache Lucene (org.apache.lucene:*) - http://lucene.apache.org/
-  * Apache PDFBox (org.apache.pdfbox:*) - http://pdfbox.apache.org/
-  * Apache POI (org.apache.poi:*) - http://poi.apache.org/
-  * Apache Solr (org.apache.solr:*) - http://lucene.apache.org/solr/
-  * Apache Xerces (xerces:*) - http://xerces.apache.org/
-  * Apache XML Commons (xml-apis:*) - http://xerces.apache.org/xml-commons/licenses.html
-  * Apache XML Project (xalan:*) - http://xml.apache.org/xalan-j/#license
-  * Databene ContiPerf (org.databene:contiperf) - http://databene.org/contiperf
-  * Rome (net.java.dev.rome:*, org.rometools:*, rome:*) - http://rometools.org/
-  * Spring Framework  (org.springframework:*) - http://www.springsource.org/spring-framework
-  * SWORD Libraries (org.swordapp:*) - http://mvnrepository.com/artifact/org.swordapp/server/2.0
+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
+---------------------------------------------------

-BSD License (http://www.opensource.org/licenses/BSD-3-Clause)
-  * DNSJava (org.dspace.dnsjava:dnsjava)- http://www.xbill.org/dnsjava/dnsjava-current/README
-  * Foresite Toolkit (com.googlecode.foresite-toolkit:*) - http://code.google.com/p/foresite-toolkit/
-  * Jaxen (jaxen:*) -  http://jaxen.codehaus.org/license.html 
-  * YUI (com.yahoo.platform.yui:*) - http://yuilibrary.com/license/
+    Apache Software License, Version 2.0:

-Common Development and Distribution License (CDDL) v1.0 (http://www.opensource.org/licenses/CDDL-1.0)
-  * JavaBeans Activation Framework (javax.activation:*) - http://www.opensource.org/licenses/CDDL-1.0  
-  * Java Mail (javax.mail:*) - http://www.opensource.org/licenses/CDDL-1.0
-  * JAX-RPC (javax.xml:jaxrpc-api) - http://java.net/projects/jax-rpc/
+        * 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/)
+        * 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)
+        * 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)
+        * 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)
+        * Jtwig Core (com.lyncode:jtwig-core:2.0.1 - http://www.lyncode.com/jtwig-core)
+        * 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)
+        * Spatial4J (com.spatial4j:spatial4j:0.4.1 - https://github.com/spatial4j/spatial4j)
+        * 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/)
+        * 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)
+        * Commons JXPath (commons-jxpath:commons-jxpath:1.3 - http://commons.apache.org/jxpath/)
+        * Commons Lang (commons-lang:commons-lang:2.6 - http://commons.apache.org/lang/)
+        * 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)
+        * jdbm (jdbm:jdbm:1.0 - no url defined)
+        * Joda time (joda-time:joda-time:2.2 - http://joda-time.sourceforge.net)
+        * Joda-Time (joda-time:joda-time:2.9.2 - http://www.joda.org/joda-time/)
+        * Apache Log4j (log4j:log4j:1.2.17 - http://logging.apache.org/log4j/1.2/)
+        * "Java Concurrency in Practice" book annotations (net.jcip:jcip-annotations:1.0 - http://jcip.net/)
+        * Ehcache Core (net.sf.ehcache:ehcache-core:2.4.3 - http://ehcache.org)
+        * opencsv (net.sf.opencsv:opencsv:2.3 - http://opencsv.sf.net)
+        * Abdera Client (org.apache.abdera:abdera-client:1.1.3 - http://abdera.apache.org/abdera-client)
+        * 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/)
+        * 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/)
+        * Cocoon Core (org.apache.cocoon:cocoon-core:2.2.0 - http://cocoon.apache.org/2.2/core-modules/core/2.2/)
+        * Cocoon Expression Language API (org.apache.cocoon:cocoon-expression-language-api:1.0.0 - http://cocoon.apache.org/2.2/core-modules/expression-language-api/1.0/)
+        * Cocoon Expression Language Implementation. (org.apache.cocoon:cocoon-expression-language-impl:1.0.0 - http://cocoon.apache.org/2.2/core-modules/expression-language-impl/1.0/)
+        * Cocoon Flowscript Block Implementation (org.apache.cocoon:cocoon-flowscript-impl:1.0.0 - http://cocoon.apache.org/2.2/blocks/flowscript/1.0/)
+        * Cocoon Linkrewriter Block Implementation (org.apache.cocoon:cocoon-linkrewriter-impl:1.0.0 - http://cocoon.apache.org/2.2/blocks/linkrewriter/1.0/)
+        * Cocoon Pipeline API (org.apache.cocoon:cocoon-pipeline-api:1.0.0 - http://cocoon.apache.org/2.2/core-modules/pipeline-api/1.0/)
+        * Cocoon Pipeline Components (org.apache.cocoon:cocoon-pipeline-components:1.0.0 - http://cocoon.apache.org/2.2/core-modules/pipeline-components/1.0/)
+        * Cocoon Pipeline Implementation (org.apache.cocoon:cocoon-pipeline-impl:1.0.0 - http://cocoon.apache.org/2.2/core-modules/pipeline-impl/1.0/)
+        * Cocoon Servlet Service Components (org.apache.cocoon:cocoon-servlet-service-components:1.0.0 - http://cocoon.apache.org/subprojects/servlet-service/1.0/servlet-service-components/1.0/)
+        * Cocoon Sitemap API (org.apache.cocoon:cocoon-sitemap-api:1.0.0 - http://cocoon.apache.org/2.2/core-modules/sitemap-api/1.0/)
+        * Cocoon Sitemap Components (org.apache.cocoon:cocoon-sitemap-components:1.0.0 - http://cocoon.apache.org/2.2/core-modules/sitemap-components/1.0/)
+        * Cocoon Sitemap Implementation (org.apache.cocoon:cocoon-sitemap-impl:1.0.0 - http://cocoon.apache.org/2.2/core-modules/sitemap-impl/1.0/)
+        * Cocoon Spring Configurator (org.apache.cocoon:cocoon-spring-configurator:1.0.2 - http://cocoon.apache.org/cocoon-spring-configurator)
+        * Cocoon Store Implementation (org.apache.cocoon:cocoon-store-impl:1.0.0 - http://cocoon.apache.org/2.2/core-modules/store-impl/1.0/)
+        * Cocoon Template Framework Block Implementation (org.apache.cocoon:cocoon-template-impl:1.1.0 - http://cocoon.apache.org/2.2/blocks/template/1.0/)
+        * Cocoon Thread API (org.apache.cocoon:cocoon-thread-api:1.0.0 - http://cocoon.apache.org/2.2/core-modules/thread-api/1.0/)
+        * Cocoon Thread Implementation (org.apache.cocoon:cocoon-thread-impl:1.0.0 - http://cocoon.apache.org/2.2/core-modules/thread-impl/1.0/)
+        * Cocoon Util (org.apache.cocoon:cocoon-util:1.0.0 - http://cocoon.apache.org/2.2/core-modules/util/1.0/)
+        * Cocoon XML API (org.apache.cocoon:cocoon-xml-api:1.0.0 - http://cocoon.apache.org/2.2/core-modules/xml-api/1.0/)
+        * 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 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 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/)
+        * 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/)
+        * Excalibur XML Utilities (org.apache.excalibur.components:excalibur-xmlutil:2.2.1 - http://www.apache.org/excalibur/excalibur-components-modules/excalibur-xmlutil/)
+        * Excalibur Instrument API (org.apache.excalibur.containerkit:excalibur-instrument-api:2.2.1 - http://www.apache.org/excalibur/excalibur-containerkit/excalibur-instrument-modules/excalibur-instrument-api/)
+        * Excalibur Logger (org.apache.excalibur.containerkit:excalibur-logger:2.2.1 - http://www.apache.org/excalibur/excalibur-containerkit/excalibur-logger/)
+        * Activation 1.1 (org.apache.geronimo.specs:geronimo-activation_1.1_spec:1.1 - http://geronimo.apache.org/maven/specs/geronimo-activation_1.1_spec/1.1)
+        * JavaMail 1.4 (org.apache.geronimo.specs:geronimo-javamail_1.4_spec:1.7.1 - http://geronimo.apache.org/maven/specs/geronimo-javamail_1.4_spec/1.7.1)
+        * Streaming API for XML (STAX API 1.0) (org.apache.geronimo.specs:geronimo-stax-api_1.0_spec:1.0.1 - http://geronimo.apache.org/specs/geronimo-stax-api_1.0_spec)
+        * Apache Hadoop Annotations (org.apache.hadoop:hadoop-annotations:2.2.0 - no url defined)
+        * Apache Hadoop Auth (org.apache.hadoop:hadoop-auth:2.2.0 - no url defined)
+        * Apache Hadoop Common (org.apache.hadoop:hadoop-common:2.2.0 - no url defined)
+        * Apache Hadoop HDFS (org.apache.hadoop:hadoop-hdfs:2.2.0 - no url defined)
+        * Apache HttpClient (org.apache.httpcomponents:httpclient:4.5.1 - http://hc.apache.org/httpcomponents-client)
+        * Apache HttpClient Cache (org.apache.httpcomponents:httpclient-cache:4.2.6 - http://hc.apache.org/httpcomponents-client)
+        * Apache HttpCore (org.apache.httpcomponents:httpcore:4.4.4 - http://hc.apache.org/httpcomponents-core-ga)
+        * Apache HttpClient Mime (org.apache.httpcomponents:httpmime:4.3.1 - http://hc.apache.org/httpcomponents-client)
+        * Apache JAMES Mime4j (Core) (org.apache.james:apache-mime4j-core:0.7.2 - http://james.apache.org/mime4j/apache-mime4j-core)
+        * Apache JAMES Mime4j (DOM) (org.apache.james:apache-mime4j-dom:0.7.2 - http://james.apache.org/mime4j/apache-mime4j-dom)
+        * Apache Jena - Libraries POM (org.apache.jena:apache-jena-libs:2.13.0 - http://jena.apache.org/apache-jena-libs/)
+        * Apache Jena - ARQ (SPARQL 1.1 Query Engine) (org.apache.jena:jena-arq:2.13.0 - http://jena.apache.org/jena-arq/)
+        * Apache Jena - Core (org.apache.jena:jena-core:2.13.0 - http://jena.apache.org/jena-core/)
+        * Apache Jena - IRI (org.apache.jena:jena-iri:1.1.2 - http://jena.apache.org/jena-iri/)
+        * Apache Jena - TDB (Native Triple Store) (org.apache.jena:jena-tdb:1.1.2 - http://jena.apache.org/jena-tdb/)
+        * Lucene Common Analyzers (org.apache.lucene:lucene-analyzers-common:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-analyzers-common)
+        * Lucene Common Analyzers (org.apache.lucene:lucene-analyzers-common:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-common)
+        * Lucene ICU Analysis Components (org.apache.lucene:lucene-analyzers-icu:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-icu)
+        * Lucene Kuromoji Japanese Morphological Analyzer (org.apache.lucene:lucene-analyzers-kuromoji:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-kuromoji)
+        * Lucene Morfologik Polish Lemmatizer (org.apache.lucene:lucene-analyzers-morfologik:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-morfologik)
+        * Lucene Phonetic Filters (org.apache.lucene:lucene-analyzers-phonetic:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-phonetic)
+        * Lucene Smart Chinese Analyzer (org.apache.lucene:lucene-analyzers-smartcn:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-smartcn)
+        * Lucene Stempel Analyzer (org.apache.lucene:lucene-analyzers-stempel:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-stempel)
+        * Lucene codecs (org.apache.lucene:lucene-codecs:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-codecs)
+        * Lucene Core (org.apache.lucene:lucene-core:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-core)
+        * Lucene Core (org.apache.lucene:lucene-core:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-core)
+        * Lucene Expressions (org.apache.lucene:lucene-expressions:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-expressions)
+        * Lucene Grouping (org.apache.lucene:lucene-grouping:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-grouping)
+        * Lucene Grouping (org.apache.lucene:lucene-grouping:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-grouping)
+        * Lucene Highlighter (org.apache.lucene:lucene-highlighter:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-highlighter)
+        * Lucene Highlighter (org.apache.lucene:lucene-highlighter:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-highlighter)
+        * Lucene Join (org.apache.lucene:lucene-join:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-join)
+        * Lucene Join (org.apache.lucene:lucene-join:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-join)
+        * Lucene Memory (org.apache.lucene:lucene-memory:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-memory)
+        * Lucene Memory (org.apache.lucene:lucene-memory:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-memory)
+        * Lucene Miscellaneous (org.apache.lucene:lucene-misc:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-misc)
+        * Lucene Miscellaneous (org.apache.lucene:lucene-misc:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-misc)
+        * Lucene Queries (org.apache.lucene:lucene-queries:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-queries)
+        * Lucene Queries (org.apache.lucene:lucene-queries:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-queries)
+        * Lucene QueryParsers (org.apache.lucene:lucene-queryparser:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-queryparser)
+        * Lucene QueryParsers (org.apache.lucene:lucene-queryparser:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-queryparser)
+        * Lucene Sandbox (org.apache.lucene:lucene-sandbox:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-sandbox)
+        * Lucene Spatial (org.apache.lucene:lucene-spatial:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-spatial)
+        * 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 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 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 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)
+        * Apache Solr Core (org.apache.solr:solr-core:4.10.4 - http://lucene.apache.org/solr-parent/solr-core)
+        * Apache Solr Solrj (org.apache.solr:solr-solrj:4.10.4 - http://lucene.apache.org/solr-parent/solr-solrj)
+        * Apache Thrift (org.apache.thrift:libthrift:0.9.2 - http://thrift.apache.org)
+        * Apache Tika core (org.apache.tika:tika-core:1.5 - http://tika.apache.org/)
+        * Apache Tika parsers (org.apache.tika:tika-parsers:1.5 - http://tika.apache.org/)
+        * Apache Tika XMP (org.apache.tika:tika-xmp:1.5 - http://tika.apache.org/)
+        * 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)
+        * 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/)
+        * Jackson (org.codehaus.jackson:jackson-core-asl:1.9.13 - http://jackson.codehaus.org)
+        * Data Mapper for Jackson (org.codehaus.jackson:jackson-mapper-asl:1.9.13 - http://jackson.codehaus.org)
+        * 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)
+        * 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)
+        * Javassist (org.javassist:javassist:3.18.1-GA - http://www.javassist.org/)
+        * 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)
+        * Servlet Specification API (org.mortbay.jetty:servlet-api:2.5-20081211 - http://jetty.mortbay.org/servlet-api)
+        * Noggit (org.noggit:noggit:0.5 - http://noggit.org)
+        * 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)
+        * 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)
+        * Spring Beans (org.springframework:spring-beans:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Beans (org.springframework:spring-beans:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Context (org.springframework:spring-context:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Context (org.springframework:spring-context:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Context Support (org.springframework:spring-context-support:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Core (org.springframework:spring-core:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Core (org.springframework:spring-core:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Expression Language (SpEL) (org.springframework:spring-expression:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Expression Language (SpEL) (org.springframework:spring-expression:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring JDBC (org.springframework:spring-jdbc:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring JDBC (org.springframework:spring-jdbc:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Object/Relational Mapping (org.springframework:spring-orm:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Object/Relational Mapping (org.springframework:spring-orm:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring TestContext Framework (org.springframework:spring-test:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Transaction (org.springframework:spring-tx:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Transaction (org.springframework:spring-tx:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Web (org.springframework:spring-web:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Web (org.springframework:spring-web:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Web MVC (org.springframework:spring-webmvc:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Web MVC (org.springframework:spring-webmvc:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
+        * spring-security-config (org.springframework.security:spring-security-config:3.2.9.RELEASE - http://spring.io/spring-security)
+        * spring-security-core (org.springframework.security:spring-security-core:3.2.9.RELEASE - http://spring.io/spring-security)
+        * spring-security-web (org.springframework.security:spring-security-web:3.2.9.RELEASE - http://spring.io/spring-security)
+        * SWORD Java API, GUI and CLI (org.swordapp:sword-common:1.1 - http://nexus.sonatype.org/oss-repository-hosting.html/sword-common)
+        * SWORD v2 :: Common Server Library (org.swordapp:sword2-server:1.0 - http://www.swordapp.org/)
+        * xml-matchers (org.xmlmatchers:xml-matchers:0.10 - http://code.google.com/p/xml-matchers/)
+        * oro (oro:oro:2.0.8 - no url defined)
+        * JUnitParams (pl.pragmatists:JUnitParams:1.0.2 - http://junitparams.googlecode.com)
+        * Rome A9 OpenSearch (rome:opensearch:0.1 - http://wiki.java.net/bin/view/Javawsxml/OpenSearch)
+        * ROME, RSS and atOM utilitiEs for Java (rome:rome:1.0 - https://rome.dev.java.net/)
+        * 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/)
+        * 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/)
+        * XML Commons Resolver Component (xml-resolver:xml-resolver:1.2 - http://xml.apache.org/commons/components/resolver/)

-Common Public License v1.0 (http://www.opensource.org/licenses/cpl1.0)
-  * JUnit (junit:*) - http://junit.org/license   
-  * WSDL4J (wsdl4j:*) - http://sourceforge.net/projects/wsdl4j/
+    BSD License:

-Lesser GPL (http://www.opensource.org/licenses/LGPL-2.1)
-  * Text-mining (org.dspace.dependencies:dspace-tm-extractors) - http://code.google.com/p/text-mining/  
-  * MaxMind GeoIP (org.dspace.dependencies:dspace-geoip) - http://geoip.cvs.sourceforge.net/viewvc/geoip/java/LICENSE
+        * AntLR Parser Generator (antlr:antlr:2.7.7 - http://www.antlr.org/)
+        * ASM Core (asm:asm:3.3.1 - http://asm.objectweb.org/asm/)
+        * 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/)
+        * 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/)
+        * yui compressor (com.yahoo.platform.yui:yuicompressor:2.3.6 - http://developer.yahoo.com/yui/compressor/)
+        * dnsjava (dnsjava:dnsjava:2.1.7 - http://www.dnsjava.org)
+        * dom4j (dom4j:dom4j:1.6.1 - http://dom4j.org)
+        * 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)
+        * 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)
+        * 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)
+        * 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)
+        * 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/)
+        * XMLUnit for Java (xmlunit:xmlunit:1.1 - http://xmlunit.sourceforge.net/)
+        * XMLUnit for Java (xmlunit:xmlunit:1.3 - http://xmlunit.sourceforge.net/)

-MIT / X11 License (or adaptations) (http://www.opensource.org/licenses/MIT)
-  * Bouncy Castle (org.bouncycastle:*) - http://www.bouncycastle.org/licence.html
-  * jmockit (org.dspace.dependencies.jmockit:dspace-jmockit) - http://code.google.com/p/jmockit/
-  * SLF4J (org.slf4j:*) - http://www.slf4j.org/license.html
+    Common Development and Distribution License (CDDL):

-Mozilla Public License (http://www.opensource.org/licenses/MPL-2.0)
-  * H2 database (com.h2database:*) - http://www.h2database.com/html/license.html
+        * JAXB Reference Implementation (com.sun.xml.bind:jaxb-impl:2.2.5 - http://jaxb.java.net/)
+        * 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)
+        * 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)
+        * jsp-api (javax.servlet:jsp-api:2.0 - no url defined)
+        * 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)
+        * 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)
+        * HK2 API module (org.glassfish.hk2:hk2-api:2.4.0-b31 - https://hk2.java.net/hk2-api)
+        * HK2 configuration module (org.glassfish.hk2:hk2-config:2.4.0-b31 - https://hk2.java.net/hk2-configuration/hk2-configuration-persistence/hk2-xml-dom/hk2-config)
+        * HK2 core module (org.glassfish.hk2:hk2-core:2.4.0-b31 - https://hk2.java.net/hk2-core)
+        * ServiceLocator Default Implementation (org.glassfish.hk2:hk2-locator:2.4.0-b31 - https://hk2.java.net/hk2-locator)
+        * Run Level Service (org.glassfish.hk2:hk2-runlevel:2.4.0-b31 - https://hk2.java.net/hk2-runlevel)
+        * HK2 Implementation Utilities (org.glassfish.hk2:hk2-utils:2.4.0-b31 - https://hk2.java.net/hk2-utils)
+        * OSGi resource locator bundle - used by various API providers that rely on META-INF/services mechanism to locate providers. (org.glassfish.hk2:osgi-resource-locator:1.0.1 - http://glassfish.org/osgi-resource-locator/)
+        * HK2 Spring Bridge (org.glassfish.hk2:spring-bridge:2.4.0-b31 - https://hk2.java.net/spring-bridge)
+        * aopalliance version 1.0 repackaged as a module (org.glassfish.hk2.external:aopalliance-repackaged:2.4.0-b31 - https://hk2.java.net/external/aopalliance-repackaged)
+        * 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)
+        * 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/)
+        * jersey-core-client (org.glassfish.jersey.core:jersey-client:2.22.1 - https://jersey.java.net/jersey-client/)
+        * jersey-core-common (org.glassfish.jersey.core:jersey-common:2.22.1 - https://jersey.java.net/jersey-common/)
+        * jersey-core-server (org.glassfish.jersey.core:jersey-server:2.22.1 - https://jersey.java.net/jersey-server/)
+        * jersey-ext-entity-filtering (org.glassfish.jersey.ext:jersey-entity-filtering:2.22.1 - https://jersey.java.net/project/jersey-entity-filtering/)
+        * jersey-spring3 (org.glassfish.jersey.ext:jersey-spring3:2.22.1 - https://jersey.java.net/project/jersey-spring3/)
+        * jersey-media-jaxb (org.glassfish.jersey.media:jersey-media-jaxb:2.22.1 - https://jersey.java.net/project/jersey-media-jaxb/)
+        * 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/)

-Other Open Source Licenses:
-  * ICU4J (com.ibm.icu:icu4j) - ICU License : http://source.icu-project.org/repos/icu/icu/trunk/license.html
-  * JDOM  (jdom:*) - JDOM License : https://github.com/hunterhacker/jdom/blob/master/LICENSE.txt
-  * PostgreSQL (postgresql:*) - PostgreSQL License (BSD-based): http://www.postgresql.org/about/licence/
+    Eclipse Public License:

----
-NOTE #1: Some individual web application files in DSpace (e.g. Javascript 
-libraries, CSS Frameworks) may have their own open source license. In that 
-scenario, we place a copy of the full text of the license alongside the 
-licensed files. You can locate these additional licenses in our codebase 
-by searching for files with a ".LICENSE" file extension.
+        * JUnit (junit:junit:4.11 - http://junit.org)
+        * AspectJ runtime (org.aspectj:aspectjrt:1.6.11 - http://www.aspectj.org)
+        * JPA 2.0 API (org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final - http://hibernate.org)
+        * 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)

-For example, on Linux you can use the 'find' command from the source directory:
+    GNU General Public License, Version 2 with the Classpath Exception:

-find . -type f -name "*.LICENSE"
----
+        * 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)

----
-NOTE #2: Although we try to keep this libraries list current, the latest 
-information about DSpace third party libraries can be found by running the 
-following Maven command(s):
+    GNU Lesser General Public License (LGPL):

-mvn project-info-reports:dependencies
+        * FindBugs-Annotations (com.google.code.findbugs:annotations:3.0.1u2 - http://findbugs.sourceforge.net/)
+        * MaxMind GeoIP Legacy API (com.maxmind.geoip:geoip-api:1.3.0 - https://github.com/maxmind/geoip-api-java)
+        * JHighlight (com.uwyn:jhighlight:1.0 - https://jhighlight.dev.java.net/)
+        * DSpace TM-Extractors Dependency (org.dspace.dependencies:dspace-tm-extractors:1.0.1 - http://projects.dspace.org/dspace-pom/dspace-tm-extractors)
+        * A Hibernate O/RM Module (org.hibernate:hibernate-core:4.2.21.Final - http://hibernate.org)
+        * A Hibernate O/RM Module (org.hibernate:hibernate-ehcache:4.2.21.Final - http://hibernate.org)
+        * Hibernate Commons Annotations (org.hibernate.common:hibernate-commons-annotations:4.0.2.Final - http://hibernate.org)
+        * im4java (org.im4java:im4java:1.4.0 - http://sourceforge.net/projects/im4java/)
+        * 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)
+        * xom (xom:xom:1.1 - http://www.xom.nu)
+        * XOM (xom:xom:1.2.5 - http://xom.nu)

-This generates a "[project]/target/site/dependencies.html" report under every 
-DSpace project directory. This report lists all dependencies and their license
-(if it can be determined by Maven).
+    ICU License:

-Additionally, you may wish to run:
+        * ICU4J (com.ibm.icu:icu4j:56.1 - http://icu-project.org/)

-mvn project-info-reports:dependancy-convergence
+    JDOM License (Apache-style license):

-This generates a summary report at 
-"[dspace]/target/site/dependancy-convergence.html" which lists all dependencies
-of all DSpace projects (though it does not list license information)
+        * jdom (jdom:jdom:1.0 - no url defined)

-For more information see the maven-project-info-reports-plugin:
-http://maven.apache.org/plugins/maven-project-info-reports-plugin/
----
+    MIT License:
+
+        * 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)
+        * 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)
+
+    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)
+        * Javassist (org.javassist:javassist:3.18.1-GA - http://www.javassist.org/)
+        * Rhino (rhino:js:1.6R7 - http://www.mozilla.org/rhino/)
+
+    Public Domain:
+
+        * AOP alliance (aopalliance:aopalliance:1.0 - http://aopalliance.sourceforge.net)
+        * Dough Lea's util.concurrent package (concurrent:concurrent:1.3.4 - no url defined)
+        * Reflections (org.reflections:reflections:0.9.9-RC1 - http://code.google.com/p/reflections/reflections/)
+        * XZ for Java (org.tukaani:xz:1.4 - http://tukaani.org/xz/java.html)
+
+    Similar to Apache License but with the acknowledgment clause removed:
+
+        * JDOM (org.jdom:jdom:1.1.3 - http://www.jdom.org)
+
+    The PostgreSQL License:
+
+        * PostgreSQL JDBC Driver - JDBC 4.2 (org.postgresql:postgresql:9.4.1211 - https://github.com/pgjdbc/pgjdbc)
+
+    license.txt:
+
+        * JPA 2.0 API (org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final - http://hibernate.org)
--- a/54
+++ b/54
@@ -1,54 +0,0 @@
-Installation instructions are included in this release package under
-
- - dspace/docs/DSpace-Manual.pdf
-
-DSpace version information can be viewed online at
- - https://wiki.duraspace.org/display/DSDOC/
-
-Documentation for the most recent stable release(s) may be downloaded
-or viewed online at
- - http://www.dspace.org/latest-release/
- - https://wiki.duraspace.org/display/DSDOC/
-
-In addition, a listing of all known contributors to DSpace software can be
-found online at:
-https://wiki.duraspace.org/display/DSPACE/DSpaceContributors
-
-Installation instructions for other versions may be different, so you
-are encouraged to obtain the appropriate version of the Documentation
-(from the links above or from the source repository).
-
-To obtain files from the repository and build, please see:
-
- - https://github.com/DSpace/DSpace/
-
-or just:
-
- - git clone git://github.com/DSpace/DSpace.git
-
-Please refer any further problems to the dspace-tech@lists.sourceforge.net
-mailing list.
-
- - http://sourceforge.net/mail/?group_id=19984
-
-
-Detailed Issue Tracking for DSpace is done on our JIRA Issue Tracker
-
- - https://jira.duraspace.org/browse/DS
-
-
-To contribute to DSpace, please see:
-
- - https://wiki.duraspace.org/display/DSPACE/How+to+Contribute+to+DSpace
-
-
-For more details about DSpace, including a list of service providers,
-places to seek help, news articles and lists of other users, please see:
-
- - http://www.dspace.org/
-
-
-DSpace source code licensing information available online at:
- - http://www.dspace.org/license/
-
-Copyright (c) 2002-2012, DuraSpace.  All rights reserved.
--- a/README.md
+++ b/README.md
@@ -0,0 +1,85 @@
+
+# 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://travis-ci.org/DSpace/DSpace.png?branch=master)](https://travis-ci.org/DSpace/DSpace)
+
+[DSpace Documentation](https://wiki.duraspace.org/display/DSDOC/) | 
+[DSpace Releases](https://github.com/DSpace/DSpace/releases) |
+[DSpace Wiki](https://wiki.duraspace.org/display/DSPACE/Home) | 
+[Support](https://wiki.duraspace.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.
+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).
+
+Past releases are all available via GitHub at https://github.com/DSpace/DSpace/releases
+
+## Documentation / Installation
+
+Documentation for each release may be viewed online or downloaded via our [Documentation Wiki](https://wiki.duraspace.org/display/DSDOC/). 
+
+The latest DSpace Installation instructions are available at:
+https://wiki.duraspace.org/display/DSDOC6x/Installing+DSpace
+
+Please be aware that, as a Java web application, DSpace requires a database (PostgreSQL or Oracle) 
+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.
+
+## 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).
+
+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.
+
+In addition, a listing of all known contributors to DSpace software can be
+found online at: https://wiki.duraspace.org/display/DSPACE/DSpaceContributors
+
+## Getting Help
+
+DSpace provides public mailing lists where you can post questions or raise topics for discussion.
+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-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
+
+DSpace also has an active service provider network. If you'd rather hire a service provider to 
+install, upgrade, customize or host DSpace, then we recommend getting in touch with one of our 
+[Registered Service Providers](http://www.dspace.org/service-providers).
+
+## Issue Tracker
+
+The DSpace Issue Tracker can be found at: https://jira.duraspace.org/projects/DS/summary
+
+## License
+
+DSpace source code is freely available under a standard [BSD 3-Clause license](https://opensource.org/licenses/BSD-3-Clause).
+The full license is available at http://www.dspace.org/license/
--- a/build.properties
+++ b/build.properties
@@ -1,137 +0,0 @@
-# DSpace build.properties
-# This file should be customised to suit your build environment.
-# Note that not all configuration is handled here, only the most common properties that tend to differ between build environments. 
-# For adjusting global settings or more complex settings, edit the relevant config file.
-
-##########################
-# SERVER CONFIGURATION #
-##########################
-
-# DSpace installation directory. Data will be stored within this directory
-dspace.dir=/dspace
-
-# DSpace host name - should match base URL.  Do not include port number
-dspace.hostname = localhost
-
-# DSpace base host URL.  Include port number etc.
-dspace.baseUrl = http://localhost:8080
-
-# Name of the site
-dspace.name = DSpace at My University
-
-# Solr server
-solr.server=http://localhost:8080/solr
-
-# Default language for metadata values
-default.language = en_US
-
-##########################
-# DATABASE CONFIGURATION #
-##########################
-
-# Database name ("oracle", or "postgres")
-db.name=postgres
-
-# Uncomment the appropriate block below for your database.
-# postgres
-db.driver=org.postgresql.Driver
-db.url=jdbc:postgresql://localhost:5432/dspace
-db.username=dspace
-db.password=dspace
-
-# oracle
-#db.driver= oracle.jdbc.OracleDriver
-#db.url=jdbc:oracle:thin:@//localhost:1521/xe
-#db.username=dspace
-#db.password=dspace
-
-# Schema name - if your database contains multiple schemas, you can avoid problems with
-# retrieving the definitions of duplicate object names by specifying
-# the schema name here that is used for DSpace by uncommenting the following entry
-db.schema = 
-
-# Maximum number of DB connections in pool
-db.maxconnections = 30
-
-# Maximum time to wait before giving up if all connections in pool are busy (milliseconds)
-db.maxwait = 5000
-
-# Maximum number of idle connections in pool (-1 = unlimited)
-db.maxidle = -1
-
-# Determine if prepared statement should be cached. (default is true)
-db.statementpool = true
-
-# Specify a name for the connection pool (useful if you have multiple applications sharing Tomcat's dbcp)
-# If not specified, defaults to 'dspacepool'
-db.poolname = dspacepool
-
-#######################
-# EMAIL CONFIGURATION #
-#######################
-
-# SMTP mail server
-mail.server = smtp.example.com
-
-# SMTP mail server authentication username and password (if required)
-# mail.server.username = myusername
-# mail.server.password = mypassword
-mail.server.username=
-mail.server.password=
-
-# SMTP mail server alternate port (defaults to 25)
-mail.server.port = 25
-
-# From address for mail
-mail.from.address = dspace-noreply@myu.edu
-
-# Currently limited to one recipient!
-mail.feedback.recipient = dspace-help@myu.edu
-
-# General site administration (Webmaster) e-mail
-mail.admin = dspace-help@myu.edu
-
-# Recipient for server errors and alerts
-#mail.alert.recipient = email-address-here
-mail.alert.recipient=
-
-# Recipient for new user registration emails
-#mail.registration.notify = email-address-here
-mail.registration.notify=
-
-
-########################
-# HANDLE CONFIGURATION #
-########################
-
-# Canonical Handle URL prefix
-#
-# By default, DSpace is configured to use http://hdl.handle.net/
-# as the canonical URL prefix when generating dc.identifier.uri
-# during submission, and in the 'identifier' displayed in JSPUI
-# item record pages.
-#
-# If you do not subscribe to CNRI's handle service, you can change this
-# to match the persistent URL service you use, or you can force DSpace
-# to use your site's URL, eg.
-#handle.canonical.prefix = ${dspace.url}/handle/
-#
-# Note that this will not alter dc.identifer.uri metadata for existing
-# items (only for subsequent submissions), but it will alter the URL 
-# in JSPUI's 'identifier' message on item record pages for existing items.
-#
-# If omitted, the canonical URL prefix will be http://hdl.handle.net/
-handle.canonical.prefix = http://hdl.handle.net/
-
-# CNRI Handle prefix
-handle.prefix = 123456789
-
-#######################
-# PROXY CONFIGURATION #
-#######################
-# uncomment and specify both properties if proxy server required
-# proxy server for external http requests - use regular hostname without port number
-http.proxy.host =
-
-# port number of proxy server
-http.proxy.port =
--- a/checkstyle-suppressions.xml
+++ b/checkstyle-suppressions.xml
@@ -0,0 +1,10 @@
+<?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>
--- a/checkstyle.xml
+++ b/checkstyle.xml
@@ -0,0 +1,144 @@
+<?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>
--- a/dspace-api/pom.xml
+++ b/dspace-api/pom.xml
@@ -1,4 +1,5 @@
-<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>
@@ -12,14 +13,37 @@
    <parent>
        <groupId>org.dspace</groupId>
        <artifactId>dspace-parent</artifactId>
-        <version>3.0-rc3</version>
+        <version>7.0-SNAPSHOT</version>
        <relativePath>..</relativePath>
    </parent>

+    <properties>
+        <!-- This is the path to the root [dspace-src] directory. -->
+        <root.basedir>${basedir}/..</root.basedir>
+    </properties>
+
    <!--
       Runtime and Compile Time dependencies for DSpace.
    -->
    <build>
+        <resources>
+            <resource>
+                <directory>src/main/resources</directory>
+                <includes>
+                    <include>maven.properties</include>
+                    <include>scm.properties</include>
+                </includes>
+                <filtering>true</filtering>
+            </resource>
+            <resource>
+                <directory>src/main/resources</directory>
+                <excludes>
+                    <exclude>maven.properties</exclude>
+                    <exclude>scm.properties</exclude>
+                </excludes>
+                <filtering>false</filtering>
+            </resource>
+        </resources>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
@@ -48,16 +72,93 @@
                    </execution>
                </executions>
            </plugin>
+            <!-- Verify OS license headers for all source code files -->
            <plugin>
-                <artifactId>maven-dependency-plugin</artifactId>
-                <version>2.3</version>
+                <groupId>com.mycila</groupId>
+                <artifactId>license-maven-plugin</artifactId>
+                <configuration>
+                    <excludes>
+                        <exclude>**/src/test/resources/**</exclude>
+                        <exclude>**/src/test/data/**</exclude>
+                        <exclude>**/.gitignore</exclude>
+                        <exclude>src/test/data/dspaceFolder/config/spiders/**</exclude>
+                        <exclude>src/main/java/org/apache/solr/handler/extraction/ExtractingParams.java</exclude>
+                    </excludes>
+                </configuration>
+            </plugin>
+
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>build-helper-maven-plugin</artifactId>
+                <version>1.9.1</version>
                <executions>
                    <execution>
-                        <id>setupTestEnvironment</id>
-                        <phase>generate-test-resources</phase>
+                        <phase>validate</phase>
                        <goals>
-                            <goal>unpack</goal>
+                            <goal>maven-version</goal>
                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>buildnumber-maven-plugin</artifactId>
+                <version>1.4</version>
+                <executions>
+                    <execution>
+                        <phase>validate</phase>
+                        <goals>
+                            <goal>create</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+
+        </plugins>
+    </build>
+
+
+    <profiles>
+        <profile>
+            <id>findbugs</id>
+            <activation>
+                <activeByDefault>false</activeByDefault>
+                <!-- property>
+                    <name>maven.test.skip</name>
+                    <value>false</value>
+                </property -->
+            </activation>
+            <build>
+                <plugins>
+                    <plugin>
+                        <groupId>org.codehaus.mojo</groupId>
+                        <artifactId>findbugs-maven-plugin</artifactId>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+
+        <!-- If Unit Testing is enabled, then setup the Unit Test Environment.
+             See also the 'skiptests' profile in Parent POM. -->
+        <profile>
+            <id>test-environment</id>
+            <activation>
+                <activeByDefault>false</activeByDefault>
+                <property>
+                    <name>maven.test.skip</name>
+                    <value>false</value>
+                </property>
+            </activation>
+            <build>
+                <plugins>
+                    <!-- Unit/Integration Testing setup: This plugin unzips the
+                         'testEnvironment.zip' file (created by dspace-parent POM), into
+                         the 'target/testing/' folder, to essentially create a test
+                         install of DSpace, against which Tests can be run. -->
+                    <plugin>
+                        <artifactId>maven-dependency-plugin</artifactId>
+                        <version>2.8</version>
                        <configuration>
                            <outputDirectory>${project.build.directory}/testing</outputDirectory>
                            <artifactItems>
@@ -70,104 +171,117 @@
                                </artifactItem>
                            </artifactItems>
                        </configuration>
+                        <executions>
+                            <execution>
+                                <id>setupTestEnvironment</id>
+                                <phase>generate-test-resources</phase>
+                                <goals>
+                                    <goal>unpack</goal>
+                                </goals>
+                            </execution>
+                            <execution>
+                                <id>setupIntegrationTestEnvironment</id>
+                                <phase>pre-integration-test</phase>
+                                <goals>
+                                    <goal>unpack</goal>
+                                </goals>
                            </execution>
                        </executions>
                    </plugin>
+
                    <!-- This plugin allows us to run a Groovy script in our Maven POM
                         (see: http://gmaven.codehaus.org/Executing+Groovy+Code )
                         We are generating a OS-agnostic version (agnostic.build.dir) of
                         the ${project.build.directory} property (full path of target dir).
-                    This is necessary so that the FileWeaver & Surefire plugins can
-                    use it to initialize the Unit Test Framework's dspace.cfg file.
+                         This is needed by the FileWeaver & Surefire plugins (see below)
+                         to initialize the Unit Test environment's dspace.cfg file.
                         Otherwise, the Unit Test Framework will not work on Windows OS.
                         This Groovy code was mostly borrowed from:
                         http://stackoverflow.com/questions/3872355/how-to-convert-file-separator-in-maven
                    -->
                    <plugin>
                        <groupId>org.codehaus.gmaven</groupId>
-                <artifactId>gmaven-plugin</artifactId>
-                <version>1.4</version>
+                        <artifactId>groovy-maven-plugin</artifactId>
+                        <version>2.0</version>
                        <executions>
                            <execution>
                                <id>setproperty</id>
-                        <phase>generate-test-resources</phase>
+                                <phase>generate-test-resources
+                                </phase> <!-- XXX I think this should be 'initialize' - MHW -->
                                <goals>
                                    <goal>execute</goal>
                                </goals>
                                <configuration>
                                    <source>
-                            pom.properties['agnostic.build.dir']=project.build.directory.replace('\\','/');
+                                        project.properties['agnostic.build.dir'] = project.build.directory.replace(File.separator, '/');
                                        println("Initializing Maven property 'agnostic.build.dir' to: " + project.properties['agnostic.build.dir']);
                                    </source>
                                </configuration>
                            </execution>
                        </executions>
                    </plugin>
-            <!-- FileWeaver plugin is in charge of initializing & "weaving" together
-                 the dspace.cfg file to be used by the Unit Testing framework -->
-            <plugin>
-                <groupId>edu.iu.ul.maven.plugins</groupId>
-                <artifactId>fileweaver</artifactId>
-                <version>1.0</version>
-                <configuration>
-                    <outputs>
-                        <output>
-                            <outputPath>${agnostic.build.dir}/testing</outputPath>
-                            <name>dspace.cfg.woven</name>
-                            <parts>
-                                <part>
-                                    <path>${agnostic.build.dir}/testing/dspace/config/dspace.cfg</path>
-                                </part>
-                                <part>
-                                    <path>${agnostic.build.dir}/testing/dspace.cfg.more</path>
-                                </part>
-                            </parts>
-                            <properties>
-                                <dspace.dir>${agnostic.build.dir}/testing/dspace</dspace.dir>
-                            </properties>
-                        </output>
-                    </outputs>
-                </configuration>
-                <executions>
-                    <execution>
-                        <id>edit-dspace-cfg</id>
-                        <phase>process-test-resources</phase>
-                        <goals>
-                            <goal>weave</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-
-            <!--
-                The ant plugin below ensures that the dspace "woven" configuration file ends up in the dspace directory
-                The dspace service manager needs this "woven" configuration file when it starts
-            -->
-            <plugin>
-              <artifactId>maven-antrun-plugin</artifactId>
-              <executions>
-                <execution>
-                  <phase>process-test-resources</phase>
-                  <configuration>
-                    <tasks>
-                        <copy file="${agnostic.build.dir}/testing/dspace.cfg.woven" tofile="${agnostic.build.dir}/testing/dspace/config/dspace.cfg" />
-                    </tasks>
-                  </configuration>
-                  <goals>
-                    <goal>run</goal>
-                  </goals>
-                </execution>
-              </executions>
-            </plugin>

+                    <!-- Run Unit Testing! This plugin just kicks off the tests (when enabled). -->
                    <plugin>
                        <artifactId>maven-surefire-plugin</artifactId>
                        <configuration>
                            <systemPropertyVariables>
-                        <dspace.dir>${agnostic.build.dir}/testing/dspace</dspace.dir>
-                        <dspace.dir.static>${basedir}/src/test/data/dspaceFolder</dspace.dir.static>
-                        <dspace.configuration>${agnostic.build.dir}/testing/dspace/config/dspace.cfg</dspace.configuration>
-                        <db.schema.path>${agnostic.build.dir}/testing/dspace/etc/h2/database_schema.sql</db.schema.path>
+                                <!-- Specify the dspace.dir to use for test environment -->
+                                <!-- This system property is loaded by AbstractDSpaceTest to initialize the test environment -->
+                                <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
+                                <!-- Turn off any DSpace logging -->
+                                <dspace.log.init.disable>true</dspace.log.init.disable>
+                            </systemPropertyVariables>
+                        </configuration>
+                    </plugin>
+
+
+                    <plugin>
+                        <groupId>org.codehaus.mojo</groupId>
+                        <artifactId>xml-maven-plugin</artifactId>
+                        <version>1.0.1</version>
+                        <executions>
+                            <execution>
+                                <id>validate-ALL-xml-and-xsl</id>
+                                <phase>process-test-resources</phase>
+                                <goals>
+                                    <goal>validate</goal>
+                                </goals>
+                            </execution>
+                        </executions>
+                        <configuration>
+                            <validationSets>
+                                <!-- validate ALL XML and XSL config files in the testing folder -->
+                                <validationSet>
+                                    <dir>${agnostic.build.dir}/testing</dir>
+                                    <includes>
+                                        <include>**/*.xml</include>
+                                        <include>**/*.xsl</include>
+                                        <include>**/*.xconf</include>
+                                    </includes>
+                                </validationSet>
+                                <!-- validate ALL XML and XSL files throughout the project -->
+                                <validationSet>
+                                    <dir>${root.basedir}</dir>
+                                    <includes>
+                                        <include>**/*.xml</include>
+                                        <include>**/*.xsl</include>
+                                        <include>**/*.xmap</include>
+                                    </includes>
+                                </validationSet>
+                            </validationSets>
+                        </configuration>
+                    </plugin>
+
+
+                    <!-- Run Integration Testing! This plugin just kicks off the tests (when enabled). -->
+                    <plugin>
+                        <artifactId>maven-failsafe-plugin</artifactId>
+                        <configuration>
+                            <systemPropertyVariables>
+                                <!-- Specify the dspace.dir to use for test environment -->
+                                <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
+                                <!-- Turn off any DSpace logging -->
                                <dspace.log.init.disable>true</dspace.log.init.disable>
                            </systemPropertyVariables>
                        </configuration>
@@ -175,7 +289,39 @@
                </plugins>
            </build>

+        </profile>
+    </profiles>
+
    <dependencies>
+        <dependency>
+            <groupId>org.hibernate</groupId>
+            <artifactId>hibernate-core</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.jboss.logging</groupId>
+                    <artifactId>jboss-logging</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <dependency>
+            <groupId>org.hibernate</groupId>
+            <artifactId>hibernate-ehcache</artifactId>
+        </dependency>
+        <dependency>
+           <groupId>org.hibernate</groupId>
+           <artifactId>hibernate-validator-cdi</artifactId>
+           <version>${hibernate-validator.version}</version>
+        </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>
@@ -193,12 +339,19 @@
            <artifactId>dspace-tm-extractors</artifactId>
        </dependency>
        <dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-core</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-analyzers</artifactId>
+            <groupId>org.apache.jena</groupId>
+            <artifactId>apache-jena-libs</artifactId>
+            <type>pom</type>
+            <exclusions>
+                <exclusion>
+                    <groupId>com.fasterxml.jackson.core</groupId>
+                    <artifactId>jackson-core</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>com.fasterxml.jackson.core</groupId>
+                    <artifactId>jackson-databind</artifactId>
+                </exclusion>
+            </exclusions>
        </dependency>
        <dependency>
            <groupId>commons-cli</groupId>
@@ -213,19 +366,18 @@
            <artifactId>commons-collections</artifactId>
        </dependency>
        <dependency>
-            <groupId>commons-dbcp</groupId>
-            <artifactId>commons-dbcp</artifactId>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-collections4</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-dbcp2</artifactId>
        </dependency>
        <dependency>
            <groupId>commons-fileupload</groupId>
            <artifactId>commons-fileupload</artifactId>
        </dependency>

-        <dependency>
-            <groupId>commons-httpclient</groupId>
-            <artifactId>commons-httpclient</artifactId>
-        </dependency>
-
        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
@@ -235,8 +387,12 @@
            <artifactId>commons-lang</artifactId>
        </dependency>
        <dependency>
-            <groupId>commons-pool</groupId>
-            <artifactId>commons-pool</artifactId>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-pool2</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>commons-validator</groupId>
+            <artifactId>commons-validator</artifactId>
        </dependency>
        <dependency>
            <groupId>javax.mail</groupId>
@@ -258,7 +414,7 @@
            </exclusions>
        </dependency>
        <dependency>
-            <groupId>jdom</groupId>
+            <groupId>org.jdom</groupId>
            <artifactId>jdom</artifactId>
        </dependency>
        <dependency>
@@ -277,10 +433,6 @@
            <groupId>org.apache.pdfbox</groupId>
            <artifactId>fontbox</artifactId>
        </dependency>
-        <dependency>
-           <groupId>org.apache.pdfbox</groupId>
-           <artifactId>jempbox</artifactId>
-        </dependency>
        <dependency>
            <groupId>org.bouncycastle</groupId>
            <artifactId>bcprov-jdk15</artifactId>
@@ -298,11 +450,7 @@
            <artifactId>poi-scratchpad</artifactId>
        </dependency>
        <dependency>
-            <groupId>org.apache.poi</groupId>
-            <artifactId>poi-ooxml</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>net.java.dev.rome</groupId>
+            <groupId>rome</groupId>
            <artifactId>rome</artifactId>
        </dependency>
        <dependency>
@@ -316,10 +464,16 @@
        <dependency>
            <groupId>xerces</groupId>
            <artifactId>xercesImpl</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>xml-apis</groupId>
+                    <artifactId>xml-apis</artifactId>
+                </exclusion>
+            </exclusions>
        </dependency>
        <dependency>
            <groupId>xml-apis</groupId>
-            <artifactId>xmlParserAPIs</artifactId>
+            <artifactId>xml-apis</artifactId>
        </dependency>
        <dependency>
            <groupId>javax.activation</groupId>
@@ -337,14 +491,19 @@
            <groupId>org.dspace</groupId>
            <artifactId>dspace-services</artifactId>
        </dependency>
+        <dependency> <!-- Keep jmockit before junit -->
+            <groupId>org.jmockit</groupId>
+            <artifactId>jmockit</artifactId>
+            <scope>test</scope>
+        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
-            <groupId>org.dspace.dependencies.jmockit</groupId>
-            <artifactId>dspace-jmockit</artifactId>
+            <groupId>org.hamcrest</groupId>
+            <artifactId>hamcrest-core</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
@@ -353,34 +512,57 @@
            <scope>test</scope>
        </dependency>
        <dependency>
-            <groupId>org.databene</groupId>
-            <artifactId>contiperf</artifactId>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-core</artifactId>
            <scope>test</scope>
        </dependency>
+
        <dependency>
            <groupId>org.rometools</groupId>
            <artifactId>rome-modules</artifactId>
            <version>1.0</version>
        </dependency>
        <dependency>
-            <groupId>gr.ekt</groupId>
-            <artifactId>biblio-transformation-engine</artifactId>
-            <version>0.82</version>
+            <groupId>gr.ekt.bte</groupId>
+            <artifactId>bte-core</artifactId>
+            <version>0.9.3.5</version>
+            <exclusions>
+                <!-- A more recent version is retrieved from another dependency -->
+                <exclusion>
+                    <groupId>org.mockito</groupId>
+                    <artifactId>mockito-core</artifactId>
+                </exclusion>
+            </exclusions>
        </dependency>
        <dependency>
-            <groupId>net.sf.opencsv</groupId>
-            <artifactId>opencsv</artifactId>
-            <version>2.3</version>
+            <groupId>gr.ekt.bte</groupId>
+            <artifactId>bte-io</artifactId>
+            <version>0.9.3.5</version>
+            <exclusions>
+                <!-- A more recent version is retrieved from another dependency -->
+                <exclusion>
+                    <groupId>org.apache.commons</groupId>
+                    <artifactId>commons-lang3</artifactId>
+                </exclusion>
+                <!-- A more recent version is retrieved from another dependency -->
+                <exclusion>
+                    <groupId>org.mockito</groupId>
+                    <artifactId>mockito-core</artifactId>
+                </exclusion>
+            </exclusions>
        </dependency>
        <dependency>
-            <groupId>org.jbibtex</groupId>
-            <artifactId>jbibtex</artifactId>
-            <version>1.0.0</version>
+            <groupId>org.apache.httpcomponents</groupId>
+            <artifactId>httpcore</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.httpcomponents</groupId>
+            <artifactId>httpclient</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.solr</groupId>
            <artifactId>solr-solrj</artifactId>
-            <version>${lucene.version}</version>
+            <version>${solr.version}</version>
            <exclusions>
                <exclusion>
                    <groupId>org.slf4j</groupId>
@@ -392,51 +574,166 @@
                </exclusion>
            </exclusions>
        </dependency>
+
        <dependency>
            <groupId>commons-configuration</groupId>
            <artifactId>commons-configuration</artifactId>
-            <version>1.8</version>
        </dependency>
        <dependency>
-            <groupId>org.dspace.dependencies</groupId>
-            <artifactId>dspace-geoip</artifactId>
-            <version>1.2.3</version>
+            <groupId>com.maxmind.geoip2</groupId>
+            <artifactId>geoip2</artifactId>
+            <version>2.11.0</version>
        </dependency>
        <dependency>
            <groupId>org.apache.ant</groupId>
            <artifactId>ant</artifactId>
        </dependency>
        <dependency>
-            <groupId>org.dspace.dnsjava</groupId>
+            <groupId>dnsjava</groupId>
            <artifactId>dnsjava</artifactId>
-            <version>2.0.6</version>
+            <version>2.1.7</version>
        </dependency>

        <dependency>
-            <groupId>org.ostermiller</groupId>
-            <artifactId>utils</artifactId>
-            <version>1.07.00</version>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-core</artifactId>
+            <version>4.10.4</version>
        </dependency>

        <dependency>
-            <groupId>org.elasticsearch</groupId>
-            <artifactId>elasticsearch</artifactId>
-            <version>0.18.6</version>
+            <groupId>com.coverity.security</groupId>
+            <artifactId>coverity-escapers</artifactId>
+            <version>1.1.1</version>
        </dependency>

        <!--  Gson: Java to Json conversion -->
        <dependency>
            <groupId>com.google.code.gson</groupId>
            <artifactId>gson</artifactId>
-            <version>2.2.1</version>
            <scope>compile</scope>
        </dependency>

        <dependency>
-            <groupId>postgresql</groupId>
+            <groupId>com.google.guava</groupId>
+            <artifactId>guava</artifactId>
+            <version>19.0</version>
+        </dependency>
+
+
+        <dependency>
+            <groupId>org.postgresql</groupId>
            <artifactId>postgresql</artifactId>
        </dependency>

+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>jdbm</groupId>
+            <artifactId>jdbm</artifactId>
+            <version>1.0</version>
+        </dependency>
+
+        <!-- For ImageMagick MediaFilters -->
+        <dependency>
+            <groupId>org.im4java</groupId>
+            <artifactId>im4java</artifactId>
+            <version>1.4.0</version>
+        </dependency>
+
+        <!-- Flyway DB API (flywaydb.org) is used to manage DB upgrades automatically. -->
+        <dependency>
+            <groupId>org.flywaydb</groupId>
+            <artifactId>flyway-core</artifactId>
+            <version>4.0.3</version>
+        </dependency>
+
+        <!-- Google Analytics -->
+        <dependency>
+            <groupId>com.google.apis</groupId>
+            <artifactId>google-api-services-analytics</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.google.api-client</groupId>
+            <artifactId>google-api-client</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.google.http-client</groupId>
+            <artifactId>google-http-client</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.google.http-client</groupId>
+            <artifactId>google-http-client-jackson2</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.google.oauth-client</groupId>
+            <artifactId>google-oauth-client</artifactId>
+        </dependency>
+        <!-- FindBugs -->
+        <dependency>
+            <groupId>com.google.code.findbugs</groupId>
+            <artifactId>jsr305</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.google.code.findbugs</groupId>
+            <artifactId>annotations</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>joda-time</groupId>
+            <artifactId>joda-time</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>javax.inject</groupId>
+            <artifactId>javax.inject</artifactId>
+            <version>1</version>
+            <type>jar</type>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.ws.commons.axiom</groupId>
+            <artifactId>axiom-impl</artifactId>
+            <!-- NOTE: SWORDv2 needs 1.2.14, required by Abdera: https://abdera.apache.org/ -->
+            <version>1.2.14</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.ws.commons.axiom</groupId>
+            <artifactId>axiom-api</artifactId>
+            <!-- NOTE: SWORDv2 needs 1.2.14, required by Abdera: https://abdera.apache.org/ -->
+            <version>1.2.14</version>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.core</groupId>
+            <artifactId>jersey-client</artifactId>
+            <version>${jersey.version}</version>
+        </dependency>
+        <!-- S3 -->
+        <dependency>
+            <groupId>com.amazonaws</groupId>
+            <artifactId>aws-java-sdk-s3</artifactId>
+            <version>1.10.50</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>joda-time</groupId>
+                    <artifactId>joda-time</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>com.fasterxml.jackson.core</groupId>
+                    <artifactId>jackson-databind</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <!-- S3 also wanted jackson... -->
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+        </dependency>
    </dependencies>

 </project>
--- a/dspace-api/src/main/java/org/apache/solr/handler/extraction/ExtractingParams.java
+++ b/dspace-api/src/main/java/org/apache/solr/handler/extraction/ExtractingParams.java
@@ -0,0 +1,163 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.solr.handler.extraction;
+
+
+/**
+ * The various Solr Parameters names to use when extracting content.
+ **/
+public interface ExtractingParams {
+
+    /**
+     * Map all generated attribute names to field names with lowercase and underscores.
+     */
+    public static final String LOWERNAMES = "lowernames";
+
+    /**
+     * if true, ignore TikaException (give up to extract text but index meta data)
+     */
+    public static final String IGNORE_TIKA_EXCEPTION = "ignoreTikaException";
+
+
+    /**
+     * The param prefix for mapping Tika metadata to Solr fields.
+     * <p>
+     * To map a field, add a name like:
+     * <pre>fmap.title=solr.title</pre>
+     *
+     * In this example, the tika "title" metadata value will be added to a Solr field named "solr.title"
+     */
+    public static final String MAP_PREFIX = "fmap.";
+
+    /**
+     * The boost value for the name of the field.  The boost can be specified by a name mapping.
+     * <p>
+     * For example
+     * <pre>
+     * map.title=solr.title
+     * boost.solr.title=2.5
+     * </pre>
+     * will boost the solr.title field for this document by 2.5
+     */
+    public static final String BOOST_PREFIX = "boost.";
+
+    /**
+     * Pass in literal values to be added to the document, as in
+     * <pre>
+     *  literal.myField=Foo
+     * </pre>
+     */
+    public static final String LITERALS_PREFIX = "literal.";
+
+
+    /**
+     * Restrict the extracted parts of a document to be indexed
+     * by passing in an XPath expression.  All content that satisfies the XPath expr.
+     * will be passed to the {@link org.apache.solr.handler.extraction.SolrContentHandler}.
+     * <p>
+     * See Tika's docs for what the extracted document looks like.
+     *
+     * @see #CAPTURE_ELEMENTS
+     */
+    public static final String XPATH_EXPRESSION = "xpath";
+
+
+    /**
+     * Only extract and return the content, do not index it.
+     */
+    public static final String EXTRACT_ONLY = "extractOnly";
+
+    /**
+     * Content output format if extractOnly is true. Default is "xml", alternative is "text".
+     */
+    public static final String EXTRACT_FORMAT = "extractFormat";
+
+    /**
+     * Capture attributes separately according to the name of the element, instead of just adding them to the string
+     * buffer
+     */
+    public static final String CAPTURE_ATTRIBUTES = "captureAttr";
+
+    /**
+     * Literal field values will by default override other values such as metadata and content. Set this to false to
+     * revert to pre-4.0 behaviour
+     */
+    public static final String LITERALS_OVERRIDE = "literalsOverride";
+
+    /**
+     * Capture the specified fields (and everything included below it that isn't capture by some other capture field)
+     * separately from the default.  This is different
+     * then the case of passing in an XPath expression.
+     * <p>
+     * The Capture field is based on the localName returned to the
+     * {@link org.apache.solr.handler.extraction.SolrContentHandler}
+     * by Tika, not to be confused by the mapped field.  The field name can then
+     * be mapped into the index schema.
+     * <p>
+     * For instance, a Tika document may look like:
+     * <pre>
+     *  &lt;html&gt;
+     *    ...
+     *    &lt;body&gt;
+     *      &lt;p&gt;some text here.  &lt;div&gt;more text&lt;/div&gt;&lt;/p&gt;
+     *      Some more text
+     *    &lt;/body&gt;
+     * </pre>
+     * By passing in the p tag, you could capture all P tags separately from the rest of the t
+     * Thus, in the example, the capture of the P tag would be: "some text here.  more text"
+     */
+    public static final String CAPTURE_ELEMENTS = "capture";
+
+    /**
+     * The type of the stream.  If not specified, Tika will use mime type detection.
+     */
+    public static final String STREAM_TYPE = "stream.type";
+
+
+    /**
+     * Optional.  The file name. If specified, Tika can take this into account while
+     * guessing the MIME type.
+     */
+    public static final String RESOURCE_NAME = "resource.name";
+
+    /**
+     * Optional. The password for this resource. Will be used instead of the rule based password lookup mechanisms
+     */
+    public static final String RESOURCE_PASSWORD = "resource.password";
+
+    /**
+     * Optional.  If specified, the prefix will be prepended to all Metadata, such that it would be possible
+     * to setup a dynamic field to automatically capture it
+     */
+    public static final String UNKNOWN_FIELD_PREFIX = "uprefix";
+
+    /**
+     * Optional.  If specified and the name of a potential field cannot be determined, the default Field specified
+     * will be used instead.
+     */
+    public static final String DEFAULT_FIELD = "defaultField";
+
+    /**
+     * Optional. If specified, loads the file as a source for password lookups for Tika encrypted documents.
+     * <p>
+     * File format is Java properties format with one key=value per line.
+     * The key is evaluated as a regex against the file name, and the value is the password
+     * The rules are evaluated top-bottom, i.e. the first match will be used
+     * If you want a fallback password to be always used, supply a .*=&lt;defaultmypassword&gt; at the end
+     */
+    public static final String PASSWORD_MAP_FILE = "passwordsFile";
+}
--- a/dspace-api/src/main/java/org/dspace/administer/CommunityFiliator.java
+++ b/dspace-api/src/main/java/org/dspace/administer/CommunityFiliator.java
@@ -9,18 +9,23 @@ package org.dspace.administer;

 import java.io.IOException;
 import java.sql.SQLException;
+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.collections.CollectionUtils;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Community;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.CommunityService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
-import org.dspace.handle.HandleManager;
-import org.dspace.storage.rdbms.DatabaseManager;
+import org.dspace.handle.factory.HandleServiceFactory;
+import org.dspace.handle.service.HandleService;

 /**
 * A command-line tool for setting/removing community/sub-community
@@ -30,10 +35,21 @@ import org.dspace.storage.rdbms.DatabaseManager;
 * @version $Revision$
 */

-public class CommunityFiliator
-{
-    public static void main(String[] argv) throws Exception
-    {
+public class CommunityFiliator {
+
+    protected CommunityService communityService;
+    protected HandleService handleService;
+
+    public CommunityFiliator() {
+        communityService = ContentServiceFactory.getInstance().getCommunityService();
+        handleService = HandleServiceFactory.getInstance().getHandleService();
+    }
+
+    /**
+     * @param argv the command line arguments given
+     * @throws Exception if error
+     */
+    public static void main(String[] argv) throws Exception {
        // create an options object and populate it
        CommandLineParser parser = new PosixParser();

@@ -54,8 +70,7 @@ 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
@@ -66,45 +81,37 @@ 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);
            }
@@ -113,63 +120,58 @@ public class CommunityFiliator
        CommunityFiliator filiator = new CommunityFiliator();
        Context c = new Context();

-        // ve are superuser!
-        c.setIgnoreAuthorization(true);
+        // 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
+     * @throws SQLException       if database error
+     * @throws AuthorizeException if authorize error
+     * @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 = child.getParentCommunity();
+        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);
@@ -177,12 +179,10 @@ public class CommunityFiliator

        // second test - circularity: parent's parents can't include proposed
        // child
-        Community[] parentDads = parent.getAllParents();
+        List<Community> parentDads = parent.getParentCommunities();

-        for (int i = 0; i < parentDads.length; i++)
-        {
-            if (parentDads[i].getID() == child.getID())
-            {
+        for (int i = 0; i < parentDads.size(); i++) {
+            if (parentDads.get(i).getID().equals(child.getID())) {
                System.out
                    .println("Error, circular parentage - child is parent of parent");
                System.exit(1);
@@ -190,7 +190,7 @@ public class CommunityFiliator
        }

        // everthing's OK
-        parent.addSubcommunity(child);
+        communityService.addSubcommunity(c, parent, child);

        // complete the pending transaction
        c.complete();
@@ -198,25 +198,29 @@ public class CommunityFiliator
                               + "' is parent of community: '" + child.getID() + "'");
    }

+    /**
+     * @param c      context
+     * @param parent parent Community
+     * @param child  child community
+     * @throws SQLException       if database error
+     * @throws AuthorizeException if authorize error
+     * @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
-        Community[] parentKids = parent.getSubcommunities();
+        List<Community> parentKids = parent.getSubcommunities();
        boolean isChild = false;

-        for (int i = 0; i < parentKids.length; i++)
-        {
-            if (parentKids[i].getID() == child.getID())
-            {
+        for (int i = 0; i < parentKids.size(); i++) {
+            if (parentKids.get(i).getID().equals(child.getID())) {
                isChild = true;

                break;
            }
        }

-        if (!isChild)
-        {
+        if (!isChild) {
            System.out
                .println("Error, child community not a child of parent community");
            System.exit(1);
@@ -224,9 +228,10 @@ public class CommunityFiliator

        // OK remove the mappings - but leave the community, which will become
        // top-level
-        DatabaseManager.updateQuery(c,
-                "DELETE FROM community2community WHERE parent_comm_id= ? "+
-                "AND child_comm_id= ? ", parent.getID(), child.getID());
+        child.getParentCommunities().remove(parent);
+        parent.getSubcommunities().remove(child);
+        communityService.update(c, child);
+        communityService.update(c, parent);

        // complete the pending transaction
        c.complete();
@@ -235,27 +240,30 @@ public class CommunityFiliator
                               + "'");
    }

-    private Community resolveCommunity(Context c, String communityID)
-            throws SQLException
-    {
+    /**
+     * 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 {
        Community community = null;

-        if (communityID.indexOf('/') != -1)
-        {
+        if (communityID.indexOf('/') != -1) {
            // has a / must be a handle
-            community = (Community) HandleManager.resolveToObject(c,
+            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
-        {
-            community = Community.find(c, Integer.parseInt(communityID));
+        } else {
+            community = communityService.find(c, UUID.fromString(communityID));
        }

        return community;
--- a/dspace-api/src/main/java/org/dspace/administer/CreateAdministrator.java
+++ b/dspace-api/src/main/java/org/dspace/administer/CreateAdministrator.java
@@ -7,21 +7,23 @@
 */
 package org.dspace.administer;

-import java.io.BufferedReader;
-import java.io.InputStreamReader;
+import java.io.Console;
+import java.util.Arrays;
 import java.util.Locale;

 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;
 import org.dspace.core.I18nUtil;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
+import org.dspace.eperson.factory.EPersonServiceFactory;
+import org.dspace.eperson.service.EPersonService;
+import org.dspace.eperson.service.GroupService;

 /**
 * A command-line tool for creating an initial administrator for setting up a
@@ -39,24 +41,26 @@ import org.dspace.eperson.Group;
 *
 * @author Robert Tansley
 * @author Richard Jones
- * 
 * @version $Revision$
 */
-public final class CreateAdministrator
-{
-	/** DSpace Context object */
-	private Context context;
+public final class CreateAdministrator {
+    /**
+     * DSpace Context object
+     */
+    private final Context context;
+
+    protected EPersonService ePersonService;
+    protected GroupService groupService;

    /**
     * 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
-     *            command-line arguments
+     * @param argv the command line arguments given
+     * @throws Exception if error
     */
    public static void main(String[] argv)
-    	throws Exception
-    {
+        throws Exception {
        CommandLineParser parser = new PosixParser();
        Options options = new Options();

@@ -71,14 +75,11 @@ 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();
        }
    }
@@ -86,25 +87,24 @@ public final class CreateAdministrator
    /**
     * constructor, which just creates and object with a ready context
     *
-     * @throws Exception
+     * @throws Exception if error
     */
-    private CreateAdministrator()
-    	throws Exception
-    {
+    protected CreateAdministrator()
+        throws Exception {
        context = new Context();
+        groupService = EPersonServiceFactory.getInstance().getGroupService();
+        ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
    }

    /**
     * Method which will negotiate with the user via the command line to
     * obtain the administrator's details
     *
-     * @throws Exception
+     * @throws Exception if error
     */
-    private void negotiateAdministratorDetails()
-    	throws Exception
-    {
-    	// For easier reading of typing
-    	BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
+    protected void negotiateAdministratorDetails()
+        throws Exception {
+        Console console = System.console();

        System.out.println("Creating an initial administrator account");

@@ -113,102 +113,90 @@ public final class CreateAdministrator
        String email = null;
        String firstName = null;
        String lastName = null;
-    	String password1 = null;
-    	String password2 = null;
+        char[] password1 = null;
+        char[] password2 = null;
        String language = I18nUtil.DEFAULTLOCALE.getLanguage();

-    	while (!dataOK)
-    	{
+        while (!dataOK) {
            System.out.print("E-mail address: ");
            System.out.flush();

-    		email = input.readLine();
-            if (email != null)
-            {
+            email = console.readLine();
+            if (!StringUtils.isBlank(email)) {
                email = email.trim();
+            } else {
+                System.out.println("Please provide an email address.");
+                continue;
            }

            System.out.print("First name: ");
            System.out.flush();

-    		firstName = input.readLine();
+            firstName = console.readLine();

-            if (firstName != null)
-            {
+            if (firstName != null) {
                firstName = firstName.trim();
            }

            System.out.print("Last name: ");
            System.out.flush();

-    		lastName = input.readLine();
+            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 = input.readLine();
+                language = console.readLine();

-                if (language != null)
-                {
+                if (language != null) {
                    language = language.trim();
                    language = I18nUtil.getSupportedLocale(new Locale(language)).getLanguage();
                }
            }

-    		System.out.println("WARNING: Password will appear on-screen.");
+            System.out.println("Password will not display on screen.");
            System.out.print("Password: ");
            System.out.flush();

-    		password1 = input.readLine();
-
-            if (password1 != null)
-            {
-                password1 = password1.trim();
-            }
+            password1 = console.readPassword();

            System.out.print("Again to confirm: ");
            System.out.flush();

-    		password2 = input.readLine();
+            password2 = console.readPassword();

-            if (password2 != null)
-            {
-                password2 = password2.trim();
-            }
-    		
-    		if (!StringUtils.isEmpty(password1) && StringUtils.equals(password1, password2))
-    		{
+            //TODO real password validation
+            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 = input.readLine();
+                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");
            }
        }

        // if we make it to here, we are ready to create an administrator
-    	createAdministrator(email, firstName, lastName, language, password1);
+        createAdministrator(email, firstName, lastName, language, String.valueOf(password1));
+
+        //Cleaning arrays that held password
+        Arrays.fill(password1, ' ');
+        Arrays.fill(password2, ' ');
    }

    /**
@@ -218,48 +206,45 @@ public final class CreateAdministrator
     * @param email    the email for the user
     * @param first    user's first name
     * @param last     user's last name
-     * @param ps	desired password
-     * 
-     * @throws Exception
+     * @param language preferred language
+     * @param pw       desired password
+     * @throws Exception if error
     */
-    private void createAdministrator(String email, String first, String last,
+    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.setIgnoreAuthorization(true);
+        context.turnOffAuthorisationSystem();

        // Find administrator group
-    	Group admins = Group.find(context, 1);
+        Group admins = groupService.findByName(context, Group.ADMIN);

-    	if (admins == null)
-    	{
+        if (admins == null) {
            throw new IllegalStateException("Error, no admin group (group 1) found");
        }

        // Create the administrator e-person
-        EPerson eperson = EPerson.findByEmail(context,email);
+        EPerson eperson = ePersonService.findByEmail(context, email);

        // check if the email belongs to a registered user,
        // if not create a new user with this email
-        if (eperson == null)
-        {
-            eperson = EPerson.create(context);
+        if (eperson == null) {
+            eperson = ePersonService.create(context);
            eperson.setEmail(email);
            eperson.setCanLogIn(true);
            eperson.setRequireCertificate(false);
            eperson.setSelfRegistered(false);
        }

-    	eperson.setLastName(last);
-    	eperson.setFirstName(first);
-    	eperson.setLanguage(language);
-    	eperson.setPassword(pw);
-    	eperson.update();
+        eperson.setLastName(context, last);
+        eperson.setFirstName(context, first);
+        eperson.setLanguage(context, language);
+        ePersonService.setPassword(eperson, pw);
+        ePersonService.update(context, eperson);

-    	admins.addMember(eperson);
-    	admins.update();
+        groupService.addMember(context, admins, eperson);
+        groupService.update(context, admins);

        context.complete();

--- a/dspace-api/src/main/java/org/dspace/administer/DCType.java
+++ b/dspace-api/src/main/java/org/dspace/administer/DCType.java
@@ -1,287 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import java.io.IOException;
-import java.sql.SQLException;
-
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.MetadataField;
-import org.dspace.content.MetadataSchema;
-import org.dspace.content.NonUniqueMetadataException;
-import org.dspace.core.Context;
-
-/**
- * Class representing a particular Dublin Core metadata type, with various
- * utility methods. In general, only used for manipulating the registry of
- * Dublin Core types in the system, so most users will not need this.
- * 
- * <p>
- * The DCType implementation has been deprecated, please use MetadataManager,
- * MetadataSchema and MetadataField instead. For backward compatibility the this
- * implementation has been updated to transparently call the new classes.
- * </p>
- *
- * @author Robert Tansley
- * @author Martin Hald
- * @version $Revision$
- * @deprecated
- */
-public class DCType
-{
-    /** Our context */
-    private Context ourContext;
-
-    /** The matching metadata field */
-    private MetadataField field = new MetadataField();
-
-    /**
-     * Create a DCType from an existing metadata field.
-     *
-     * @param context
-     * @param field
-     * @deprecated
-     */
-    public DCType(Context context, MetadataField field)
-    {
-        this.ourContext = context;
-        this.field = field;
-    }
-
-    /**
-     * Default constructor.
-     * 
-     * @param context
-     * @deprecated
-     */
-    public DCType(Context context)
-    {
-        this.ourContext = context;
-    }
-
-    /**
-     * Utility method for quick access to an element and qualifier given the
-     * type ID.
-     * 
-     * @param context
-     *            context, in case DC types need to be read in from DB
-     * @param id
-     *            the DC type ID
-     * @return a two-String array, string 0 is the element, string 1 is the
-     *         qualifier
-     * @deprecated
-     */
-    public static String[] quickFind(Context context, int id)
-            throws SQLException
-    {
-        MetadataField field = MetadataField.find(context, id);
-
-        String[] result = new String[2];
-
-        if (field == null)
-        {
-        return result;
-    }
-        else
-        {
-            result[0] = field.getElement();
-            result[1] = field.getQualifier();
-            return result;
-        }
-    }
-
-    /**
-     * Get a metadata field from the database.
-     * 
-     * @param context
-     *            DSpace context object
-     * @param id
-     *            ID of the dublin core type
-     * 
-     * @return the metadata field, or null if the ID is invalid.
-     * @deprecated
-     */
-    public static DCType find(Context context, int id) throws SQLException
-    {
-        MetadataField field = MetadataField.find(context, id);
-        return new DCType(context, field);
-    }
-
-    /**
-     * Find a given Dublin Core type. Returns <code>null</code> if the Dublin
-     * Core type doesn't exist.
-     * 
-     * @param context
-     *            the DSpace context to use
-     * @param element
-     *            the element to find
-     * @param qualifier
-     *            the qualifier, or <code>null</code> to find an unqualified
-     *            type
-     * 
-     * @return the Dublin Core type, or <code>null</code> if there isn't a
-     *         corresponding type in the registry
-     * @throws AuthorizeException
-     * @deprecated
-     */
-    public static DCType findByElement(Context context, String element,
-            String qualifier) throws SQLException, AuthorizeException
-    {
-        MetadataField field = MetadataField.findByElement(context,
-                MetadataSchema.DC_SCHEMA_ID, element, qualifier);
-
-        if (field == null)
-        {
-            return null;
-        }
-        else
-        {
-            return new DCType(context, field);
-        }
-    }
-
-    /**
-     * Retrieve all Dublin Core types from the registry
-     * 
-     * @return an array of all the Dublin Core types
-     * @deprecated
-     */
-    public static DCType[] findAll(Context context) throws SQLException
-    {
-
-        MetadataField field[] = MetadataField.findAll(context);
-        DCType[] typeArray = new DCType[field.length];
-
-        for (int ii = 0; ii < field.length; ii++)
-        {
-            typeArray[ii] = new DCType(context, field[ii]);
-        }
-
-        // Return the array
-        return typeArray;
-    }
-
-    /**
-     * Create a new Dublin Core type
-     * 
-     * @param context
-     *            DSpace context object
-     * @return the newly created DCType
-     * @throws NonUniqueMetadataException
-     * @throws IOException
-     * @deprecated
-     */
-    public static DCType create(Context context) throws SQLException,
-            AuthorizeException, IOException, NonUniqueMetadataException
-        {
-        MetadataField field = new MetadataField();
-        field.setSchemaID(MetadataSchema.DC_SCHEMA_ID);
-        field.create(context);
-        return new DCType(context, field);
-    }
-
-    /**
-     * Delete this DC type. This won't work if there are any DC values in the
-     * database of this type - they need to be updated first. An
-     * <code>SQLException</code> (referential integrity violation) will be
-     * thrown in this case.
-     * @deprecated
-     */
-    public void delete() throws SQLException, AuthorizeException
-    {
-        field.delete(ourContext);
-    }
-
-    /**
-     * Get the internal identifier of this metadata field
-     * 
-     * @return the internal identifier
-     */
-    public int getID()
-    {
-        return field.getFieldID();
-    }
-
-    /**
-     * Get the DC element
-     * 
-     * @return the element
-     */
-    public String getElement()
-    {
-        return field.getElement();
-    }
-
-    /**
-     * Set the DC element
-     * 
-     * @param s
-     *            the new element
-     */
-    public void setElement(String s)
-    {
-        field.setElement(s);
-    }
-
-    /**
-     * Get the DC qualifier, if any.
-     * 
-     * @return the DC qualifier, or <code>null</code> if this is an
-     *         unqualified element
-     */
-    public String getQualifier()
-    {
-        return field.getQualifier();
-    }
-
-    /**
-     * Set the DC qualifier
-     * 
-     * @param s
-     *            the DC qualifier, or <code>null</code> if this is an
-     *            unqualified element
-     */
-    public void setQualifier(String s)
-    {
-        field.setQualifier(s);
-    }
-
-    /**
-     * Get the scope note - information about the DC type and its use
-     * 
-     * @return the scope note
-     */
-    public String getScopeNote()
-    {
-        return field.getScopeNote();
-    }
-
-    /**
-     * Set the scope note
-     * 
-     * @param s
-     *            the new scope note
-     */
-    public void setScopeNote(String s)
-    {
-        field.setScopeNote(s);
-    }
-
-    /**
-     * Update the dublin core registry
-     *
-     * @throws IOException
-     * @throws NonUniqueMetadataException
-     * @deprecated
-     */
-    public void update() throws SQLException, AuthorizeException,
-            NonUniqueMetadataException, IOException
-        {
-        field.update(ourContext);
-    }
-}
--- a/dspace-api/src/main/java/org/dspace/administer/MetadataExporter.java
+++ b/dspace-api/src/main/java/org/dspace/administer/MetadataExporter.java
@@ -12,6 +12,7 @@ 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;
@@ -24,6 +25,9 @@ import org.apache.xml.serialize.OutputFormat;
 import org.apache.xml.serialize.XMLSerializer;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.MetadataFieldService;
+import org.dspace.content.service.MetadataSchemaService;
 import org.dspace.core.Context;
 import org.xml.sax.SAXException;

@@ -35,27 +39,37 @@ import org.xml.sax.SAXException;
 * from the metadata schemas for the repository.
 *
 * The form of the XML is as follows
- * 
+ * {@code
 * <metadata-schemas>
 * <schema>
 * <name>dc</name>
 * <namespace>http://dublincore.org/documents/dcmi-terms/</namespace>
 * </schema>
 * </metadata-schemas>
+ * }
 */
-public class MetadataExporter
-{
+public class MetadataExporter {
+
+    protected static MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance()
+                                                                                        .getMetadataSchemaService();
+    protected static MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance()
+                                                                                      .getMetadataFieldService();

    /**
-     * @param args
-     * @throws ParseException 
-     * @throws SAXException 
-     * @throws IOException 
-     * @throws SQLException 
-     * @throws RegistryExportException 
+     * Default constructor
     */
-    public static void main(String[] args) throws ParseException, SQLException, IOException, SAXException, RegistryExportException
-    {
+    private MetadataExporter() { }
+
+    /**
+     * @param args commandline arguments
+     * @throws ParseException          if parser error
+     * @throws SAXException            if XML parse error
+     * @throws IOException             if IO error
+     * @throws SQLException            if database error
+     * @throws RegistryExportException if export error
+     */
+    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();
@@ -66,29 +80,35 @@ 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');
        }

        saveRegistry(file, schema);
    }

-    public static void saveRegistry(String file, String schema) throws SQLException, IOException, SAXException, RegistryExportException
-    {
+    /**
+     * Save a registry to a filepath
+     *
+     * @param file   filepath
+     * @param schema schema definition to save
+     * @throws SQLException            if database error
+     * @throws IOException             if IO error
+     * @throws SAXException            if XML error
+     * @throws RegistryExportException if export error
+     */
+    public static void saveRegistry(String file, String schema)
+        throws SQLException, IOException, SAXException, RegistryExportException {
        // create a context
        Context context = new Context();
-        context.setIgnoreAuthorization(true);
+        context.turnOffAuthorisationSystem();

        OutputFormat xmlFormat = new OutputFormat(Method.XML, "UTF-8", true);
        xmlFormat.setLineWidth(120);
@@ -102,30 +122,25 @@ public class MetadataExporter
        // Save the schema definition(s)
        saveSchema(context, xmlSerializer, schema);

-        MetadataField[] mdFields = null;
+        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 = MetadataSchema.find(context, schema);
-            if (mdSchema == null)
-            {
+            MetadataSchema mdSchema = metadataSchemaService.find(context, schema);
+            if (mdSchema == null) {
                throw new RegistryExportException("no schema to export");
            }

            // Get the metadata fields only for the specified schema
-            mdFields = MetadataField.findAllInSchema(context, mdSchema.getSchemaID());
-        }
-        else
-        {
+            mdFields = metadataFieldService.findAllInSchema(context, mdSchema);
+        } else {
            // Get the metadata fields for all the schemas
-            mdFields = MetadataField.findAll(context);
+            mdFields = metadataFieldService.findAll(context);
        }

        // Output the metadata fields
-        for (MetadataField mdField : mdFields)
-        {
+        for (MetadataField mdField : mdFields) {
            saveType(context, xmlSerializer, mdField);
        }

@@ -138,29 +153,26 @@ public class MetadataExporter

    /**
     * Serialize the schema registry. If the parameter 'schema' is null or empty, save all schemas
-     * @param context
-     * @param xmlSerializer
-     * @param schema
-     * @throws SQLException
-     * @throws SAXException
-     * @throws RegistryExportException
+     *
+     * @param context       DSpace Context
+     * @param xmlSerializer XML serializer
+     * @param schema        schema (may be null to save all)
+     * @throws SQLException            if database error
+     * @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 = MetadataSchema.find(context, schema);
+            MetadataSchema mdSchema = metadataSchemaService.find(context, schema);

            saveSchema(xmlSerializer, mdSchema);
-        }
-        else
-        {
+        } else {
            // Find all schemas
-            MetadataSchema[] mdSchemas = MetadataSchema.findAll(context);
+            List<MetadataSchema> mdSchemas = metadataSchemaService.findAll(context);

-            for (MetadataSchema mdSchema : mdSchemas)
-            {
+            for (MetadataSchema mdSchema : mdSchemas) {
                saveSchema(xmlSerializer, mdSchema);
            }
        }
@@ -169,30 +181,27 @@ public class MetadataExporter
    /**
     * Serialize a single schema (namespace) registry entry
     *
-     * @param xmlSerializer
-     * @param mdSchema
-     * @throws SAXException
-     * @throws RegistryExportException
+     * @param xmlSerializer XML serializer
+     * @param mdSchema      DSpace metadata schema
+     * @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;
        }
@@ -216,19 +225,18 @@ public class MetadataExporter
    /**
     * Serialize a single metadata field registry entry to xml
     *
-     * @param context
-     * @param xmlSerializer
-     * @param mdField
-     * @throws SAXException
-     * @throws RegistryExportException
-     * @throws SQLException
-     * @throws IOException 
+     * @param context       DSpace context
+     * @param xmlSerializer xml serializer
+     * @param mdField       DSpace metadata field
+     * @throws SAXException            if XML error
+     * @throws RegistryExportException if export error
+     * @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");
        }

@@ -239,8 +247,7 @@ 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");
        }

@@ -258,53 +265,50 @@ 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");
        }

        xmlSerializer.endElement("dc-type");
    }

+    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
     */
-    static Map<Integer, String> schemaMap = new HashMap<Integer, String>();
-    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(Integer.valueOf(mdField.getSchemaID()));
+        String name = schemaMap.get(mdField.getMetadataSchema().getID());

-        if (name == null)
-        {
+        if (name == null) {
            // Name not retrieved before, so get the schema now
-            MetadataSchema mdSchema = MetadataSchema.find(context, mdField.getSchemaID());
-            if (mdSchema != null)
-            {
+            MetadataSchema mdSchema = metadataSchemaService.find(context, mdField.getMetadataSchema().getID());
+            if (mdSchema != null) {
                name = mdSchema.getName();
-                schemaMap.put(Integer.valueOf(mdSchema.getSchemaID()), name);
-            }
-            else
-            {
+                schemaMap.put(mdSchema.getID(), name);
+            } else {
                // Can't find the schema
                throw new RegistryExportException("Can't get schema name for field");
            }
@@ -315,8 +319,7 @@ 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";
--- a/dspace-api/src/main/java/org/dspace/administer/MetadataImporter.java
+++ b/dspace-api/src/main/java/org/dspace/administer/MetadataImporter.java
@@ -9,7 +9,6 @@ package org.dspace.administer;

 import java.io.IOException;
 import java.sql.SQLException;
-
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;

@@ -18,19 +17,20 @@ 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;
 import org.dspace.content.NonUniqueMetadataException;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.MetadataFieldService;
+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;

 /**
@@ -42,6 +42,7 @@ import org.xml.sax.SAXException;
 *
 * The format of the XML file is as follows:
 *
+ * {@code
 * <dspace-dc-types>
 * <dc-type>
 * <schema>icadmin</schema>
@@ -53,17 +54,42 @@ import org.xml.sax.SAXException;
 * [....]
 *
 * </dspace-dc-types>
+ * }
 */
-public class MetadataImporter
-{
+public class MetadataImporter {
+    protected static MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance()
+                                                                                        .getMetadataSchemaService();
+    protected static MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance()
+                                                                                      .getMetadataFieldService();
+
+    /**
+     * 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
+     * @throws ParseException               if parse error
+     * @throws SQLException                 if database error
+     * @throws IOException                  if IO error
+     * @throws TransformerException         if transformer error
+     * @throws ParserConfigurationException if config error
+     * @throws AuthorizeException           if authorization error
+     * @throws SAXException                 if parser error
+     * @throws NonUniqueMetadataException   if duplicate metadata
+     * @throws RegistryImportException      if import fails
+     **/
    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
@@ -74,12 +100,9 @@ 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);
        }
@@ -92,14 +115,25 @@ public class MetadataImporter
     * Load the data from the specified file path into the database
     *
     * @param file        the file path containing the source data
+     * @param forceUpdate whether to force update
+     * @throws SQLException                 if database error
+     * @throws IOException                  if IO error
+     * @throws TransformerException         if transformer error
+     * @throws ParserConfigurationException if config error
+     * @throws AuthorizeException           if authorization error
+     * @throws SAXException                 if parser error
+     * @throws NonUniqueMetadataException   if duplicate metadata
+     * @throws RegistryImportException      if import fails
     */
    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 {
            // create a context
-        Context context = new Context();
-        context.setIgnoreAuthorization(true);
+            context = new Context();
+            context.turnOffAuthorisationSystem();

            // read the XML
            Document document = RegistryImporter.loadXML(file);
@@ -108,8 +142,7 @@ 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);
            }
@@ -118,81 +151,73 @@ 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();
+            }
+        }
    }

    /**
     * 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
-     * @throws NonUniqueMetadataException
+     * @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
+     * @throws AuthorizeException         if authorization error
+     * @throws NonUniqueMetadataException if duplicate metadata
+     * @throws RegistryImportException    if import fails
     */
    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");
        }

-        System.out.print("Registering Schema: " + name + " - " + namespace + " ... ");
-        
        // check to see if the schema already exists
-        MetadataSchema s = MetadataSchema.find(context, name);
+        MetadataSchema s = metadataSchemaService.find(context, name);

-        if (s == null)
-        {
+        if (s == null) {
            // Schema does not exist - create
-            MetadataSchema schema = new MetadataSchema(namespace, name);
-            schema.create(context);
-            System.out.println("created");
-        }
-        else
-        {
+            log.info("Registering Schema " + name + " (" + namespace + ")");
+            metadataSchemaService.create(context, name, namespace);
+        } else {
            // Schema exists - if it's the same namespace, allow the type imports to continue
-            if (s.getNamespace().equals(namespace))
-            {
-                System.out.println("already exists, skipping to type import");
+            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);
-                s.update(context);
-                System.out.println("namespace updated (" + name + " = " + namespace + ")");
-            }
-            else
-            {
-                // Don't update the existing namespace - abort abort abort
-                System.out.println("schema exists, but with different namespace");
-                System.out.println("was: " + s.getNamespace());
-                System.out.println("xml: " + namespace);
-                System.out.println("aborting - use -u to force the update");
-                
-                throw new RegistryImportException("schema already registered with different namespace - use -u to update");
+                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.");
            }
        }

@@ -203,16 +228,18 @@ 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
-     * @throws NonUniqueMetadataException
+     * @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
+     * @throws AuthorizeException         if authorization error
+     * @throws NonUniqueMetadataException if duplicate metadata
+     * @throws RegistryImportException    if import fails
     */
    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");
@@ -220,42 +247,38 @@ 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;
        }

-        System.out.print("Registering Metadata: " + schema + "." + element + "." + qualifier + " ... ");

        // Find the matching schema object
-        MetadataSchema schemaObj = MetadataSchema.find(context, schema);
+        MetadataSchema schemaObj = metadataSchemaService.find(context, schema);

-        if (schemaObj == null)
-        {
-            throw new RegistryImportException("Schema '" + schema + "' is not registered");
+        if (schemaObj == null) {
+            throw new RegistryImportException("Schema '" + schema + "' is not registered and does not exist.");
        }

-        MetadataField mf = MetadataField.findByElement(context, schemaObj.getSchemaID(), element, qualifier);
-        if (mf != null)
-        {
-            System.out.println("already exists, skipping");
+        MetadataField mf = metadataFieldService.findByElement(context, schemaObj, element, qualifier);
+        if (mf != null) {
+            // Metadata field already exists, skipping it
            return;
        }

-        MetadataField field = new MetadataField();
-        field.setSchemaID(schemaObj.getSchemaID());
-        field.setElement(element);
-        field.setQualifier(qualifier);
-        field.setScopeNote(scopeNote);
-        field.create(context);
-        System.out.println("created");
+        // Actually create this metadata field as it doesn't yet exist
+        String fieldName = schema + "." + element + "." + qualifier;
+        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);
    }

    /**
     * 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";
--- a/dspace-api/src/main/java/org/dspace/administer/RegistryExportException.java
+++ b/dspace-api/src/main/java/org/dspace/administer/RegistryExportException.java
@@ -12,44 +12,39 @@ 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();
    }

    /**
     * create an exception with only a message
     *
-     * @param message
+     * @param message exception message
     */
-    public RegistryExportException(String message)
-    {
+    public RegistryExportException(String message) {
        super(message);
    }

    /**
     * create an exception with an inner exception and a message
     *
-     * @param   message
-     * @param   e
+     * @param message exception message
+     * @param e       reference to Throwable
     */
-    public RegistryExportException(String message, Throwable e)
-    {
+    public RegistryExportException(String message, Throwable e) {
        super(message, e);
    }

    /**
     * create an exception with an inner exception
     *
-     * @param   e
+     * @param e reference to Throwable
     */
-    public RegistryExportException(Throwable e)
-    {
+    public RegistryExportException(Throwable e) {
        super(e);
    }

--- a/dspace-api/src/main/java/org/dspace/administer/RegistryImportException.java
+++ b/dspace-api/src/main/java/org/dspace/administer/RegistryImportException.java
@@ -12,44 +12,39 @@ 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();
    }

    /**
     * create an exception with only a message
     *
-     * @param message
+     * @param message error message
     */
-    public RegistryImportException(String message)
-    {
+    public RegistryImportException(String message) {
        super(message);
    }

    /**
     * create an exception with an inner exception and a message
     *
-     * @param	message
-     * @param	e
+     * @param message error message
+     * @param e       throwable
     */
-    public RegistryImportException(String message, Throwable e)
-    {
+    public RegistryImportException(String message, Throwable e) {
        super(message, e);
    }

    /**
     * create an exception with an inner exception
     *
-     * @param	e
+     * @param e throwable
     */
-    public RegistryImportException(Throwable e)
-    {
+    public RegistryImportException(Throwable e) {
        super(e);
    }

--- a/dspace-api/src/main/java/org/dspace/administer/RegistryImporter.java
+++ b/dspace-api/src/main/java/org/dspace/administer/RegistryImporter.java
@@ -9,18 +9,15 @@ 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;

 /**
@@ -31,19 +28,24 @@ import org.xml.sax.SAXException;
 * I am the author, really I ripped these methods off from other
 * classes
 */
-public class RegistryImporter
-{
+public class RegistryImporter {
+
+    /**
+     * Default constructor
+     */
+    private 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();

@@ -64,21 +66,17 @@ 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
-     * 
+     * @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>
+     * @throws TransformerException if error
     */
    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;
        }
@@ -86,8 +84,7 @@ public class RegistryImporter
        // Get the #text
        Node dataNode = childNode.getFirstChild();

-        if (dataNode == null)
-        {
+        if (dataNode == null) {
            return null;
        }

@@ -112,23 +109,19 @@ 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
-     * 
+     * @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>
+     * @throws TransformerException if error
     */
    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();

--- a/dspace-api/src/main/java/org/dspace/administer/RegistryLoader.java
+++ b/dspace-api/src/main/java/org/dspace/administer/RegistryLoader.java
@@ -10,7 +10,8 @@ package org.dspace.administer;
 import java.io.File;
 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;
@@ -20,9 +21,8 @@ import org.apache.log4j.Logger;
 import org.apache.xpath.XPathAPI;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.BitstreamFormat;
-import org.dspace.content.MetadataField;
-import org.dspace.content.MetadataSchema;
-import org.dspace.content.NonUniqueMetadataException;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.BitstreamFormatService;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
 import org.w3c.dom.Document;
@@ -43,88 +43,86 @@ 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() { }
+
    /**
     * For invoking via the command line
     *
-     * @param argv
-     *            command-line arguments
+     * @param argv the command line arguments given
+     * @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 | -dc) registry-file.xml";
+            + " (-bitstream | -metadata) registry-file.xml";

        Context context = null;

-        try
-        {
+        try {
            context = new Context();

            // Can't update registries anonymously, so we need to turn off
            // authorisation
-            context.setIgnoreAuthorization(true);
+            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("-dc"))
-            {
-                loadDublinCoreTypes(context, argv[1]);
-            }
-            else
-            {
+            } else if (argv[0].equalsIgnoreCase("-metadata")) {
+                // Call MetadataImporter, as it handles Metadata schema updates
+                MetadataImporter.loadRegistry(argv[1], true);
+            } else {
                System.err.println(usage);
            }

+            // Commit changes and close Context
            context.complete();

            System.exit(0);
-        }
-        catch (ArrayIndexOutOfBoundsException ae)
-        {
+        } catch (ArrayIndexOutOfBoundsException ae) {
            System.err.println(usage);

-            if (context != null)
-            {
-                context.abort();
-            }
-
            System.exit(1);
-        }
-        catch (Exception e)
-        {
+        } catch (Exception e) {
            log.fatal(LogManager.getHeader(context, "error_loading_registries",
                                           ""), e);

-            if (context != null)
-            {
-                context.abort();
-            }
-
            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();
+            }
        }
    }

    /**
     * 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
+     * @throws ParserConfigurationException if config error
+     * @throws AuthorizeException           if authorization error
+     * @throws SAXException                 if parser error
     */
    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
@@ -132,8 +130,7 @@ 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);
        }
@@ -146,15 +143,16 @@ 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
+     * @throws AuthorizeException   if authorization error
     */
    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");
@@ -168,124 +166,32 @@ public class RegistryLoader

        String[] extensions = getRepeatedElementData(node, "extension");

+        // Check if this format already exists in our registry (by mime type)
+        BitstreamFormat exists = bitstreamFormatService.findByMIMEType(context, mimeType);
+
+        // If not found by mimeType, check by short description (since this must also be unique)
+        if (exists == null) {
+            exists = bitstreamFormatService.findByShortDescription(context, shortDesc);
+        }
+
+        // If it doesn't exist, create it..otherwise skip it.
+        if (exists == null) {
            // Create the format object
-        BitstreamFormat format = BitstreamFormat.create(context);
+            BitstreamFormat format = bitstreamFormatService.create(context);

            // Fill it out with the values
            format.setMIMEType(mimeType);
-        format.setShortDescription(shortDesc);
+            bitstreamFormatService.setShortDescription(context, format, shortDesc);
            format.setDescription(desc);
            format.setSupportLevel(supportLevel);
            format.setInternal(internal);
-        format.setExtensions(extensions);
+            ArrayList<String> extensionList = new ArrayList<>();
+            extensionList.addAll(Arrays.asList(extensions));
+            format.setExtensions(extensionList);

            // Write to database
-        format.update();
+            bitstreamFormatService.update(context, format);
        }
-
-    /**
-     * Load Dublin Core types
-     * 
-     * @param context
-     *            DSpace context object
-     * @param filename
-     *            the filename of the XML file to load
-     * @throws NonUniqueMetadataException
-     */
-    public static void loadDublinCoreTypes(Context context, String filename)
-            throws SQLException, IOException, ParserConfigurationException,
-            SAXException, TransformerException, AuthorizeException,
-            NonUniqueMetadataException
-    {
-        Document document = loadXML(filename);
-
-        // Get the nodes corresponding to schemas
-        NodeList schemaNodes = XPathAPI.selectNodeList(document,
-                "/dspace-dc-types/dc-schema");
-
-        // Add each schema
-        for (int i = 0; i < schemaNodes.getLength(); i++)
-        {
-            Node n = schemaNodes.item(i);
-            loadMDSchema(context, n);
-        }
-        
-        // Get the nodes corresponding to fields
-        NodeList typeNodes = XPathAPI.selectNodeList(document,
-                "/dspace-dc-types/dc-type");
-
-        // Add each one as a new field to the schema
-        for (int i = 0; i < typeNodes.getLength(); i++)
-        {
-            Node n = typeNodes.item(i);
-            loadDCType(context, n);
-        }
-
-        log.info(LogManager.getHeader(context, "load_dublin_core_types",
-                "number_loaded=" + typeNodes.getLength()));
-    }
-
-    /**
-     * Load Dublin Core Schemas
-     * 
-     * @param context
-     * @param node
-     */
-    private static void loadMDSchema(Context context, Node node) 
-    		throws TransformerException, SQLException, AuthorizeException, 
-    		NonUniqueMetadataException
-    {
-    	// Get the values
-        String shortname = getElementData(node, "name");
-        String namespace = getElementData(node, "namespace");
-
-        // Check if the schema exists already
-        MetadataSchema schema = MetadataSchema.find(context, shortname);
-        if (schema == null)
-        {
-        	// If not create it.
-        	schema = new MetadataSchema();
-        	schema.setNamespace(namespace);
-        	schema.setName(shortname);
-        	schema.create(context);
-        }
-    }
-    
-    /**
-     * 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
-     * @throws NonUniqueMetadataException
-     */
-    private static void loadDCType(Context context, Node node)
-            throws SQLException, IOException, TransformerException,
-            AuthorizeException, NonUniqueMetadataException
-    {
-        // Get the values
-        String schema = getElementData(node, "schema");
-        String element = getElementData(node, "element");
-        String qualifier = getElementData(node, "qualifier");
-        String scopeNote = getElementData(node, "scope_note");
-
-        // If the schema is not provided default to DC
-        if (schema == null)
-        {
-            schema = MetadataSchema.DC_SCHEMA;
-        }
-
-        // Find the matching schema object
-        MetadataSchema schemaObj = MetadataSchema.find(context, schema);
-        
-        MetadataField field = new MetadataField();
-        field.setSchemaID(schemaObj.getSchemaID());
-        field.setElement(element);
-        field.setQualifier(qualifier);
-        field.setScopeNote(scopeNote);
-        field.create(context);
    }

    // ===================== XML Utility Methods =========================
@@ -293,14 +199,14 @@ public class RegistryLoader
    /**
     * 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 config error
+     * @throws SAXException                 if parser error
     */
    private static Document loadXML(String filename) throws IOException,
-            ParserConfigurationException, SAXException
-    {
+        ParserConfigurationException, SAXException {
        DocumentBuilder builder = DocumentBuilderFactory.newInstance()
                                                        .newDocumentBuilder();

@@ -319,21 +225,17 @@ 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
-     * 
+     * @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>
+     * @throws TransformerException if transformer error
     */
    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;
        }
@@ -341,8 +243,7 @@ public class RegistryLoader
        // Get the #text
        Node dataNode = childNode.getFirstChild();

-        if (dataNode == null)
-        {
+        if (dataNode == null) {
            return null;
        }

@@ -367,23 +268,19 @@ 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
-     * 
+     * @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>
+     * @throws TransformerException if transformer error
     */
    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();

--- a/dspace-api/src/main/java/org/dspace/administer/StructBuilder.java
+++ b/dspace-api/src/main/java/org/dspace/administer/StructBuilder.java
@@ -14,7 +14,6 @@ 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;
@@ -28,8 +27,12 @@ import org.apache.xpath.XPathAPI;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.CollectionService;
+import org.dspace.content.service.CommunityService;
 import org.dspace.core.Context;
-import org.dspace.eperson.EPerson;
+import org.dspace.eperson.factory.EPersonServiceFactory;
+import org.dspace.eperson.service.EPersonService;
 import org.jdom.Element;
 import org.jdom.output.XMLOutputter;
 import org.w3c.dom.Document;
@@ -42,7 +45,7 @@ import org.xml.sax.SAXException;
 * an XML file.
 *
 * The XML file structure needs to be:
- * 
+ * {@code
 * <import_structure>
 * <community>
 * <name>....</name>
@@ -52,42 +55,56 @@ import org.xml.sax.SAXException;
 * </collection>
 * </community>
 * </import_structure>
- * 
+ * }
 * 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
 *
 * @author Richard Jones
- *
 */

-public class StructBuilder
-{
-    /** the output xml document which will contain updated information about the 
+public class StructBuilder {
+    /**
+     * 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"));

-    /** a hashtable to hold metadata for the collection being worked on */
+    /**
+     * a hashtable to hold metadata for the collection being worked on
+     */
    private static Map<String, String> collectionMap = new HashMap<String, String>();

-    /** a hashtable to hold metadata for the community being worked on */
+    /**
+     * a hashtable to hold metadata for the community being worked on
+     */
    private static Map<String, String> communityMap = new HashMap<String, String>();

+    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
     *
     * This is of the form:
     *
-     * StructBuilder -f [xml source] -e [administrator email] -o [output file]
+     * {@code StructBuilder -f [xml source] -e [administrator email] -o [output file]}
     *
     * The output file will contain exactly the same as the source xml document, but
     * with the handle for each imported item added as an attribute.
+     *
+     * @param argv the command line arguments given
+     * @throws Exception if an error occurs
     */
    public static void main(String[] argv)
-    	throws Exception
-    {
+        throws Exception {
        CommandLineParser parser = new PosixParser();

        Options options = new Options();
@@ -102,23 +119,19 @@ public class StructBuilder
        String eperson = null;
        String output = null;

-    	if (line.hasOption('f'))
-    	{
+        if (line.hasOption('f')) {
            file = line.getOptionValue('f');
        }

-    	if (line.hasOption('e'))
-    	{
+        if (line.hasOption('e')) {
            eperson = line.getOptionValue('e');
        }

-    	if (line.hasOption('o'))
-    	{
+        if (line.hasOption('o')) {
            output = line.getOptionValue('o');
        }

-    	if (output == null || eperson == null || file == null)
-    	{
+        if (output == null || eperson == null || file == null) {
            usage();
            System.exit(0);
        }
@@ -127,7 +140,7 @@ public class StructBuilder
        Context context = new Context();

        // set the context
-        context.setCurrentUser(EPerson.findByEmail(context, eperson));
+        context.setCurrentUser(ePersonService.findByEmail(context, eperson));

        // load the XML
        Document document = loadXML(file);
@@ -159,20 +172,16 @@ public class StructBuilder

        // generate the output
        Element root = xmlOutput.getRootElement();
-        for (int i = 0; i < elements.length; i++)
-        {
+        for (int i = 0; i < elements.length; i++) {
            root.addContent(elements[i]);
        }

        // finally write the string into the output file
-        try 
-        {
+        try {
            BufferedWriter out = new BufferedWriter(new FileWriter(output));
            out.write(new XMLOutputter().outputString(xmlOutput));
            out.close();
-        } 
-        catch (IOException e) 
-        {
+        } catch (IOException e) {
            System.out.println("Unable to write to output file " + output);
            System.exit(0);
        }
@@ -183,10 +192,11 @@ public class StructBuilder
    /**
     * Output the usage information
     */
-    private static void usage()
-    {
+    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");
+        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;
    }

@@ -195,12 +205,10 @@ public class StructBuilder
     * fails it generates an error and ceases execution
     *
     * @param document the XML document object
-     * @throws TransformerException
-     * 
+     * @throws TransformerException if transformer error
     */
    private static void validate(org.w3c.dom.Document document)
-    	throws TransformerException
-    {
+        throws TransformerException {
        StringBuffer err = new StringBuffer();
        boolean trip = false;

@@ -208,22 +216,19 @@ public class StructBuilder
        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)
-        {
+        if (first.getLength() == 0) {
            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);
        }
@@ -236,23 +241,19 @@ public class StructBuilder
     * @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
-    {
+        throws TransformerException {
        StringBuffer err = new StringBuffer();
        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)
-	        {
+            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");
@@ -262,8 +263,7 @@ public class StructBuilder
            // validate sub communities
            NodeList subCommunities = XPathAPI.selectNodeList(n, "community");
            String comErrs = validateCommunities(subCommunities, level + 1);
-	        if (comErrs != null)
-	        {
+            if (comErrs != null) {
                err.append(comErrs);
                trip = true;
            }
@@ -271,15 +271,13 @@ public class StructBuilder
            // validate collections
            NodeList collections = XPathAPI.selectNodeList(n, "collection");
            String colErrs = validateCollections(collections, level + 1);
-	        if (colErrs != null)
-	        {
+            if (colErrs != null) {
                err.append(colErrs);
                trip = true;
            }
        }

-        if (trip)
-        {
+        if (trip) {
            errs = err.toString();
        }

@@ -292,22 +290,18 @@ public class StructBuilder
     *
     * @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
-    {
+        throws TransformerException {
        StringBuffer err = new StringBuffer();
        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)
-	        {
+            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");
@@ -315,8 +309,7 @@ public class StructBuilder
            }
        }

-        if (trip)
-        {
+        if (trip) {
            errs = err.toString();
        }

@@ -326,14 +319,11 @@ 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();

@@ -346,19 +336,15 @@ 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();
            }
        }
@@ -373,41 +359,33 @@ 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, Exception {
        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)
-            {
-                community = parent.createSubcommunity();
-            }
-            else
-            {
-                community = Community.create(null, context);
+            if (parent != null) {
+                community = communityService.create(parent, context);
+            } else {
+                community = communityService.create(null, context);
            }

            // default the short description to be an empty string
-            community.setMetadata("short_description", " ");
+            communityService.setMetadata(context, community, "short_description", " ");

            // 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)
-                {
-                    community.setMetadata(entry.getValue(), getStringValue(nl.item(0)));
+                if (nl.getLength() == 1) {
+                    communityService.setMetadata(context, community, entry.getValue(), getStringValue(nl.item(0)));
                }
            }

@@ -420,7 +398,7 @@ public class StructBuilder
            // difficult
            // to isolate the community that already exists without hitting
            // the database directly.
-            community.update();
+            communityService.update(context, community);

            // build the element with the handle that identifies the new
            // community
@@ -433,34 +411,30 @@ public class StructBuilder
            element.setAttribute("identifier", community.getHandle());

            Element nameElement = new Element("name");
-            nameElement.setText(community.getMetadata("name"));
+            nameElement.setText(communityService.getMetadata(community, "name"));
            element.addContent(nameElement);

-            if (community.getMetadata("short_description") != null)
-            {
+            if (communityService.getMetadata(community, "short_description") != null) {
                Element descriptionElement = new Element("description");
-                descriptionElement.setText(community.getMetadata("short_description"));
+                descriptionElement.setText(communityService.getMetadata(community, "short_description"));
                element.addContent(descriptionElement);
            }

-            if (community.getMetadata("introductory_text") != null)
-            {
+            if (communityService.getMetadata(community, "introductory_text") != null) {
                Element introElement = new Element("intro");
-                introElement.setText(community.getMetadata("introductory_text"));
+                introElement.setText(communityService.getMetadata(community, "introductory_text"));
                element.addContent(introElement);
            }

-            if (community.getMetadata("copyright_text") != null)
-            {
+            if (communityService.getMetadata(community, "copyright_text") != null) {
                Element copyrightElement = new Element("copyright");
-                copyrightElement.setText(community.getMetadata("copyright_text"));
+                copyrightElement.setText(communityService.getMetadata(community, "copyright_text"));
                element.addContent(copyrightElement);
            }

-            if (community.getMetadata("side_bar_text") != null)
-            {
+            if (communityService.getMetadata(community, "side_bar_text") != null) {
                Element sidebarElement = new Element("sidebar");
-                sidebarElement.setText(community.getMetadata("side_bar_text"));
+                sidebarElement.setText(communityService.getMetadata(community, "side_bar_text"));
                element.addContent(sidebarElement);
            }

@@ -473,12 +447,10 @@ 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]);
            }

@@ -494,81 +466,70 @@ 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, IOException, Exception {
        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 = parent.createCollection();
+            Collection collection = collectionService.create(context, parent);

            // default the short description to the empty string
-            collection.setMetadata("short_description", " ");
+            collectionService.setMetadata(context, collection, "short_description", " ");

            // 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)
-                {
-                    collection.setMetadata(entry.getValue(), getStringValue(nl.item(0)));
+                if (nl.getLength() == 1) {
+                    collectionService.setMetadata(context, collection, entry.getValue(), getStringValue(nl.item(0)));
                }
            }

-            collection.update();
+            collectionService.update(context, collection);

            element.setAttribute("identifier", collection.getHandle());

            Element nameElement = new Element("name");
-            nameElement.setText(collection.getMetadata("name"));
+            nameElement.setText(collectionService.getMetadata(collection, "name"));
            element.addContent(nameElement);

-            if (collection.getMetadata("short_description") != null)
-            {
+            if (collectionService.getMetadata(collection, "short_description") != null) {
                Element descriptionElement = new Element("description");
-                descriptionElement.setText(collection.getMetadata("short_description"));
+                descriptionElement.setText(collectionService.getMetadata(collection, "short_description"));
                element.addContent(descriptionElement);
            }

-            if (collection.getMetadata("introductory_text") != null)
-            {
+            if (collectionService.getMetadata(collection, "introductory_text") != null) {
                Element introElement = new Element("intro");
-                introElement.setText(collection.getMetadata("introductory_text"));
+                introElement.setText(collectionService.getMetadata(collection, "introductory_text"));
                element.addContent(introElement);
            }

-            if (collection.getMetadata("copyright_text") != null)
-            {
+            if (collectionService.getMetadata(collection, "copyright_text") != null) {
                Element copyrightElement = new Element("copyright");
-                copyrightElement.setText(collection.getMetadata("copyright_text"));
+                copyrightElement.setText(collectionService.getMetadata(collection, "copyright_text"));
                element.addContent(copyrightElement);
            }

-            if (collection.getMetadata("side_bar_text") != null)
-            {
+            if (collectionService.getMetadata(collection, "side_bar_text") != null) {
                Element sidebarElement = new Element("sidebar");
-                sidebarElement.setText(collection.getMetadata("side_bar_text"));
+                sidebarElement.setText(collectionService.getMetadata(collection, "side_bar_text"));
                element.addContent(sidebarElement);
            }

-            if (collection.getMetadata("license") != null)
-            {
+            if (collectionService.getMetadata(collection, "license") != null) {
                Element sidebarElement = new Element("license");
-                sidebarElement.setText(collection.getMetadata("license"));
+                sidebarElement.setText(collectionService.getMetadata(collection, "license"));
                element.addContent(sidebarElement);
            }

-            if (collection.getMetadata("provenance_description") != null)
-            {
+            if (collectionService.getMetadata(collection, "provenance_description") != null) {
                Element sidebarElement = new Element("provenance");
-                sidebarElement.setText(collection.getMetadata("provenance_description"));
+                sidebarElement.setText(collectionService.getMetadata(collection, "provenance_description"));
                element.addContent(sidebarElement);
            }

--- a/dspace-api/src/main/java/org/dspace/administer/Upgrade101To11.java
+++ b/dspace-api/src/main/java/org/dspace/administer/Upgrade101To11.java
@@ -1,97 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import org.dspace.content.DCDate;
-import org.dspace.core.Context;
-import org.dspace.storage.rdbms.DatabaseManager;
-import org.dspace.storage.rdbms.TableRow;
-import org.dspace.storage.rdbms.TableRowIterator;
-
-/**
- * A command-line tool for performing necessary tweaks in the database for the
- * new last_modified column in the item table.
- * 
- * @author Robert Tansley
- * @version $Revision$
- */
-public class Upgrade101To11
-{
-    /**
-     * For invoking via the command line
-     * 
-     * @param argv
-     *            command-line arguments
-     */
-    public static void main(String[] argv)
-    {
-        Context context = null;
-
-        try
-        {
-            context = new Context();
-
-            // Deal with withdrawn items first.
-            // last_modified takes the value of the deletion date
-            TableRowIterator tri = DatabaseManager.queryTable(context, "item",
-                    "SELECT * FROM item WHERE withdrawal_date IS NOT NULL");
-
-            while (tri.hasNext())
-            {
-                TableRow row = tri.next();
-                DCDate d = new DCDate(row.getStringColumn("withdrawal_date"));
-                row.setColumn("last_modified", d.toDate());
-                DatabaseManager.update(context, row);
-            }
-            tri.close();
-
-            // Next, update those items with a date.available
-            tri = DatabaseManager.query(context,
-                        "SELECT item.item_id, dcvalue.text_value FROM item, dctyperegistry, "+
-                        "dcvalue WHERE item.item_id=dcvalue.item_id AND dcvalue.dc_type_id="+
-                        "dctyperegistry.dc_type_id AND dctyperegistry.element LIKE 'date' "+
-                        "AND dctyperegistry.qualifier LIKE 'available'");
-
-            while (tri.hasNext())
-            {
-                TableRow resultRow = tri.next();
-                DCDate d = new DCDate(resultRow.getStringColumn("text_value"));
-
-                // Can't update the row, have to do a separate query
-                TableRow itemRow = DatabaseManager.find(context, "item",
-                        resultRow.getIntColumn("item_id"));
-                itemRow.setColumn("last_modified", d.toDate());
-                DatabaseManager.update(context, itemRow);
-            }
-            tri.close();
-
-            // Finally, for all items that have no date.available or withdrawal
-            // date, set the update time to now!
-            DatabaseManager.updateQuery(context,
-                        "UPDATE item SET last_modified=now() WHERE last_modified IS NULL");
-
-            context.complete();
-
-            System.out.println("Last modified dates set");
-
-            System.exit(0);
-        }
-        catch (Exception e)
-        {
-            System.err.println("Exception occurred:" + e);
-            e.printStackTrace();
-
-            if (context != null)
-            {
-                context.abort();
-            }
-
-            System.exit(1);
-        }
-    }
-}
--- a/dspace-api/src/main/java/org/dspace/administer/Upgrade11To12.java
+++ b/dspace-api/src/main/java/org/dspace/administer/Upgrade11To12.java
@@ -1,198 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import org.dspace.content.Bitstream;
-import org.dspace.content.BitstreamFormat;
-import org.dspace.content.Bundle;
-import org.dspace.content.Collection;
-import org.dspace.content.Item;
-import org.dspace.content.ItemIterator;
-import org.dspace.core.Context;
-
-/**
- * Command-line tool for making changes to DSpace database when updating from
- * version 1.1/1.1.1 to 1.2.
- * <P>
- * The changes are:
- * <ul>
- * <li>Setting owning collection field for items
- * <li>Reorganising content bitstreams into one bundle named ORIGINAL, license
- * bitstreams into a bundle named LICENSE
- * <li>Setting the sequence_id numbers in the bitstream table. This happens as
- * item.update() is called on every item.
- * <li>If a (newly-reorganised) 'ORIGINAL' bundle contains a text/html
- * bitstream, that bitstream is set to the primary bitstream for HTML support.
- * </ul>
- */
-public class Upgrade11To12
-{
-    public static void main(String[] argv) throws Exception
-    {
-        Context c = new Context();
-
-        // ve are superuser!
-        c.setIgnoreAuthorization(true);
-
-        ItemIterator ii = null;
-
-        // first set owning Collections
-        Collection[] collections = Collection.findAll(c);
-
-        System.out.println("Setting item owningCollection fields in database");
-
-        for (int q = 0; q < collections.length; q++)
-        {
-            ii = collections[q].getItems();
-
-            while (ii.hasNext())
-            {
-                Item myItem = ii.next();
-
-                // set it if it's not already set
-                if (myItem.getOwningCollection() == null)
-                {
-                    myItem.setOwningCollection(collections[q]);
-                    myItem.update();
-                    System.out.println("Set owner of item " + myItem.getID()
-                            + " to collection " + collections[q].getID());
-                }
-            }
-        }
-
-        // commit pending transactions before continuing
-        c.commit();
-
-        // now combine some bundles
-        ii = Item.findAll(c);
-
-        while (ii.hasNext())
-        {
-            boolean skipItem = false;
-            Item myItem = ii.next();
-
-            int licenseBundleIndex = -1; // array index of license bundle (we'll
-                                         // skip this one often)
-            int primaryBundleIndex = -1; // array index of our primary bundle
-                                         // (all bitstreams assemble here)
-
-            System.out.println("Processing item #: " + myItem.getID());
-
-            Bundle[] myBundles = myItem.getBundles();
-
-            // look for bundles with multiple bitstreams
-            // (if any found, we'll skip this item)
-            for (int i = 0; i < myBundles.length; i++)
-            {
-                // skip if bundle is already named
-                if (myBundles[i].getName() != null)
-                {
-                    System.out
-                            .println("Skipping this item - named bundles already found");
-                    skipItem = true;
-
-                    break;
-                }
-
-                Bitstream[] bitstreams = myBundles[i].getBitstreams();
-
-                // skip this item if we already have bundles combined in this
-                // item
-                if (bitstreams.length > 1)
-                {
-                    System.out
-                            .println("Skipping this item - compound bundles already found");
-                    skipItem = true;
-
-                    break;
-                }
-
-                // is this the license? check the format
-                BitstreamFormat bf = bitstreams[0].getFormat();
-
-                if ("License".equals(bf.getShortDescription()))
-                {
-                    System.out.println("Found license!");
-
-                    if (licenseBundleIndex == -1)
-                    {
-                        licenseBundleIndex = i;
-                        System.out.println("License bundle set to: " + i);
-                    }
-                    else
-                    {
-                        System.out
-                                .println("ERROR - multiple license bundles in item - skipping");
-                        skipItem = true;
-
-                        break;
-                    }
-                }
-                else
-                {
-                    // not a license, if primary isn't set yet, set it
-                    if (primaryBundleIndex == -1)
-                    {
-                        primaryBundleIndex = i;
-                        System.out.println("Primary bundle set to: " + i);
-                    }
-                }
-            }
-
-            if (!skipItem)
-            {
-                // name the primary and license bundles
-                if (primaryBundleIndex != -1)
-                {
-                    myBundles[primaryBundleIndex].setName("ORIGINAL");
-                    myBundles[primaryBundleIndex].update();
-                }
-
-                if (licenseBundleIndex != -1)
-                {
-                    myBundles[licenseBundleIndex].setName("LICENSE");
-                    myBundles[licenseBundleIndex].update();
-                }
-
-                for (int i = 0; i < myBundles.length; i++)
-                {
-                    Bitstream[] bitstreams = myBundles[i].getBitstreams();
-
-                    // now we can safely assume no bundles with multiple
-                    // bitstreams
-                    if (bitstreams.length > 0 && (i != primaryBundleIndex) && (i != licenseBundleIndex))
-                    {
-                        // only option left is a bitstream to be combined
-                        // with primary bundle
-                        // and remove now-redundant bundle
-                        myBundles[primaryBundleIndex]
-                                .addBitstream(bitstreams[0]); // add to
-                                                              // primary
-                        myItem.removeBundle(myBundles[i]); // remove this
-                                                           // bundle
-
-                        System.out.println("Bitstream from bundle " + i
-                                + " moved to primary bundle");
-
-                        // flag if HTML bitstream
-                        if (bitstreams[0].getFormat().getMIMEType().equals(
-                                "text/html"))
-                        {
-                            System.out
-                                    .println("Set primary bitstream to HTML file in item #"
-                                            + myItem.getID()
-                                            + " for HTML support.");
-                        }
-                    }
-                }
-            }
-        }
-
-        c.complete();
-    }
-}
--- a/dspace-api/src/main/java/org/dspace/app/bulkedit/BulkEditChange.java
+++ b/dspace-api/src/main/java/org/dspace/app/bulkedit/BulkEditChange.java
@@ -7,68 +7,93 @@
 */
 package org.dspace.app.bulkedit;

-import org.dspace.content.Item;
-import org.dspace.content.DCValue;
-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 */
-    private List<DCValue> adds;
+    /**
+     * The List of hashtables with the new elements
+     */
+    private List<BulkEditMetadataValue> adds;

-    /** The List of hashtables with the removed elements */
-    private List<DCValue> removes;
+    /**
+     * The List of hashtables with the removed elements
+     */
+    private List<BulkEditMetadataValue> removes;

-    /** The List of hashtables with the unchanged elements */
-    private List<DCValue> constant;
+    /**
+     * The List of hashtables with the unchanged elements
+     */
+    private List<BulkEditMetadataValue> constant;

-    /** The List of the complete set of new values (constant + adds) */
-    private List<DCValue> complete;
+    /**
+     * 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;
@@ -77,12 +102,12 @@ public class BulkEditChange
        newOwningCollection = null;

        // Initialise the arrays
-        adds = new ArrayList<DCValue>();
-        removes = new ArrayList<DCValue>();
-        constant = new ArrayList<DCValue>();
-        complete = new ArrayList<DCValue>();
-        oldMappedCollections = new ArrayList<Collection>();
-        newMappedCollections = new ArrayList<Collection>();
+        adds = new ArrayList<>();
+        removes = new ArrayList<>();
+        constant = new ArrayList<>();
+        complete = new ArrayList<>();
+        oldMappedCollections = new ArrayList<>();
+        newMappedCollections = new ArrayList<>();
    }

    /**
@@ -90,20 +115,19 @@ public class BulkEditChange
     *
     * @param i The Item to store
     */
-    public BulkEditChange(Item i)
-    {
+    public BulkEditChange(Item i) {
        // Store the item
        item = i;
        newItem = false;
        empty = true;

        // Initialise the arrays
-        adds = new ArrayList<DCValue>();
-        removes = new ArrayList<DCValue>();
-        constant = new ArrayList<DCValue>();
-        complete = new ArrayList<DCValue>();
-        oldMappedCollections = new ArrayList<Collection>();
-        newMappedCollections = new ArrayList<Collection>();
+        adds = new ArrayList<>();
+        removes = new ArrayList<>();
+        constant = new ArrayList<>();
+        complete = new ArrayList<>();
+        oldMappedCollections = new ArrayList<>();
+        newMappedCollections = new ArrayList<>();
    }

    /**
@@ -111,8 +135,7 @@ public class BulkEditChange
     *
     * @param i The item
     */
-    public void setItem(Item i)
-    {
+    public void setItem(Item i) {
        // Store the item
        item = i;
    }
@@ -122,8 +145,7 @@ public class BulkEditChange
     *
     * @param dcv The value to add
     */
-    public void registerAdd(DCValue dcv)
-    {
+    public void registerAdd(BulkEditMetadataValue dcv) {
        // Add the added value
        adds.add(dcv);
        complete.add(dcv);
@@ -135,8 +157,7 @@ public class BulkEditChange
     *
     * @param dcv The value to remove
     */
-    public void registerRemove(DCValue dcv)
-    {
+    public void registerRemove(BulkEditMetadataValue dcv) {
        // Add the removed value
        removes.add(dcv);
        empty = false;
@@ -147,8 +168,7 @@ public class BulkEditChange
     *
     * @param dcv The value to keep unchanged
     */
-    public void registerConstant(DCValue dcv)
-    {
+    public void registerConstant(BulkEditMetadataValue dcv) {
        // Add the removed value
        constant.add(dcv);
        complete.add(dcv);
@@ -159,8 +179,7 @@ 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;
@@ -171,27 +190,22 @@ 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;
        }
@@ -203,8 +217,7 @@ 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;

@@ -218,8 +231,7 @@ 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;
@@ -230,8 +242,7 @@ public class BulkEditChange
     *
     * @return The item
     */
-    public Item getItem()
-    {
+    public Item getItem() {
        // Return the item
        return item;
    }
@@ -241,8 +252,7 @@ public class BulkEditChange
     *
     * @return the list of elements and their values that have been added.
     */
-    public List<DCValue> getAdds()
-    {
+    public List<BulkEditMetadataValue> getAdds() {
        // Return the array
        return adds;
    }
@@ -252,8 +262,7 @@ public class BulkEditChange
     *
     * @return the list of elements and their values that have been removed.
     */
-    public List<DCValue> getRemoves()
-    {
+    public List<BulkEditMetadataValue> getRemoves() {
        // Return the array
        return removes;
    }
@@ -263,8 +272,7 @@ public class BulkEditChange
     *
     * @return the list of unchanged values
     */
-    public List<DCValue> getConstant()
-    {
+    public List<BulkEditMetadataValue> getConstant() {
        // Return the array
        return constant;
    }
@@ -274,8 +282,7 @@ public class BulkEditChange
     *
     * @return the list of all values
     */
-    public List<DCValue> getComplete()
-    {
+    public List<BulkEditMetadataValue> getComplete() {
        // Return the array
        return complete;
    }
@@ -285,8 +292,7 @@ public class BulkEditChange
     *
     * @return the list of new mapped collections
     */
-    public List<Collection> getNewMappedCollections()
-    {
+    public List<Collection> getNewMappedCollections() {
        // Return the array
        return newMappedCollections;
    }
@@ -296,8 +302,7 @@ public class BulkEditChange
     *
     * @return the list of old mapped collections
     */
-    public List<Collection> getOldMappedCollections()
-    {
+    public List<Collection> getOldMappedCollections() {
        // Return the array
        return oldMappedCollections;
    }
@@ -307,8 +312,7 @@ public class BulkEditChange
     *
     * @return the old owning collection
     */
-    public Collection getOldOwningCollection()
-    {
+    public Collection getOldOwningCollection() {
        // Return the old owning collection
        return oldOwningCollection;
    }
@@ -318,8 +322,7 @@ public class BulkEditChange
     *
     * @return the new owning collection
     */
-    public Collection getNewOwningCollection()
-    {
+    public Collection getNewOwningCollection() {
        // Return the new owning collection
        return newOwningCollection;
    }
@@ -329,8 +332,7 @@ 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;
    }
@@ -340,8 +342,7 @@ 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;
    }
@@ -360,8 +361,7 @@ 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;
    }
@@ -380,8 +380,7 @@ 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;
    }
@@ -400,8 +399,7 @@ public class BulkEditChange
     *
     * @return Whether or not changes have been made
     */
-    public boolean hasChanges()
-    {
+    public boolean hasChanges() {
        return !empty;
    }
 }
--- a/dspace-api/src/main/java/org/dspace/app/bulkedit/BulkEditMetadataValue.java
+++ b/dspace-api/src/main/java/org/dspace/app/bulkedit/BulkEditMetadataValue.java
@@ -0,0 +1,83 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.bulkedit;
+
+/**
+ * Value class used for metadata value edits used by the bulk edit.
+ *
+ * @author kevinvandevelde at atmire.com
+ */
+public class BulkEditMetadataValue {
+
+    private String schema;
+    private String element;
+    private String qualifier;
+    private String language;
+    private String value;
+    private String authority;
+    private int confidence;
+
+    public BulkEditMetadataValue() {
+    }
+
+    public void setSchema(String schema) {
+        this.schema = schema;
+    }
+
+    public void setElement(String element) {
+        this.element = element;
+    }
+
+    public void setQualifier(String qualifier) {
+        this.qualifier = qualifier;
+    }
+
+    public void setLanguage(String language) {
+        this.language = language;
+    }
+
+    public void setValue(String value) {
+        this.value = value;
+    }
+
+    public void setAuthority(String authority) {
+        this.authority = authority;
+    }
+
+    public void setConfidence(int confidence) {
+        this.confidence = confidence;
+    }
+
+    public String getSchema() {
+        return schema;
+    }
+
+    public String getElement() {
+        return element;
+    }
+
+    public String getQualifier() {
+        return qualifier;
+    }
+
+    public String getLanguage() {
+        return language;
+    }
+
+    public String getValue() {
+        return value;
+    }
+
+    public String getAuthority() {
+        return authority;
+    }
+
+    public int getConfidence() {
+        return confidence;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/bulkedit/DSpaceCSV.java
+++ b/dspace-api/src/main/java/org/dspace/app/bulkedit/DSpaceCSV.java
@@ -7,15 +7,41 @@
 */
 package org.dspace.app.bulkedit;

-import org.dspace.content.*;
-import org.dspace.content.Collection;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Context;
-
-import java.util.*;
-import java.util.regex.Pattern;
+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.io.*;
+import java.util.regex.Pattern;
+
+import org.dspace.authority.AuthorityValue;
+import org.dspace.authority.factory.AuthorityServiceFactory;
+import org.dspace.authority.service.AuthorityValueService;
+import org.dspace.content.Collection;
+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.core.Context;
+import org.dspace.services.factory.DSpaceServicesFactory;

 /**
 * Utility class to read and write CSV files
@@ -31,41 +57,70 @@ import java.io.*;
 *
 * @author Stuart Lewis
 */
-public class DSpaceCSV implements Serializable
-{
-    /** The headings of the CSV file */
-    private List<String> headings;
+public class DSpaceCSV implements Serializable {
+    /**
+     * The headings of the CSV file
+     */
+    protected List<String> headings;

-    /** An array list of CSV lines */
-    private List<DSpaceCSVLine> lines;
+    /**
+     * An array list of CSV lines
+     */
+    protected List<DSpaceCSVLine> lines;

-    /** A counter of how many CSV lines this object holds */
-    private int counter;
+    /**
+     * A counter of how many CSV lines this object holds
+     */
+    protected int counter;

-    /** The value separator (defaults to double pipe '||') */
-    protected static String valueSeparator;
+    /**
+     * The value separator (defaults to double pipe '||')
+     */
+    protected String valueSeparator;

-    /** The value separator in an escaped form for using in regexs */
-    protected static String escapedValueSeparator;
+    /**
+     * The value separator in an escaped form for using in regexes
+     */
+    protected String escapedValueSeparator;

-    /** The field separator (defaults to comma) */
-    protected static String fieldSeparator;
+    /**
+     * The field separator (defaults to comma)
+     */
+    protected String fieldSeparator;

-    /** The field separator in an escaped form for using in regexs */
-    protected static String escapedFieldSeparator;
+    /**
+     * The field separator in an escaped form for using in regexes
+     */
+    protected String escapedFieldSeparator;

-    /** The authority separator (defaults to dobule colon '::') */
-    protected static String authoritySeparator;
+    /**
+     * The authority separator (defaults to double colon '::')
+     */
+    protected String authoritySeparator;

-    /** The authority separator in an escaped form for using in regexs */
-    protected static String escapedAuthoritySeparator;
+    /**
+     * 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();


-    /** Whether to export all metadata such as handles and provenance information */
-    private boolean exportAll;
+    /**
+     * Whether to export all metadata such as handles and provenance information
+     */
+    protected boolean exportAll;

-    /** A list of metadata elements to ignore */
-    private Map<String, String> ignore;
+    /**
+     * A list of metadata elements to ignore
+     */
+    protected Map<String, String> ignore;


    /**
@@ -73,8 +128,7 @@ 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();

@@ -87,48 +141,45 @@ 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);
-                }
-                // Store the action
-                else if ("action".equals(element))
-                {
+                } else if ("action".equals(element)) { // Store the action
                    // Store the heading
                    headings.add(element);
+                } else if (!"id".equals(element)) {
+                    String authorityPrefix = "";
+                    AuthorityValue authorityValueType = authorityValueService.getAuthorityValueType(element);
+                    if (authorityValueType != null) {
+                        String authorityType = authorityValueType.getAuthorityType();
+                        authorityPrefix = element.substring(0, authorityType.length() + 1);
+                        element = element.substring(authorityPrefix.length());
                    }
-                else if (!"id".equals(element))
-                {
+
                    // Verify that the heading is valid in the metadata registry
                    String[] clean = element.split("\\[");
                    String[] parts = clean[0].split("\\.");
@@ -147,7 +198,7 @@ public class DSpaceCSV implements Serializable
                    }

                    // Check that the scheme exists
-                    MetadataSchema foundSchema = MetadataSchema.find(c, metadataSchema);
+                    MetadataSchema foundSchema = metadataSchemaService.find(c, metadataSchema);
                    if (foundSchema == null) {
                        throw new MetadataImportInvalidHeadingException(clean[0],
                                                                        MetadataImportInvalidHeadingException.SCHEMA,
@@ -155,8 +206,8 @@ public class DSpaceCSV implements Serializable
                    }

                    // Check that the metadata element exists in the schema
-                    int schemaID = foundSchema.getSchemaID();
-                    MetadataField foundField = MetadataField.findByElement(c, schemaID, metadataElement, metadataQualifier);
+                    MetadataField foundField = metadataFieldService
+                        .findByElement(c, foundSchema, metadataElement, metadataQualifier);
                    if (foundField == null) {
                        throw new MetadataImportInvalidHeadingException(clean[0],
                                                                        MetadataImportInvalidHeadingException.ELEMENT,
@@ -164,7 +215,7 @@ public class DSpaceCSV implements Serializable
                    }

                    // Store the heading
-                    headings.add(element);
+                    headings.add(authorityPrefix + element);
                }
            }

@@ -172,8 +223,7 @@ 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);
@@ -212,11 +262,8 @@ public class DSpaceCSV implements Serializable
                    addItem(lineRead);
                }
            }
-        }
-        finally
-        {
-            if (input != null)
-            {
+        } finally {
+            if (input != null) {
                input.close();
            }
        }
@@ -225,8 +272,7 @@ public class DSpaceCSV implements Serializable
    /**
     * Initialise this class with values from dspace.cfg
     */
-    private void init()
-    {
+    protected void init() {
        // Set the value separator
        setValueSeparator();

@@ -237,28 +283,28 @@ public class DSpaceCSV implements Serializable
        setAuthoritySeparator();

        // Create the headings
-        headings = new ArrayList<String>();
+        headings = new ArrayList<>();

        // Create the blank list of items
-        lines = new ArrayList<DSpaceCSVLine>();
+        lines = new ArrayList<>();

        // Initialise the counter
        counter = 0;

        // Set the metadata fields to ignore
-        ignore = new HashMap<String, String>();
-        String toIgnore = ConfigurationManager.getProperty("bulkedit", "ignore-on-export");
-        if ((toIgnore == null) || ("".equals(toIgnore.trim())))
-        {
-            // Set a default value
-            toIgnore = "dc.date.accessioned, dc.date.available, " +
-                       "dc.date.updated, dc.description.provenance";
-        }
-        String[] toIgnoreArray = toIgnore.split(",");
-        for (String toIgnoreString : toIgnoreArray)
-        {
-            if (!"".equals(toIgnoreString.trim()))
-            {
+        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())) {
                ignore.put(toIgnoreString.trim(), toIgnoreString.trim());
            }
        }
@@ -286,16 +332,13 @@ public class DSpaceCSV implements Serializable
     *
     * If not set, defaults to double pipe '||'
     */
-    private void setValueSeparator()
-    {
+    private void setValueSeparator() {
        // Get the value separator
-        valueSeparator = ConfigurationManager.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 = "||";
        }

@@ -315,32 +358,22 @@ 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 = ConfigurationManager.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 = ",";
        }

@@ -357,16 +390,13 @@ public class DSpaceCSV implements Serializable
     *
     * If not set, defaults to double colon '::'
     */
-    private void setAuthoritySeparator()
-    {
+    private void setAuthoritySeparator() {
        // Get the value separator
-        authoritySeparator = ConfigurationManager.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 = "::";
        }

@@ -380,11 +410,15 @@ 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) {
+            return;
+        }
+
        // Create the CSV line
        DSpaceCSVLine line = new DSpaceCSVLine(i.getID());

@@ -393,48 +427,43 @@ public class DSpaceCSV implements Serializable
        line.add("collection", owningCollectionHandle);

        // Add in any mapped collections
-        Collection[] collections = i.getCollections();
-        for (Collection c : collections)
-        {
+        List<Collection> collections = i.getCollections();
+        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
-        DCValue md[] = i.getMetadata(Item.ANY, Item.ANY, Item.ANY, Item.ANY);
-        for (DCValue value : md)
-        {
+        List<MetadataValue> md = itemService.getMetadata(i, Item.ANY, Item.ANY, Item.ANY, Item.ANY);
+        for (MetadataValue value : md) {
+            MetadataField metadataField = value.getMetadataField();
+            MetadataSchema metadataSchema = metadataField.getMetadataSchema();
            // Get the key (schema.element)
-            String key = value.schema + "." + value.element;
+            String key = metadataSchema.getName() + "." + metadataField.getElement();

            // Add the qualifier if there is one (schema.element.qualifier)
-            if (value.qualifier != null)
-            {
-                key = key + "." + value.qualifier;
+            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.language != null)
-            {
-                key = key + "[" + value.language + "]";
+            if (value.getLanguage() != null) {
+                key = key + "[" + value.getLanguage() + "]";
            }

            // Store the item
-            if (exportAll || okToExport(value))
-            {
+            if (exportAll || okToExport(metadataField)) {
                // Add authority and confidence if authority is not null
-                String mdValue = value.value;
-                if (value.authority != null && !"".equals(value.authority))
-                {
-                    mdValue += authoritySeparator + value.authority + authoritySeparator + value.confidence;
+                String mdValue = value.getValue();
+                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);
                }
            }
@@ -449,12 +478,10 @@ 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
-    {
-        // Check to see if the last character is a field separator, which hides the last empy column
+    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 += " ";
@@ -462,20 +489,17 @@ public class DSpaceCSV implements Serializable

        // Split up on field separator
        String[] parts = line.split(escapedFieldSeparator);
-        ArrayList<String> bits = new ArrayList<String>();
+        ArrayList<String> bits = new ArrayList<>();
        bits.addAll(Arrays.asList(parts));

        // 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);
@@ -490,10 +514,8 @@ 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);
            }
@@ -502,10 +524,8 @@ 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);
            }
@@ -517,18 +537,12 @@ 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
-            {
-                csvLine = new DSpaceCSVLine(Integer.parseInt(id));
-            }
-            catch (NumberFormatException nfe)
-            {
+        } else {
+            try {
+                csvLine = new DSpaceCSVLine(UUID.fromString(id));
+            } 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");
@@ -538,13 +552,10 @@ 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 = "";
                }

@@ -556,10 +567,8 @@ 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);
                    }
                }
@@ -575,8 +584,7 @@ public class DSpaceCSV implements Serializable
     *
     * @return The lines
     */
-    public final List<DSpaceCSVLine> getCSVLines()
-    {
+    public final List<DSpaceCSVLine> getCSVLines() {
        // Return the lines
        return lines;
    }
@@ -586,22 +594,20 @@ 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";
-        Collections.sort(headings);
-        for (String value : headings)
-        {
+        List<String> headingsCopy = new ArrayList<>(headings);
+        Collections.sort(headingsCopy);
+        for (String value : headingsCopy) {
            csvLines[0] = csvLines[0] + fieldSeparator + value;
        }

        Iterator<DSpaceCSVLine> i = lines.iterator();
        int c = 1;
-        while (i.hasNext())
-        {
-            csvLines[c++] = i.next().toCSV(headings);
+        while (i.hasNext()) {
+            csvLines[c++] = i.next().toCSV(headingsCopy, fieldSeparator, valueSeparator);
        }

        return csvLines;
@@ -611,11 +617,9 @@ 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(
@@ -633,16 +637,14 @@ public class DSpaceCSV implements Serializable
     *
     * The list can be configured via the key ignore-on-export in bulkedit.cfg
     *
-     * @param md The DCValue to examine
+     * @param md The Metadatum to examine
     * @return Whether or not it is OK to export this element
     */
-    private final boolean okToExport(DCValue md)
-    {
+    protected boolean okToExport(MetadataField md) {
        // Now compare with the list to ignore
-        String key = md.schema + "." + md.element;
-        if (md.qualifier != null)
-        {
-            key += "." + md.qualifier;
+        String key = md.getMetadataSchema().getName() + "." + md.getElement();
+        if (md.getQualifier() != null) {
+            key += "." + md.getQualifier();
        }
        if (ignore.get(key) != null) {
            return false;
@@ -657,8 +659,7 @@ public class DSpaceCSV implements Serializable
     *
     * @return The headings
     */
-    public List<String> getHeadings()
-    {
+    public List<String> getHeadings() {
        return headings;
    }

@@ -667,15 +668,22 @@ public class DSpaceCSV implements Serializable
     *
     * @return The formatted String as a csv
     */
-    public final String toString()
-    {
+    @Override
+    public final String toString() {
        // Return the csv as one long string
-        StringBuffer csvLines = new StringBuffer();
+        StringBuilder csvLines = new StringBuilder();
        String[] lines = this.getCSVLinesAsStringArray();
-        for (String line : lines)
-        {
+        for (String line : lines) {
            csvLines.append(line).append("\n");
        }
        return csvLines.toString();
    }
+
+    public String getAuthoritySeparator() {
+        return authoritySeparator;
+    }
+
+    public String getEscapedAuthoritySeparator() {
+        return escapedAuthoritySeparator;
+    }
 }
--- a/dspace-api/src/main/java/org/dspace/app/bulkedit/DSpaceCSVLine.java
+++ b/dspace-api/src/main/java/org/dspace/app/bulkedit/DSpaceCSVLine.java
@@ -9,44 +9,78 @@ package org.dspace.app.bulkedit;

 import java.io.Serializable;
 import java.util.ArrayList;
-import java.util.HashMap;
+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;

 /**
 * 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 */
-    private int id;
+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 */
-    private Map<String, ArrayList> items;
+    /**
+     * 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
+     */
+    private transient final Comparator<? super String> headerComparator = new Comparator<String>() {
+        @Override
+        public int compare(String md1, String md2) {
+            // The metadata coming from an external source should be processed after the others
+            AuthorityValue source1 = authorityValueService.getAuthorityValueType(md1);
+            AuthorityValue source2 = authorityValueService.getAuthorityValueType(md2);
+
+            int compare;
+            if (source1 == null && source2 != null) {
+                compare = -1;
+            } else if (source1 != null && source2 == null) {
+                compare = 1;
+            } else {
+                // the order of the rest does not matter
+                compare = md1.compareTo(md2);
+            }
+            return compare;
+        }
+    };

    /**
     * Create a new CSV line
     *
     * @param itemId The item ID of the line
     */
-    public DSpaceCSVLine(int itemId)
-    {
+    public DSpaceCSVLine(UUID itemId) {
        // Store the ID + separator, and initialise the hashtable
        this.id = itemId;
-        items = new HashMap<String, ArrayList>();
+        items = new TreeMap<>(headerComparator);
+//        this.items = new HashMap<String, ArrayList>();
    }

    /**
     * Create a new CSV line for a new item
     */
-    public DSpaceCSVLine()
-    {
-        // Set the ID to be -1, and initialise the hashtable
-        this.id = -1;
-        this.items = new HashMap<String, ArrayList>();
+    public DSpaceCSVLine() {
+        // Set the ID to be null, and initialise the hashtable
+        this.id = null;
+        this.items = new TreeMap<>(headerComparator);
    }

    /**
@@ -54,8 +88,7 @@ public class DSpaceCSVLine implements Serializable
     *
     * @return The item ID
     */
-    public int getID()
-    {
+    public UUID getID() {
        // Return the ID
        return id;
    }
@@ -66,17 +99,14 @@ 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);
        }
    }
@@ -87,8 +117,7 @@ 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);
    }
@@ -98,8 +127,7 @@ 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) {
@@ -114,8 +142,7 @@ 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();
    }
@@ -124,24 +151,23 @@ public class DSpaceCSVLine implements Serializable
     * Write this line out as a CSV formatted string, in the order given by the headings provided
     *
     * @param headings       The headings which define the order the elements must be presented in
+     * @param fieldSeparator separator between metadata fields
+     * @param valueSeparator separator between metadata values (within a field)
     * @return The CSV formatted String
     */
-    protected String toCSV(List<String> headings)
-    {
+    protected String toCSV(List<String> headings, String fieldSeparator, String valueSeparator) {
        StringBuilder bits = new StringBuilder();

        // Add the id
-        bits.append("\"").append(id).append("\"").append(DSpaceCSV.fieldSeparator);
-        bits.append(valueToCSV(items.get("collection")));
+        bits.append("\"").append(id).append("\"").append(fieldSeparator);
+        bits.append(valueToCSV(items.get("collection"), valueSeparator));

        // Add the rest of the elements
-        for (String heading : headings)
-        {
-            bits.append(DSpaceCSV.fieldSeparator);
+        for (String heading : headings) {
+            bits.append(fieldSeparator);
            List<String> values = items.get(heading);
-            if (values != null && !"collection".equals(heading))
-            {
-                bits.append(valueToCSV(values));
+            if (values != null && !"collection".equals(heading)) {
+                bits.append(valueToCSV(values, valueSeparator));
            }
        }

@@ -152,32 +178,26 @@ public class DSpaceCSVLine implements Serializable
     * Internal method to create a CSV formatted String joining a given set of elements
     *
     * @param values         The values to create the string from
+     * @param valueSeparator value separator
     * @return The line as a CSV formatted String
     */
-    protected String valueToCSV(List<String> values)
-    {
+    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)
-                {
-                    str.append(DSpaceCSV.valueSeparator);
+            for (String value : values) {
+                if (str.length() > 0) {
+                    str.append(valueSeparator);
                }

                str.append(value);
--- a/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExport.java
+++ b/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataExport.java
@@ -7,29 +7,51 @@
 */
 package org.dspace.app.bulkedit;

-import org.apache.commons.cli.*;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;

-import org.dspace.content.*;
+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.factory.ContentServiceFactory;
+import org.dspace.content.service.ItemService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
-import org.dspace.handle.HandleManager;
-
-import java.util.ArrayList;
-import java.sql.SQLException;
-import java.util.List;
+import org.dspace.handle.factory.HandleServiceFactory;

 /**
 * Metadata exporter to allow the batch export of metadata into a file
 *
 * @author Stuart Lewis
 */
-public class MetadataExport
-{
-    /** The items to export */
-    private ItemIterator toExport;
+public class MetadataExport {
+    /**
+     * The items to export
+     */
+    protected Iterator<Item> toExport;

-    /** Whether to export all metadata, or just normally edited metadata */
-    private boolean exportAll;
+    protected ItemService itemService;
+
+    protected Context context;
+
+    /**
+     * Whether to export all metadata, or just normally edited metadata
+     */
+    protected boolean exportAll;
+
+    protected MetadataExport() {
+        itemService = ContentServiceFactory.getInstance().getItemService();
+    }

    /**
     * Set up a new metadata export
@@ -38,11 +60,13 @@ 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, ItemIterator toExport, boolean exportAll)
-    {
+    public MetadataExport(Context c, Iterator<Item> toExport, boolean exportAll) {
+        itemService = ContentServiceFactory.getInstance().getItemService();
+
        // Store the export settings
        this.toExport = toExport;
        this.exportAll = exportAll;
+        this.context = c;
    }

    /**
@@ -52,16 +76,15 @@ 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)
-    {
-        try
-        {
+    public MetadataExport(Context c, Community toExport, boolean exportAll) {
+        itemService = ContentServiceFactory.getInstance().getItemService();
+
+        try {
            // Try to export the community
-            this.toExport = new ItemIterator(c, buildFromCommunity(toExport, new ArrayList<Integer>(), 0));
+            this.toExport = buildFromCommunity(c, toExport, 0);
            this.exportAll = exportAll;
-        }
-        catch (SQLException sqle)
-        {
+            this.context = c;
+        } catch (SQLException sqle) {
            // Something went wrong...
            System.err.println("Error running exporter:");
            sqle.printStackTrace(System.err);
@@ -72,48 +95,47 @@ public class MetadataExport
    /**
     * Build an array list of item ids that are in a community (include sub-communities and collections)
     *
+     * @param context   DSpace context
     * @param community The community to build from
-     * @param itemIDs The itemID (used for recursion - use an empty ArrayList)
     * @param indent    How many spaces to use when writing out the names of items added
     * @return The list of item ids
-     * @throws SQLException
+     * @throws SQLException if database error
     */
-    private List<Integer> buildFromCommunity(Community community, List<Integer> itemIDs, int indent)
-                                                                               throws SQLException
-    {
+    protected Iterator<Item> buildFromCommunity(Context context, Community community, int indent)
+        throws SQLException {
        // Add all the collections
-        Collection[] collections = community.getCollections();
-        for (Collection collection : collections)
-        {
-            for (int i = 0; i < indent; i++)
-            {
+        List<Collection> collections = community.getCollections();
+        Iterator<Item> result = null;
+        for (Collection collection : collections) {
+            for (int i = 0; i < indent; i++) {
                System.out.print(" ");
            }

-            ItemIterator items = collection.getAllItems();
-            while (items.hasNext())
-            {
-                int id = items.next().getID();
-                // Only add if not already included (so mapped items only appear once)
-                if (!itemIDs.contains(id))
-                {
-                    itemIDs.add(id);
-                }
-            }
-        }
+            Iterator<Item> items = itemService.findByCollection(context, collection);
+            result = addItemsToResult(result, items);

+        }
        // Add all the sub-communities
-        Community[] communities = community.getSubcommunities();
-        for (Community subCommunity : communities)
-        {
-            for (int i = 0; i < indent; i++)
-            {
+        List<Community> communities = community.getSubcommunities();
+        for (Community subCommunity : communities) {
+            for (int i = 0; i < indent; i++) {
                System.out.print(" ");
            }
-            buildFromCommunity(subCommunity, itemIDs, indent + 1);
+            Iterator<Item> items = buildFromCommunity(context, subCommunity, indent + 1);
+            result = addItemsToResult(result, items);
        }

-        return itemIDs;
+        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;
    }

    /**
@@ -121,22 +143,26 @@ 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())
-            {
-                csv.addItem(toExport.next());
+            while (toExport.hasNext()) {
+                Item item = toExport.next();
+                csv.addItem(item);
+                context.uncacheEntity(item);
            }

+            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();
            return null;
        }
    }
@@ -147,8 +173,7 @@ 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);
@@ -161,9 +186,9 @@ public class MetadataExport
     * main method to run the metadata exporter
     *
     * @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();

@@ -171,83 +196,70 @@ 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);
        }
        String filename = line.getOptionValue('f');

        // Create a context
-        Context c = new Context();
+        Context c = new Context(Context.Mode.READ_ONLY);
        c.turnOffAuthorisationSystem();

        // The things we'll export
-        ItemIterator toExport = null;
+        Iterator<Item> toExport = null;
        MetadataExport exporter = null;

        // Export everything?
        boolean exportAll = line.hasOption('a');

+        ContentServiceFactory contentServiceFactory = ContentServiceFactory.getInstance();
        // Check we have an item OK
-        if (!line.hasOption('i'))
-        {
+        ItemService itemService = contentServiceFactory.getItemService();
+        if (!line.hasOption('i')) {
            System.out.println("Exporting whole repository WARNING: May take some time!");
-            exporter = new MetadataExport(c, Item.findAll(c), exportAll);
-        }
-        else
-        {
+            exporter = new MetadataExport(c, itemService.findAll(c), exportAll);
+        } else {
            String handle = line.getOptionValue('i');
-            DSpaceObject dso = HandleManager.resolveToObject(c, handle);
-            if (dso == null)
-            {
+            DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(c, handle);
+            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<Integer> item = new ArrayList<Integer>();
-                item.add(dso.getID());
-                exporter = new MetadataExport(c, new ItemIterator(c, item), exportAll);
-            }
-            else if (dso.getType() == Constants.COLLECTION)
-            {
+                List<Item> item = new ArrayList<>();
+                item.add((Item) dso);
+                exporter = new MetadataExport(c, item.iterator(), exportAll);
+            } else if (dso.getType() == Constants.COLLECTION) {
                System.out.println("Exporting collection '" + dso.getName() + "' (" + handle + ")");
                Collection collection = (Collection) dso;
-                toExport = collection.getAllItems();
+                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);
            }
--- a/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImport.java
+++ b/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImport.java
--- a/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImportException.java
+++ b/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImportException.java
@@ -12,15 +12,13 @@ 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);
    }

@@ -30,8 +28,7 @@ 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);
    }
 }
--- a/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImportInvalidHeadingException.java
+++ b/dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImportInvalidHeadingException.java
@@ -12,27 +12,40 @@ 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;


@@ -41,9 +54,9 @@ public class MetadataImportInvalidHeadingException extends Exception
     *
     * @param message   the error message
     * @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;
@@ -55,8 +68,7 @@ public class MetadataImportInvalidHeadingException extends Exception
     *
     * @return the type of the exception
     */
-    public String getType()
-    {
+    public String getType() {
        return "" + type;
    }

@@ -65,8 +77,7 @@ public class MetadataImportInvalidHeadingException extends Exception
     *
     * @return the invalid heading
     */
-    public String getBadHeader()
-    {
+    public String getBadHeader() {
        return badHeading;
    }

@@ -75,8 +86,7 @@ public class MetadataImportInvalidHeadingException extends Exception
     *
     * @return the invalid column number
     */
-    public int getColumn()
-    {
+    public int getColumn() {
        return column;
    }

@@ -85,20 +95,16 @@ public class MetadataImportInvalidHeadingException extends Exception
     *
     * @return The exception message
     */
-    public String getMessage()
-    {
-        if (type == SCHEMA)
-        {
-            return "Unknown metadata schema in row " + column + ": " + badHeading;
-        } else if (type == ELEMENT)
-        {
-            return "Unknown metadata element in row " + column + ": " + badHeading;
-        } else if (type == MISSING)
-        {
-            return "Row with missing header: Row " + column;
-        } else
-        {
-            return "Bad metadata declaration in row " + column + ": " + badHeading;
+    @Override
+    public String getMessage() {
+        if (type == SCHEMA) {
+            return "Unknown metadata schema in column " + column + ": " + badHeading;
+        } else if (type == ELEMENT) {
+            return "Unknown metadata element in column " + column + ": " + badHeading;
+        } else if (type == MISSING) {
+            return "Row with missing header: column " + column;
+        } else {
+            return "Bad metadata declaration in column" + column + ": " + badHeading;
        }
    }
 }
--- a/dspace-api/src/main/java/org/dspace/app/bulkedit/package-info.java
+++ b/dspace-api/src/main/java/org/dspace/app/bulkedit/package-info.java
@@ -0,0 +1,21 @@
+/**
+ * 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/
+ */
+
+/**
+ * <p>The DSpace Batch Metadata Editor, which uses a CSV file to export/import
+ * item metadata.</p>
+ * <ul>
+ *   <li>works on items, communities, collections or the whole site</li>
+ *   <li>can also create new items, delete items and withdraw/restore them</li>
+ *   <li>cannot export/import bitstreams</li>
+ * </ul>
+ */
+
+package org.dspace.app.bulkedit;
+
+
--- a/dspace-api/src/main/java/org/dspace/app/checker/ChecksumChecker.java
+++ b/dspace-api/src/main/java/org/dspace/app/checker/ChecksumChecker.java
@@ -8,10 +8,12 @@
 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 org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
@@ -23,42 +25,43 @@ 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.BitstreamInfoDAO;
 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.ListDispatcher;
 import org.dspace.checker.ResultsLogger;
 import org.dspace.checker.ResultsPruner;
 import org.dspace.checker.SimpleDispatcher;
+import org.dspace.content.Bitstream;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.BitstreamService;
+import org.dspace.core.Context;
 import org.dspace.core.Utils;

 /**
 * Command line access to the checksum checker. Options are listed in the
- * documentation for the main method.</p>
+ * documentation for the main method.
 *
 * @author Jim Downing
 * @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();
+
    /**
     * 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>
@@ -77,9 +80,11 @@ 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)
-    {
+    public static void main(String[] args) throws SQLException {
        // set up command line parser
        CommandLineParser parser = new PosixParser();
        CommandLine line = null;
@@ -103,42 +108,37 @@ 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;
+        try {
+            context = new Context();
+

            // Prune stage
-        if (line.hasOption('p'))
-        {
+            if (line.hasOption('p')) {
                ResultsPruner rp = null;
-            try
-            {
+                try {
                    rp = (line.getOptionValue('p') != null) ? ResultsPruner
-                        .getPruner(line.getOptionValue('p')) : ResultsPruner
-                        .getDefaultPruner();
-            }
-            catch (FileNotFoundException e)
-            {
+                        .getPruner(context, line.getOptionValue('p')) : ResultsPruner
+                        .getDefaultPruner(context);
+                } catch (FileNotFoundException e) {
                    LOG.error("File not found", e);
                    System.exit(1);
                }
@@ -153,77 +153,55 @@ public final class ChecksumChecker

            // process should loop infinitely through
            // most_recent_checksum table
-        if (line.hasOption('l'))
-        {
-            dispatcher = new SimpleDispatcher(new BitstreamInfoDAO(), processStart, false); 
-        }
-        else if (line.hasOption('L'))
-        {
-            dispatcher = new SimpleDispatcher(new BitstreamInfoDAO(), processStart, true);
-        }
-        else if (line.hasOption('b'))
-        {
+            if (line.hasOption('l')) {
+                dispatcher = new SimpleDispatcher(context, processStart, false);
+            } else if (line.hasOption('L')) {
+                dispatcher = new SimpleDispatcher(context, processStart, true);
+            } else if (line.hasOption('b')) {
                // check only specified bitstream(s)
                String[] ids = line.getOptionValues('b');
-            List<Integer> idList = new ArrayList<Integer>(ids.length);
+                List<Bitstream> bitstreams = new ArrayList<>(ids.length);

-            for (int i = 0; i < ids.length; i++)
-            {
-                try
-                {
-                    idList.add(Integer.valueOf(ids[i]));
-                }
-                catch (NumberFormatException nfe)
-                {
+                for (int i = 0; i < ids.length; i++) {
+                    try {
+                        bitstreams.add(bitstreamService.find(context, UUID.fromString(ids[i])));
+                    } catch (NumberFormatException nfe) {
                        System.err.println("The following argument: " + ids[i]
                                               + " is not an integer");
                        System.exit(0);
                    }
                }
-            dispatcher = new ListDispatcher(idList);
-        }
-
-        else if (line.hasOption('a'))
-        {
-            dispatcher = new HandleDispatcher(new BitstreamInfoDAO(), line.getOptionValue('a'));
-        }
-        else if (line.hasOption('d'))
-        {
+                dispatcher = new IteratorDispatcher(bitstreams.iterator());
+            } else if (line.hasOption('a')) {
+                dispatcher = new HandleDispatcher(context, line.getOptionValue('a'));
+            } else if (line.hasOption('d')) {
                // run checker process for specified duration
-            try
-            {
+                try {
                    dispatcher = new LimitedDurationDispatcher(
-                        new SimpleDispatcher(new BitstreamInfoDAO(), processStart, true), new Date(
+                        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'))
-        {
-        	int count = Integer.valueOf(line.getOptionValue('c')).intValue();
+            } 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(
-                    new BitstreamInfoDAO(), processStart, false), count);
-        }
-        else
-        {
+                    context, processStart, false), count);
+            } else {
                dispatcher = new LimitedCountDispatcher(new SimpleDispatcher(
-                    new BitstreamInfoDAO(), processStart, false), 1);
+                    context, processStart, false), 1);
            }

            ResultsLogger logger = new ResultsLogger(processStart);
-        CheckerCommand checker = new CheckerCommand();
+            CheckerCommand checker = new CheckerCommand(context);
            // verbose reporting
-        if (line.hasOption('v'))
-        {
+            if (line.hasOption('v')) {
                checker.setReportVerbose(true);
            }

@@ -231,7 +209,13 @@ public final class ChecksumChecker
            checker.setDispatcher(dispatcher);
            checker.setCollector(logger);
            checker.process();
-        System.exit(0);
+            context.complete();
+            context = null;
+        } finally {
+            if (context != null) {
+                context.abort();
+            }
+        }
    }

    /**
@@ -239,24 +223,19 @@ 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);
--- a/dspace-api/src/main/java/org/dspace/app/configuration/APISpringLoader.java
+++ b/dspace-api/src/main/java/org/dspace/app/configuration/APISpringLoader.java
@@ -7,16 +7,14 @@
 */
 package org.dspace.app.configuration;

-import org.dspace.kernel.config.SpringLoader;
-import org.dspace.services.ConfigurationService;
-
 import java.io.File;
 import java.net.MalformedURLException;

+import org.dspace.kernel.config.SpringLoader;
+import org.dspace.services.ConfigurationService;
+
 /**
- * User: kevin (kevin at atmire.com)
- * Date: 3-aug-2011
- * Time: 11:31:21
+ * @author Kevin Van de Velde (kevin at atmire dot com)
 */
 public class APISpringLoader implements SpringLoader {

--- a/dspace-api/src/main/java/org/dspace/app/harvest/Harvest.java
+++ b/dspace-api/src/main/java/org/dspace/app/harvest/Harvest.java
@@ -9,7 +9,9 @@ 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;
@@ -17,30 +19,39 @@ import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.PosixParser;
 import org.dspace.authorize.AuthorizeException;
-import org.dspace.browse.IndexBrowse;
 import org.dspace.content.Collection;
 import org.dspace.content.DSpaceObject;
-import org.dspace.harvest.HarvestedCollection;
 import org.dspace.content.Item;
-import org.dspace.content.ItemIterator;
-import org.dspace.harvest.OAIHarvester;
-import org.dspace.harvest.OAIHarvester.HarvestingException;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.CollectionService;
+import org.dspace.content.service.ItemService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;
-import org.dspace.handle.HandleManager;
+import org.dspace.eperson.factory.EPersonServiceFactory;
+import org.dspace.eperson.service.EPersonService;
+import org.dspace.handle.factory.HandleServiceFactory;
+import org.dspace.harvest.HarvestedCollection;
+import org.dspace.harvest.HarvestingException;
+import org.dspace.harvest.OAIHarvester;
+import org.dspace.harvest.factory.HarvestServiceFactory;
+import org.dspace.harvest.service.HarvestedCollectionService;

 /**
 * Test class for harvested collections.
 *
 * @author Alexey Maslov
 */
-public class Harvest
-{
+public class Harvest {
    private static Context context;

-    public static void main(String[] argv) throws Exception
-    {
+    private static final HarvestedCollectionService harvestedCollectionService =
+        HarvestServiceFactory.getInstance().getHarvestedCollectionService();
+    private static final EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
+    private static final CollectionService collectionService =
+        ContentServiceFactory.getInstance().getCollectionService();
+
+    public static void main(String[] argv) throws Exception {
        // create an options object and populate it
        CommandLineParser parser = new PosixParser();

@@ -56,12 +67,19 @@ public class Harvest
        options.addOption("P", "purge", 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");

@@ -75,27 +93,21 @@ 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 -s 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(
+                "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.exit(0);
@@ -151,21 +163,17 @@ public class Harvest

        // Instantiate our class
        Harvest harvester = new Harvest();
-        harvester.context = new Context();
+        harvester.context = new Context(Context.Mode.BATCH_EDIT);


        // 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.
-        else if ("run".equals(command))
-        {
-            if (collection == null || eperson == null)
-            {
+            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)");
@@ -173,41 +181,33 @@ 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)
-        else if ("purgeAll".equals(command))
-        {
-        	if (eperson == null)
-            {
+            if (eperson == null) {
                System.out
                    .println("Error - an eperson must be provided");
                System.out.println(" (run with -h flag for details)");
                System.exit(1);
            }

-        	List<Integer> cids = HarvestedCollection.findAll(context);
-        	System.out.println("Purging the following collections (deleting items and resetting harvest status): " + cids.toString());
-	    	for (Integer cid : cids) 
-	    	{
-	    		harvester.purgeCollection(cid.toString(), eperson);
+            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());
+                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.
-        else if ("purge".equals(command))
-        {
-            if (collection == null || eperson == null)
-            {
+            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)");
@@ -218,39 +218,34 @@ 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
-        else if ("config".equals(command))
-        {
-            if (collection == null)
-            {
+            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);
        }
    }

@@ -265,39 +260,30 @@ 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 = HandleManager.resolveToObject(context, collectionID);
+                    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;
                    }
-                }
-                // not a handle, try and treat it as an integer collection
-                // database ID
-                else
-                {
-                    System.out.println("Looking up by id: " + collectionID + ", parsed as '" + Integer.parseInt(collectionID) + "', " + "in context: " + context);
-                    targetCollection = Collection.find(context, Integer.parseInt(collectionID));
+                } 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);
+                    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();
        }

@@ -305,33 +291,31 @@ 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);
        System.out.println(collection.getID());

        try {
-    		HarvestedCollection hc = HarvestedCollection.find(context, collection.getID());
+            HarvestedCollection hc = harvestedCollectionService.find(context, collection);
            if (hc == null) {
-        		hc = HarvestedCollection.create(context, collection.getID());
+                hc = harvestedCollectionService.create(context, collection);
            }

            context.turnOffAuthorisationSystem();
            hc.setHarvestParams(type, oaiSource, oaiSetId, mdConfigId);
            hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
-    		hc.update();
+            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();
            }
        }
@@ -345,47 +329,45 @@ 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 
-    	{
-    		EPerson eperson = EPerson.findByEmail(context, email);
+        try {
+            EPerson eperson = ePersonService.findByEmail(context, email);
            context.setCurrentUser(eperson);
            context.turnOffAuthorisationSystem();

-    		ItemIterator it = collection.getAllItems();
-    		IndexBrowse ib = new IndexBrowse(context);
+            ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+            Iterator<Item> it = itemService.findByCollection(context, collection);
            int i = 0;
            while (it.hasNext()) {
                i++;
                Item item = it.next();
                System.out.println("Deleting: " + item.getHandle());
-    			ib.itemRemoved(item);
-    			collection.removeItem(item);
-    			// commit every 50 items
+                collectionService.removeItem(context, collection, item);
+                context.uncacheEntity(item);// Dispatch events every 50 items
                if (i % 50 == 0) {
-    				context.commit();
+                    context.dispatchEvents();
                    i = 0;
                }
            }

-    		HarvestedCollection hc = HarvestedCollection.find(context, collection.getID());
+            HarvestedCollection hc = harvestedCollectionService.find(context, collection);
            if (hc != null) {
-	    		hc.setHarvestResult(null,"");
+                hc.setLastHarvested(null);
+                hc.setHarvestMessage("");
                hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
                hc.setHarvestStartTime(null);
-	    		hc.update();
+                harvestedCollectionService.update(context, hc);
            }
            context.restoreAuthSystemState();
-    		context.commit();
-    	} 
-    	catch (Exception e) {
+            context.dispatchEvents();
+        } catch (Exception e) {
            System.out.println("Changes could not be committed");
            e.printStackTrace();
            System.exit(1);
-    	}
-    	finally {
+        } finally {
            context.restoreAuthSystemState();
        }
    }
@@ -401,11 +383,10 @@ public class Harvest
        OAIHarvester harvester = null;
        try {
            Collection collection = resolveCollection(collectionID);
-        	HarvestedCollection hc = HarvestedCollection.find(context, collection.getID());
+            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);
@@ -417,67 +398,87 @@ public class Harvest

        try {
            // Harvest will not work for an anonymous user
-        	EPerson eperson = EPerson.findByEmail(context, email);
+            EPerson eperson = ePersonService.findByEmail(context, email);
            System.out.println("Harvest started... ");
            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);
        }

        System.out.println("Harvest complete. ");
    }

-    
    /**
-     * 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 
-    	{
-	    	List<Integer> cids = HarvestedCollection.findAll(context);
-	    	for (Integer cid : cids) 
-	    	{
-	    		HarvestedCollection hc = HarvestedCollection.find(context, cid);
+        try {
+            List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context);
+            for (HarvestedCollection harvestedCollection : harvestedCollections) {
                //hc.setHarvestResult(null,"");
-	    		hc.setHarvestStartTime(null);
-	    		hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
-	    		hc.update();
+                harvestedCollection.setHarvestStartTime(null);
+                harvestedCollection.setHarvestStatus(HarvestedCollection.STATUS_READY);
+                harvestedCollectionService.update(context, harvestedCollection);
            }
-	    	context.commit();
            System.out.println("success. ");
-    	}
-    	catch (Exception ex) {
+        } catch (Exception ex) {
            System.out.println("failed. ");
            ex.printStackTrace();
        }
    }

-    
    /**
     * 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... ");
-	    	OAIHarvester.startNewScheduler();
+            HarvestServiceFactory.getInstance().getHarvestSchedulingService().startNewScheduler();
            System.out.println("running. ");
-    	}
-    	catch (Exception ex) {
+        } catch (Exception ex) {
            ex.printStackTrace();
        }
    }

+    /**
+     * See if the responder is alive and working.
+     *
+     * @param server         address of the responder's host.
+     * @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) {
+        List<String> errors;
+
+        System.out.print("Testing basic PMH access:  ");
+        errors = OAIHarvester.verifyOAIharvester(server, set,
+                                                 (null != metadataFormat) ? metadataFormat : "dc", false);
+        if (errors.isEmpty()) {
+            System.out.println("OK");
+        } 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()) {
+            System.out.println("OK");
+        } else {
+            for (String error : errors) {
+                System.err.println(error);
+            }
+        }
+    }
 }
--- a/dspace-api/src/main/java/org/dspace/app/itemexport/ItemExport.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemexport/ItemExport.java
--- a/dspace-api/src/main/java/org/dspace/app/itemexport/ItemExportCLITool.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemexport/ItemExportCLITool.java
@@ -0,0 +1,246 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.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.dspace.app.itemexport.factory.ItemExportServiceFactory;
+import org.dspace.app.itemexport.service.ItemExportService;
+import org.dspace.content.Collection;
+import org.dspace.content.Item;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.CollectionService;
+import org.dspace.content.service.ItemService;
+import org.dspace.core.Constants;
+import org.dspace.core.Context;
+import org.dspace.handle.factory.HandleServiceFactory;
+import org.dspace.handle.service.HandleService;
+
+/**
+ * Item exporter to create simple AIPs for DSpace content. Currently exports
+ * individual items, or entire collections. For instructions on use, see
+ * printUsage() method.
+ * <P>
+ * ItemExport creates the simple AIP package that the importer also uses. It
+ * consists of:
+ * <P>
+ * /exportdir/42/ (one directory per item) / dublin_core.xml - qualified dublin
+ * core in RDF schema / contents - text file, listing one file per line / file1
+ * - files contained in the item / file2 / ...
+ * <P>
+ * issues -doesn't handle special characters in metadata (needs to turn {@code &'s} into
+ * {@code &amp;}, etc.)
+ * <P>
+ * Modified by David Little, UCSD Libraries 12/21/04 to allow the registration
+ * of files (bitstreams) into DSpace.
+ *
+ * @author David Little
+ * @author Jay Paz
+ */
+public class ItemExportCLITool {
+
+    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 {
+        // create an options object and populate it
+        CommandLineParser parser = new PosixParser();
+
+        Options options = new Options();
+
+        options.addOption("t", "type", true, "type: COLLECTION or ITEM");
+        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("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)");
+        options.addOption("h", "help", false, "help");
+
+        // as pointed out by Peter Dietz this provides similar functionality to export metadata
+        // but it is needed since it directly exports to Simple Archive Format (SAF)
+        options.addOption("x", "exclude-bitstreams", false, "do not export bitstreams");
+
+        CommandLine line = parser.parse(options, argv);
+
+        String typeString = null;
+        String destDirName = null;
+        String myIDString = null;
+        int seqStart = -1;
+        int myType = -1;
+
+        Item myItem = null;
+        Collection mycollection = null;
+
+        if (line.hasOption('h')) {
+            HelpFormatter myhelp = new HelpFormatter();
+            myhelp.printHelp("ItemExport\n", options);
+            System.out
+                .println("\nfull collection: ItemExport -t COLLECTION -i ID -d dest -n number");
+            System.out
+                .println("singleitem:       ItemExport -t ITEM -i ID -d dest -n number");
+
+            System.exit(0);
+        }
+
+        if (line.hasOption('t')) { // type
+            typeString = line.getOptionValue('t');
+
+            if ("ITEM".equals(typeString)) {
+                myType = Constants.ITEM;
+            } else if ("COLLECTION".equals(typeString)) {
+                myType = Constants.COLLECTION;
+            }
+        }
+
+        if (line.hasOption('i')) { // id
+            myIDString = line.getOptionValue('i');
+        }
+
+        if (line.hasOption('d')) { // dest
+            destDirName = line.getOptionValue('d');
+        }
+
+        if (line.hasOption('n')) { // number
+            seqStart = Integer.parseInt(line.getOptionValue('n'));
+        }
+
+        boolean migrate = false;
+        if (line.hasOption('m')) { // number
+            migrate = true;
+        }
+
+        boolean zip = false;
+        String zipFileName = "";
+        if (line.hasOption('z')) {
+            zip = true;
+            zipFileName = line.getOptionValue('z');
+        }
+
+        boolean excludeBitstreams = false;
+        if (line.hasOption('x')) {
+            excludeBitstreams = true;
+        }
+
+        // now validate the args
+        if (myType == -1) {
+            System.out
+                .println("type must be either COLLECTION or ITEM (-h for help)");
+            System.exit(1);
+        }
+
+        if (destDirName == null) {
+            System.out
+                .println("destination directory must be set (-h for help)");
+            System.exit(1);
+        }
+
+        if (seqStart == -1) {
+            System.out
+                .println("sequence start number must be set (-h for help)");
+            System.exit(1);
+        }
+
+        if (myIDString == null) {
+            System.out
+                .println("ID must be set to either a database ID or a handle (-h for help)");
+            System.exit(1);
+        }
+
+        Context c = new Context(Context.Mode.READ_ONLY);
+        c.turnOffAuthorisationSystem();
+
+        if (myType == Constants.ITEM) {
+            // first, is myIDString a handle?
+            if (myIDString.indexOf('/') != -1) {
+                myItem = (Item) handleService.resolveToObject(c, myIDString);
+
+                if ((myItem == null) || (myItem.getType() != Constants.ITEM)) {
+                    myItem = null;
+                }
+            } else {
+                myItem = itemService.find(c, UUID.fromString(myIDString));
+            }
+
+            if (myItem == null) {
+                System.out
+                    .println("Error, item cannot be found: " + myIDString);
+            }
+        } 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 = null;
+                }
+            } else if (myIDString != null) {
+                mycollection = collectionService.find(c, UUID.fromString(myIDString));
+            }
+
+            if (mycollection == null) {
+                System.out.println("Error, collection cannot be found: "
+                                       + myIDString);
+                System.exit(1);
+            }
+        }
+
+        if (zip) {
+            Iterator<Item> items;
+            if (myItem != null) {
+                List<Item> myItems = new ArrayList<>();
+                myItems.add(myItem);
+                items = myItems.iterator();
+            } 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) {
+                // it's only a single item
+                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
+                Iterator<Item> i = itemService.findByCollection(c, mycollection);
+                itemExportService.exportItem(c, i, destDirName, seqStart, migrate, excludeBitstreams);
+            }
+        }
+
+        c.complete();
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemexport/ItemExportException.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemexport/ItemExportException.java
@@ -10,20 +10,17 @@ 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;
    }
 }
--- a/dspace-api/src/main/java/org/dspace/app/itemexport/ItemExportServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemexport/ItemExportServiceImpl.java
--- a/dspace-api/src/main/java/org/dspace/app/itemexport/factory/ItemExportServiceFactory.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemexport/factory/ItemExportServiceFactory.java
@@ -0,0 +1,27 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.itemexport.factory;
+
+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
+ *
+ * @author kevinvandevelde at atmire.com
+ */
+public abstract class ItemExportServiceFactory {
+
+    public abstract ItemExportService getItemExportService();
+
+    public static ItemExportServiceFactory getInstance() {
+        return DSpaceServicesFactory.getInstance().getServiceManager()
+                                    .getServiceByName("itemExportServiceFactory", ItemExportServiceFactory.class);
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemexport/factory/ItemExportServiceFactoryImpl.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemexport/factory/ItemExportServiceFactoryImpl.java
@@ -0,0 +1,28 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.itemexport.factory;
+
+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
+ *
+ * @author kevinvandevelde at atmire.com
+ */
+public class ItemExportServiceFactoryImpl extends ItemExportServiceFactory {
+
+    @Autowired(required = true)
+    private ItemExportService itemExportService;
+
+    @Override
+    public ItemExportService getItemExportService() {
+        return itemExportService;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemexport/service/ItemExportService.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemexport/service/ItemExportService.java
@@ -0,0 +1,270 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.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;
+
+/**
+ * Item exporter to create simple AIPs for DSpace content. Currently exports
+ * individual items, or entire collections. For instructions on use, see
+ * printUsage() method.
+ * <P>
+ * ItemExport creates the simple AIP package that the importer also uses. It
+ * consists of:
+ * <P>
+ * /exportdir/42/ (one directory per item) / dublin_core.xml - qualified dublin
+ * core in RDF schema / contents - text file, listing one file per line / file1
+ * - files contained in the item / file2 / ...
+ * <P>
+ * issues -doesn't handle special characters in metadata (needs to turn {@code &'s} into
+ * {@code &amp;}, etc.)
+ * <P>
+ * Modified by David Little, UCSD Libraries 12/21/04 to allow the registration
+ * of files (bitstreams) into DSpace.
+ *
+ * @author David Little
+ * @author Jay Paz
+ */
+public interface ItemExportService {
+
+    /**
+     * used for export download
+     */
+    public static final String COMPRESSED_EXPORT_MIME_TYPE = "application/zip";
+
+    public void exportItem(Context c, Iterator<Item> i,
+                           String destDirName, int seqStart, boolean migrate,
+                           boolean excludeBitstreams) throws Exception;
+
+    /**
+     * Method to perform an export and save it as a zip file.
+     *
+     * @param context           The DSpace Context
+     * @param items             The items to export
+     * @param destDirName       The directory to save the export in
+     * @param zipFileName       The name to save the zip file as
+     * @param seqStart          The first number in the sequence
+     * @param migrate           Whether to use the migrate option or not
+     * @param excludeBitstreams Whether to exclude bitstreams or not
+     * @throws Exception if error
+     */
+    public void exportAsZip(Context context, Iterator<Item> items,
+                            String destDirName, String zipFileName,
+                            int seqStart, boolean migrate,
+                            boolean excludeBitstreams) throws Exception;
+
+    /**
+     * Convenience methot to create export a single Community, Collection, or
+     * Item
+     *
+     * @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
+     */
+    public void createDownloadableExport(DSpaceObject dso,
+                                         Context context, boolean migrate) throws Exception;
+
+    /**
+     * 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 migrate   Whether to use the migrate option or not
+     * @throws Exception if error
+     */
+    public void createDownloadableExport(List<DSpaceObject> dsObjects,
+                                         Context context, boolean migrate) throws Exception;
+
+    /**
+     * 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 migrate         Whether to use the migrate option or not
+     * @throws Exception if error
+     */
+    public void createDownloadableExport(DSpaceObject dso,
+                                         Context context, String additionalEmail, boolean migrate) throws Exception;
+
+    /**
+     * 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 migrate         Whether to use the migrate option or not
+     * @throws Exception if error
+     */
+    public void createDownloadableExport(List<DSpaceObject> dsObjects,
+                                         Context context, String additionalEmail, boolean migrate) throws Exception;
+
+
+    /**
+     * 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
+     * @return String representing the file name in the form of
+     * 'export_yyy_MMM_dd_count_epersonID'
+     * @throws Exception if error
+     */
+    public String assembleFileName(String type, EPerson eperson,
+                                   Date date) throws Exception;
+
+
+    /**
+     * 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
+     * @return String representing a directory in the form of
+     * org.dspace.app.itemexport.download.dir/epersonID
+     * @throws Exception if error
+     */
+    public String getExportDownloadDirectory(EPerson ePerson)
+        throws Exception;
+
+
+    /**
+     * Returns config file entry for org.dspace.app.itemexport.work.dir
+     *
+     * @return String representing config file entry for
+     * org.dspace.app.itemexport.work.dir
+     * @throws Exception if error
+     */
+    public String getExportWorkDirectory() throws Exception;
+
+    /**
+     * 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
+     * @return an input stream of the file to be downloaded
+     * @throws Exception if error
+     */
+    public InputStream getExportDownloadInputStream(String fileName,
+                                                    EPerson eperson) throws Exception;
+
+    /**
+     * 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
+     * @throws Exception if error
+     */
+    public long getExportFileSize(Context context, String fileName) throws Exception;
+
+    /**
+     * 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.
+     * @return date as long
+     * @throws Exception if error
+     * @see java.io.File#lastModified()
+     */
+    public long getExportFileLastModified(Context context, String fileName)
+        throws Exception;
+
+    /**
+     * The file name of the export archive contains the eperson id of the person
+     * 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
+     * @return true if it is the same person false otherwise
+     */
+    public boolean canDownload(Context context, String fileName);
+
+    /**
+     * Reads the download directory for the eperson to see if any export
+     * archives are available
+     *
+     * @param eperson EPerson object
+     * @return a list of file names representing export archives that have been
+     * processed
+     * @throws Exception if error
+     */
+    public List<String> getExportsAvailable(EPerson eperson)
+        throws Exception;
+
+    /**
+     * A clean up method that is ran before a new export archive is created. It
+     * 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
+     * @throws Exception if error
+     */
+    public void deleteOldExportArchives(EPerson eperson) throws Exception;
+
+    /**
+     * A clean up method that is ran before a new export archive is created. It
+     * uses the config file entry 'org.dspace.app.itemexport.life.span.hours' to
+     * determine if the current exports are too old and need purgeing
+     * Removes all old exports, not just those for the person doing the export.
+     *
+     * @throws Exception if error
+     */
+    public void deleteOldExportArchives() throws Exception;
+
+    /**
+     * Since the archive is created in a new thread we are unable to communicate
+     * with calling method about success or failure. We accomplis this
+     * 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
+     *                 the email
+     * @throws MessagingException if error
+     */
+    public void emailSuccessMessage(Context context, EPerson eperson,
+                                    String fileName) throws MessagingException;
+
+    /**
+     * Since the archive is created in a new thread we are unable to communicate
+     * with calling method about success or failure. We accomplis this
+     * 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
+     * @throws MessagingException if error
+     */
+    public void emailErrorMessage(EPerson eperson, String error)
+        throws MessagingException;
+
+    /**
+     * Zip source to target
+     *
+     * @param strSource source file
+     * @param target    target file
+     * @throws Exception if error
+     */
+    public void zip(String strSource, String target) throws Exception;
+
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemimport/BTEBatchImportService.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemimport/BTEBatchImportService.java
@@ -0,0 +1,106 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.itemimport;
+
+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 {
+
+    TransformationEngine transformationEngine;
+    Map<String, DataLoader> dataLoaders = new HashMap<String, DataLoader>();
+    Map<String, String> outputMap = new HashMap<String, String>();
+
+    /**
+     * Default constructor
+     */
+    public BTEBatchImportService() {
+        super();
+    }
+
+    /**
+     * Setter method for dataLoaders parameter
+     *
+     * @param dataLoaders map of data loaders
+     */
+    public void setDataLoaders(Map<String, DataLoader> dataLoaders) {
+        this.dataLoaders = dataLoaders;
+    }
+
+    /**
+     * Get data loaders
+     *
+     * @return the map of DataLoaders
+     */
+    public Map<String, DataLoader> getDataLoaders() {
+        return dataLoaders;
+    }
+
+    /**
+     * Get output map
+     *
+     * @return the outputMapping
+     */
+    public Map<String, String> getOutputMap() {
+        return outputMap;
+    }
+
+    /**
+     * Setter method for the outputMapping
+     *
+     * @param outputMap the output mapping
+     */
+    public void setOutputMap(Map<String, String> outputMap) {
+        this.outputMap = outputMap;
+    }
+
+    /**
+     * Get transformation engine
+     *
+     * @return transformation engine
+     */
+    public TransformationEngine getTransformationEngine() {
+        return transformationEngine;
+    }
+
+    /**
+     * set transformation engine
+     *
+     * @param transformationEngine transformation engine
+     */
+    public void setTransformationEngine(TransformationEngine transformationEngine) {
+        this.transformationEngine = transformationEngine;
+    }
+
+    /**
+     * Getter of file data loaders
+     *
+     * @return List of file data loaders
+     */
+    public List<String> getFileDataLoaders() {
+        List<String> result = new ArrayList<String>();
+
+        for (String key : dataLoaders.keySet()) {
+            DataLoader dl = dataLoaders.get(key);
+            if (dl instanceof FileDataLoader) {
+                result.add(key);
+            }
+        }
+        return result;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemimport/BatchUpload.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemimport/BatchUpload.java
@@ -0,0 +1,229 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.itemimport;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.LineNumberReader;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.GregorianCalendar;
+import java.util.List;
+
+/**
+ * @author kstamatis
+ */
+public class BatchUpload {
+
+    private Date date;
+    private File dir;
+    private boolean successful;
+    private int itemsImported;
+    private int totalItems = 0;
+    private List<String> handlesImported = new ArrayList<String>();
+    private String errorMsg = "";
+    private String errorMsgHTML = "";
+
+    /**
+     * Initialize with directory
+     *
+     * @param dirPath directory path
+     */
+    public BatchUpload(String dirPath) {
+
+        this.initializeWithFile(new File(dirPath));
+
+    }
+
+    /**
+     * Initialize with directory
+     *
+     * @param dir directory path
+     */
+    public BatchUpload(File dir) {
+
+        this.initializeWithFile(dir);
+
+    }
+
+    /**
+     * Initialize with directory
+     *
+     * @param dir directory path
+     */
+    private void initializeWithFile(File dir) {
+
+        this.dir = dir;
+
+        String dirName = dir.getName();
+        long timeMillis = Long.parseLong(dirName);
+        Calendar calendar = new GregorianCalendar();
+        calendar.setTimeInMillis(timeMillis);
+        this.date = calendar.getTime();
+
+        try {
+            this.itemsImported = countLines(dir + File.separator + "mapfile");
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+
+        for (File file : dir.listFiles()) {
+            if (file.isDirectory()) {
+                this.totalItems = file.list().length;
+            }
+        }
+
+        this.successful = this.totalItems == this.itemsImported;
+
+        //Parse possible error message
+
+        File errorFile = new File(dir + File.separator + "error.txt");
+        if (errorFile.exists()) {
+            try {
+                readFile(dir + File.separator + "error.txt");
+            } catch (IOException e) {
+                // TODO Auto-generated catch block
+                e.printStackTrace();
+            }
+        }
+    }
+
+    /**
+     * Count lines in file
+     *
+     * @param filename file name
+     * @return lines in file
+     * @throws IOException if IO error
+     */
+    private int countLines(String filename) throws IOException {
+        LineNumberReader reader = new LineNumberReader(new FileReader(filename));
+        int cnt = 0;
+        String lineRead = "";
+        while ((lineRead = reader.readLine()) != null) {
+            String[] parts = lineRead.split(" ");
+            if (parts.length > 1) {
+                handlesImported.add(parts[1].trim());
+            } else {
+                handlesImported.add(lineRead);
+            }
+        }
+
+        cnt = reader.getLineNumber();
+        reader.close();
+        return cnt;
+    }
+
+    /**
+     * Read a file
+     *
+     * @param filename file name
+     * @throws IOException if IO error
+     */
+    private void readFile(String filename) throws IOException {
+        LineNumberReader reader = new LineNumberReader(new FileReader(filename));
+        String lineRead = "";
+        while ((lineRead = reader.readLine()) != null) {
+            this.errorMsg += lineRead + "\n";
+
+            if (lineRead.startsWith("\tat ")) {
+                this.errorMsgHTML += "<span class=\"batchimport-error-tab\">" + lineRead + "</span><br/>";
+            } else if (lineRead.startsWith("Caused by")) {
+                this.errorMsgHTML += "<span class=\"batchimport-error-caused\">" + lineRead + "</span><br/>";
+            } else {
+                this.errorMsgHTML += lineRead + "<br/>";
+            }
+        }
+        reader.close();
+    }
+
+    /**
+     * Get date
+     *
+     * @return Date
+     */
+    public Date getDate() {
+        return date;
+    }
+
+    /**
+     * Get path to directory
+     *
+     * @return directory
+     */
+    public File getDir() {
+        return dir;
+    }
+
+    /**
+     * Whether successulf
+     *
+     * @return true or false
+     */
+    public boolean isSuccessful() {
+        return successful;
+    }
+
+    /**
+     * Get items imported
+     *
+     * @return number of items
+     */
+    public int getItemsImported() {
+        return itemsImported;
+    }
+
+    /**
+     * Get total items
+     *
+     * @return total
+     */
+    public int getTotalItems() {
+        return totalItems;
+    }
+
+    /**
+     * Get formatted date (DD/MM/YY)
+     *
+     * @return date as string
+     */
+    public String getDateFormatted() {
+        SimpleDateFormat df = new SimpleDateFormat("dd/MM/yyyy - HH:mm");
+
+        return df.format(date);
+    }
+
+    /**
+     * Get handles of imported files
+     *
+     * @return list of handles
+     */
+    public List<String> getHandlesImported() {
+        return handlesImported;
+    }
+
+    /**
+     * Get error message
+     *
+     * @return error message
+     */
+    public String getErrorMsg() {
+        return errorMsg;
+    }
+
+    /**
+     * Get error message as HTML
+     *
+     * @return error message string as HTML
+     */
+    public String getErrorMsgHTML() {
+        return errorMsgHTML;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemimport/DataLoaderService.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemimport/DataLoaderService.java
@@ -1,52 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemimport;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import gr.ekt.transformationengine.core.DataLoader;
-
-
-
-
-/**
- * This class acts as a Service in the procedure ot batch import using the Biblio-Transformation-Engine
- */
-public class DataLoaderService
-{
-
-    Map<String, DataLoader> dataLoaders = new HashMap<String, DataLoader>();
-    
-    /**
-     * Default constructor
-     */
-    public DataLoaderService()
-    {
-        super();
-    }
-
-    /**
-     * Setter method for dataLoaders parameter
-     * @param dataLoaders
-     */
-    public void setDataLoaders(Map<String, DataLoader> dataLoaders)
-    {
-        this.dataLoaders = dataLoaders;
-    }
-
-    /**
-     * 
-     * @return the map of DataLoaders
-     */
-    public Map<String, DataLoader> getDataLoaders()
-    {
-        return dataLoaders;
-    }
-    
-}
--- a/dspace-api/src/main/java/org/dspace/app/itemimport/ItemImport.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemimport/ItemImport.java
--- a/dspace-api/src/main/java/org/dspace/app/itemimport/ItemImportCLITool.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemimport/ItemImportCLITool.java
@@ -0,0 +1,431 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.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.dspace.app.itemimport.factory.ItemImportServiceFactory;
+import org.dspace.app.itemimport.service.ItemImportService;
+import org.dspace.content.Collection;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.CollectionService;
+import org.dspace.core.Constants;
+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;
+
+/**
+ * Import items into DSpace. The conventional use is upload files by copying
+ * them. DSpace writes the item's bitstreams into its assetstore. Metadata is
+ * also loaded to the DSpace database.
+ * <P>
+ * A second use assumes the bitstream files already exist in a storage
+ * resource accessible to DSpace. In this case the bitstreams are 'registered'.
+ * That is, the metadata is loaded to the DSpace database and DSpace is given
+ * the location of the file which is subsumed into DSpace.
+ * <P>
+ * The distinction is controlled by the format of lines in the 'contents' file.
+ * See comments in processContentsFile() below.
+ * <P>
+ * Modified by David Little, UCSD Libraries 12/21/04 to
+ * allow the registration of files (bitstreams) into DSpace.
+ */
+public class ItemImportCLITool {
+
+    private static boolean template = false;
+
+    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 {
+        Date startTime = new Date();
+        int status = 0;
+
+        try {
+            // create an options object and populate it
+            CommandLineParser parser = new PosixParser();
+
+            Options options = new Options();
+
+            options.addOption("a", "add", false, "add items to DSpace");
+            options.addOption("b", "add-bte", false, "add items to DSpace via Biblio-Transformation-Engine (BTE)");
+            options.addOption("r", "replace", false, "replace items in mapfile");
+            options.addOption("d", "delete", false,
+                              "delete items listed in mapfile");
+            options.addOption("i", "inputtype", true, "input type in case of BTE import");
+            options.addOption("s", "source", true, "source of items (directory)");
+            options.addOption("z", "zip", true, "name of zip file");
+            options.addOption("c", "collection", true,
+                              "destination collection(s) Handle or database ID");
+            options.addOption("m", "mapfile", true, "mapfile items in mapfile");
+            options.addOption("e", "eperson", true,
+                              "email of eperson doing importing");
+            options.addOption("w", "workflow", false,
+                              "send submission through collection's workflow");
+            options.addOption("n", "notify", false,
+                              "if sending submissions through the workflow, send notification emails");
+            options.addOption("t", "test", false,
+                              "test run - do not actually import items");
+            options.addOption("p", "template", false, "apply template");
+            options.addOption("R", "resume", false,
+                              "resume a failed import (add only)");
+            options.addOption("q", "quiet", false, "don't display metadata");
+
+            options.addOption("h", "help", false, "help");
+
+            CommandLine line = parser.parse(options, argv);
+
+            String command = null; // add replace remove, etc
+            String bteInputType = null; //ris, endnote, tsv, csv, bibtex
+            String sourcedir = null;
+            String mapfile = null;
+            String eperson = null; // db ID or email
+            String[] collections = null; // db ID or handles
+            boolean isTest = false;
+            boolean isResume = false;
+            boolean useWorkflow = false;
+            boolean useWorkflowSendEmail = false;
+            boolean isQuiet = false;
+
+            if (line.hasOption('h')) {
+                HelpFormatter myhelp = new HelpFormatter();
+                myhelp.printHelp("ItemImport\n", options);
+                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");
+                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.");
+
+                System.exit(0);
+            }
+
+            if (line.hasOption('a')) {
+                command = "add";
+            }
+
+            if (line.hasOption('r')) {
+                command = "replace";
+            }
+
+            if (line.hasOption('d')) {
+                command = "delete";
+            }
+
+            if (line.hasOption('b')) {
+                command = "add-bte";
+            }
+
+            if (line.hasOption('i')) {
+                bteInputType = line.getOptionValue('i');
+            }
+
+            if (line.hasOption('w')) {
+                useWorkflow = true;
+                if (line.hasOption('n')) {
+                    useWorkflowSendEmail = true;
+                }
+            }
+
+            if (line.hasOption('t')) {
+                isTest = true;
+                System.out.println("**Test Run** - not actually importing items.");
+            }
+
+            if (line.hasOption('p')) {
+                template = true;
+            }
+
+            if (line.hasOption('s')) { // source
+                sourcedir = line.getOptionValue('s');
+            }
+
+            if (line.hasOption('m')) { // mapfile
+                mapfile = line.getOptionValue('m');
+            }
+
+            if (line.hasOption('e')) { // eperson
+                eperson = line.getOptionValue('e');
+            }
+
+            if (line.hasOption('c')) { // collections
+                collections = line.getOptionValues('c');
+            }
+
+            if (line.hasOption('R')) {
+                isResume = true;
+                System.out
+                    .println("**Resume import** - attempting to import items not already imported");
+            }
+
+            if (line.hasOption('q')) {
+                isQuiet = true;
+            }
+
+            boolean zip = false;
+            String zipfilename = "";
+            if (line.hasOption('z')) {
+                zip = true;
+                zipfilename = line.getOptionValue('z');
+            }
+
+            //By default assume collections will be given on the command line
+            boolean commandLineCollections = true;
+            // now validate
+            // must have a command set
+            if (command == null) {
+                System.out
+                    .println("Error - must run with either add, replace, or remove (run with -h flag for details)");
+                System.exit(1);
+            } else if ("add".equals(command) || "replace".equals(command)) {
+                if (sourcedir == null) {
+                    System.out
+                        .println("Error - a source directory containing items must be set");
+                    System.out.println(" (run with -h flag for details)");
+                    System.exit(1);
+                }
+
+                if (mapfile == null) {
+                    System.out
+                        .println("Error - a map file to hold importing results must be specified");
+                    System.out.println(" (run with -h flag for details)");
+                    System.exit(1);
+                }
+
+                if (eperson == null) {
+                    System.out
+                        .println("Error - an eperson to do the importing must be specified");
+                    System.out.println(" (run with -h flag for details)");
+                    System.exit(1);
+                }
+
+                if (collections == null) {
+                    System.out.println("No collections given. Assuming 'collections' file inside item directory");
+                    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
+
+                if (mapfile == null) {
+                    System.out
+                        .println("Error - a map file to hold importing results must be specified");
+                    System.out.println(" (run with -h flag for details)");
+                    System.exit(1);
+                }
+
+                if (eperson == null) {
+                    System.out
+                        .println("Error - an eperson to do the importing must be specified");
+                    System.out.println(" (run with -h flag for details)");
+                    System.exit(1);
+                }
+
+                if (collections == null) {
+                    System.out.println("No collections given. Assuming 'collections' file inside item directory");
+                    commandLineCollections = false;
+                }
+
+                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");
+                    System.out.println(" (run with -h flag for details)");
+                    System.exit(1);
+                }
+            } else if ("delete".equals(command)) {
+                if (eperson == null) {
+                    System.out
+                        .println("Error - an eperson to do the importing must be specified");
+                    System.exit(1);
+                }
+
+                if (mapfile == null) {
+                    System.out.println("Error - a map file must be specified");
+                    System.exit(1);
+                }
+            }
+
+            // can only resume for adds
+            if (isResume && !"add".equals(command) && !"add-bte".equals(command)) {
+                System.out
+                    .println("Error - resume option only works with the --add or the --add-bte commands");
+                System.exit(1);
+            }
+
+            // do checks around mapfile - if mapfile exists and 'add' is selected,
+            // resume must be chosen
+            File myFile = new File(mapfile);
+
+            if (!isResume && "add".equals(command) && myFile.exists()) {
+                System.out.println("Error - the mapfile " + mapfile
+                                       + " already exists.");
+                System.out
+                    .println("Either delete it or use --resume if attempting to resume an aborted import.");
+                System.exit(1);
+            }
+
+            ItemImportService myloader = ItemImportServiceFactory.getInstance().getItemImportService();
+            myloader.setTest(isTest);
+            myloader.setResume(isResume);
+            myloader.setUseWorkflow(useWorkflow);
+            myloader.setUseWorkflowSendEmail(useWorkflowSendEmail);
+            myloader.setQuiet(isQuiet);
+
+            // create a context
+            Context c = new Context(Context.Mode.BATCH_EDIT);
+
+            // find the EPerson, assign to context
+            EPerson myEPerson = null;
+
+            if (eperson.indexOf('@') != -1) {
+                // @ sign, must be an email
+                myEPerson = epersonService.findByEmail(c, eperson);
+            } else {
+                myEPerson = epersonService.find(c, UUID.fromString(eperson));
+            }
+
+            if (myEPerson == null) {
+                System.out.println("Error, eperson cannot be found: " + eperson);
+                System.exit(1);
+            }
+
+            c.setCurrentUser(myEPerson);
+
+            // find collections
+            List<Collection> mycollections = null;
+
+            // don't need to validate collections set if command is "delete"
+            // also if no collections are given in the command line
+            if (!"delete".equals(command) && commandLineCollections) {
+                System.out.println("Destination collections:");
+
+                mycollections = new ArrayList<>();
+
+                // validate each collection arg to see if it's a real collection
+                for (int i = 0; i < collections.length; i++) {
+                    // is the ID a handle?
+                    if (collections[i].indexOf('/') != -1) {
+                        // string has a / so it must be a handle - try and resolve
+                        // it
+                        mycollections.add((Collection) handleService
+                            .resolveToObject(c, collections[i]));
+
+                        // resolved, now make sure it's a collection
+                        if ((mycollections.get(i) == null)
+                            || (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
+                        mycollections.set(i, collectionService.find(c, UUID.fromString(collections[i])));
+                    }
+
+                    // was the collection valid?
+                    if (mycollections.get(i) == null) {
+                        throw new IllegalArgumentException("Cannot resolve "
+                                                               + collections[i] + " to collection");
+                    }
+
+                    // print progress info
+                    String owningPrefix = "";
+
+                    if (i == 0) {
+                        owningPrefix = "Owning ";
+                    }
+
+                    System.out.println(owningPrefix + " Collection: "
+                                           + mycollections.get(i).getName());
+                }
+            } // end of validating collections
+
+            try {
+                // If this is a zip archive, unzip it first
+                if (zip) {
+                    sourcedir = myloader.unzip(sourcedir, zipfilename);
+                }
+
+
+                c.turnOffAuthorisationSystem();
+
+                if ("add".equals(command)) {
+                    myloader.addItems(c, mycollections, sourcedir, mapfile, template);
+                } else if ("replace".equals(command)) {
+                    myloader.replaceItems(c, mycollections, sourcedir, mapfile, template);
+                } else if ("delete".equals(command)) {
+                    myloader.deleteItems(c, mapfile);
+                } else if ("add-bte".equals(command)) {
+                    myloader.addBTEItems(c, mycollections, sourcedir, mapfile, template, bteInputType, null);
+                }
+
+                // complete all transactions
+                c.complete();
+            } catch (Exception e) {
+                c.abort();
+                e.printStackTrace();
+                System.out.println(e);
+                status = 1;
+            }
+
+            // Delete the unzipped file
+            try {
+                if (zip) {
+                    System.gc();
+                    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());
+            }
+
+
+            if (isTest) {
+                System.out.println("***End of Test Run***");
+            }
+        } finally {
+            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.exit(status);
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemimport/ItemImportServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemimport/ItemImportServiceImpl.java
--- a/dspace-api/src/main/java/org/dspace/app/itemimport/factory/ItemImportServiceFactory.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemimport/factory/ItemImportServiceFactory.java
@@ -0,0 +1,27 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.itemimport.factory;
+
+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
+ *
+ * @author kevinvandevelde at atmire.com
+ */
+public abstract class ItemImportServiceFactory {
+
+    public abstract ItemImportService getItemImportService();
+
+    public static ItemImportServiceFactory getInstance() {
+        return DSpaceServicesFactory.getInstance().getServiceManager()
+                                    .getServiceByName("itemImportServiceFactory", ItemImportServiceFactory.class);
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemimport/factory/ItemImportServiceFactoryImpl.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemimport/factory/ItemImportServiceFactoryImpl.java
@@ -0,0 +1,28 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.itemimport.factory;
+
+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
+ *
+ * @author kevinvandevelde at atmire.com
+ */
+public class ItemImportServiceFactoryImpl extends ItemImportServiceFactory {
+
+    @Autowired(required = true)
+    private ItemImportService itemImportService;
+
+    @Override
+    public ItemImportService getItemImportService() {
+        return itemImportService;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemimport/service/ItemImportService.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemimport/service/ItemImportService.java
@@ -0,0 +1,253 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.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 items into DSpace. The conventional use is upload files by copying
+ * them. DSpace writes the item's bitstreams into its assetstore. Metadata is
+ * also loaded to the DSpace database.
+ * <P>
+ * A second use assumes the bitstream files already exist in a storage
+ * resource accessible to DSpace. In this case the bitstreams are 'registered'.
+ * That is, the metadata is loaded to the DSpace database and DSpace is given
+ * the location of the file which is subsumed into DSpace.
+ * <P>
+ * The distinction is controlled by the format of lines in the 'contents' file.
+ * See comments in processContentsFile() below.
+ * <P>
+ * Modified by David Little, UCSD Libraries 12/21/04 to
+ * allow the registration of files (bitstreams) into DSpace.
+ */
+public interface ItemImportService {
+
+
+    /**
+     * @param c             DSpace Context
+     * @param mycollections List of Collections
+     * @param sourceDir     source location
+     * @param mapFile       map file
+     * @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;
+
+    /**
+     * Add items
+     *
+     * @param c             DSpace Context
+     * @param mycollections List of Collections
+     * @param sourceDir     source location
+     * @param mapFile       map file
+     * @param template      whether to use template item
+     * @throws Exception if error
+     */
+    public void addItems(Context c, List<Collection> mycollections,
+                         String sourceDir, String mapFile, boolean template) throws Exception;
+
+    /**
+     * Unzip a file
+     *
+     * @param zipfile file
+     * @return unzip location
+     * @throws IOException if error
+     */
+    public String unzip(File zipfile) throws IOException;
+
+    /**
+     * Unzip a file to a destination
+     *
+     * @param zipfile file
+     * @param destDir destination directory
+     * @return unzip location
+     * @throws IOException if error
+     */
+    public String unzip(File zipfile, String destDir) throws IOException;
+
+    /**
+     * Unzip a file in a specific source directory
+     *
+     * @param sourcedir   source directory
+     * @param zipfilename file name
+     * @return unzip location
+     * @throws IOException if error
+     */
+    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
+     *
+     * @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
+     * @param resumeDir        In case of a resume request, the directory that containsthe old mapfile and data
+     * @param inputType        The input type of the data (bibtex, csv, etc.), in case of local file
+     * @param context          The context
+     * @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;
+
+    /**
+     * Since the BTE batch import is done in a new thread we are unable to communicate
+     * with calling method about success or failure. We accomplish this
+     * 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
+     * @throws MessagingException if error
+     */
+    public void emailSuccessMessage(Context context, EPerson eperson,
+                                    String fileName) throws MessagingException;
+
+    /**
+     * Since the BTE batch import is done in a new thread we are unable to communicate
+     * with calling method about success or failure. We accomplis this
+     * 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
+     * @throws MessagingException if error
+     */
+    public void emailErrorMessage(EPerson eperson, String error)
+        throws MessagingException;
+
+
+    /**
+     * Get imports available for a person
+     *
+     * @param eperson EPerson object
+     * @return List of batch uploads
+     * @throws Exception if error
+     */
+    public List<BatchUpload> getImportsAvailable(EPerson eperson)
+        throws Exception;
+
+    /**
+     * Get import upload directory
+     *
+     * @param ePerson EPerson object
+     * @return directory
+     * @throws Exception if error
+     */
+    public String getImportUploadableDirectory(EPerson ePerson)
+        throws Exception;
+
+    /**
+     * Delete a batch by ID
+     *
+     * @param c        DSpace Context
+     * @param uploadId identifier
+     * @throws Exception if error
+     */
+    public void deleteBatchUpload(Context c, String uploadId) throws Exception;
+
+    /**
+     * Replace items
+     *
+     * @param c             DSpace Context
+     * @param mycollections List of Collections
+     * @param sourcedir     source directory
+     * @param mapfile       map file
+     * @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;
+
+    /**
+     * Delete items via mapfile
+     *
+     * @param c       DSpace Context
+     * @param mapfile map file
+     * @throws Exception if error
+     */
+    public void deleteItems(Context c, String mapfile) throws Exception;
+
+    /**
+     * Add items
+     *
+     * @param c             DSpace Context
+     * @param mycollections List of Collections
+     * @param sourcedir     source directory
+     * @param mapfile       map file
+     * @param template      whether to use template item
+     * @param bteInputType  The input type of the data (bibtex, csv, etc.), in case of local file
+     * @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;
+
+    /**
+     * 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;
+
+    /**
+     * Cleanup
+     */
+    public void cleanupZipTemp();
+
+    /**
+     * 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);
+
+    /**
+     * @param useWorkflowSendMail whether to send mail
+     */
+    public void setUseWorkflowSendEmail(boolean useWorkflowSendMail);
+
+    /**
+     * Set quiet flag
+     *
+     * @param isQuiet true or false
+     */
+    public void setQuiet(boolean isQuiet);
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingAvailabilityBitstreamStrategy.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingAvailabilityBitstreamStrategy.java
@@ -0,0 +1,93 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.itemmarking;
+
+import java.io.UnsupportedEncodingException;
+import java.sql.SQLException;
+import java.util.List;
+
+import org.dspace.app.util.Util;
+import org.dspace.content.Bitstream;
+import org.dspace.content.Bundle;
+import org.dspace.content.Item;
+import org.dspace.content.service.ItemService;
+import org.dspace.core.Constants;
+import org.dspace.core.Context;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * This is an item marking Strategy class that tries to mark an item availability
+ * based on the existence of bitstreams within the ORIGINAL bundle.
+ *
+ * @author Kostas Stamatis
+ */
+public class ItemMarkingAvailabilityBitstreamStrategy implements ItemMarkingExtractor {
+
+    private String availableImageName;
+    private String nonAvailableImageName;
+
+    @Autowired(required = true)
+    protected ItemService itemService;
+
+    public ItemMarkingAvailabilityBitstreamStrategy() {
+
+    }
+
+    @Override
+    public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
+        throws SQLException {
+
+        List<Bundle> bundles = itemService.getBundles(item, "ORIGINAL");
+        if (bundles.size() == 0) {
+            ItemMarkingInfo markInfo = new ItemMarkingInfo();
+            markInfo.setImageName(nonAvailableImageName);
+
+            return markInfo;
+        } else {
+            Bundle originalBundle = bundles.iterator().next();
+            if (originalBundle.getBitstreams().size() == 0) {
+                ItemMarkingInfo markInfo = new ItemMarkingInfo();
+                markInfo.setImageName(nonAvailableImageName);
+
+                return markInfo;
+            } else {
+                Bitstream bitstream = originalBundle.getBitstreams().get(0);
+
+                ItemMarkingInfo signInfo = new ItemMarkingInfo();
+                signInfo.setImageName(availableImageName);
+                signInfo.setTooltip(bitstream.getName());
+
+
+                String bsLink = "";
+
+                bsLink = bsLink + "bitstream/"
+                    + item.getHandle() + "/"
+                    + bitstream.getSequenceID() + "/";
+
+                try {
+                    bsLink = bsLink + Util.encodeBitstreamName(bitstream.getName(), Constants.DEFAULT_ENCODING);
+                } catch (UnsupportedEncodingException e) {
+
+                    e.printStackTrace();
+                }
+
+                signInfo.setLink(bsLink);
+
+                return signInfo;
+            }
+        }
+    }
+
+    public void setAvailableImageName(String availableImageName) {
+        this.availableImageName = availableImageName;
+    }
+
+    public void setNonAvailableImageName(String nonAvailableImageName) {
+        this.nonAvailableImageName = nonAvailableImageName;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingCollectionStrategy.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingCollectionStrategy.java
@@ -0,0 +1,49 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.itemmarking;
+
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.dspace.content.Collection;
+import org.dspace.content.Item;
+import org.dspace.core.Context;
+
+/**
+ * This is an item marking Strategy class that tries to mark an item
+ * based on the collection the items belong to
+ *
+ * @author Kostas Stamatis
+ */
+public class ItemMarkingCollectionStrategy implements ItemMarkingExtractor {
+
+    Map<String, ItemMarkingInfo> mapping = new HashMap<String, ItemMarkingInfo>();
+
+    public ItemMarkingCollectionStrategy() {
+    }
+
+    @Override
+    public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
+        throws SQLException {
+
+        if (mapping != null) {
+            for (Collection collection : item.getCollections()) {
+                if (mapping.containsKey(collection.getHandle())) {
+                    return mapping.get(collection.getHandle());
+                }
+            }
+        }
+
+        return null;
+    }
+
+    public void setMapping(Map<String, ItemMarkingInfo> mapping) {
+        this.mapping = mapping;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingExtractor.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingExtractor.java
@@ -0,0 +1,23 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.itemmarking;
+
+import java.sql.SQLException;
+
+import org.dspace.content.Item;
+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)
+        throws SQLException;
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingInfo.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingInfo.java
@@ -0,0 +1,56 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.itemmarking;
+
+/**
+ * Simple DTO to transfer data about the marking info for an item
+ *
+ * @author Kostas Stamatis
+ */
+public class ItemMarkingInfo {
+    private String imageName;
+    private String classInfo;
+    private String tooltip;
+    private String link;
+
+    public ItemMarkingInfo() {
+        super();
+    }
+
+    public String getImageName() {
+        return imageName;
+    }
+
+    public void setImageName(String imageName) {
+        this.imageName = imageName;
+    }
+
+    public String getTooltip() {
+        return tooltip;
+    }
+
+    public void setTooltip(String tooltip) {
+        this.tooltip = tooltip;
+    }
+
+    public String getLink() {
+        return link;
+    }
+
+    public void setLink(String link) {
+        this.link = link;
+    }
+
+    public String getClassInfo() {
+        return classInfo;
+    }
+
+    public void setClassInfo(String classInfo) {
+        this.classInfo = classInfo;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingMetadataStrategy.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingMetadataStrategy.java
@@ -0,0 +1,64 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.itemmarking;
+
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.dspace.content.Item;
+import org.dspace.content.MetadataValue;
+import org.dspace.content.service.ItemService;
+import org.dspace.core.Context;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * This is an item marking Strategy class that tries to mark an item
+ * based on the existence of a specific value within the values of a specific
+ * metadata field
+ *
+ * @author Kostas Stamatis
+ */
+public class ItemMarkingMetadataStrategy implements ItemMarkingExtractor {
+
+    @Autowired(required = true)
+    protected ItemService itemService;
+
+    private String metadataField;
+    Map<String, ItemMarkingInfo> mapping = new HashMap<String, ItemMarkingInfo>();
+
+    public ItemMarkingMetadataStrategy() {
+    }
+
+    @Override
+    public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
+        throws SQLException {
+
+        if (metadataField != null && mapping != null) {
+            List<MetadataValue> vals = itemService.getMetadataByMetadataString(item, metadataField);
+            if (vals.size() > 0) {
+                for (MetadataValue value : vals) {
+                    String type = value.getValue();
+                    if (mapping.containsKey(type)) {
+                        return mapping.get(type);
+                    }
+                }
+            }
+        }
+        return null;
+    }
+
+    public void setMetadataField(String metadataField) {
+        this.metadataField = metadataField;
+    }
+
+    public void setMapping(Map<String, ItemMarkingInfo> mapping) {
+        this.mapping = mapping;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/ActionManager.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/ActionManager.java
@@ -16,21 +16,25 @@ 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> {

-	private Map<Class<? extends UpdateAction>, UpdateAction> registry 
+    protected Map<Class<? extends UpdateAction>, UpdateAction> registry
        = new LinkedHashMap<Class<? extends UpdateAction>, 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);
        }
@@ -39,11 +43,9 @@ 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();
    }

@@ -53,25 +55,24 @@ public class ActionManager implements Iterable<UpdateAction> {
     *
     * @return iterator for UpdateActions
     */
-	public Iterator<UpdateAction> iterator()
-	{
-		return new Iterator<UpdateAction>() 
-		{ 			
+    @Override
+    public Iterator<UpdateAction> iterator() {
+        return new Iterator<UpdateAction>() {
            private Iterator<Class<? extends UpdateAction>> itr = registry.keySet().iterator();

-			public boolean hasNext()
-			{
+            @Override
+            public boolean hasNext() {
                return itr.hasNext();
            }

-			public UpdateAction next()
-			{
+            @Override
+            public UpdateAction next() {
                return registry.get(itr.next());
            }

            //not supported
-			public void remove()
-			{
+            @Override
+            public void remove() {
                throw new UnsupportedOperationException();
            }
        };
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/AddBitstreamsAction.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/AddBitstreamsAction.java
@@ -17,54 +17,59 @@ import java.util.ArrayList;
 import java.util.List;

 import org.dspace.authorize.AuthorizeException;
-import org.dspace.authorize.AuthorizeManager;
-import org.dspace.authorize.ResourcePolicy;
+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.FormatIdentifier;
-import org.dspace.content.InstallItem;
 import org.dspace.content.Item;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.BitstreamFormatService;
+import org.dspace.content.service.InstallItemService;
 import org.dspace.core.Context;
 import org.dspace.eperson.Group;
+import org.dspace.eperson.factory.EPersonServiceFactory;
+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 {

-	public AddBitstreamsAction()
-	{
+    protected AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
+    protected BitstreamFormatService bitstreamFormatService = ContentServiceFactory.getInstance()
+                                                                                   .getBitstreamFormatService();
+    protected GroupService groupService = EPersonServiceFactory.getInstance().getGroupService();
+    protected InstallItemService installItemService = ContentServiceFactory.getInstance().getInstallItemService();
+
+    public AddBitstreamsAction() {
        //empty
    }

    /**
     * Adds bitstreams from the archive as listed in the contents file.
     *
-	 *  @param context
-	 *  @param itarch
-	 *  @param isTest
-	 *  @param suppressUndo
-	 *  @throws IllegalArgumentException
-	 *  @throws ParseException
-	 *  @throws IOException
-	 *  @throws AuthorizeException
-	 *  @throws SQLException
+     * @param context      DSpace Context
+     * @param itarch       Item Archive
+     * @param isTest       test flag
+     * @param suppressUndo undo flag
+     * @throws IOException              if IO error
+     * @throws IllegalArgumentException if arg exception
+     * @throws SQLException             if database error
+     * @throws AuthorizeException       if authorization error
+     * @throws ParseException           if parse error
     */
+    @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;
        }
@@ -73,32 +78,59 @@ 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)
-		{        				
-			addBitstream(context, itarch, item, dir, ce, suppressUndo, isTest);
+        for (ContentsEntry ce : contents) {
+            String targetBundleName = addBitstream(context, itarch, item, dir, ce, suppressUndo, isTest);
+            if (!targetBundleName.equals("")
+                && !targetBundleName.equals("THUMBNAIL")
+                && !targetBundleName.equals("TEXT")) {
+                bitstream_bundles_updated++;
            }
        }

-	private void addBitstream(Context context, ItemArchive itarch, Item item, File dir, 
+        if (alterProvenance && bitstream_bundles_updated > 0) {
+            DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
+
+            String append = ". Added " + Integer.toString(bitstream_bundles_updated)
+                + " bitstream(s) on " + DCDate.getCurrent() + " : "
+                + installItemService.getBitstreamProvenanceMessage(context, item);
+            MetadataUtilities.appendMetadata(context, item, dtom, false, append);
+        }
+    }
+
+    /**
+     * Add bitstream
+     *
+     * @param context      DSpace Context
+     * @param itarch       Item Archive
+     * @param item         DSpace Item
+     * @param dir          directory
+     * @param ce           contents entry for bitstream
+     * @param suppressUndo undo flag
+     * @param isTest       test flag
+     * @return bundle name
+     * @throws IOException              if IO error
+     * @throws IllegalArgumentException if arg exception
+     * @throws SQLException             if database error
+     * @throws AuthorizeException       if authorization error
+     * @throws ParseException           if parse error
+     */
+    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);

@@ -108,40 +140,29 @@ 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
-	        Bundle[] bundles = item.getBundles(newBundleName);
+            List<Bundle> bundles = itemService.getBundles(item, newBundleName);
            Bundle targetBundle = null;

-	        if (bundles.length < 1)
-	        {
+            if (bundles.size() < 1) {
                // not found, create a new one
-	            targetBundle = item.createBundle(newBundleName);
-	        }
-	        else
-	        {
+                targetBundle = bundleService.create(context, item, newBundleName);
+            } else {
                //verify bundle + name are not duplicates
-	        	for (Bundle b : bundles)
-	        	{
-	        		Bitstream[] bitstreams = b.getBitstreams();
-	        		for (Bitstream bsm : bitstreams)
-	        		{
-	        			if (bsm.getName().equals(ce.filename))
-	        			{
+                for (Bundle b : bundles) {
+                    List<Bitstream> bitstreams = b.getBitstreams();
+                    for (Bitstream bsm : bitstreams) {
+                        if (bsm.getName().equals(ce.filename)) {
                            throw new IllegalArgumentException("Duplicate bundle + filename cannot be added: "
                                                                   + b.getName() + " + " + bsm.getName());
                        }
@@ -149,55 +170,39 @@ public class AddBitstreamsAction extends UpdateBitstreamsAction {
                }

                // select first bundle
-	            targetBundle = bundles[0];
+                targetBundle = bundles.iterator().next();
            }

-	        bs = targetBundle.createBitstream(bis);	
-	        bs.setName(ce.filename);
+            bs = bitstreamService.create(context, targetBundle, bis);
+            bs.setName(context, ce.filename);

            // Identify the format
            // FIXME - guessing format guesses license.txt incorrectly as a text file format!
-	        BitstreamFormat fmt = FormatIdentifier.guessFormat(context, bs);
-	    	bs.setFormat(fmt);
+            BitstreamFormat fmt = bitstreamFormatService.guessFormat(context, bs);
+            bitstreamService.setFormat(context, bs, fmt);

-	        if (ce.description != null)
-	        {
-	        	bs.setDescription(ce.description);
+            if (ce.description != null) {
+                bs.setDescription(context, ce.description);
            }

-	        if ((ce.permissionsActionId != -1) && (ce.permissionsGroupName != null))
-	        {
-				Group group = Group.findByName(context, ce.permissionsGroupName);
+            if ((ce.permissionsActionId != -1) && (ce.permissionsGroupName != null)) {
+                Group group = groupService.findByName(context, ce.permissionsGroupName);

-				if (group != null)
-				{
-			        AuthorizeManager.removeAllPolicies(context, bs);  // remove the default policy
-			        ResourcePolicy rp = ResourcePolicy.create(context);
-			        rp.setResource(bs);
-			        rp.setAction(ce.permissionsActionId);
-			        rp.setGroup(group);		
-			        rp.update();
+                if (group != null) {
+                    authorizeService.removeAllPolicies(context, bs);  // remove the default policy
+                    authorizeService.createResourcePolicy(context, bs, group, null, ce.permissionsActionId, null);
                }
            }

-	        if (alterProvenance && !targetBundle.getName().equals("THUMBNAIL") 
-	        		&& !targetBundle.getName().equals("TEXT"))
-	        {
-	        	DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
+            //update after all changes are applied
+            bitstreamService.update(context, bs);

-	        	String append = "Bitstream added on " + DCDate.getCurrent() + " : " 
-	        	                + InstallItem.getBitstreamProvenanceMessage(item);
-	        	MetadataUtilities.appendMetadata(item, dtom, false, append);
-	        }
-	        
-	        //update after all changes are applied, even metadata ones
-	        bs.update();
-        
-	        if (!suppressUndo)
-	        {
+            if (!suppressUndo) {
                itarch.addUndoDeleteContents(bs.getID());
            }
+            return targetBundle.getName();
        }
+        return "";
    }

 }
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/AddMetadataAction.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/AddMetadataAction.java
@@ -8,104 +8,101 @@
 package org.dspace.app.itemupdate;

 import java.sql.SQLException;
+import java.util.List;

 import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.DCValue;
 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;
 import org.dspace.core.Context;

 /**
 * Action to add metadata to item
- *
 */
 public class AddMetadataAction extends UpdateMetadataAction {

+    protected MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance()
+                                                                                 .getMetadataSchemaService();
+    protected MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance().getMetadataFieldService();
+
    /**
     * Adds metadata specified in the source archive
     *
-	 *  @param context
-	 *  @param itarch
-	 *  @param isTest
-	 *  @param suppressUndo
-	 *  @throws AuthorizeException
-	 *  @throws SQLException
+     * @param context      DSpace Context
+     * @param itarch       item archive
+     * @param isTest       test flag
+     * @param suppressUndo undo flag
+     * @throws AuthorizeException if authorization error
+     * @throws SQLException       if database error
     */
+    @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
-					DCValue[] ardcv = null;
-					ardcv = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
+                    List<MetadataValue> ardcv = null;
+                    ardcv = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);

                    boolean found = false;
-					for (DCValue dcv : ardcv)
-					{
-						if (dcv.value.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 = MetadataSchema.find(context, dtom.schema);
+                            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
-	        	        	{
-		        	        	int schemaID = foundSchema.getSchemaID();
-		        	        	MetadataField foundField = MetadataField.findByElement(context, schemaID, 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
-						{
-							item.addMetadata(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 (DCValue dcval : ardcv)
-								{							
-									itarch.addUndoMetadataField(DtoMetadata.create(dcval.schema, dcval.element, 
-											dcval.qualifier, dcval.language, dcval.value));
+                                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()));
                                }

                            }
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/BitstreamFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/BitstreamFilter.java
@@ -7,17 +7,17 @@
 */
 package org.dspace.app.itemupdate;

-import java.io.IOException;
-import java.util.Properties;
-import java.io.InputStream;
 import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Properties;
+
 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 {

@@ -26,33 +26,27 @@ public abstract class BitstreamFilter {
    /**
     * The filter method
     *
-	 * @param bitstream
+     * @param bitstream Bitstream
     * @return whether the bitstream matches the criteria
-	 * @throws BitstreamFilterException
+     * @throws BitstreamFilterException if filter error
     */
    public abstract boolean accept(Bitstream bitstream) throws BitstreamFilterException;

    /**
-	 * 
     * @param filepath - The complete path for the properties file
-	 * @throws IOException
+     * @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();
            }
        }
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/BitstreamFilterByBundleName.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/BitstreamFilterByBundleName.java
@@ -8,56 +8,47 @@
 package org.dspace.app.itemupdate;

 import java.sql.SQLException;
+import java.util.List;

 import org.dspace.content.Bitstream;
 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
    }

    /**
     * Filter bitstream based on bundle name found in properties file
     *
-	 *    @param bitstream
-	 *    @throws BitstreamFilterException
+     * @param bitstream Bitstream
     * @return whether bitstream is in bundle
-	 *    
+     * @throws BitstreamFilterException if filter error
     */
+    @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
-		{
-			Bundle[] bundles = bitstream.getBundles();
-			for (Bundle b : bundles)
-			{
-				if (b.getName().equals(bundleName))
-				{
+        try {
+            List<Bundle> bundles = bitstream.getBundles();
+            for (Bundle b : bundles) {
+                if (b.getName().equals(bundleName)) {
                    return true;
                }
            }
-		}
-		catch(SQLException e)
-		{
+        } catch (SQLException e) {
            throw new BitstreamFilterException(e);
        }
        return false;
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/BitstreamFilterByFilename.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/BitstreamFilterByFilename.java
@@ -7,21 +7,20 @@
 */
 package org.dspace.app.itemupdate;

-import java.util.regex.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;

 import org.dspace.content.Bitstream;

 /**
 * BitstreamFilter implementation to filter by filename pattern
- *
 */
 public class BitstreamFilterByFilename extends BitstreamFilter {

-	private Pattern pattern;
-	private String filenameRegex;
+    protected Pattern pattern;
+    protected String filenameRegex;

-	public BitstreamFilterByFilename()
-	{
+    public BitstreamFilterByFilename() {
        //empty
    }

@@ -29,15 +28,15 @@ public class BitstreamFilterByFilename extends BitstreamFilter {
     * Tests bitstream by matching the regular expression in the
     * properties against the bitstream name
     *
+     * @param bitstream Bitstream
     * @return whether bitstream name matches the regular expression
+     * @throws BitstreamFilterException if filter error
     */
-	public boolean accept(Bitstream bitstream) throws BitstreamFilterException
-	{		
-		if (filenameRegex == null)
-		{
+    @Override
+    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);
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/BitstreamFilterException.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/BitstreamFilterException.java
@@ -9,20 +9,25 @@ 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(String msg)
-	{
+    public BitstreamFilterException() {
+    }
+
+    /**
+     * @param msg exception message
+     */
+    public BitstreamFilterException(String msg) {
        super(msg);
    }
-	public BitstreamFilterException(Exception e)
-	{
+
+    /**
+     * @param e exception
+     */
+    public BitstreamFilterException(Exception e) {
        super(e);
    }

--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/ContentsEntry.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/ContentsEntry.java
@@ -8,7 +8,8 @@
 package org.dspace.app.itemupdate;

 import java.text.ParseException;
-import java.util.regex.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;

 import org.dspace.core.Constants;

@@ -21,14 +22,13 @@ import org.dspace.core.Constants;
 * it looks from the source code that the ordering or elements is not fixed
 *
 * e.g.:
+ * {@code
 * 48217870-MIT.pdf\tbundle: bundlename\tpermissions: -r 'MIT Users'\tdescription: Full printable version (MIT only)
 * 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:";
@@ -41,12 +41,11 @@ public class ContentsEntry
    final int permissionsActionId;
    final String description;

-	private ContentsEntry(String filename, 
+    protected ContentsEntry(String filename,
                            String bundlename,
                            int permissionsActionId,
                            String permissionsGroupName,
-			             String description)
-	{
+                            String description) {
        this.filename = filename;
        this.bundlename = bundlename;
        this.permissionsActionId = permissionsActionId;
@@ -57,13 +56,12 @@ public class ContentsEntry
    /**
     * Factory method parses a line from the Contents Entry file
     *
-	 * @param line
+     * @param line line as string
     * @return the parsed ContentsEntry object
-	 * @throws ParseException
+     * @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);

@@ -73,46 +71,33 @@ 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);
                }
            }
@@ -120,30 +105,23 @@ 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);
        }

--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/DeleteBitstreamsAction.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/DeleteBitstreamsAction.java
@@ -26,84 +26,64 @@ 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
     *
-	 *  @param context
-	 *  @param itarch
-	 *  @param isTest
-	 *  @param suppressUndo
-	 *  @throws IllegalArgumentException
-	 *  @throws ParseException
-	 *  @throws IOException
-	 *  @throws AuthorizeException
-	 *  @throws SQLException
+     * @param context      DSpace Context
+     * @param itarch       item archive
+     * @param isTest       test flag
+     * @param suppressUndo undo flag
+     * @throws IOException              if IO error
+     * @throws IllegalArgumentException if arg exception
+     * @throws SQLException             if database error
+     * @throws AuthorizeException       if authorization error
+     * @throws ParseException           if parse error
     */
+    @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
-		{
-			List<Integer> list = MetadataUtilities.readDeleteContentsFile(f);
-			if (list.isEmpty())
-			{
+        } else {
+            List<String> list = MetadataUtilities.readDeleteContentsFile(f);
+            if (list.isEmpty()) {
                ItemUpdate.pr("Warning: empty delete_contents file for item " + itarch.getDirectoryName());
-			}
-			else
-			{
-				for (int id : list)
-				{
-					try
-					{
-			    		Bitstream bs = Bitstream.find(context, id);
-			    		if (bs == null)
-			    		{
+            } else {
+                for (String id : list) {
+                    try {
+                        Bitstream bs = bitstreamService.findByIdOrLegacyId(context, id);
+                        if (bs == null) {
                            ItemUpdate.pr("Bitstream not found by id: " + id);
-			    		}
-			    		else
-			    		{
-				    		Bundle[] bundles = bs.getBundles();
-				    		for (Bundle b : bundles)
-				    		{
-				    			if (isTest)
-				    			{
+                        } else {
+                            List<Bundle> bundles = bs.getBundles();
+                            for (Bundle b : bundles) {
+                                if (isTest) {
                                    ItemUpdate.pr("Delete bitstream with id = " + id);
-				    			}
-				    			else
-				    			{
-				    				b.removeBitstream(bs); 
+                                } 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() + "; ";
-				            	Item item = bundles[0].getItems()[0];
+                                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)
-					    		{
-					    			MetadataUtilities.appendMetadata(item, dtom, false, append);
+                                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());
                    }
                }
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/DeleteBitstreamsByFilterAction.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/DeleteBitstreamsByFilterAction.java
@@ -28,77 +28,67 @@ 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 {

-	private BitstreamFilter filter;
+    protected BitstreamFilter filter;

    /**
     * Set filter
     *
-	 * @param filter
+     * @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;
    }

    /**
     * Delete bitstream
     *
-	 *  @param context
-	 *  @param itarch
-	 *  @param isTest
-	 *  @param suppressUndo
-	 *  @throws IllegalArgumentException
-	 *  @throws ParseException
-	 *  @throws IOException
-	 *  @throws AuthorizeException
-	 *  @throws SQLException
+     * @param context      DSpace Context
+     * @param itarch       item archive
+     * @param isTest       test flag
+     * @param suppressUndo undo flag
+     * @throws IOException              if IO error
+     * @throws SQLException             if database error
+     * @throws AuthorizeException       if authorization error
+     * @throws ParseException           if parse error
+     * @throws BitstreamFilterException if filter error
     */
+    @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();
-		Bundle[] bundles = item.getBundles();
+        List<Bundle> bundles = item.getBundles();

-		for (Bundle b : bundles)    
-		{
-			Bitstream[] bitstreams = b.getBitstreams();
+        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());
                        }
-	    				b.removeBitstream(bs); 
+                        bundleService.removeBitstream(context, b, bs);
                        ItemUpdate.pr("Deleted " + bundleName + " bitstream " + bs.getName()
                                          + " with id = " + bs.getID());
                    }
@@ -106,13 +96,11 @@ 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(", ");
            }

@@ -120,9 +108,8 @@ public class DeleteBitstreamsByFilterAction extends UpdateBitstreamsAction {

            ItemUpdate.pr("Append provenance with: " + sb.toString());

-    		if (!isTest)
-    		{
-    			MetadataUtilities.appendMetadata(item, dtom, false, sb.toString());
+            if (!isTest) {
+                MetadataUtilities.appendMetadata(context, item, dtom, false, sb.toString());
            }
        }
    }
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/DeleteMetadataAction.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/DeleteMetadataAction.java
@@ -7,57 +7,58 @@
 */
 package org.dspace.app.itemupdate;

+import java.sql.SQLException;
 import java.text.ParseException;
+import java.util.List;

 import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.DCValue;
 import org.dspace.content.Item;
+import org.dspace.content.MetadataField;
+import org.dspace.content.MetadataSchema;
+import org.dspace.content.MetadataValue;
 import org.dspace.core.Context;

 /**
 * Action to delete metadata
- * 
- *
 */
 public class DeleteMetadataAction extends UpdateMetadataAction {

    /**
     * Delete metadata from item
     *
-	 *  @param context
-	 *  @param itarch
-	 *  @param isTest
-	 *  @param suppressUndo
-	 *  @throws ParseException
-	 *  @throws AuthorizeException
+     * @param context      DSpace Context
+     * @param itarch       Item Archive
+     * @param isTest       test flag
+     * @param suppressUndo undo flag
+     * @throws SQLException       if database error
+     * @throws AuthorizeException if authorization error
+     * @throws ParseException     if parse error
     */
+    @Override
    public void execute(Context context, ItemArchive itarch, boolean isTest,
-            boolean suppressUndo) throws AuthorizeException, ParseException 
-	{
+                        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, "");
-			DCValue[] ardcv = item.getMetadata(f);
+            List<MetadataValue> ardcv = itemService.getMetadataByMetadataString(item, f);

            ItemUpdate.pr("Metadata to be deleted: ");
-			for (DCValue dcv : ardcv)
-			{
+            for (MetadataValue dcv : ardcv) {
                ItemUpdate.pr("  " + MetadataUtilities.getDCValueString(dcv));
            }

-			if (!isTest)
-			{
-				if (!suppressUndo)
-				{
-					for (DCValue dcv : ardcv)
-					{
-						itarch.addUndoMetadataField(DtoMetadata.create(dcv.schema, dcv.element, 
-								dcv.qualifier, dcv.language, dcv.value));					
+            if (!isTest) {
+                if (!suppressUndo) {
+                    for (MetadataValue dcv : ardcv) {
+                        MetadataField metadataField = dcv.getMetadataField();
+                        MetadataSchema metadataSchema = metadataField.getMetadataSchema();
+                        itarch.addUndoMetadataField(
+                            DtoMetadata.create(metadataSchema.getName(), metadataField.getElement(),
+                                               metadataField.getQualifier(), dcv.getLanguage(), dcv.getValue()));
                    }
                }

-				item.clearMetadata(dummy.schema, dummy.element, dummy.qualifier, Item.ANY);	
+                itemService.clearMetadata(context, item, dummy.schema, dummy.element, dummy.qualifier, Item.ANY);
            }
        }
    }
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/DerivativeTextBitstreamFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/DerivativeTextBitstreamFilter.java
@@ -11,12 +11,10 @@ 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");
    }
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/DtoMetadata.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/DtoMetadata.java
@@ -8,6 +8,7 @@
 package org.dspace.app.itemupdate;

 import java.text.ParseException;
+
 import org.dspace.content.Item;

 /**
@@ -16,22 +17,19 @@ import org.dspace.content.Item;
 *
 * Adds some utility methods
 *
- *   Really not at all general enough but supports Dublin Core and the compound form notation <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;

-	private 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;
@@ -42,23 +40,21 @@ 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'
     * @param language  null or empty
-	 * @param value      
+     * @param value     value
     * @return DtoMetadata object
+     * @throws IllegalArgumentException if arg error
     */
    public static DtoMetadata create(String schema,
                                     String element,
                                     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);
@@ -67,19 +63,18 @@ class DtoMetadata
    /**
     * Factory method to create metadata object
     *
-	 * 
     * @param compoundForm of the form <schema>.<element>[.<qualifier>]
     * @param language     null or empty
-	 * @param value      
+     * @param value        value
+     * @throws ParseException           if parse error
+     * @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];
        }

@@ -90,56 +85,44 @@ 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);
@@ -148,8 +131,7 @@ class DtoMetadata
        return s;
    }

-	public String getValue()
-	{
+    public String getValue() {
        return value;
    }

--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/ItemArchive.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/ItemArchive.java
@@ -10,64 +10,70 @@ package org.dspace.app.itemupdate;
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileWriter;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
-import java.io.InputStream;
+import java.io.FileWriter;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.OutputStream;
 import java.io.PrintWriter;
 import java.sql.SQLException;
 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.content.ItemIterator;
+import org.dspace.app.util.LocalSchemaFilenameFilter;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.DSpaceObject;
 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.HandleManager;
-
+import org.dspace.handle.factory.HandleServiceFactory;
+import org.dspace.handle.service.HandleService;
 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);

    public static final String DUBLIN_CORE_XML = "dublin_core.xml";

-    private static DocumentBuilder builder = null;
-    private static Transformer transformer = null;
+    protected static DocumentBuilder builder = null;
+    protected Transformer transformer = null;

-	private List<DtoMetadata> dtomList = null; 
-	private List<DtoMetadata> undoDtomList = new ArrayList<DtoMetadata>();
+    protected List<DtoMetadata> dtomList = null;
+    protected List<DtoMetadata> undoDtomList = new ArrayList<DtoMetadata>();

-	private List<Integer> undoAddContents = new ArrayList<Integer>(); // for undo of add
+    protected List<UUID> undoAddContents = new ArrayList<>(); // for undo of add

-	private Item item;
-	private File dir;  // directory name in source archive for this item
-	private String dirname; //convenience
+    protected Item item;
+    protected File dir;  // directory name in source archive for this item
+    protected String dirname; //convenience
+
+    protected HandleService handleService;
+    protected ItemService itemService;

    //constructors
-	private ItemArchive() 
-	{
-		// nothing
+    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
@@ -77,40 +83,40 @@ public class ItemArchive {
     * @param dir       - The directory File in the source archive
     * @param itemField - The metadata field in which the Item identifier is located
     *                  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
+            File file[] = dir.listFiles(new LocalSchemaFilenameFilter());
+            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);
        }

@@ -119,21 +125,23 @@ public class ItemArchive {
        return itarch;
    }

-	private static DocumentBuilder getDocumentBuilder()
-	throws ParserConfigurationException
-	{
-		if (builder == null)
-		{
+    protected static DocumentBuilder getDocumentBuilder()
+        throws ParserConfigurationException {
+        if (builder == null) {
            builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
        }
        return builder;
    }

-	private static Transformer getTransformer()
-	throws TransformerConfigurationException
-	{
-		if (transformer == null)
-		{
+    /**
+     * Getter for Transformer
+     *
+     * @return Transformer
+     * @throws TransformerConfigurationException if config error
+     */
+    protected Transformer getTransformer()
+        throws TransformerConfigurationException {
+        if (transformer == null) {
            transformer = TransformerFactory.newInstance().newTransformer();
        }
        return transformer;
@@ -141,55 +149,55 @@ 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
+     *
+     * @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
+     *
+     * @param bitstreamId bitstream ID
     */
-	public void addUndoDeleteContents(int bitstreamId)
-	{
+    public void addUndoDeleteContents(UUID bitstreamId) {
        this.undoAddContents.add(bitstreamId);
    }

@@ -200,13 +208,14 @@ public class ItemArchive {
     * 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");
        }

@@ -214,21 +223,17 @@ 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);
        }

        String handle = uri.substring(ItemUpdate.HANDLE_PREFIX.length());

-		DSpaceObject dso = HandleManager.resolveToObject(context, handle);  
-		if (dso instanceof Item)
-		{
+        DSpaceObject dso = handleService.resolveToObject(context, handle);
+        if (dso instanceof Item) {
            item = (Item) dso;
-		}
-		else
-		{
+        } else {
            ItemUpdate.pr("Warning: item not instantiated");
            throw new IllegalArgumentException("Item " + handle + " not instantiated.");
        }
@@ -239,53 +244,50 @@ 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
-     * @throws Exception
+     * @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

-	    ItemIterator itr = Item.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++;
        }

-		itr.close(); 
-		
        ItemUpdate.prv("items matching = " + count);

-		if (count != 1)
-		{
+        if (count != 1) {
            throw new Exception("" + count + " items matching item identifier: " + dtom.value);
        }

        return item;
    }

-    private DtoMetadata  getMetadataField(String compoundForm)
-    {
-    	for (DtoMetadata dtom : dtomList)
-    	{
-			if (dtom.matches(compoundForm, false))
-			{
+    /**
+     * Get DtoMetadata field
+     *
+     * @param compoundForm compound form
+     * @return DtoMetadata field
+     */
+    private DtoMetadata getMetadataField(String compoundForm) {
+        for (DtoMetadata dtom : dtomList) {
+            if (dtom.matches(compoundForm, false)) {
                return dtom;
            }
        }
@@ -295,51 +297,44 @@ public class ItemArchive {
    /**
     * write undo directory and files to Disk in archive format
     *
-     * 
     * @param undoDir - the root directory of the undo archive
+     * @throws IOException                       if IO error
+     * @throws ParserConfigurationException      if config error
+     * @throws TransformerConfigurationException if transformer config error
+     * @throws TransformerException              if transformer error
+     * @throws FileNotFoundException             if file not found
     */
    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 (Integer i : undoAddContents)
-                    {
+                    for (UUID i : undoAddContents) {
                        pw.println(i);
                    }
-                }
-                finally
-                {
+                } finally {
                    pw.close();
                }
            }
-        }
-        finally
-        {
-            if (out != null)
-            {
+        } finally {
+            if (out != null) {
                out.close();
            }
        }
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/ItemUpdate.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/ItemUpdate.java
@@ -9,9 +9,9 @@ package org.dspace.app.itemupdate;

 import java.io.BufferedWriter;
 import java.io.File;
-import java.io.FilenameFilter;
 import java.io.FileNotFoundException;
 import java.io.FileWriter;
+import java.io.FilenameFilter;
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.ArrayList;
@@ -20,6 +20,7 @@ import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.UUID;

 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
@@ -28,12 +29,15 @@ import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.PosixParser;
 import org.dspace.content.Item;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.ItemService;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;
+import org.dspace.eperson.factory.EPersonServiceFactory;
+import org.dspace.eperson.service.EPersonService;

 /**
- *   
 * Provides some batch editing capabilities for items in DSpace:
 * Metadata fields - Add, Delete
 * Bitstreams - Add, Delete
@@ -58,9 +62,7 @@ import org.dspace.eperson.EPerson;
 * 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 {

@@ -74,45 +76,44 @@ public class ItemUpdate {

    public static boolean verbose = false;

-	static
-	{
+    protected static final EPersonService epersonService = EPersonServiceFactory.getInstance().getEPersonService();
+    protected static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+
+    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()
-    {
-        public boolean accept(File dir, String n)
-        {
+    static FilenameFilter directoryFilter = new FilenameFilter() {
+        @Override
+        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()
-    {
-        public boolean accept(File dir, String n)
-        {
+    static FilenameFilter fileFilter = new FilenameFilter() {
+        @Override
+        public boolean accept(File dir, String n) {
            File f = new File(dir.getAbsolutePath() + File.separatorChar + n);
            return (f.isFile());
        }
    };

    // instance variables
-    private ActionManager actionMgr = new ActionManager(); 
-    private List<String> undoActionList = new ArrayList<String>();  
-    private String eperson;
+    protected ActionManager actionMgr = new ActionManager();
+    protected List<String> undoActionList = new ArrayList<String>();
+    protected String eperson;

    /**
-     * 
-     * @param argv
+     * @param argv the command line arguments given
     */
-    public static void main(String[] argv)
-    {
+    public static void main(String[] argv) {
        // create an options object and populate it
        CommandLineParser parser = new PosixParser();

@@ -123,20 +124,23 @@ 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");

@@ -154,12 +158,10 @@ 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("");
@@ -173,91 +175,79 @@ 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);
                }
@@ -265,138 +255,127 @@ 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());
                }
            }

            pr("ItemUpdate - initializing run on " + (new Date()).toString());

-	        context = new Context();  
+            context = new Context(Context.Mode.BATCH_EDIT);
            iu.setEPerson(context, iu.eperson);
-	        context.setIgnoreAuthorization(true);
+            context.turnOffAuthorisationSystem();

            HANDLE_PREFIX = ConfigurationManager.getProperty("handle.canonical.prefix");
-	    	if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0)
-	    	{
+            if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0) {
                HANDLE_PREFIX = "http://hdl.handle.net/";
            }

            iu.processArchive(context, sourcedir, itemField, metadataIndexName, alterProvenance, isTest);

            context.complete();  // complete all transactions
-	        context.setIgnoreAuthorization(false);
-        }
-        catch (Exception e)
-        {
-            if (context != null && context.isValid())
-            {
+        } catch (Exception e) {
+            if (context != null && context.isValid()) {
                context.abort();
-            	context.setIgnoreAuthorization(false);
            }
            e.printStackTrace();
            pr(e.toString());
            status = 1;
+        } finally {
+            context.restoreAuthSystemState();
        }

-        if (isTest)
-        {
+        if (isTest) {
            pr("***End of Test Run***");
-        }
-        else
-        {
+        } else {
            pr("End.");

        }
        System.exit(status);
    }

-    private void processArchive(Context context, String sourceDirPath, String itemField,
+    /**
+     * process an archive
+     *
+     * @param context           DSpace Context
+     * @param sourceDirPath     source path
+     * @param itemField         item field
+     * @param metadataIndexName index name
+     * @param alterProvenance   whether to alter provenance
+     * @param isTest            test flag
+     * @throws Exception if error
+     */
+    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);
        }
@@ -407,90 +386,73 @@ 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();
-    				item.update();  //need to update before commit
-    				context.commit();  
-	    			item.decache();
+                    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();
            }
        }
@@ -502,48 +464,42 @@ public class ItemUpdate {


    /**
-     * 
     * to avoid overwriting the undo source tree on repeated processing
     * sequence numbers are added and checked
     *
     * @param sourceDir - the original source directory
     * @return the directory of the undo archive
-     * @throws FileNotFoundException
-     * @throws IOException
+     * @throws FileNotFoundException if file doesn't exist
+     * @throws IOException           if IO error
     */
-	private File initUndoArchive(File sourceDir)
-	throws FileNotFoundException, IOException
-	{				
-		File parentDir = sourceDir.getAbsoluteFile().getParentFile(); 
-		if (parentDir == null)
-		{
-			throw new FileNotFoundException("Parent directory of archive directory not found; unable to write UndoArchive; no processing performed");    			
+    protected File initUndoArchive(File sourceDir)
+        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");
        }

        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())
-		{
-        	pr("ERROR creating  Undo Archive directory ");
-        	throw new IOException("ERROR creating  Undo Archive directory ");
+        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;
        }
@@ -552,29 +508,31 @@ public class ItemUpdate {

    //private void write

-    private void setEPerson(Context context, String eperson)
-    throws Exception
-    {
-        if (eperson == null)
-        {
+    /**
+     * 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) {
            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 = EPerson.findByEmail(context, eperson);
-        }
-        else
-        {
-            myEPerson = EPerson.find(context, Integer.parseInt(eperson));
+            myEPerson = epersonService.findByEmail(context, eperson);
+        } 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");
        }
@@ -586,21 +544,20 @@ 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
+     *
+     * @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
+     *
+     * @param s String
     */
-    static void prv(String s)
-    {
-    	if (verbose) 
-    	{
+    static void prv(String s) {
+        if (verbose) {
            System.out.println(s);
        }
    }
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/MetadataUtilities.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/MetadataUtilities.java
@@ -11,14 +11,13 @@ import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
-import java.io.InputStream;
 import java.io.IOException;
+import java.io.InputStream;
 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;
@@ -31,7 +30,15 @@ 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.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;
 import org.w3c.dom.NamedNodeMap;
@@ -39,12 +46,6 @@ import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 import org.xml.sax.SAXException;

-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.DCValue;
-import org.dspace.content.Item;
-import org.dspace.content.MetadataSchema;
-import org.dspace.core.ConfigurationManager;
-

 /**
 * Miscellaneous methods for metadata handling that build on the API
@@ -52,67 +53,60 @@ import org.dspace.core.ConfigurationManager;
 * in context in ItemUpdate.
 *
 * The XML methods were based on those in ItemImport
- * 
- *
 */
 public class MetadataUtilities {

+    protected static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+
    /**
-     * 
-     *  Working around Item API to delete a value-specific DCValue
+     * 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
     * add them back, minus the one to actually delete
     *
-     * 
-     * @param item
-     * @param dtom
-     * @param isLanguageStrict - 
-     * 
+     * @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
     */
-    public static boolean deleteMetadataByValue(Item item, DtoMetadata dtom, boolean isLanguageStrict)
-    {   	
-    	DCValue[] ar = null;
+    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
-    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);  
-    	}
-    	else
-    	{
-    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);  
+        if (isLanguageStrict) {   // get all for given type
+            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
+        } else {
+            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
        }

        boolean found = false;

        //build new set minus the one to delete
        List<String> vals = new ArrayList<String>();
-    	for (DCValue dcv : ar)
-    	{
-    		if (dcv.value.equals(dtom.value))
-    		{
+        for (MetadataValue dcv : ar) {
+            if (dcv.getValue().equals(dtom.value)) {
                found = true;
-    		}
-    		else
-    		{
-    			vals.add(dcv.value);
+            } else {
+                vals.add(dcv.getValue());
            }
        }

-    	if (found)  //remove all for given type  ??synchronize this block??
-    	{   
-        	if (isLanguageStrict)
-        	{           		
-        		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-        	}
-        	else
-        	{
-        		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
+        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 {
+                itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
            }

-    		item.addMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals.toArray(new String[vals.size()]));   	
+            itemService.addMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals);
        }
        return found;
    }
@@ -120,83 +114,71 @@ public class MetadataUtilities {
    /**
     * Append text to value metadata field to item
     *
-     * @param item
-     * @param dtom
-     * @param isLanguageStrict
-     * @param textToAppend
+     * @param context          DSpace Context
+     * @param item             DSpace Item
+     * @param dtom             metadata field
+     * @param isLanguageStrict if strict
+     * @param textToAppend     text to append
     * @throws IllegalArgumentException - When target metadata field is not found
+     * @throws SQLException             if database error
     */
-    public static void appendMetadata(Item item, DtoMetadata dtom, boolean isLanguageStrict, 
+    public static void appendMetadata(Context context, Item item, DtoMetadata dtom, boolean isLanguageStrict,
                                      String textToAppend)
-    throws IllegalArgumentException
-    {   	
-    	DCValue[] ar = null;
+        throws IllegalArgumentException, SQLException {
+        List<MetadataValue> ar = null;

        // get all values for given element/qualifier
-    	if (isLanguageStrict)  // get all for given element/qualifier
-    	{   
-    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);  
-    	}
-    	else
-    	{
-    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);  
+        if (isLanguageStrict) {  // get all for given element/qualifier
+            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
+        } else {
+            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
        }

-    	if (ar.length == 0)
-    	{
+        if (ar.size() == 0) {
            throw new IllegalArgumentException("Metadata to append to not found");
        }

        int idx = 0;  //index of field to change
-    	if (ar.length > 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.length; i++) 
-    	{
-    		if (i == idx)
-    		{
-    			vals.add(ar[i].value + textToAppend);
-    		}
-    		else
-    		{
-    			vals.add(ar[i].value);
+        for (int i = 0; i < ar.size(); i++) {
+            if (i == idx) {
+                vals.add(ar.get(i).getValue() + textToAppend);
+            } else {
+                vals.add(ar.get(i).getValue());
            }
        }

-    	if (isLanguageStrict)
-    	{           		
-    		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-    	}
-    	else
-    	{
-    		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
+        if (isLanguageStrict) {
+            itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
+        } else {
+            itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
        }

-		item.addMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals.toArray(new String[vals.size()]));   	
+        itemService.addMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals);
    }

    /**
     * Modification of method from ItemImporter.loadDublinCore
     * as a Factory method
     *
-     * @param docBuilder  - 
+     * @param docBuilder DocumentBuilder
     * @param is         - InputStream of dublin_core.xml
     * @return list of DtoMetadata representing the metadata fields relating to an Item
-     * @throws SQLException
-     * @throws IOException
-     * @throws ParserConfigurationException
-     * @throws SAXException
-     * @throws TransformerException
-     * @throws AuthorizeException
+     * @throws SQLException                 if database error
+     * @throws IOException                  if IO error
+     * @throws ParserConfigurationException if parser config error
+     * @throws SAXException                 if XML error
+     * @throws TransformerException         if transformer error
+     * @throws AuthorizeException           if authorization error
     */
    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>();
@@ -206,55 +188,43 @@ 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");
            }

@@ -268,39 +238,31 @@ public class MetadataUtilities {
    /**
     * Write dublin_core.xml
     *
-     * @param docBuilder
-     * @param dtomList
+     * @param docBuilder DocumentBuilder
+     * @param dtomList   List of metadata fields
     * @return xml document
-     * @throws ParserConfigurationException
-     * @throws TransformerConfigurationException
-     * @throws TransformerException
+     * @throws ParserConfigurationException      if parser config error
+     * @throws TransformerConfigurationException if transformer config error
+     * @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);
@@ -312,39 +274,37 @@ public class MetadataUtilities {

    /**
     * write xml document to output stream
-     * @param doc
-     * @param transformer
-     * @param out
-     * @throws IOException
-     * @throws TransformerException
+     *
+     * @param doc         XML Document
+     * @param transformer XML Transformer
+     * @param out         OutputStream
+     * @throws IOException          if IO Error
+     * @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
+
    /**
     * Lookup an attribute from a DOM node.
-     * @param n
-     * @param name
-     * @return
+     *
+     * @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();
            }
        }
@@ -354,19 +314,17 @@ public class MetadataUtilities {

    /**
     * Return the String value of a Node.
-     * @param node
-     * @return
+     *
+     * @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();
            }
        }
@@ -375,44 +333,37 @@ public class MetadataUtilities {
    }

    /**
-     * 		rewrite of ItemImport's functionality
-     *      but just the parsing of the file, not the processing of its elements
+     * Rewrite of ItemImport's functionality
+     * but just the parsing of the file, not the processing of its elements.
     *
-     *      
-     * @validate  flag to verify matching files in tree
-     * @return
+     * @param f file
+     * @return list of ContentsEntry
+     * @throws FileNotFoundException if file doesn't exist
+     * @throws IOException           if IO error
+     * @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
            }
        }
@@ -421,52 +372,33 @@ public class MetadataUtilities {
    }

    /**
-     * 
-     * @param f
-     * @return
-     * @throws FileNotFoundException
-     * @throws IOException
+     * @param f file
+     * @return list of lines as strings
+     * @throws FileNotFoundException if file doesn't exist
+     * @throws IOException           if IO Error
     */
-    public static List<Integer> readDeleteContentsFile(File f)
-    throws FileNotFoundException, IOException
-    {
-    	List<Integer> list = new ArrayList<Integer>();
+    public static List<String> readDeleteContentsFile(File f)
+        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;
                }

-	            int n = 0;
-	            try
-	            {
-	            	n = Integer.parseInt(line);
-		    		list.add(n);	    		
+                list.add(line);
            }
-	            catch(NumberFormatException e)
-	            {
-	            	ItemUpdate.pr("Error reading delete contents line:" + e.toString());
-	            }            	
-	    	}
-    	}
-    	finally
-    	{
-    		try
-    		{
+        } finally {
+            try {
                in.close();
-    		}
-    		catch(IOException e)
-    		{
+            } catch (IOException e) {
                //skip
            }
        }
@@ -475,54 +407,55 @@ public class MetadataUtilities {
    }

    /**
-     *    Get display of DCValue    
+     * Get display of Metadatum
     *
-     * @param dcv
-     * @return string displaying elements of the DCValue
+     * @param dcv MetadataValue
+     * @return string displaying elements of the Metadatum
     */
-    public static String getDCValueString(DCValue dcv)
-    {
-    	return "schema: " + dcv.schema + "; element: " + dcv.element + "; qualifier: " + dcv.qualifier +
-    	       "; language: " + dcv.language + "; value: " + dcv.value;
+    public static String getDCValueString(MetadataValue dcv) {
+        MetadataField metadataField = dcv.getMetadataField();
+        MetadataSchema metadataSchema = metadataField.getMetadataSchema();
+        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();
    }

    /**
-	 *    Parses metadata field given in the form <schema>.<element>[.<qualifier>|.*]
+     * Parses metadata field given in the form {@code <schema>.<element>[.<qualifier>|.*]}
     * checks for correct number of elements (2 or 3) and for empty strings
     *
+     * @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);
        }

--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/OriginalBitstreamFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/OriginalBitstreamFilter.java
@@ -8,6 +8,7 @@
 package org.dspace.app.itemupdate;

 import java.sql.SQLException;
+import java.util.List;

 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
@@ -17,36 +18,29 @@ 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
+     * @throws BitstreamFilterException if filter error
     */
+    @Override
    public boolean accept(Bitstream bitstream)
-	throws BitstreamFilterException
-	{		
-		try
-		{
-			Bundle[] bundles = bitstream.getBundles();
-			for (Bundle b : bundles)
-			{
-				if (b.getName().equals("ORIGINAL"))
-				{
+        throws BitstreamFilterException {
+        try {
+            List<Bundle> bundles = bitstream.getBundles();
+            for (Bundle bundle : bundles) {
+                if (bundle.getName().equals("ORIGINAL")) {
                    return true;
                }
            }
-		}
-		catch(SQLException e)
-		{
+        } catch (SQLException e) {
            throw new BitstreamFilterException(e);
        }
        return false;
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/OriginalWithDerivativesBitstreamFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/OriginalWithDerivativesBitstreamFilter.java
@@ -8,6 +8,8 @@
 package org.dspace.app.itemupdate;

 import java.sql.SQLException;
+import java.util.List;
+
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;

@@ -16,41 +18,33 @@ 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 
-{
-	private String[] bundlesToEmpty = { "ORIGINAL", "TEXT", "THUMBNAIL" };	
+public class OriginalWithDerivativesBitstreamFilter extends BitstreamFilter {
+    protected String[] bundlesToEmpty = {"ORIGINAL", "TEXT", "THUMBNAIL"};

-	public OriginalWithDerivativesBitstreamFilter()
-	{
+    public OriginalWithDerivativesBitstreamFilter() {
        //empty
    }

    /**
     * Tests bitstream for membership in specified bundles (ORIGINAL, TEXT, THUMBNAIL)
     *
-	 * @param bitstream
-	 * @throws BitstreamFilterException
+     * @param bitstream Bitstream
     * @return true if bitstream is in specified bundles
+     * @throws BitstreamFilterException if error
     */
+    @Override
    public boolean accept(Bitstream bitstream)
-	throws BitstreamFilterException
-	{		
-		try
-		{
-			Bundle[] bundles = bitstream.getBundles();
-			for (Bundle b : bundles)
-			{
-				for (String bn : bundlesToEmpty)
-				{
-					if (b.getName().equals(bn))
-					{
+        throws BitstreamFilterException {
+        try {
+            List<Bundle> bundles = bitstream.getBundles();
+            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;
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/ThumbnailBitstreamFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/ThumbnailBitstreamFilter.java
@@ -11,12 +11,10 @@ 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");
    }
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/UpdateAction.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/UpdateAction.java
@@ -7,22 +7,25 @@
 */
 package org.dspace.app.itemupdate;

+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.ItemService;
 import org.dspace.core.Context;

 /**
 * Interface for actions to update an item
- *
 */
-public interface UpdateAction 
-{
+public interface UpdateAction {
+    public ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+
+
    /**
     * Action to update item
     *
-	 * @param context
-	 * @param itarch
-	 * @param isTest
-	 * @param suppressUndo
-	 * @throws Exception
+     * @param context      DSpace context
+     * @param itarch       item archive
+     * @param isTest       test flag
+     * @param suppressUndo undo flag
+     * @throws Exception if error
     */
    public void execute(Context context, ItemArchive itarch, boolean isTest, boolean suppressUndo)
        throws Exception;
--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/UpdateBitstreamsAction.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/UpdateBitstreamsAction.java
@@ -7,32 +7,36 @@
 */
 package org.dspace.app.itemupdate;

+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.BitstreamService;
+import org.dspace.content.service.BundleService;
+
 /**
 * Base class for Bitstream actions
- * 
- *
 */
 public abstract class UpdateBitstreamsAction implements UpdateAction {

    protected boolean alterProvenance = true;

+
+    protected BundleService bundleService = ContentServiceFactory.getInstance().getBundleService();
+    protected BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();
+
    /**
     * Set variable to indicate that the dc.description.provenance field may
     * be changed as a result of Bitstream changes by ItemUpdate
-	 * @param alterProvenance
+     *
+     * @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;
    }

--- a/dspace-api/src/main/java/org/dspace/app/itemupdate/UpdateMetadataAction.java
+++ b/dspace-api/src/main/java/org/dspace/app/itemupdate/UpdateMetadataAction.java
@@ -13,12 +13,10 @@ import java.util.Set;
 /**
 * This abstract subclass for metadata actions
 * maintains a collection for the target metadata fields
- *   expressed as a string in the compound notation ( <schema>.<element>.<qualifier> )
+ * expressed as a string in the compound notation ( {@code <schema>.<element>.<qualifier>} )
 * 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 {

@@ -36,11 +34,10 @@ public abstract class UpdateMetadataAction implements UpdateAction {
    /**
     * Set target fields
     *
-	 * @param targetFields
+     * @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);
        }

@@ -48,11 +45,11 @@ public abstract class UpdateMetadataAction implements UpdateAction {

    /**
     * Add array of target fields to update
-	 * @param targetFields
+     *
+     * @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);
        }

@@ -61,7 +58,7 @@ public abstract class UpdateMetadataAction implements UpdateAction {
    /**
     * Add single field to update
     *
-	 * @param targetField
+     * @param targetField target field to update
     */
    public void addTargetField(String targetField) {
        this.targetFields.add(targetField);
--- a/dspace-api/src/main/java/org/dspace/app/launcher/CommandRunner.java
+++ b/dspace-api/src/main/java/org/dspace/app/launcher/CommandRunner.java
@@ -0,0 +1,104 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.launcher;
+
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+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 {
+
+    /**
+     * Default constructor
+     */
+    private CommandRunner() { }
+
+    /**
+     * @param args the command line arguments given
+     * @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) {
+            runManyCommands(args[0]);
+        } else {
+            runManyCommands("-");
+        }
+        // There is no sensible way to use the status returned by runManyCommands().
+        // If called from the command line then we would want to return it
+        // through System.exit().  But if called (normally) from ScriptLauncher,
+        // there is no way to return it and we don't want to interrupt
+        // ScriptLauncher.
+        //
+        // "'tis a puzzlement." -- the King of Siam
+    }
+
+    /**
+     * Read a file of command lines and execute each in turn.
+     *
+     * @param script the file of command lines to be executed.
+     * @return status code
+     * @throws IOException           if IO error
+     * @throws FileNotFoundException if file doesn't exist
+     */
+    static int runManyCommands(String script)
+        throws FileNotFoundException, IOException {
+        Reader input;
+        if ("-".equals(script)) {
+            input = new InputStreamReader(System.in);
+        } else {
+            input = new FileReader(script);
+        }
+
+        StreamTokenizer tokenizer = new StreamTokenizer(input);
+
+        tokenizer.eolIsSignificant(true);
+
+        tokenizer.ordinaryChar('-');
+        tokenizer.wordChars('-', '-');
+
+        tokenizer.ordinaryChars('0', '9');
+        tokenizer.wordChars('0', '9');
+
+        tokenizer.ordinaryChar('.');
+        tokenizer.wordChars('.', '.');
+
+        tokenizer.ordinaryChar('@');
+        tokenizer.wordChars('@', '@');
+
+        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) {
+                    status = ScriptLauncher.runOneCommand(commandConfigs, tokens.toArray(new String[tokens.size()]));
+                    if (status > 0) {
+                        break;
+                    }
+                    tokens.clear();
+                }
+            } else {
+                tokens.add(tokenizer.sval);
+            }
+        }
+
+        return status;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/launcher/ScriptLauncher.java
+++ b/dspace-api/src/main/java/org/dspace/app/launcher/ScriptLauncher.java
@@ -7,15 +7,18 @@
 */
 package org.dspace.app.launcher;

-import org.dspace.core.ConfigurationManager;
+import java.io.FileNotFoundException;
+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;
 import org.jdom.Document;
 import org.jdom.Element;
 import org.jdom.input.SAXBuilder;
-import java.util.List;
-import java.lang.reflect.Method;

 /**
 * A DSpace script launcher.
@@ -23,89 +26,121 @@ import java.lang.reflect.Method;
 * @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
     *
     * @param args Any parameters required to be passed to the scripts it executes
+     * @throws IOException           if IO error
+     * @throws FileNotFoundException if file doesn't exist
     */
    public static void main(String[] args)
-    {
-        // Check that there is at least one argument
-        if (args.length < 1)
-        {
-            System.err.println("You must provide at least one command argument");
-            display();
-            System.exit(1);
-        }
-
+        throws FileNotFoundException, IOException {
        // Initialise the service manager kernel
        try {
            kernelImpl = DSpaceKernelInit.getKernel(null);
-            if (!kernelImpl.isRunning())
-            {
-                kernelImpl.start(ConfigurationManager.getProperty("dspace.dir"));
+            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 filter init: " + e.getMessage();
-            System.err.println(message + ":" + e);
+            String message = "Failure during kernel init: " + e.getMessage();
+            System.err.println(message);
+            e.printStackTrace();
            throw new IllegalStateException(message, e);
        }

-        // Parse the configuration file looking for the command entered
-        Document doc = getConfig();
+        // Load up the ScriptLauncher's configuration
+        Document commandConfigs = getConfig();
+
+        // Check that there is at least one argument (if not display command options)
+        if (args.length < 1) {
+            System.err.println("You must provide at least one command argument");
+            display(commandConfigs);
+            System.exit(1);
+        }
+
+        // Look up command in the configuration, and execute.
+        int status;
+        status = runOneCommand(commandConfigs, args);
+
+        // Destroy the service kernel if it is still alive
+        if (kernelImpl != null) {
+            kernelImpl.destroy();
+            kernelImpl = null;
+        }
+
+        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
+     */
+    public static int runOneCommand(Document commandConfigs, String[] args, DSpaceKernelImpl kernelImpl) {
        String request = args[0];
-        Element root = doc.getRootElement();
+        Element root = commandConfigs.getRootElement();
        List<Element> commands = root.getChildren("command");
-        for (Element command : commands)
-        {
-            if (request.equalsIgnoreCase(command.getChild("name").getValue()))
-            {
+        Element command = null;
+        for (Element candidate : commands) {
+            if (request.equalsIgnoreCase(candidate.getChild("name").getValue())) {
+                command = candidate;
+                break;
+            }
+        }
+
+        if (null == command) {
+            // The command wasn't found
+            System.err.println("Command not found: " + args[0]);
+            display(commandConfigs);
+            return 1;
+        }
+
        // 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");
-                            System.exit(1);
+                    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);
-                        System.exit(1);
+                return 1;
            }

            // Strip the leading argument from the args, and add the arguments
@@ -114,26 +149,20 @@ 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;
@@ -141,25 +170,24 @@ 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;
            }

            // Establish the request service startup
-                    RequestService requestService = kernelImpl.getServiceManager().getServiceByName(RequestService.class.getName(), RequestService.class);
+            RequestService requestService = kernelImpl.getServiceManager().getServiceByName(
+                RequestService.class.getName(), RequestService.class);
            if (requestService == null) {
-                        throw new IllegalStateException("Could not get the DSpace RequestService to start the request transaction");
+                throw new IllegalStateException(
+                    "Could not get the DSpace RequestService to start the request transaction");
            }

            // Establish a request related to the current session
@@ -167,8 +195,7 @@ public class ScriptLauncher
            requestService.startRequest();

            // Run the main() method
-                    try
-                    {
+            try {
                Object[] arguments = {useargs};

                // Useful for debugging, so left in the code...
@@ -184,50 +211,20 @@ 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);

-                    	if (kernelImpl != null)
-                        {
-                            kernelImpl.destroy();
-                            kernelImpl = null;
-                        }
-
                // Exceptions from the script are reported as a 'cause'
                Throwable cause = e.getCause();
                System.err.println("Exception: " + cause.getMessage());
                cause.printStackTrace();
-                        System.exit(1);
+                return 1;
            }
-
-                }
-
-                // Destroy the service kernel
-                if (kernelImpl != null)
-                {
-                    kernelImpl.destroy();
-                    kernelImpl = null;
        }

        // Everything completed OK
-                System.exit(0);
-            }
-        }
-
-        // Destroy the service kernel if it is still alive
-        if (kernelImpl != null)
-        {
-            kernelImpl.destroy();
-            kernelImpl = null;
-        }
-
-        // The command wasn't found
-        System.err.println("Command not found: " + args[0]);
-        display();
-        System.exit(1);
+        return 0;
    }

    /**
@@ -235,22 +232,23 @@ public class ScriptLauncher
     *
     * @return The XML configuration file Document
     */
-    private static Document getConfig()
-    {
+    protected static Document getConfig() {
+        return getConfig(kernelImpl);
+    }
+
+    public static Document getConfig(DSpaceKernelImpl kernelImpl) {
        // Load the launcher configuration file
-        String config = ConfigurationManager.getProperty("dspace.dir") +
+        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();
            System.exit(1);
        }
        return doc;
@@ -258,14 +256,24 @@ public class ScriptLauncher

    /**
     * Display the commands that the current launcher config file knows about
+     *
+     * @param commandConfigs configs as Document
     */
-    private static void display()
-    {
-        Document doc = getConfig();
-        List<Element> commands = doc.getRootElement().getChildren("command");
+    private static void display(Document commandConfigs) {
+        // List all command elements
+        List<Element> commands = commandConfigs.getRootElement().getChildren("command");
+
+        // Sort the commands by name.
+        // 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) {
+            sortedCommands.put(command.getChild("name").getValue(), command);
+        }
+
+        // Display the sorted list
        System.out.println("Usage: dspace [command-name] {parameters}");
-        for (Element command : commands)
-        {
+        for (Element command : sortedCommands.values()) {
            System.out.println(" - " + command.getChild("name").getValue() +
                                   ": " + command.getChild("description").getValue());
        }
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/Brand.java
+++ b/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.
@@ -20,8 +20,7 @@ import java.awt.Rectangle;
 * 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;
@@ -34,13 +33,11 @@ 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;
@@ -55,46 +52,34 @@ 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]);
            }
        }
@@ -111,48 +96,37 @@ 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();

-		bWidth = fm.stringWidth(brandText.getText()) + xOffset * 2 + 1;
-		bHeight = fm.getHeight();
+        int bx = 0;
+        int by = 0;

+        if (brandText.getLocation().equals(BrandText.TL)) {
            bx = 0;
            by = 0;
-
-		if (brandText.getLocation().equals(BrandText.TL))
-		{
-			bx = 0;
-			by = 0;
-		}
-		else if (brandText.getLocation().equals(BrandText.TR))
-		{
+        } 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);
-		tx = bx + xOffset;
-		ty = by + fm.getAscent();
+        int tx = bx + xOffset;
+        int ty = by + fm.getAscent();

        g2.setColor(Color.black);
        g2.fill(box);
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/BrandText.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/BrandText.java
@@ -13,15 +13,22 @@ 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;
@@ -34,8 +41,7 @@ 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;
    }
@@ -45,8 +51,7 @@ class BrandText
     *
     * @return String one the class location constants e.g. <code>Identifier.BL</code>
     */
-	public String getLocation()
-	{
+    public String getLocation() {
        return location;
    }

@@ -56,8 +61,7 @@ class BrandText
     *
     * @return String the text associated with the Identifier object
     */
-	public String getText()
-	{
+    public String getText() {
        return text;
    }

@@ -67,8 +71,7 @@ class BrandText
     *
     * @param location one of the class location constants
     */
-	public void setLocation(String location)
-	{
+    public void setLocation(String location) {
        this.location = location;
    }

@@ -78,8 +81,7 @@ 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;
    }
 }
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/BrandedPreviewJPEGFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/BrandedPreviewJPEGFilter.java
@@ -7,64 +7,61 @@
 */
 package org.dspace.app.mediafilter;

-import java.awt.Graphics2D;
 import java.awt.image.BufferedImage;
-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;
 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
 * no bigger than. Creates only JPEGs.
+ *
+ * @author Jason Sherman jsherman@usao.edu
 */
-public class BrandedPreviewJPEGFilter extends MediaFilter
-{
-    public String getFilteredName(String oldFilename)
-    {
+public class BrandedPreviewJPEGFilter extends MediaFilter {
+    @Override
+    public String getFilteredName(String oldFilename) {
        return oldFilename + ".preview.jpg";
    }

    /**
     * @return String bundle name
-     *  
     */
-    public String getBundleName()
-    {
+    @Override
+    public String getBundleName() {
        return "BRANDED_PREVIEW";
    }

    /**
     * @return String bitstreamformat
     */
-    public String getFormatString()
-    {
+    @Override
+    public String getFormatString() {
        return "JPEG";
    }

    /**
     * @return String description
     */
-    public String getDescription()
-    {
+    @Override
+    public String getDescription() {
        return "Generated Branded Preview";
    }


    /**
-     * @param source
-     *            source input stream
-     * 
+     * @param currentItem item
+     * @param source      source input stream
+     * @param verbose     verbose mode
     * @return InputStream the resulting input stream
+     * @throws Exception if error
     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception
-    {
+    @Override
+    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+        throws Exception {
        // read in bitstream's image
        BufferedImage buf = ImageIO.read(source);

@@ -73,89 +70,17 @@ public class BrandedPreviewJPEGFilter extends MediaFilter
            .getIntProperty("webui.preview.maxwidth");
        float ymax = (float) ConfigurationManager
            .getIntProperty("webui.preview.maxheight");
+        boolean blurring = (boolean) ConfigurationManager
+            .getBooleanProperty("webui.preview.blurring");
+        boolean hqscaling = (boolean) ConfigurationManager
+            .getBooleanProperty("webui.preview.hqscaling");
        int brandHeight = ConfigurationManager.getIntProperty("webui.preview.brand.height");
        String brandFont = ConfigurationManager.getProperty("webui.preview.brand.font");
        int brandFontPoint = ConfigurationManager.getIntProperty("webui.preview.brand.fontpoint");

-        // 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 (MediaFilterManager.isVerbose)
-        {
-            System.out.println("original size: " + xsize + "," + ysize);
-        }
-
-        // scale by x first if needed
-        if (xsize > xmax)
-        {
-            // calculate scaling factor so that xsize * scale = new size (max)
-            float scaleFactor = xmax / xsize;
-
-            // if verbose flag is set, print out extracted text
-            // to STDOUT
-            if (MediaFilterManager.isVerbose)
-            {
-                System.out.println("x scale factor: " + scaleFactor);
-            }
-
-            // now reduce x size
-            // and y size
-            xsize = xsize * scaleFactor;
-            ysize = ysize * scaleFactor;
-
-            // if verbose flag is set, print out extracted text
-            // to STDOUT
-            if (MediaFilterManager.isVerbose)
-            {
-                System.out.println("new size: " + xsize + "," + ysize);
-            }
-        }
-
-        // scale by y if needed
-        if (ysize > ymax)
-        {
-            float scaleFactor = ymax / ysize;
-
-            // now reduce x size
-            // and y size
-            xsize = xsize * scaleFactor;
-            ysize = ysize * scaleFactor;
-        }
-
-        // if verbose flag is set, print details to STDOUT
-        if (MediaFilterManager.isVerbose)
-        {
-            System.out.println("created thumbnail size: " + xsize + ", "
-                    + ysize);
-        }
-
-        // create an image buffer for the preview with the new xsize, ysize
-        // we add
-        BufferedImage branded = new BufferedImage((int) xsize, (int) ysize + brandHeight,
-                BufferedImage.TYPE_INT_RGB);
-
-        // now render the image into the preview buffer
-        Graphics2D g2d = branded.createGraphics();
-        g2d.drawImage(buf, 0, 0, (int) xsize, (int) ysize, null);
-        
-        Brand brand = new Brand((int) xsize, brandHeight, new Font(brandFont, Font.PLAIN, brandFontPoint), 5);
-		BufferedImage brandImage = brand.create(ConfigurationManager.getProperty("webui.preview.brand"),
-												ConfigurationManager.getProperty("webui.preview.brand.abbrev"),
-												MediaFilterManager.getCurrentItem() == null ? "" : "hdl:" + MediaFilterManager.getCurrentItem().getHandle());
-		
-		g2d.drawImage(brandImage, (int)0, (int)ysize, (int) xsize, (int) 20, null);
-
-        // now create an input stream for the thumbnail buffer and return it
-        ByteArrayOutputStream baos = new ByteArrayOutputStream();
-
-        ImageIO.write(branded, "jpeg", baos);
-
-        // now get the array
-        ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
-
-        return bais; // hope this gets written out before its garbage collected!
+        JPEGFilter jpegFilter = new JPEGFilter();
+        return jpegFilter
+            .getThumbDim(currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, brandHeight, brandFontPoint,
+                         brandFont);
    }
 }
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/ExcelFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/ExcelFilter.java
@@ -0,0 +1,99 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.mediafilter;
+
+import java.io.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.dspace.content.Item;
+
+/*
+ * ExcelFilter
+ *
+ * Entries you must add to dspace.cfg:
+ *
+ * filter.plugins = blah, \
+ *     Excel Text Extractor
+ *
+ * plugin.named.org.dspace.app.mediafilter.FormatFilter = \
+ *     blah = blah, \
+ *     org.dspace.app.mediafilter.ExcelFilter = Excel Text Extractor
+ *
+ * #Configure each filter's input Formats
+ * filter.org.dspace.app.mediafilter.ExcelFilter.inputFormats = Microsoft Excel, Microsoft Excel XML
+ *
+ */
+public class ExcelFilter extends MediaFilter {
+
+    private static Logger log = Logger.getLogger(ExcelFilter.class);
+
+    public String getFilteredName(String oldFilename) {
+        return oldFilename + ".txt";
+    }
+
+    /**
+     * @return String bundle name
+     */
+    public String getBundleName() {
+        return "TEXT";
+    }
+
+    /**
+     * @return String bitstream format
+     */
+    public String getFormatString() {
+        return "Text";
+    }
+
+    /**
+     * @return String description
+     */
+    public String getDescription() {
+        return "Extracted text";
+    }
+
+    /**
+     * @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 {
+        String extractedText = null;
+
+        try {
+            POITextExtractor theExtractor = ExtractorFactory.createExtractor(source);
+            if (theExtractor instanceof ExcelExtractor) {
+                // for xls file
+                extractedText = (theExtractor).getText();
+            } else if (theExtractor instanceof XSSFExcelExtractor) {
+                // for xlsx file
+                extractedText = (theExtractor).getText();
+            }
+        } catch (Exception e) {
+            log.error("Error filtering bitstream: " + e.getMessage(), e);
+            throw e;
+        }
+
+        if (extractedText != null) {
+            // generate an input stream with the extracted text
+            return IOUtils.toInputStream(extractedText, StandardCharsets.UTF_8);
+        }
+
+        return null;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/FormatFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/FormatFilter.java
@@ -18,13 +18,11 @@ 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
     */
@@ -44,18 +42,21 @@ public interface FormatFilter
    public String getFormatString();

    /**
-     * @return string to describe the newly-generated Bitstream's - how it was
+     * @return string to describe the newly-generated Bitstream - how it was
     * produced is a good idea
     */
    public String getDescription();

    /**
-     * @param source
-     *            input stream
+     * Read the source stream and produce the filtered content.
     *
-     * @return result of filter's transformation, written out to a bitstream
+     * @param item    Item
+     * @param source  input stream
+     * @param verbose verbosity flag
+     * @return result of filter's transformation as a byte stream.
+     * @throws Exception if error
     */
-    public InputStream getDestinationStream(InputStream source)
+    public InputStream getDestinationStream(Item item, InputStream source, boolean verbose)
        throws Exception;

    /**
@@ -66,18 +67,15 @@ 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 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
     */
-    public boolean preProcessBitstream(Context c, Item item, Bitstream source)
+    public boolean preProcessBitstream(Context c, Item item, Bitstream source, boolean verbose)
        throws Exception;

    /**
@@ -88,14 +86,11 @@ 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
     */
    public void postProcessBitstream(Context c, Item item, Bitstream generatedBitstream)
        throws Exception;
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/HTMLFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/HTMLFilter.java
@@ -9,58 +9,58 @@ package org.dspace.app.mediafilter;

 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 {

-    public String getFilteredName(String oldFilename)
-    {
+    @Override
+    public String getFilteredName(String oldFilename) {
        return oldFilename + ".txt";
    }

    /**
     * @return String bundle name
-     *  
     */
-    public String getBundleName()
-    {
+    @Override
+    public String getBundleName() {
        return "TEXT";
    }

    /**
     * @return String bitstreamformat
     */
-    public String getFormatString()
-    {
+    @Override
+    public String getFormatString() {
        return "Text";
    }

    /**
     * @return String description
     */
-    public String getDescription()
-    {
+    @Override
+    public String getDescription() {
        return "Extracted text";
    }

    /**
-     * @param source
-     *            source input stream
-     * 
+     * @param currentItem item
+     * @param source      source input stream
+     * @param verbose     verbose mode
     * @return InputStream the resulting input stream
+     * @throws Exception if error
     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception
-    {
+    @Override
+    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+        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();
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/ImageMagickImageThumbnailFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/ImageMagickImageThumbnailFilter.java
@@ -0,0 +1,52 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.mediafilter;
+
+import java.io.ByteArrayInputStream;
+import java.io.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 {
+
+    /**
+     * @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 {
+        File f = inputStreamToTempFile(source, "imthumb", ".tmp");
+        File f2 = null;
+        try {
+            f2 = getThumbnailFile(f, verbose);
+            byte[] bytes = Files.readAllBytes(f2.toPath());
+            return new ByteArrayInputStream(bytes);
+        } finally {
+            //noinspection ResultOfMethodCallIgnored
+            f.delete();
+            if (f2 != null) {
+                //noinspection ResultOfMethodCallIgnored
+                f2.delete();
+            }
+        }
+    }
+
+
+}
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/ImageMagickPdfThumbnailFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/ImageMagickPdfThumbnailFilter.java
@@ -0,0 +1,43 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.mediafilter;
+
+import java.io.ByteArrayInputStream;
+import java.io.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 {
+        File f = inputStreamToTempFile(source, "impdfthumb", ".pdf");
+        File f2 = null;
+        File f3 = null;
+        try {
+            f2 = getImageFile(f, 0, verbose);
+            f3 = getThumbnailFile(f2, verbose);
+            byte[] bytes = Files.readAllBytes(f3.toPath());
+            return new ByteArrayInputStream(bytes);
+        } finally {
+            //noinspection ResultOfMethodCallIgnored
+            f.delete();
+            if (f2 != null) {
+                //noinspection ResultOfMethodCallIgnored
+                f2.delete();
+            }
+            if (f3 != null) {
+                //noinspection ResultOfMethodCallIgnored
+                f3.delete();
+            }
+        }
+    }
+
+}
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/ImageMagickThumbnailFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/ImageMagickThumbnailFilter.java
@@ -0,0 +1,202 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.mediafilter;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
+
+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.IM4JavaException;
+import org.im4java.core.IMOperation;
+import org.im4java.core.Info;
+import org.im4java.process.ProcessStarter;
+
+/**
+ * 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 abstract class ImageMagickThumbnailFilter extends MediaFilter {
+    protected static int width = 180;
+    protected static int height = 120;
+    private static boolean flatten = true;
+    static String bitstreamDescription = "IM Thumbnail";
+    static final String defaultPattern = "Generated Thumbnail";
+    static Pattern replaceRegex = Pattern.compile(defaultPattern);
+    protected final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+
+    static String cmyk_profile;
+    static String srgb_profile;
+
+    static {
+        String pre = ImageMagickThumbnailFilter.class.getName();
+        String s = ConfigurationManager.getProperty(pre + ".ProcessStarter");
+        ProcessStarter.setGlobalSearchPath(s);
+        width = ConfigurationManager.getIntProperty("thumbnail.maxwidth", width);
+        height = ConfigurationManager.getIntProperty("thumbnail.maxheight", height);
+        flatten = ConfigurationManager.getBooleanProperty(pre + ".flatten", flatten);
+        String description = ConfigurationManager.getProperty(pre + ".bitstreamDescription");
+        cmyk_profile = ConfigurationManager.getProperty(pre + ".cmyk_profile");
+        srgb_profile = ConfigurationManager.getProperty(pre + ".srgb_profile");
+        if (description != null) {
+            bitstreamDescription = description;
+        }
+        try {
+            String patt = ConfigurationManager.getProperty(pre + ".replaceRegex");
+            replaceRegex = Pattern.compile(patt == null ? defaultPattern : patt);
+        } catch (PatternSyntaxException e) {
+            System.err.println("Invalid thumbnail replacement pattern: " + e.getMessage());
+        }
+    }
+
+    public ImageMagickThumbnailFilter() {
+    }
+
+    @Override
+    public String getFilteredName(String oldFilename) {
+        return oldFilename + ".jpg";
+    }
+
+    /**
+     * @return String bundle name
+     */
+    @Override
+    public String getBundleName() {
+        return "THUMBNAIL";
+    }
+
+    /**
+     * @return String bitstreamformat
+     */
+    @Override
+    public String getFormatString() {
+        return "JPEG";
+    }
+
+    /**
+     * @return String bitstreamDescription
+     */
+    @Override
+    public String getDescription() {
+        return bitstreamDescription;
+    }
+
+    public File inputStreamToTempFile(InputStream source, String prefix, String suffix) throws IOException {
+        File f = File.createTempFile(prefix, suffix);
+        f.deleteOnExit();
+        FileOutputStream fos = new FileOutputStream(f);
+
+        byte[] buffer = new byte[1024];
+        int len = source.read(buffer);
+        while (len != -1) {
+            fos.write(buffer, 0, len);
+            len = source.read(buffer);
+        }
+        fos.close();
+        return f;
+    }
+
+    public File getThumbnailFile(File f, boolean verbose)
+        throws IOException, InterruptedException, IM4JavaException {
+        File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
+        f2.deleteOnExit();
+        ConvertCmd cmd = new ConvertCmd();
+        IMOperation op = new IMOperation();
+        op.autoOrient();
+        op.addImage(f.getAbsolutePath());
+        op.thumbnail(width, height);
+        op.addImage(f2.getAbsolutePath());
+        if (verbose) {
+            System.out.println("IM Thumbnail Param: " + op);
+        }
+        cmd.run(op);
+        return f2;
+    }
+
+    public File getImageFile(File f, int page, boolean verbose)
+        throws IOException, InterruptedException, IM4JavaException {
+        File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
+        f2.deleteOnExit();
+        ConvertCmd cmd = new ConvertCmd();
+        IMOperation op = new IMOperation();
+        String s = "[" + page + "]";
+        op.addImage(f.getAbsolutePath() + s);
+        if (flatten) {
+            op.flatten();
+        }
+        // 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);
+            String imageClass = imageInfo.getImageClass();
+            if (imageClass.contains("CMYK")) {
+                op.profile(cmyk_profile);
+                op.profile(srgb_profile);
+            }
+        }
+        op.addImage(f2.getAbsolutePath());
+        if (verbose) {
+            System.out.println("IM Image Param: " + op);
+        }
+        cmd.run(op);
+        return f2;
+    }
+
+    @Override
+    public boolean preProcessBitstream(Context c, Item item, Bitstream source, boolean verbose) throws Exception {
+        String nsrc = source.getName();
+        for (Bundle b : itemService.getBundles(item, "THUMBNAIL")) {
+            for (Bitstream bit : b.getBitstreams()) {
+                String n = bit.getName();
+                if (n != null) {
+                    if (nsrc != null) {
+                        if (!n.startsWith(nsrc)) {
+                            continue;
+                        }
+                    }
+                }
+                String description = bit.getDescription();
+                // If anything other than a generated thumbnail
+                // is found, halt processing
+                if (description != null) {
+                    if (replaceRegex.matcher(description).matches()) {
+                        if (verbose) {
+                            System.out.println(description + " " + nsrc
+                                                   + " matches pattern and is replacable.");
+                        }
+                        continue;
+                    }
+                    if (description.equals(bitstreamDescription)) {
+                        if (verbose) {
+                            System.out.println(bitstreamDescription + " " + nsrc
+                                                   + " is replacable.");
+                        }
+                        continue;
+                    }
+                }
+                System.out.println("Custom Thumbnail exists for " + nsrc + " for item "
+                                       + item.getHandle() + ".  Thumbnail will not be generated. ");
+                return false;
+            }
+        }
+
+        return true; // assume that the thumbnail is a custom one
+    }
+
+}
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/JPEGFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/JPEGFilter.java
@@ -7,92 +7,113 @@
 */
 package org.dspace.app.mediafilter;

+import java.awt.Color;
+import java.awt.Font;
 import java.awt.Graphics2D;
+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.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.InputStream;
-
 import javax.imageio.ImageIO;

+import org.dspace.content.Item;
 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
 * no bigger than. Creates only JPEGs.
+ *
+ * @author Jason Sherman jsherman@usao.edu
 */
-public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
-{
-    public String getFilteredName(String oldFilename)
-    {
+public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats {
+    @Override
+    public String getFilteredName(String oldFilename) {
        return oldFilename + ".jpg";
    }

    /**
     * @return String bundle name
-     *  
     */
-    public String getBundleName()
-    {
+    @Override
+    public String getBundleName() {
        return "THUMBNAIL";
    }

    /**
     * @return String bitstreamformat
     */
-    public String getFormatString()
-    {
+    @Override
+    public String getFormatString() {
        return "JPEG";
    }

    /**
     * @return String description
     */
-    public String getDescription()
-    {
+    @Override
+    public String getDescription() {
        return "Generated Thumbnail";
    }

    /**
-     * @param source
-     *            source input stream
-     * 
+     * @param currentItem item
+     * @param source      source input stream
+     * @param verbose     verbose mode
     * @return InputStream the resulting input stream
+     * @throws Exception if error
     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception
-    {
+    @Override
+    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+        throws Exception {
        // read in bitstream's image
        BufferedImage buf = ImageIO.read(source);

+        return getThumb(currentItem, buf, verbose);
+    }
+
+    public InputStream getThumb(Item currentItem, BufferedImage buf, boolean verbose)
+        throws Exception {
        // get config params
        float xmax = (float) ConfigurationManager
            .getIntProperty("thumbnail.maxwidth");
        float ymax = (float) ConfigurationManager
            .getIntProperty("thumbnail.maxheight");
+        boolean blurring = (boolean) ConfigurationManager
+            .getBooleanProperty("thumbnail.blurring");
+        boolean hqscaling = (boolean) ConfigurationManager
+            .getBooleanProperty("thumbnail.hqscaling");

+        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 {
        // 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 (MediaFilterManager.isVerbose)
-        {
+        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 (MediaFilterManager.isVerbose)
-            {
+            if (verbose) {
                System.out.println("x scale factor: " + scale_factor);
            }

@@ -103,15 +124,13 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats

            // if verbose flag is set, print out extracted text
            // to STDOUT
-            if (MediaFilterManager.isVerbose)
-            {
-                System.out.println("new size: " + xsize + "," + ysize);
+            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
@@ -121,9 +140,8 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
        }

        // if verbose flag is set, print details to STDOUT
-        if (MediaFilterManager.isVerbose)
-        {
-            System.out.println("created thumbnail size: " + xsize + ", "
+        if (verbose) {
+            System.out.println("size after fitting to maximum height: " + xsize + ", "
                                   + ysize);
        }

@@ -131,10 +149,34 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
        BufferedImage thumbnail = new BufferedImage((int) xsize, (int) ysize,
                                                    BufferedImage.TYPE_INT_RGB);

+        // Use blurring if selected in config.
+        // a little blur before scaling does wonders for keeping moire in check.
+        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) {
+            // 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);
+        }
+
        // now render the image into the thumbnail buffer
        Graphics2D g2d = thumbnail.createGraphics();
        g2d.drawImage(buf, 0, 0, (int) xsize, (int) ysize, null);

+        if (brandHeight != 0) {
+            Brand brand = new Brand((int) xsize, brandHeight, new Font(brandFont, Font.PLAIN, brandFontPoint), 5);
+            BufferedImage brandImage = brand.create(ConfigurationManager.getProperty("webui.preview.brand"),
+                                                    ConfigurationManager.getProperty("webui.preview.brand.abbrev"),
+                                                    currentItem == null ? "" : "hdl:" + currentItem.getHandle());
+
+            g2d.drawImage(brandImage, (int) 0, (int) ysize, (int) xsize, (int) 20, null);
+        }
+
        // now create an input stream for the thumbnail buffer and return it
        ByteArrayOutputStream baos = new ByteArrayOutputStream();

@@ -147,20 +189,127 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
    }


-    public String[] getInputMIMETypes()
-    {
+    @Override
+    public String[] getInputMIMETypes() {
        return ImageIO.getReaderMIMETypes();
    }

-    public String[] getInputDescriptions()
-    {
+    @Override
+    public String[] getInputDescriptions() {
        return null;
    }

-    public String[] getInputExtensions()
-    {
+    @Override
+    public String[] getInputExtensions() {
        // Temporarily disabled as JDK 1.6 only
        // return ImageIO.getReaderFileSuffixes();
        return null;
    }
+
+    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();
+        BufferedImage normal = new BufferedImage(w, h, type);
+        Graphics2D g2d = normal.createGraphics();
+        g2d.drawImage(buf, 0, 0, w, h, Color.WHITE, null);
+        g2d.dispose();
+        return normal;
+    }
+
+    /**
+     * Convenience method that returns a blurred instance of the
+     * provided {@code BufferedImage}.
+     *
+     * @param buf buffered image
+     * @return updated BufferedImage
+     */
+    public BufferedImage getBlurredInstance(BufferedImage buf) {
+        buf = getNormalizedInstance(buf);
+
+        // kernel for blur op
+        float[] matrix = {
+            0.111f, 0.111f, 0.111f,
+            0.111f, 0.111f, 0.111f,
+            0.111f, 0.111f, 0.111f,
+        };
+
+        // perform the blur and return the blurred version.
+        BufferedImageOp blur = new ConvolveOp(new Kernel(3, 3, matrix));
+        BufferedImage blurbuf = blur.filter(buf, null);
+        return blurbuf;
+    }
+
+    /**
+     * Convenience method that returns a scaled instance of the
+     * provided {@code BufferedImage}.
+     *
+     * @param buf           the original image to be scaled
+     * @param targetWidth   the desired width of the scaled instance,
+     *                      in pixels
+     * @param targetHeight  the desired height of the scaled instance,
+     *                      in pixels
+     * @param hint          one of the rendering hints that corresponds to
+     *                      {@code RenderingHints.KEY_INTERPOLATION} (e.g.
+     *                      {@code RenderingHints.VALUE_INTERPOLATION_NEAREST_NEIGHBOR},
+     *                      {@code RenderingHints.VALUE_INTERPOLATION_BILINEAR},
+     *                      {@code RenderingHints.VALUE_INTERPOLATION_BICUBIC})
+     * @param higherQuality if true, this method will use a multi-step
+     *                      scaling technique that provides higher quality than the usual
+     *                      one-step technique (only useful in downscaling cases, where
+     *                      {@code targetWidth} or {@code targetHeight} is
+     *                      smaller than the original dimensions, and generally only when
+     *                      the {@code BILINEAR} hint is specified)
+     * @return a scaled version of the original {@code BufferedImage}
+     */
+    public BufferedImage getScaledInstance(BufferedImage buf,
+                                           int targetWidth,
+                                           int targetHeight,
+                                           Object hint,
+                                           boolean higherQuality) {
+        int type = (buf.getTransparency() == Transparency.OPAQUE) ?
+            BufferedImage.TYPE_INT_RGB : BufferedImage.TYPE_INT_ARGB;
+        BufferedImage scalebuf = (BufferedImage) buf;
+        int w;
+        int h;
+        if (higherQuality) {
+            // Use multi-step technique: start with original size, then
+            // scale down in multiple passes with drawImage()
+            // until the target size is reached
+            w = buf.getWidth();
+            h = buf.getHeight();
+        } else {
+            // Use one-step technique: scale directly from original
+            // size to target size with a single drawImage() call
+            w = targetWidth;
+            h = targetHeight;
+        }
+
+        do {
+            if (higherQuality && w > targetWidth) {
+                w /= 2;
+                if (w < targetWidth) {
+                    w = targetWidth;
+                }
+            }
+
+            if (higherQuality && h > targetHeight) {
+                h /= 2;
+                if (h < targetHeight) {
+                    h = targetHeight;
+                }
+            }
+
+            BufferedImage tmp = new BufferedImage(w, h, type);
+            Graphics2D g2d = tmp.createGraphics();
+            g2d.setRenderingHint(RenderingHints.KEY_INTERPOLATION, hint);
+            g2d.drawImage(scalebuf, 0, 0, w, h, Color.WHITE, null);
+            g2d.dispose();
+
+            scalebuf = tmp;
+        } while (w != targetWidth || h != targetHeight);
+
+        return scalebuf;
+    }
 }
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilter.java
@@ -18,8 +18,7 @@ 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().
@@ -28,20 +27,17 @@ 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 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
     */
-    public boolean preProcessBitstream(Context c, Item item, Bitstream source)
-            throws Exception
-    {
+    @Override
+    public boolean preProcessBitstream(Context c, Item item, Bitstream source, boolean verbose)
+        throws Exception {
        return true;  //default to no pre-processing
    }

@@ -53,18 +49,15 @@ 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
     */
+    @Override
    public void postProcessBitstream(Context c, Item item, Bitstream generatedBitstream)
-            throws Exception
-    {
+        throws Exception {
        //default to no post-processing necessary
    }
 }
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterCLITool.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterCLITool.java
@@ -0,0 +1,325 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.mediafilter;
+
+import java.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.dspace.app.mediafilter.factory.MediaFilterServiceFactory;
+import org.dspace.app.mediafilter.service.MediaFilterService;
+import org.dspace.content.Collection;
+import org.dspace.content.Community;
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.Item;
+import org.dspace.core.Constants;
+import org.dspace.core.Context;
+import org.dspace.core.SelfNamedPlugin;
+import org.dspace.core.factory.CoreServiceFactory;
+import org.dspace.handle.factory.HandleServiceFactory;
+import org.dspace.services.factory.DSpaceServicesFactory;
+
+/**
+ * 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
+ * MFM: -v verbose outputs all extracted text to STDOUT; -f force forces all
+ * bitstreams to be processed, even if they have been before; -n noindex does not
+ * recreate index after processing bitstreams; -i [identifier] limits processing
+ * scope to a community, collection or item; and -m [max] limits processing to a
+ * maximum number of items.
+ */
+public class MediaFilterCLITool {
+
+    //key (in dspace.cfg) which lists all enabled filters by name
+    private static final String MEDIA_FILTER_PLUGINS_KEY = "filter.plugins";
+
+    //prefix (in dspace.cfg) for all filter properties
+    private static final String FILTER_PREFIX = "filter";
+
+    //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 {
+        // set headless for non-gui workstations
+        System.setProperty("java.awt.headless", "true");
+
+        // create an options object and populate it
+        CommandLineParser parser = new PosixParser();
+
+        int status = 0;
+
+        Options options = new Options();
+
+        options.addOption("v", "verbose", false,
+                          "print all extracted text and other details to STDOUT");
+        options.addOption("q", "quiet", false,
+                          "do not print anything except in the event of errors.");
+        options.addOption("f", "force", false,
+                          "force all bitstreams to be processed");
+        options.addOption("i", "identifier", true,
+                          "ONLY process bitstreams belonging to identifier");
+        options.addOption("m", "maximum", true,
+                          "process no more than maximum items");
+        options.addOption("h", "help", false, "help");
+
+        //create a "plugin" option (to specify specific MediaFilter plugins to run)
+        OptionBuilder.withLongOpt("plugins");
+        OptionBuilder.withValueSeparator(',');
+        OptionBuilder.withDescription(
+            "ONLY run the specified Media Filter plugin(s)\n" +
+                "listed from '" + MEDIA_FILTER_PLUGINS_KEY + "' in dspace.cfg.\n" +
+                "Separate multiple with a comma (,)\n" +
+                "(e.g. MediaFilterManager -p \n\"Word Text Extractor\",\"PDF Text Extractor\")");
+        Option pluginOption = OptionBuilder.create('p');
+        pluginOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args
+        options.addOption(pluginOption);
+
+        //create a "skip" option (to specify communities/collections/items to skip)
+        OptionBuilder.withLongOpt("skip");
+        OptionBuilder.withValueSeparator(',');
+        OptionBuilder.withDescription(
+            "SKIP the bitstreams belonging to identifier\n" +
+                "Separate multiple identifiers with a comma (,)\n" +
+                "(e.g. MediaFilterManager -s \n 123456789/34,123456789/323)");
+        Option skipOption = OptionBuilder.create('s');
+        skipOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args
+        options.addOption(skipOption);
+
+        boolean isVerbose = false;
+        boolean isQuiet = false;
+        boolean isForce = false; // default to not forced
+        String identifier = null; // object scope limiter
+        int max2Process = Integer.MAX_VALUE;
+        Map<String, List<String>> filterFormats = new HashMap<>();
+
+        CommandLine line = null;
+        try {
+            line = parser.parse(options, argv);
+        } 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')) {
+            HelpFormatter myhelp = new HelpFormatter();
+            myhelp.printHelp("MediaFilterManager\n", options);
+
+            System.exit(0);
+        }
+
+        if (line.hasOption('v')) {
+            isVerbose = true;
+        }
+
+        isQuiet = line.hasOption('q');
+
+        if (line.hasOption('f')) {
+            isForce = true;
+        }
+
+        if (line.hasOption('i')) {
+            identifier = line.getOptionValue('i');
+        }
+
+        if (line.hasOption('m')) {
+            max2Process = Integer.parseInt(line.getOptionValue('m'));
+            if (max2Process <= 1) {
+                System.out.println("Invalid maximum value '" +
+                                       line.getOptionValue('m') + "' - ignoring");
+                max2Process = Integer.MAX_VALUE;
+            }
+        }
+
+        String filterNames[] = null;
+        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
+                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 {
+            //retrieve list of all enabled media filter plugins!
+            filterNames = DSpaceServicesFactory.getInstance().getConfigurationService()
+                                               .getArrayProperty(MEDIA_FILTER_PLUGINS_KEY);
+        }
+
+        MediaFilterService mediaFilterService = MediaFilterServiceFactory.getInstance().getMediaFilterService();
+        mediaFilterService.setForce(isForce);
+        mediaFilterService.setQuiet(isQuiet);
+        mediaFilterService.setVerbose(isVerbose);
+        mediaFilterService.setMax2Process(max2Process);
+
+        //initialize an array of our enabled filters
+        List<FormatFilter> filterList = new ArrayList<FormatFilter>();
+
+        //set up each filter
+        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] + "'");
+                System.exit(1);
+            } else {
+                filterList.add(filter);
+
+                String filterClassName = filter.getClass().getName();
+
+                String pluginName = null;
+
+                //If this filter is a SelfNamedPlugin,
+                //then the input formats it accepts may differ for
+                //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())) {
+                    //Get the plugin instance name for this class
+                    pluginName = ((SelfNamedPlugin) filter).getPluginInstanceName();
+                }
+
+
+                //Retrieve our list of supported formats from dspace.cfg
+                //For SelfNamedPlugins, format of key is:
+                //  filter.<class-name>.<plugin-name>.inputFormats
+                //For other MediaFilters, format of key is:
+                //  filter.<class-name>.inputFormats
+                String[] formats =
+                    DSpaceServicesFactory.getInstance().getConfigurationService().getArrayProperty(
+                        FILTER_PREFIX + "." + filterClassName +
+                            (pluginName != null ? "." + pluginName : "") +
+                            "." + INPUT_FORMATS_SUFFIX);
+
+                //add to internal map of filters to supported 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 : ""),
+                                      Arrays.asList(formats));
+                }
+            } //end if filter!=null
+        } //end for
+
+        //If verbose, print out loaded mediafilter info
+        if (isVerbose) {
+            System.out.println("The following MediaFilters are enabled: ");
+            Iterator<String> i = filterFormats.keySet().iterator();
+            while (i.hasNext()) {
+                String filterName = i.next();
+                System.out.println("Full Filter Name: " + filterName);
+                String pluginName = null;
+                if (filterName.contains(MediaFilterService.FILTER_PLUGIN_SEPARATOR)) {
+                    String[] fields = filterName.split(MediaFilterService.FILTER_PLUGIN_SEPARATOR);
+                    filterName = fields[0];
+                    pluginName = fields[1];
+                }
+
+                System.out.println(filterName +
+                                       (pluginName != null ? " (Plugin: " + pluginName + ")" : ""));
+            }
+        }
+
+        mediaFilterService.setFilterFormats(filterFormats);
+        //store our filter list into an internal array
+        mediaFilterService.setFilterClasses(filterList);
+
+
+        //Retrieve list of identifiers to skip (if any)
+        String skipIds[] = null;
+        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
+                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");
+                HelpFormatter myhelp = new HelpFormatter();
+                myhelp.printHelp("MediaFilterManager\n", options);
+                System.exit(0);
+            }
+
+            //save to a global skip list
+            mediaFilterService.setSkipList(Arrays.asList(skipIds));
+        }
+
+        Context c = null;
+
+        try {
+            c = new Context();
+
+            // have to be super-user to do the filtering
+            c.turnOffAuthorisationSystem();
+
+            // now apply the filters
+            if (identifier == null) {
+                mediaFilterService.applyFiltersAllItems(c);
+            } else {
+                // restrict application scope to identifier
+                DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(c, identifier);
+                if (dso == null) {
+                    throw new IllegalArgumentException("Cannot resolve "
+                                                           + identifier + " to a DSpace object");
+                }
+
+                switch (dso.getType()) {
+                    case Constants.COMMUNITY:
+                        mediaFilterService.applyFiltersCommunity(c, (Community) dso);
+                        break;
+                    case Constants.COLLECTION:
+                        mediaFilterService.applyFiltersCollection(c, (Collection) dso);
+                        break;
+                    case Constants.ITEM:
+                        mediaFilterService.applyFiltersItem(c, (Item) dso);
+                        break;
+                    default:
+                        break;
+                }
+            }
+
+            c.complete();
+            c = null;
+        } catch (Exception e) {
+            status = 1;
+        } finally {
+            if (c != null) {
+                c.abort();
+            }
+        }
+        System.exit(status);
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterManager.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterManager.java
@@ -1,838 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.List;
-
-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.dspace.authorize.AuthorizeManager;
-import org.dspace.content.Bitstream;
-import org.dspace.content.BitstreamFormat;
-import org.dspace.content.Bundle;
-import org.dspace.content.Collection;
-import org.dspace.content.Community;
-import org.dspace.content.DCDate;
-import org.dspace.content.DSpaceObject;
-import org.dspace.content.Item;
-import org.dspace.content.ItemIterator;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.core.PluginManager;
-import org.dspace.core.SelfNamedPlugin;
-import org.dspace.handle.HandleManager;
-import org.dspace.search.DSIndexer;
-
-/**
- * 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
- * MFM: -v verbose outputs all extracted text to STDOUT; -f force forces all
- * bitstreams to be processed, even if they have been before; -n noindex does not
- * recreate index after processing bitstreams; -i [identifier] limits processing 
- * scope to a community, collection or item; and -m [max] limits processing to a
- * maximum number of items.
- */
-public class MediaFilterManager
-{
-	//key (in dspace.cfg) which lists all enabled filters by name
-    public static final String MEDIA_FILTER_PLUGINS_KEY = "filter.plugins";
-	
-    //prefix (in dspace.cfg) for all filter properties
-    public static final String FILTER_PREFIX = "filter";
-    
-    //suffix (in dspace.cfg) for input formats supported by each filter
-    public static final String INPUT_FORMATS_SUFFIX = "inputFormats";
-    
-    static boolean updateIndex = true; // default to updating index
-
-    static boolean isVerbose = false; // default to not verbose
-
-    static boolean isQuiet = false; // default is noisy
-
-    static boolean isForce = false; // default to not forced
-    
-    static String identifier = null; // object scope limiter
-    
-    static int max2Process = Integer.MAX_VALUE;  // maximum number items to process
-    
-    static int processed = 0;   // number items processed
-    
-    private static Item currentItem = null;   // current item being processed
-    
-    private static FormatFilter[] filterClasses = null;
-    
-    private static Map<String, List<String>> filterFormats = new HashMap<String, List<String>>();
-    
-    private static List<String> skipList = null; //list of identifiers to skip during processing
-    
-    //separator in filterFormats Map between a filter class name and a plugin name,
-    //for MediaFilters which extend SelfNamedPlugin (\034 is "file separator" char)
-    public static final String FILTER_PLUGIN_SEPARATOR = "\034";
-    
-    public static void main(String[] argv) throws Exception
-    {
-        // set headless for non-gui workstations
-        System.setProperty("java.awt.headless", "true");
-
-        // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
-
-        int status = 0;
-
-        Options options = new Options();
-        
-        options.addOption("v", "verbose", false,
-                "print all extracted text and other details to STDOUT");
-        options.addOption("q", "quiet", false,
-                "do not print anything except in the event of errors.");
-        options.addOption("f", "force", false,
-                "force all bitstreams to be processed");
-        options.addOption("n", "noindex", false,
-                "do NOT update the search index after filtering bitstreams");
-        options.addOption("i", "identifier", true,
-        		"ONLY process bitstreams belonging to identifier");
-        options.addOption("m", "maximum", true,
-				"process no more than maximum items");
-        options.addOption("h", "help", false, "help");
-
-        //create a "plugin" option (to specify specific MediaFilter plugins to run)
-        OptionBuilder.withLongOpt("plugins");
-        OptionBuilder.withValueSeparator(',');
-        OptionBuilder.withDescription(
-                       "ONLY run the specified Media Filter plugin(s)\n" +
-                       "listed from '" + MEDIA_FILTER_PLUGINS_KEY + "' in dspace.cfg.\n" + 
-                       "Separate multiple with a comma (,)\n" +
-                       "(e.g. MediaFilterManager -p \n\"Word Text Extractor\",\"PDF Text Extractor\")");                
-        Option pluginOption = OptionBuilder.create('p');
-        pluginOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args
-        options.addOption(pluginOption);	
-        
-         //create a "skip" option (to specify communities/collections/items to skip)
-        OptionBuilder.withLongOpt("skip");
-        OptionBuilder.withValueSeparator(',');
-        OptionBuilder.withDescription(
-                "SKIP the bitstreams belonging to identifier\n" + 
-                "Separate multiple identifiers with a comma (,)\n" +
-                "(e.g. MediaFilterManager -s \n 123456789/34,123456789/323)");                
-        Option skipOption = OptionBuilder.create('s');
-        skipOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args
-        options.addOption(skipOption);    
-        
-        CommandLine line = null;
-        try
-        {
-            line = parser.parse(options, argv);
-        }
-        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'))
-        {
-            HelpFormatter myhelp = new HelpFormatter();
-            myhelp.printHelp("MediaFilterManager\n", options);
-
-            System.exit(0);
-        }
-
-        if (line.hasOption('v'))
-        {
-            isVerbose = true;
-        }
-
-        isQuiet = line.hasOption('q');
-
-        if (line.hasOption('n'))
-        {
-            updateIndex = false;
-        }
-
-        if (line.hasOption('f'))
-        {
-            isForce = true;
-        }
-        
-        if (line.hasOption('i'))
-        {
-        	identifier = line.getOptionValue('i');
-        }
-        
-        if (line.hasOption('m'))
-        {
-        	max2Process = Integer.parseInt(line.getOptionValue('m'));
-        	if (max2Process <= 1)
-        	{
-        		System.out.println("Invalid maximum value '" + 
-        				     		line.getOptionValue('m') + "' - ignoring");
-        		max2Process = Integer.MAX_VALUE;
-        	}
-        }
-
-        String filterNames[] = null;
-        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
-                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
-        { 
-            //retrieve list of all enabled media filter plugins!
-            String enabledPlugins = ConfigurationManager.getProperty(MEDIA_FILTER_PLUGINS_KEY);
-            filterNames = enabledPlugins.split(",\\s*");
-        }
-                
-        //initialize an array of our enabled filters
-        List<FormatFilter> filterList = new ArrayList<FormatFilter>();
-                
-        //set up each filter
-        for(int i=0; i< filterNames.length; i++)
-        {
-            //get filter of this name & add to list of filters
-            FormatFilter filter = (FormatFilter) PluginManager.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
-            {   
-                filterList.add(filter);
-                       
-                String filterClassName = filter.getClass().getName();
-                           
-                String pluginName = null;
-                           
-                //If this filter is a SelfNamedPlugin,
-                //then the input formats it accepts may differ for
-                //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()) )
-                {
-                    //Get the plugin instance name for this class
-                    pluginName = ((SelfNamedPlugin) filter).getPluginInstanceName();
-                }
-            
-                
-                //Retrieve our list of supported formats from dspace.cfg
-                //For SelfNamedPlugins, format of key is:  
-                //  filter.<class-name>.<plugin-name>.inputFormats
-                //For other MediaFilters, format of key is: 
-                //  filter.<class-name>.inputFormats
-                String formats = ConfigurationManager.getProperty(
-                    FILTER_PREFIX + "." + filterClassName + 
-                    (pluginName!=null ? "." + pluginName : "") +
-                    "." + INPUT_FORMATS_SUFFIX);
-            
-                //add to internal map of filters to supported formats	
-                if (formats != null)
-                {
-                    //For SelfNamedPlugins, map key is:  
-                    //  <class-name><separator><plugin-name>
-                    //For other MediaFilters, map key is just:
-                    //  <class-name>
-                    filterFormats.put(filterClassName + 
-        	            (pluginName!=null ? FILTER_PLUGIN_SEPARATOR + pluginName : ""),
-        	            Arrays.asList(formats.split(",[\\s]*")));
-                }
-            }//end if filter!=null
-        }//end for
-        
-        //If verbose, print out loaded mediafilter info
-        if(isVerbose)
-        {   
-            System.out.println("The following MediaFilters are enabled: ");
-            Iterator<String> i = filterFormats.keySet().iterator();
-            while(i.hasNext())
-            {
-                String filterName = i.next();
-                System.out.println("Full Filter Name: " + filterName);
-                String pluginName = null;
-                if(filterName.contains(FILTER_PLUGIN_SEPARATOR))
-                {
-                    String[] fields = filterName.split(FILTER_PLUGIN_SEPARATOR);
-                    filterName=fields[0];
-                    pluginName=fields[1];
-                }
-                 
-                System.out.println(filterName +
-                        (pluginName!=null? " (Plugin: " + pluginName + ")": ""));
-             }
-        }
-              
-        //store our filter list into an internal array
-        filterClasses = (FormatFilter[]) filterList.toArray(new FormatFilter[filterList.size()]);
-        
-        
-        //Retrieve list of identifiers to skip (if any)
-        String skipIds[] = null;
-        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
-                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");
-                HelpFormatter myhelp = new HelpFormatter();
-                myhelp.printHelp("MediaFilterManager\n", options);
-                System.exit(0);
-            }
-            
-            //save to a global skip list
-            skipList = Arrays.asList(skipIds);
-        }
-        
-        Context c = null;
-
-        try
-        {
-            c = new Context();
-
-            // have to be super-user to do the filtering
-            c.turnOffAuthorisationSystem();
-
-            // now apply the filters
-            if (identifier == null)
-            {
-            	applyFiltersAllItems(c);
-            }
-            else  // restrict application scope to identifier
-            {
-            	DSpaceObject dso = HandleManager.resolveToObject(c, identifier);
-            	if (dso == null)
-            	{
-            		throw new IllegalArgumentException("Cannot resolve "
-                                + identifier + " to a DSpace object");
-            	}
-            	
-            	switch (dso.getType())
-            	{
-            		case Constants.COMMUNITY:
-            						applyFiltersCommunity(c, (Community)dso);
-            						break;					
-            		case Constants.COLLECTION:
-            						applyFiltersCollection(c, (Collection)dso);
-            						break;						
-            		case Constants.ITEM:
-            						applyFiltersItem(c, (Item)dso);
-            						break;
-            	}
-            }
-          
-            // update search index?
-            if (updateIndex)
-            {
-                if (!isQuiet)
-                {
-                    System.out.println("Updating search index:");
-                }
-                DSIndexer.setBatchProcessingMode(true);
-                try
-                {
-                    DSIndexer.updateIndex(c);
-                }
-                finally
-                {
-                    DSIndexer.setBatchProcessingMode(false);
-                }
-            }
-
-            c.complete();
-            c = null;
-        }
-        catch (Exception e)
-        {
-            status = 1;
-        }
-        finally
-        {
-            if (c != null)
-            {
-                c.abort();
-            }
-        }
-        System.exit(status);
-    }
-
-    public static void applyFiltersAllItems(Context c) 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
-            Community[] topLevelCommunities = Community.findAllTop(c);
-          
-            for(int i=0; i<topLevelCommunities.length; i++)
-            {
-                applyFiltersCommunity(c, topLevelCommunities[i]);
-            }
-        }
-        else 
-        {
-            //otherwise, just find every item and process
-            ItemIterator i = Item.findAll(c);
-            try
-            {
-                while (i.hasNext() && processed < max2Process)
-                {
-                    applyFiltersItem(c, i.next());
-                }
-            }
-            finally
-            {
-                if (i != null)
-                {
-                    i.close();
-                }
-            }
-        }
-    }
-    
-    public static void applyFiltersCommunity(Context c, Community community)
-                                             throws Exception
-    {   //only apply filters if community not in skip-list
-        if(!inSkipList(community.getHandle()))
-        {    
-           	Community[] subcommunities = community.getSubcommunities();
-           	for (int i = 0; i < subcommunities.length; i++)
-           	{
-           		applyFiltersCommunity(c, subcommunities[i]);
-           	}
-           	
-           	Collection[] collections = community.getCollections();
-           	for (int j = 0; j < collections.length; j++)
-           	{
-           		applyFiltersCollection(c, collections[j]);
-           	}
-        }
-    }
-        
-    public static void applyFiltersCollection(Context c, Collection collection)
-                                              throws Exception
-    {
-        //only apply filters if collection not in skip-list
-        if(!inSkipList(collection.getHandle()))
-        {
-            ItemIterator i = collection.getItems();
-            try
-            {
-                while (i.hasNext() && processed < max2Process)
-                {
-                    applyFiltersItem(c, i.next());
-                }
-            }
-            finally
-            {
-                if (i != null)
-                {
-                    i.close();
-                }
-            }
-        }
-    }
-       
-    public static void applyFiltersItem(Context c, Item item) throws Exception
-    {
-        //only apply filters if item not in skip-list
-        if(!inSkipList(item.getHandle()))
-        {
-    	  //cache this item in MediaFilterManager
-    	  //so it can be accessed by MediaFilters as necessary
-    	  currentItem = item;
-    	
-          if (filterItem(c, item))
-          {
-        	  // commit changes after each filtered item
-        	  c.commit();
-              // increment processed count
-              ++processed;
-          }
-          // clear item objects from context cache and internal cache
-          item.decache();
-          currentItem = null;
-        }  
-    }
-
-    /**
-     * Iterate through the item's bitstreams in the ORIGINAL bundle, applying
-     * filters if possible.
-     * 
-     * @return true if any bitstreams processed, 
-     *         false if none
-     */
-    public static boolean filterItem(Context c, Item myItem) throws Exception
-    {
-        // get 'original' bundles
-        Bundle[] myBundles = myItem.getBundles("ORIGINAL");
-        boolean done = false;
-        for (int i = 0; i < myBundles.length; i++)
-        {
-        	// now look at all of the bitstreams
-            Bitstream[] myBitstreams = myBundles[i].getBitstreams();
-            
-            for (int k = 0; k < myBitstreams.length; k++)
-            {
-            	done |= filterBitstream(c, myItem, myBitstreams[k]);
-            }
-        }
-        return done;
-    }
-
-    /**
-     * Attempt to filter a bitstream.
-     * 
-     * An exception will be thrown if the media filter class cannot be
-     * instantiated.  Exceptions from filtering will be logged to STDOUT and
-     * swallowed.
-     * 
-     * @return true if bitstream processed, 
-     *         false if no applicable filter or already processed
-     */
-    public static boolean filterBitstream(Context c, Item myItem,
-            Bitstream myBitstream) throws Exception
-    {
-    	boolean filtered = false;
-    	
-    	// iterate through filter classes. A single format may be actioned
-    	// by more than one filter
-    	for (int i = 0; i < filterClasses.length; i++)
-    	{
-    		//List fmts = (List)filterFormats.get(filterClasses[i].getClass().getName());
-    	    String pluginName = null;
-    	               
-    	    //if this filter class is a SelfNamedPlugin,
-    	    //its list of supported formats is different for
-    	    //differently named "plugin"
-    	    if( SelfNamedPlugin.class.isAssignableFrom(filterClasses[i].getClass()) )
-    	    {
-    	        //get plugin instance name for this media filter
-    	        pluginName = ((SelfNamedPlugin)filterClasses[i]).getPluginInstanceName();
-    	    }
-    	               
-    	    //Get list of supported formats for the filter (and possibly named plugin)
-    	    //For SelfNamedPlugins, map key is:  
-    	    //  <class-name><separator><plugin-name>
-    	    //For other MediaFilters, map key is just:
-    	    //  <class-name>
-    	    List<String> fmts = filterFormats.get(filterClasses[i].getClass().getName() +
-    	                       (pluginName!=null ? FILTER_PLUGIN_SEPARATOR + pluginName : ""));
-    	   
-    	    if (fmts.contains(myBitstream.getFormat().getShortDescription()))
-    		{
-            	try
-            	{
-		            // only update item if bitstream not skipped
-		            if (processBitstream(c, myItem, myBitstream, filterClasses[i]))
-            	    {
-		           		myItem.update(); // Make sure new bitstream has a sequence
-		                                 	// number
-		           		filtered = true;
-		            }
-            	}
-                catch (Exception e)
-                {
-                	String handle = myItem.getHandle();
-                	Bundle[] bundles = myBitstream.getBundles();
-                	long size = myBitstream.getSize();
-                	String checksum = myBitstream.getChecksum() + " ("+myBitstream.getChecksumAlgorithm()+")";
-                	int assetstore = myBitstream.getStoreNumber();
-   
-                	// Printout helpful information to find the errored bitstream.
-                	System.out.println("ERROR filtering, skipping bitstream:\n");
-                	System.out.println("\tItem Handle: "+ handle);
-                	for (Bundle bundle : bundles)
-                	{
-                		System.out.println("\tBundle Name: " + bundle.getName());
-                	}
-                	System.out.println("\tFile Size: " + size);
-                	System.out.println("\tChecksum: " + checksum);
-                	System.out.println("\tAsset Store: " + assetstore);
-                	System.out.println(e);
-                    e.printStackTrace();
-                }
-    		}
-            else if (filterClasses[i] instanceof SelfRegisterInputFormats)
-            {
-                // Filter implements self registration, so check to see if it should be applied
-                // given the formats it claims to support
-                SelfRegisterInputFormats srif = (SelfRegisterInputFormats)filterClasses[i];
-                boolean applyFilter = false;
-
-                // Check MIME type
-                String[] mimeTypes = srif.getInputMIMETypes();
-                if (mimeTypes != null)
-                {
-                    for (String mimeType : mimeTypes)
-                    {
-                        if (mimeType.equalsIgnoreCase(myBitstream.getFormat().getMIMEType()))
-                        {
-                            applyFilter = true;
-                        }
-                    }
-                }
-
-                // Check description
-                if (!applyFilter)
-                {
-                    String[] descriptions = srif.getInputDescriptions();
-                    if (descriptions != null)
-                    {
-                        for (String desc : descriptions)
-                        {
-                            if (desc.equalsIgnoreCase(myBitstream.getFormat().getShortDescription()))
-                            {
-                                applyFilter = true;
-                            }
-                        }
-                    }
-                }
-
-                // Check extensions
-                if (!applyFilter)
-                {
-                    String[] extensions = srif.getInputExtensions();
-                    if (extensions != null)
-                    {
-                        for (String ext : extensions)
-                        {
-                            String[] formatExtensions = myBitstream.getFormat().getExtensions();
-                            if (formatExtensions != null && ArrayUtils.contains(formatExtensions, ext))
-                            {
-                                applyFilter = true;
-                            }
-                        }
-                    }
-                }
-
-                // Filter claims to handle this type of file, so attempt to apply it
-                if (applyFilter)
-                {
-                    try
-                    {
-                        // only update item if bitstream not skipped
-                        if (processBitstream(c, myItem, myBitstream, filterClasses[i]))
-                        {
-                               myItem.update(); // Make sure new bitstream has a sequence
-                                                 // number
-                               filtered = true;
-                        }
-                    }
-                    catch (Exception e)
-                    {
-                        System.out.println("ERROR filtering, skipping bitstream #"
-                                + myBitstream.getID() + " " + e);
-                        e.printStackTrace();
-                    }
-                }
-            }
-    	}
-        return filtered;
-    }
-    
-    /**
-     * A utility class that calls the virtual methods
-     * from the current MediaFilter class.
-     * It scans the bitstreams in an item, and decides if a bitstream has 
-     * already been filtered, and if not or if overWrite is set, invokes the 
-     * filter.
-     * 
-     * @param c
-     *            context
-     * @param item
-     *            item containing bitstream to process
-     * @param source
-     *            source bitstream to process
-     * @param formatFilter
-     *            FormatFilter to perform filtering
-     * 
-     * @return true if new rendition is created, false if rendition already
-     *         exists and overWrite is not set
-     */
-    public static boolean processBitstream(Context c, Item item, Bitstream source, FormatFilter formatFilter)
-            throws Exception
-    {
-        //do pre-processing of this bitstream, and if it fails, skip this bitstream!
-    	if(!formatFilter.preProcessBitstream(c, item, source))
-        {
-            return false;
-        }
-        	
-    	boolean overWrite = MediaFilterManager.isForce;
-        
-        // 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
-
-        Bundle[] bundles = item.getBundles(formatFilter.getBundleName());
-
-        // check if destination bitstream exists
-        if (bundles.length > 0)
-        {
-            // only finds the last match (FIXME?)
-            for (int i = 0; i < bundles.length; i++)
-            {
-                Bitstream[] bitstreams = bundles[i].getBitstreams();
-
-                for (int j = 0; j < bitstreams.length; j++)
-                {
-                    if (bitstreams[j].getName().equals(newName))
-                    {
-                        targetBundle = bundles[i];
-                        existingBitstream = bitstreams[j];
-                    }
-                }
-            }
-        }
-
-        // if exists and overwrite = false, exit
-        if (!overWrite && (existingBitstream != null))
-        {
-            if (!isQuiet)
-            {
-                System.out.println("SKIPPED: bitstream " + source.getID()
-                        + " (item: " + item.getHandle() + ") because '" + newName + "' already exists");
-            }
-
-            return false;
-        }
-        
-        InputStream destStream = formatFilter.getDestinationStream(source.retrieve());
-        if (destStream == null)
-        {
-            if (!isQuiet)
-            {
-                System.out.println("SKIPPED: bitstream " + source.getID()
-                        + " (item: " + item.getHandle() + ") because filtering was unsuccessful");
-            }
-
-            return false;
-        }
-
-        // create new bundle if needed
-        if (bundles.length < 1)
-        {
-            targetBundle = item.createBundle(formatFilter.getBundleName());
-        }
-        else
-        {
-            // take the first match
-            targetBundle = bundles[0];
-        }
-
-        Bitstream b = targetBundle.createBitstream(destStream);
-
-        // Now set the format and name of the bitstream
-        b.setName(newName);
-        b.setSource("Written by FormatFilter " + formatFilter.getClass().getName() +
-        			" on " + DCDate.getCurrent() + " (GMT)."); 
-        b.setDescription(formatFilter.getDescription());
-
-        // Find the proper format
-        BitstreamFormat bf = BitstreamFormat.findByShortDescription(c,
-                formatFilter.getFormatString());
-        b.setFormat(bf);
-        b.update();
-        
-        //Inherit policies from the source bitstream
-        //(first remove any existing policies)
-        AuthorizeManager.removeAllPolicies(c, b);
-        AuthorizeManager.inheritPolicies(c, source, b);
-
-        // fixme - set date?
-        // we are overwriting, so remove old bitstream
-        if (existingBitstream != null)
-        {
-            targetBundle.removeBitstream(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(c, item, b);
-        
-        return true;
-    }
-    
-    /**
-     * Return the item that is currently being processed/filtered
-     * by the MediaFilterManager.
-     * <p>
-     * This allows FormatFilters to retrieve the Item object
-     * in case they need access to item-level information for their format
-     * transformations/conversions.
-     * 
-     * @return current Item being processed by MediaFilterManager
-     */
-    public static Item getCurrentItem()
-    {
-        return currentItem;
-    }
-    
-    /**
-     * Check whether or not to skip processing the given identifier.
-     * 
-     * @param identifier
-     *            identifier (handle) of a community, collection or item
-     *            
-     * @return true if this community, collection or item should be skipped
-     *          during processing.  Otherwise, return false.
-     */
-    public static 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
-        {
-            return false;
-        }
-    }
-    
-}
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterServiceImpl.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/MediaFilterServiceImpl.java
@@ -0,0 +1,469 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.mediafilter;
+
+import java.io.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.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.core.Constants;
+import org.dspace.core.Context;
+import org.dspace.core.SelfNamedPlugin;
+import org.dspace.eperson.Group;
+import org.dspace.eperson.service.GroupService;
+import org.dspace.services.ConfigurationService;
+import org.springframework.beans.factory.InitializingBean;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * 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
+ * MFM: -v verbose outputs all extracted text to STDOUT; -f force forces all
+ * bitstreams to be processed, even if they have been before; -n noindex does not
+ * recreate index after processing bitstreams; -i [identifier] limits processing
+ * scope to a community, collection or item; and -m [max] limits processing to a
+ * maximum number of items.
+ */
+public class MediaFilterServiceImpl implements MediaFilterService, InitializingBean {
+    @Autowired(required = true)
+    protected AuthorizeService authorizeService;
+    @Autowired(required = true)
+    protected BitstreamFormatService bitstreamFormatService;
+    @Autowired(required = true)
+    protected BitstreamService bitstreamService;
+    @Autowired(required = true)
+    protected BundleService bundleService;
+    @Autowired(required = true)
+    protected CollectionService collectionService;
+    @Autowired(required = true)
+    protected CommunityService communityService;
+    @Autowired(required = true)
+    protected GroupService groupService;
+    @Autowired(required = true)
+    protected ItemService itemService;
+    @Autowired(required = true)
+    protected ConfigurationService configurationService;
+
+    protected int max2Process = Integer.MAX_VALUE;  // maximum number items to process
+
+    protected int processed = 0;   // number items processed
+
+    protected Item currentItem = null;   // current item being processed
+
+    protected List<FormatFilter> filterClasses = null;
+
+    protected Map<String, List<String>> filterFormats = new HashMap<>();
+
+    protected List<String> skipList = null; //list of identifiers to skip during processing
+
+    protected final List<String> publicFiltersClasses = new ArrayList<>();
+
+    protected boolean isVerbose = false;
+    protected boolean isQuiet = false;
+    protected boolean isForce = false; // default to not forced
+
+    protected MediaFilterServiceImpl() {
+
+    }
+
+    @Override
+    public void afterPropertiesSet() throws Exception {
+        String[] publicPermissionFilters = configurationService
+            .getArrayProperty("filter.org.dspace.app.mediafilter.publicPermission");
+
+        if (publicPermissionFilters != null) {
+            for (String filter : publicPermissionFilters) {
+                publicFiltersClasses.add(filter.trim());
+            }
+        }
+    }
+
+    @Override
+    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);
+
+            for (Community topLevelCommunity : topLevelCommunities) {
+                applyFiltersCommunity(context, topLevelCommunity);
+            }
+        } else {
+            //otherwise, just find every item and process
+            Iterator<Item> itemIterator = itemService.findAll(context);
+            while (itemIterator.hasNext() && processed < max2Process) {
+                applyFiltersItem(context, itemIterator.next());
+            }
+        }
+    }
+
+    @Override
+    public void applyFiltersCommunity(Context context, Community community)
+        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);
+            }
+
+            List<Collection> collections = community.getCollections();
+            for (Collection collection : collections) {
+                applyFiltersCollection(context, collection);
+            }
+        }
+    }
+
+    @Override
+    public void applyFiltersCollection(Context context, Collection collection)
+        throws Exception {
+        //only apply filters if collection not in skip-list
+        if (!inSkipList(collection.getHandle())) {
+            Iterator<Item> itemIterator = itemService.findAllByCollection(context, collection);
+            while (itemIterator.hasNext() && processed < max2Process) {
+                applyFiltersItem(context, itemIterator.next());
+            }
+        }
+    }
+
+    @Override
+    public void applyFiltersItem(Context c, Item item) throws Exception {
+        //only apply filters if item not in skip-list
+        if (!inSkipList(item.getHandle())) {
+            //cache this item in MediaFilterManager
+            //so it can be accessed by MediaFilters as necessary
+            currentItem = item;
+
+            if (filterItem(c, item)) {
+                // increment processed count
+                ++processed;
+            }
+            // clear item objects from context cache and internal cache
+            c.uncacheEntity(currentItem);
+            currentItem = null;
+        }
+    }
+
+    @Override
+    public boolean filterItem(Context context, Item myItem) throws Exception {
+        // get 'original' bundles
+        List<Bundle> myBundles = itemService.getBundles(myItem, "ORIGINAL");
+        boolean done = false;
+        for (Bundle myBundle : myBundles) {
+            // now look at all of the bitstreams
+            List<Bitstream> myBitstreams = myBundle.getBitstreams();
+
+            for (Bitstream myBitstream : myBitstreams) {
+                done |= filterBitstream(context, myItem, myBitstream);
+            }
+        }
+        return done;
+    }
+
+    @Override
+    public boolean filterBitstream(Context context, Item myItem,
+                                   Bitstream myBitstream) throws Exception {
+        boolean filtered = false;
+
+        // iterate through filter classes. A single format may be actioned
+        // by more than one filter
+        for (FormatFilter filterClass : filterClasses) {
+            //List fmts = (List)filterFormats.get(filterClasses[i].getClass().getName());
+            String pluginName = null;
+
+            //if this filter class is a SelfNamedPlugin,
+            //its list of supported formats is different for
+            //differently named "plugin"
+            if (SelfNamedPlugin.class.isAssignableFrom(filterClass.getClass())) {
+                //get plugin instance name for this media filter
+                pluginName = ((SelfNamedPlugin) filterClass).getPluginInstanceName();
+            }
+
+            //Get list of supported formats for the filter (and possibly named plugin)
+            //For SelfNamedPlugins, map key is:
+            //  <class-name><separator><plugin-name>
+            //For other MediaFilters, map key is just:
+            //  <class-name>
+            List<String> fmts = filterFormats.get(filterClass.getClass().getName() +
+                                                      (pluginName != null ? FILTER_PLUGIN_SEPARATOR + pluginName : ""));
+
+            if (fmts.contains(myBitstream.getFormat(context).getShortDescription())) {
+                try {
+                    // only update item if bitstream not skipped
+                    if (processBitstream(context, myItem, myBitstream, filterClass)) {
+                        itemService.update(context, myItem); // Make sure new bitstream has a sequence
+                        // number
+                        filtered = true;
+                    }
+                } catch (Exception e) {
+                    String handle = myItem.getHandle();
+                    List<Bundle> bundles = myBitstream.getBundles();
+                    long size = myBitstream.getSize();
+                    String checksum = myBitstream.getChecksum() + " (" + myBitstream.getChecksumAlgorithm() + ")";
+                    int assetstore = myBitstream.getStoreNumber();
+
+                    // Printout helpful information to find the errored bitstream.
+                    System.out.println("ERROR filtering, skipping bitstream:\n");
+                    System.out.println("\tItem Handle: " + handle);
+                    for (Bundle bundle : bundles) {
+                        System.out.println("\tBundle Name: " + bundle.getName());
+                    }
+                    System.out.println("\tFile Size: " + size);
+                    System.out.println("\tChecksum: " + checksum);
+                    System.out.println("\tAsset Store: " + assetstore);
+                    System.out.println(e);
+                    e.printStackTrace();
+                }
+            } else if (filterClass instanceof SelfRegisterInputFormats) {
+                // Filter implements self registration, so check to see if it should be applied
+                // given the formats it claims to support
+                SelfRegisterInputFormats srif = (SelfRegisterInputFormats) filterClass;
+                boolean applyFilter = false;
+
+                // Check MIME type
+                String[] mimeTypes = srif.getInputMIMETypes();
+                if (mimeTypes != null) {
+                    for (String mimeType : mimeTypes) {
+                        if (mimeType.equalsIgnoreCase(myBitstream.getFormat(context).getMIMEType())) {
+                            applyFilter = true;
+                        }
+                    }
+                }
+
+                // Check description
+                if (!applyFilter) {
+                    String[] descriptions = srif.getInputDescriptions();
+                    if (descriptions != null) {
+                        for (String desc : descriptions) {
+                            if (desc.equalsIgnoreCase(myBitstream.getFormat(context).getShortDescription())) {
+                                applyFilter = true;
+                            }
+                        }
+                    }
+                }
+
+                // Check extensions
+                if (!applyFilter) {
+                    String[] extensions = srif.getInputExtensions();
+                    if (extensions != null) {
+                        for (String ext : extensions) {
+                            List<String> formatExtensions = myBitstream.getFormat(context).getExtensions();
+                            if (formatExtensions != null && formatExtensions.contains(ext)) {
+                                applyFilter = true;
+                            }
+                        }
+                    }
+                }
+
+                // Filter claims to handle this type of file, so attempt to apply it
+                if (applyFilter) {
+                    try {
+                        // only update item if bitstream not skipped
+                        if (processBitstream(context, myItem, myBitstream, filterClass)) {
+                            itemService.update(context, myItem); // Make sure new bitstream has a sequence
+                            // number
+                            filtered = true;
+                        }
+                    } catch (Exception e) {
+                        System.out.println("ERROR filtering, skipping bitstream #"
+                                               + myBitstream.getID() + " " + e);
+                        e.printStackTrace();
+                    }
+                }
+            }
+        }
+        return filtered;
+    }
+
+    @Override
+    public boolean processBitstream(Context context, Item item, Bitstream source, FormatFilter formatFilter)
+        throws Exception {
+        //do pre-processing of this bitstream, and if it fails, skip this bitstream!
+        if (!formatFilter.preProcessBitstream(context, item, source, isVerbose)) {
+            return false;
+        }
+
+        boolean overWrite = isForce;
+
+        // 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) {
+            // 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;
+                        existingBitstream = bitstream;
+                    }
+                }
+            }
+        }
+
+        // if exists and overwrite = false, exit
+        if (!overWrite && (existingBitstream != null)) {
+            if (!isQuiet) {
+                System.out.println("SKIPPED: bitstream " + source.getID()
+                                       + " (item: " + item.getHandle() + ") because '" + newName + "' already exists");
+            }
+
+            return false;
+        }
+
+        if (isVerbose) {
+            System.out.println("PROCESSING: bitstream " + source.getID()
+                                   + " (item: " + item.getHandle() + ")");
+        }
+
+        InputStream destStream;
+        try {
+            System.out.println("File: " + newName);
+            destStream = formatFilter.getDestinationStream(item, bitstreamService.retrieve(context, source), isVerbose);
+            if (destStream == null) {
+                if (!isQuiet) {
+                    System.out.println("SKIPPED: bitstream " + source.getID()
+                                           + " (item: " + item.getHandle() + ") because filtering was unsuccessful");
+                }
+
+                return false;
+            }
+        } catch (OutOfMemoryError oome) {
+            System.out.println("!!! OutOfMemoryError !!!");
+            return false;
+        }
+
+        // create new bundle if needed
+        if (bundles.size() < 1) {
+            targetBundle = bundleService.create(context, item, formatFilter.getBundleName());
+        } else {
+            // take the first match
+            targetBundle = bundles.get(0);
+        }
+
+        Bitstream b = bitstreamService.create(context, targetBundle, destStream);
+
+        // Now set the format and name of the bitstream
+        b.setName(context, newName);
+        b.setSource(context, "Written by FormatFilter " + formatFilter.getClass().getName() +
+            " on " + DCDate.getCurrent() + " (GMT).");
+        b.setDescription(context, formatFilter.getDescription());
+
+        // Find the proper format
+        BitstreamFormat bf = bitstreamFormatService.findByShortDescription(context,
+                                                                           formatFilter.getFormatString());
+        bitstreamService.setFormat(context, b, bf);
+        bitstreamService.update(context, b);
+
+        //Set permissions on the derivative bitstream
+        //- First remove any existing policies
+        authorizeService.removeAllPolicies(context, b);
+
+        //- Determine if this is a public-derivative format
+        if (publicFiltersClasses.contains(formatFilter.getClass().getSimpleName())) {
+            //- Set derivative bitstream to be publicly accessible
+            Group anonymous = groupService.findByName(context, Group.ANONYMOUS);
+            authorizeService.addPolicy(context, b, Constants.READ, anonymous);
+        } else {
+            //- Inherit policies from the source bitstream
+            authorizeService.inheritPolicies(context, source, b);
+        }
+
+        // fixme - set date?
+        // we are overwriting, so remove old bitstream
+        if (existingBitstream != null) {
+            bundleService.removeBitstream(context, targetBundle, existingBitstream);
+        }
+
+        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() {
+        return currentItem;
+    }
+
+    @Override
+    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 {
+            return false;
+        }
+    }
+
+    @Override
+    public void setVerbose(boolean isVerbose) {
+        this.isVerbose = isVerbose;
+    }
+
+    @Override
+    public void setQuiet(boolean isQuiet) {
+        this.isQuiet = isQuiet;
+    }
+
+    @Override
+    public void setForce(boolean isForce) {
+        this.isForce = isForce;
+    }
+
+    @Override
+    public void setMax2Process(int max2Process) {
+        this.max2Process = max2Process;
+    }
+
+    @Override
+    public void setFilterClasses(List<FormatFilter> filterClasses) {
+        this.filterClasses = filterClasses;
+    }
+
+    @Override
+    public void setSkipList(List<String> skipList) {
+        this.skipList = skipList;
+    }
+
+    @Override
+    public void setFilterFormats(Map<String, List<String>> filterFormats) {
+        this.filterFormats = filterFormats;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/PDFBoxThumbnail.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/PDFBoxThumbnail.java
@@ -0,0 +1,94 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.mediafilter;
+
+import java.awt.image.BufferedImage;
+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;
+
+/**
+ * Create JPEG thumbnails from PDF cover page using PDFBox.
+ * Based on 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
+ * no bigger than. Creates only JPEGs.
+ *
+ * @author Ivan Masár helix84@centrum.sk
+ * @author Jason Sherman jsherman@usao.edu
+ */
+public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFormats {
+    @Override
+    public String getFilteredName(String oldFilename) {
+        return oldFilename + ".jpg";
+    }
+
+    /**
+     * @return String bundle name
+     */
+    @Override
+    public String getBundleName() {
+        return "THUMBNAIL";
+    }
+
+    /**
+     * @return String bitstreamformat
+     */
+    @Override
+    public String getFormatString() {
+        return "JPEG";
+    }
+
+    /**
+     * @return String description
+     */
+    @Override
+    public String getDescription() {
+        return "Generated Thumbnail";
+    }
+
+    /**
+     * @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 {
+        PDDocument doc = PDDocument.load(source);
+        PDFRenderer renderer = new PDFRenderer(doc);
+        BufferedImage buf = renderer.renderImage(0);
+//        ImageIO.write(buf, "PNG", new File("custom-render.png"));
+        doc.close();
+
+        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;
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/PDFFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/PDFFilter.java
@@ -18,7 +18,8 @@ import java.io.Writer;

 import org.apache.log4j.Logger;
 import org.apache.pdfbox.pdmodel.PDDocument;
-import org.apache.pdfbox.util.PDFTextStripper;
+import org.apache.pdfbox.text.PDFTextStripper;
+import org.dspace.content.Item;
 import org.dspace.core.ConfigurationManager;

 /*
@@ -27,118 +28,98 @@ 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);

-    public String getFilteredName(String oldFilename)
-    {
+    @Override
+    public String getFilteredName(String oldFilename) {
        return oldFilename + ".txt";
    }

    /**
     * @return String bundle name
-     *
     */
-    public String getBundleName()
-    {
+    @Override
+    public String getBundleName() {
        return "TEXT";
    }

    /**
     * @return String bitstreamformat
     */
-    public String getFormatString()
-    {
+    @Override
+    public String getFormatString() {
        return "Text";
    }

    /**
     * @return String description
     */
-    public String getDescription()
-    {
+    @Override
+    public String getDescription() {
        return "Extracted text";
    }

    /**
-     * @param source
-     *            source input stream
-     *
+     * @param currentItem item
+     * @param source      source input stream
+     * @param verbose     verbose mode
     * @return InputStream the resulting input stream
+     * @throws Exception if error
     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception
-    {
-        try
-        {
+    @Override
+    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+        throws Exception {
+        try {
            boolean useTemporaryFile = ConfigurationManager.getBooleanProperty("pdffilter.largepdfs", false);

            // get input stream from bitstream
            // pass to filter, get string back
            PDFTextStripper pts = new PDFTextStripper();
+            pts.setSortByPosition(true);
            PDDocument pdfDoc = null;
            Writer writer = null;
            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;
            }
        }
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/PoiWordFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/PoiWordFilter.java
@@ -0,0 +1,71 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.mediafilter;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import org.apache.poi.POITextExtractor;
+import org.apache.poi.extractor.ExtractorFactory;
+import org.apache.poi.openxml4j.exceptions.OpenXML4JException;
+import org.apache.xmlbeans.XmlException;
+import org.dspace.content.Item;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Extract flat text from Microsoft Word documents (.doc, .docx).
+ */
+public class PoiWordFilter
+    extends MediaFilter {
+    private static final Logger LOG = LoggerFactory.getLogger(PoiWordFilter.class);
+
+    @Override
+    public String getFilteredName(String oldFilename) {
+        return oldFilename + ".txt";
+    }
+
+    @Override
+    public String getBundleName() {
+        return "TEXT";
+    }
+
+    @Override
+    public String getFormatString() {
+        return "Text";
+    }
+
+    @Override
+    public String getDescription() {
+        return "Extracted text";
+    }
+
+    @Override
+    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+        throws Exception {
+        String text;
+        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) {
+            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) {
+            System.out.println(text);
+        }
+
+        // return the extracted text as a stream.
+        return new ByteArrayInputStream(text.getBytes());
+    }
+}
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/PowerPointFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/PowerPointFilter.java
@@ -10,33 +10,31 @@ package org.dspace.app.mediafilter;
 import java.io.ByteArrayInputStream;
 import java.io.InputStream;

-import org.apache.poi.extractor.ExtractorFactory;
-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.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.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);

-    public String getFilteredName(String oldFilename)
-    {
+    @Override
+    public String getFilteredName(String oldFilename) {
        return oldFilename + ".txt";
    }

    /**
     * @return String bundle name
-     * 
     */
-    public String getBundleName()
-    {
+    @Override
+    public String getBundleName() {
        return "TEXT";
    }

@@ -45,31 +43,31 @@ public class PowerPointFilter extends MediaFilter
     *
     * TODO: Check that this is correct
     */
-    public String getFormatString()
-    {
+    @Override
+    public String getFormatString() {
        return "Text";
    }

    /**
     * @return String description
     */
-    public String getDescription()
-    {
+    @Override
+    public String getDescription() {
        return "Extracted text";
    }

    /**
-     * @param source
-     *            source input stream
-     * 
+     * @param currentItem item
+     * @param source      source input stream
+     * @param verbose     verbose mode
     * @return InputStream the resulting input stream
+     * @throws Exception if error
     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception
-    {
+    @Override
+    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+        throws Exception {

-        try
-        {
+        try {

            String extractedText = null;
            new ExtractorFactory();
@@ -80,29 +78,22 @@ 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);
-            }
-
-            // Legacy PowerPoint files
-            else if (pptExtractor instanceof PowerPointExtractor)
-            {
+            } else if (pptExtractor instanceof PowerPointExtractor) { // Legacy PowerPoint files

                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 (MediaFilterManager.isVerbose)
-                {
+                if (verbose) {
                    System.out.println(extractedText);
                }

@@ -112,9 +103,7 @@ public class PowerPointFilter extends MediaFilter

                return bais;
            }
-        }
-        catch (Exception e)
-        {
+        } catch (Exception e) {
            log.error("Error filtering bitstream: " + e.getMessage(), e);
            throw e;
        }
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/SelfRegisterInputFormats.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/SelfRegisterInputFormats.java
@@ -11,8 +11,7 @@ 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();
--- a/dspace-api/src/main/java/org/dspace/app/mediafilter/WordFilter.java
+++ b/dspace-api/src/main/java/org/dspace/app/mediafilter/WordFilter.java
@@ -8,11 +8,11 @@
 package org.dspace.app.mediafilter;

 import java.io.ByteArrayInputStream;
-import java.io.InputStream;
 import java.io.IOException;
+import java.io.InputStream;

 import org.apache.log4j.Logger;
-
+import org.dspace.content.Item;
 import org.textmining.extraction.TextExtractor;
 import org.textmining.extraction.word.WordTextExtractorFactory;

@@ -22,62 +22,59 @@ 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);

-    public String getFilteredName(String oldFilename)
-    {
+    @Override
+    public String getFilteredName(String oldFilename) {
        return oldFilename + ".txt";
    }

    /**
     * @return String bundle name
-     *  
     */
-    public String getBundleName()
-    {
+    @Override
+    public String getBundleName() {
        return "TEXT";
    }

    /**
     * @return String bitstreamformat
     */
-    public String getFormatString()
-    {
+    @Override
+    public String getFormatString() {
        return "Text";
    }

    /**
     * @return String description
     */
-    public String getDescription()
-    {
+    @Override
+    public String getDescription() {
        return "Extracted text";
    }

    /**
-     * @param source
-     *            source input stream
-     * 
+     * @param currentItem item
+     * @param source      source input stream
+     * @param verbose     verbose mode
     * @return InputStream the resulting input stream
+     * @throws Exception if error
     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception
-    {
+    @Override
+    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+        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 (MediaFilterManager.isVerbose)
-            {
+            if (verbose) {
                System.out.println(extractedText);
            }

@@ -86,9 +83,7 @@ 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);
--- a/Show More
+++ b/Show More